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Biological and Biochemical Foundations of Living Systems
Foundational Concept 1
Biomolecules have unique properties that determine how they contribute to the structure and
function of cells, and how they participate in the processes necessary to maintain life.

Content Category 1A: Structure and function of proteins and their constituent amino
acids Macromolecules formed from amino acids adopt well-defined, three-dimensional
structures with chemical properties that are responsible for their participation in virtually every
process occurring within and between cells. The three-dimensional structure of proteins is a
direct consequence of the nature of the covalently-bonded sequence of amino acids, their
chemical and physical properties, and the way in which the whole assembly interacts with water.
Enzymes are proteins that interact in highly regio- and stereo-specific ways with dissolved
solutes. They either facilitate the chemical transformation of these solutes, or allow for their
transport innocuously. Dissolved solutes compete for protein-binding sites, and protein
conformational dynamics give rise to mechanisms capable of controlling enzymatic activity. The
infinite variability of potential amino acid sequences allows for adaptable responses to
pathogenic organisms and materials. The rigidity of some amino acid sequences makes them
suitable for structural roles in complex living systems. Content in this category covers a range of
protein behaviors which originate from the unique chemistry of amino acids themselves. Amino
acid classifications and protein structural elements are covered. Special emphasis is placed on
enzyme catalysis, including mechanistic considerations, kinetics, models of enzyme-substrate
interaction, and regulation. The topics and subtopics in this category are the following:

Amino Acids (BC, OC)


Descriptions
Absolute configuration at the position

L and D is different from R and S. L is not always S, and D is not always
R.
If the priority of NH2 > COOH > R, then L=S and D=R. For example, L-
Alanine = S-Alanine.
If the priority of NH2 > R > COOH, then L=R, and D=S. For example, L-
Cysteine = R-Cysteine.
L-amino acids are the more common in nature, and are the type found in
proteins. D-amino acids are less common in nature, and are never found
in proteins.
all mammalian amino acids have L configuration which corresponds to S
stereocenter (cysteine is backwards). So NH2 is always wedged
Amino acids as dipolar ions

At low pH, amino acids exist in the cationic form .
At high pH, amino acids exist in the anionic form .
At pH = pI, amino acids exist in the zwitterion form, which is overall
neutral.
on average the amino group has pka of 9, carboxylic acid has pka of 2.
So isoelectric point (pI) of average amino aicid is (9+2)/2=5.5. If the R
group has a charge then average the furthest one with the middle one.
if pH is lower than the pI then it will be protonated into cationic form.
When pH is greater than the PI the solution will be basic, rmaking it
anionic
Classifications
Acidic or basic
If the R group contains carboxylic acid, then it's an acidic amino
acid. There are two acidic amino acids: aspartic acid and glutamic
acid.
 If the R group contains an amine group, then it's a basic amino
acid. There are three basic amino acids: lysine, arginine, and
histidine.
Hydrophobic or hydrophilic
Hydrophobic:
alkyl
glycine, alanine, valine, methionine, leucine,
isoleucine, proline
aromatic
phenylalanine, tryptophan, tyrosin
Hydrophilic: If the R group contains acids, bases, amines or
alcohols.
neutral
serine, threonine, asparagine, glutamine, cysteine,
(all have O or S)
Acidic
aspartic acid, glutamic acid
Base
Histidine, lysine, Arginine (has nitrogen atoms)
Reactions
Sulfur linkage for cysteine and cystine
Cysteine can be easily oxidized to form a dimer containing disulfide
bridge between two cysteines- forms cystine

Peptide linkage: polypeptides and proteins

Peptide bond = amide bond.
The peptide bond is formed by the amine group attacking the carbonyl
carbon.
Hydrolysis

The peptide bond is very difficult to hydrolyze. It requires a strong base,
or a biological enzyme. (biological enzyme more specific)

Protein Structure (BIO, BC, OC)

Structure
1 structure of proteins
Primary structure = sequence.
The primary structure of proteins is read from the N-terminus to the C-
terminus.

2 structure of proteins
Secondary structure = repetitive motifs formed by backbone interactions.
Backbone interactions = hydrogen bonding between the NH and C=O
The two most common secondary structures are helices and pleated
sheets.
The helix is right-handed, with the R groups sticking outward.
In sheets, R groups stick out above and below the sheet.
3 structure of proteins; role of proline, cystine, hydrophobic bonding
interactions between R groups (3d formation of protein)
cystine- form covalent disulfide bonds between two cysteine
hydrophobic side chains push away from water towards the center
of the protein
alpha helix
proline-secondary amino group is held in a rigid formation that
reduces the structural flexibility of polypeptide regions containing
proline. Found in tight turns (also disrupts alpha helix/beta pleated
sheet formation due to inducing turns/bends in the protein
structure. )
glycine moves freely, so not good alpha helix former. Others are
tyrosine, glysine, and serine
 methionine, alanine, leucine, glutamate, and lysine (MALEK) have
high helix forming properties
also called a 3.613-helix, denote number of residues per turn
beta sheet
Large aromatic residues (Tyr, Phe and Trp) and -branched amino
acids (Thr, Val, Ile) are favored to be found in strands in the
middle of sheets
made up of beta strands (stretch of 3-10 amino acids)
4 structure of proteins (BIO, BC)
two or more polypeptide chains bind together. Same forces act
quaternary as tertiary (disulfide bonds, ionic interactions, hydrogen
bonds, van der waals, hydrophobic side chain
Protein exceptions/ special cases
histidine

side chain with pka 6.5 (close to physiological pH) so it is protonated and
deprotonated in body. Usually at active site of protein to
stabilize/destabilize
Proline and Glycine


proline has secondary amino so it introduces kinks into the helix

glycine is extremely flexible so it also introduces kinks
Cysteine


Can form a disulfide bridge between the two thiol groups.

extracellular is oxidizing environment, so promotes formation of disulfide
bridges. intracellular is reducing environment

Conformational stability
Denaturing and folding
when a protein conformation disrupted and it starts losing secondary,
tertiary, and quaternary structure
folding- the protein folds into a conformation that allows it to act as a
enzyme
conformation= folded 3D structure and is active
denature= unfolded, inactive
temperature denatures secondary, tertiary, and quaternary. primary still
preserved
Acid- break ionic bonds so destroys tertiary and quaternary bonds.
Protonated acidic side chains, destroying salt bridges that help maintain
tertiary protein structures
chemical- disrupts secondary, tertiary, quaternary
enzymes- disrupts everything-primary, secondary, tertiary, quaternary.
(not technically denaturing because denaturation does not disrupt primary
structure or alter peptide bonds

Hydrophobic interactions
hydrophobic side chains push away from water towards the center of the
protein
Solvation layer (entropy) (BC)
in presence of hydrophobic R groups on the protein, surrounding
molecules assemble into an organized structure known as a solvation
layer that forces these hydrophobic groups to the inner area of the protein
Separation techniques
Isoelectric point
pH at which a particular molecule carries no net charge (but both ends
are charged, not neutral)
Affects the solubility of a molecule at certain pH environments
The protein will move in a pH gradient gel until the pH is equal to the
isoelectric point when in electrophoresis. protein that is in a pH region
below its isoelectric point will be positively charged and so will migrate
towards the cathode (negatively charged electrode)
Electrophoresis
Protein flows through pores in polyacrylamide gel. Larger protein stays at
top, smaller proteins flow faster
Flow cytometry
Can be used to separate cells by phase in cell cycle by tagging with DNA
dyes.

Non-Enzymatic Protein Function (BIO, BC)

Some examples of non-enzymatic proteins are receptors, ion channels, transport
proteins, motor proteins and antibodies
The binding of molecules is done by receptors and ion channels
Affinity and specificity is the key
Transport proteins
High concentration of transport proteins = high affinity for certain
molecules
Low concentration = low affinity
Hemoglobin works as a crucial transport protein in a human body by
delivering oxygen to muscle tissues
Immune system
Antibodies are part of the adaptive immune system. Their function is to
find foreign antigens (e.g. viruses) and to target them for destruction
Motor proteins produce forces and allow for cellular motility
Myosin generates forces by contracting muscles
Kinesin is for intracellular transport
Dynein is for intracellular transport and provides motility of cilia

Enzyme Structure and Function (BIO, BC)
Function of enzymes in catalyzing biological reactions
 reduce the energy of activation to push a reaction forward. also reduces the
energy for the reverse reaction
Enzyme classification by reaction type

Reduction of activation energy

fastest rate of reaction is one with the smallest hump
Substrates and enzyme specificity
specific enzyme only catalyzes specific reactions
Active Site Model
lock and key model- active site of the enzyme has a specific shape like a lock
that only fits a specific substrate, the key

Induced-fit Model
shape of both enzyme and substrate are altered when binding
Mechanism of catalysis
Cofactors- nonprotein component to enzymes. can be coenzymes or metals
Coenzymes- cofactors that are organic molecules
 Water-soluble vitamins- many water soluble vitamins act as coezymes
Water soluble are B and C
Effects of local conditions on enzyme activity
Enzyme: a catalytic protein that increases chemical reaction by reducing
activation energy
An enzymes activity can be affected by:
Temperature
An optimal temperature for humans is around 37 degree Celsius
(normal body temperature)
Too high or low temperature from the optimal temperature will
cause enzymes to dysfunction
pH
An optimal pH is neutral, but various around different parts of the
body
For example, pH in stomach is very low for digestion
Too high or low pH from the optimal pH will cause enzymes to
dysfunction
Chemicals
Competitive and noncompetitive inhibitors can regulate enzyme
activity as well
Competitive inhibitor binds to the active site, competing
with the substrate
Non-competitive inhibitor binds to another site of an
enzyme that causes shape change of active site to inhibit
binding of substrate

Control of Enzyme Activity (BIO, BC)

Kinetics
General (catalysis)
Lower the activation energy of a reaction (forward and backwards)
MichaelisMenten
km=[s] at max V = (k-1+kcat)/K1
constant indicates how highly concentrated the substrate must be to
speed the reaction. inversely proportional to enzyme substrate affinity
Cooperativity
positive cooperative-at low concentrations of substrate, small increases in
concentration increase enzyme efficiency, allow other substrates to bind
more easily.
negative cooperative- opposite of positive cooperative

Feedback regulation
negative feedback- one of the products downstream comes back and inhibits the
enzymatic activity of earlier reactions
positive feedback- product returns to earlier step to activate associated enzyme.
Inhibition types

Competitive
competitive inhibitor does not slow down the vmax but increases the Km
compete with substrate by binding reversibly with the active site
Non-competitive
bind at site other than the active site.
lowers vmax, but keeps km (similar to irreversible inhibitor)
Mixed (BC)
bind at site of enzyme other than active site and does not prevent
substrate binding. Can bind to enzyme alone or enzyme substrate
complex. The preference of the inhibitor dictate the effect on km and
vmax. lowers vmax and increases KM
Uncompetitive (BC)
mixed substrate. Bind to enzyme substrate complex. Does not resemble
the substrate, commonly act on more than one type of enzyme.
Unlike competitive inhibitors, they cannot be overcome by excess
substrate, so lower vmax. Km also decreases
Regulatory enzymes
Allosteric enzymes
bind at a site that is not the enzymes activity site
Covalently-modified enzymes
often irreversible inhibitors that destroy the enzyme (except for
phosphorylation)
Zymogen
inactive form of enzymes. when specific bonds on zymogens are cleaved,
they become irreversible active. activity may be instigated by other
enzymes, or changes in environment.
Content Category 1B: Transmission of genetic information from the gene to the protein
Biomolecules and biomolecular assemblies interact in specific, highly-regulated ways to transfer
sequence information between biopolymers in living organisms. By storing and transferring
biological information, DNA and RNA enable living organisms to reproduce their complex
components from one generation to the next. The nucleotide monomers of these biopolymers,
being joined by phosphodiester linkages, form a polynucleotide molecule with a backbone
composed of repeating sugar-phosphate units and appendages of nitrogenous bases. The
unique sequence of bases in each gene provides specific information to the cell. DNA molecules
are composed of two polynucleotides that spiral around an imaginary axis, forming a double
helix. The two polynucleotides are held together by hydrogen bonds between the paired bases
and van der Waals interactions between the stacked bases. The pairing between the bases of
two polynucleotides is very specific, and its complementarity allows for a precise replication of
the DNA molecule. The DNA inherited by an organism leads to specific traits by dictating the
synthesis of the biomolecules (RNA molecules and proteins) involved in protein synthesis. While
every cell in a multicellular organism inherits the same DNA, its expression is precisely
regulated such that different genes are expressed by cells at different stages of development,
by cells in different tissues, and by cells exposed to different stimuli. The topics included in this
category concern not only the molecular mechanisms of the transmission of genetic information
from the gene to the protein (transcription and translation), but also the biosynthesis of the
important molecules and molecular assemblies that are involved in these mechanisms. The
control of gene expression in prokaryotes and eukaryotes is also included. Broadly speaking,
the field of biotechnology uses biological systems, living organisms, or derivatives thereof, to
make or modify products or processes for specific use. The biotechnological techniques
emphasized in this category, however, are those that take advantage of the complementary
structure of double-stranded DNA molecules to synthesize, sequence, and amplify them, and to
analyze and identify unknown polynucleotide sequences. Included within this treatment of
biotechnology are those practical applications which directly impact humans, such as medical
applications, human gene therapy, and pharmaceuticals. Content in this category covers the
biopolymers, including ribonucleic acid (RNA), deoxyribonucleic acid (DNA), proteins, and the
biochemical processes involved in carrying out the transfer of biological information from DNA.
The topics and subtopics in this category are the following:

Nucleic Acid Structure and Function (BIO, BC)

Description
composed of a base, a phosphate group, and a sugar. basis for dna
Nucleotide = base (Adenine, Guanine, Thymine, Cytosine) + sugar + phosphate.
Nucleoside = base + sugar = Adenosine, Guanosine, Thymidine, Cytidine.
Base can either be purines A and G (the big ones with 2 rings) (Pure as gold) or
pyrimidines T, C, U (the small ones with 1 ring).
The phosphate group gives DNA its acidity.
Joined by phosphodiester bonds-two of the hydroxyl groups in phosphoric acid
react with hydroxyl groups on other molecules to form two ester bonds.

Nucleotides and nucleosides
Sugar phosphate backbone

Pyrimidine, purine residues


Deoxyribonucleic acid (DNA): double helix, WatsonCrick model of DNA structure

The "double" in the double helix means that DNA is found in a double-stranded
form - 2 single-stranded chains of DNA stuck to each other via hydrogen bonding
of the base pairs. (watson crick model)
The 2 single-strands are anti-parallel to each other. Going from 5' to 3' of one
strand means going from 3' to 5' of the other strand.
The "helix" in the double helix means that the entire thing is wound up in a spiral.

Base pairing specificity: A with T, G with C
A forms 2 hydrogen bonds with T.
G forms 3 hydrogen bonds with C.
GC bonds are stronger. DNA with high GC content will be harder to break apart.
Complementary strands of DNA hydrogen bond with each other.
5'-ATGC-3' will be complementary to 5'-GCAT-3' or 3'-TACG-5', but NOT 5'-
TACG-3'. make sure you get the 5's and 3's right.
keto forms are the predominant in physiological conditions

Function in transmission of genetic information (BIO)
Because of the complementary nature of base pairing, DNA can transmit genetic
information through replication.
DNA denaturation, reannealing, hybridization
denaturation of nucleic acids such as DNA due to high temperatures is the
separation of a double strand into two single strands, which occurs when the
hydrogen bonds between the strands are broken.
Reannealing or correctly annealing, is the process by which two single strands of
DNA combine to form double-stranded DNA
Hybridization is the process of combining two complementary single-stranded
DNA or RNA molecules and allowing them to form a single double-stranded
molecule through base pairing.

DNA Replication (BIO)

 Mechanism of replication: separation of strands, specific coupling of free nucleic acids
First, the double stranded DNA must separate, or unwind. To do this:
DNA gyrase (class II topoisomerase) relieve strain when helicase is
unwinding gene
Helicase is responsible for unwinding the DNA at the replication fork.
Single-strand binding protein (SSB) is responsible for keeping the DNA
unwound after the helicase. SSBs stabilize single-stranded DNA by
binding to it.
Next, you start making DNA that is complementary to the newly
unwound/separated DNA. Note, all biological DNA synthesis occurs from the 5' to
the 3' end.
Primase gets this started by laying down a short RNA primer on the
unwound DNA. The primer is made of RNA, but is complementary to the
DNA sequence. Later, this RNA is replaced with DNA.
DNA polymerase then takes over and makes DNA that is complementary
to the unwound DNA.
DNA synthesis occurs on both strands of the unwound DNA. The
synthesis that proceeds in the direction of the replication fork is the
leading strand. The synthesis that proceeds in the opposite direction to
the replication fork is the lagging strand. The lagging strand contains
Okazaki fragments.
Finally, RNA primers are replaced with DNA by a special DNA polymerase. The
Okazaki fragments in the lagging strands (parent 5-3)are then stitched together
by DNA ligase.
DNA synthesis is bidirectional: 2 replication forks form and proceeds in opposite
directions (like an expanding bubble).
Biological DNA synthesis always proceeds from the 5' end to the 3' end.
DNA polymerase has proof-reading activity, which means it corrects any mistakes
(mutations) it makes.
DNA poly III corrects errors in 3 to 5 while replicating dna in 5 to 3. DNA
poly I synthesize DNA, correct in 3 to 5, but also 5 to 3 exonuclease
activity to remove RNA primer and replace with DNA
RNA polymerase does not correct errors
Replication occurs once every cell generation, during the S phase. (Cell division
may occur twice in meiosis, but replication still occurs once only)

Semi-conservative nature of replication
Newly synthesized DNA contains one old strand and one new strand.
Specific enzymes involved in replication
Topoisomerase (dna gyrus)- This enzyme introduces a single-strand nick in the
DNA, enabling it to swivel and thereby relieve the accumulated winding strain
generated during unwinding of the double helix.
Single Strand Binding Proteins- Responsible for holding the replication fork of
DNA open while polymerases read the templates and prepare for synthesis.
Helicase- Uses the hydrolysis of ATP to "unzip" or unwind the DNA helix at the
replication fork to allow the resulting single strands to be copied.
 Primase- Polymerises nucleotide triphosphates in a 5' to 3' direction. The enzyme
synthesises RNA primers to act as a template for future Okazaki fragments to
build on to.
DNA Polymerase III- In charge of synthesizing nucleotides onto the leading end
in the classic 5' to 3' direction.
DNA Polymerase I- In charge of synthesizing nucleotides onto primers on the
lagging strand, forming Okazaki fragments. However, this enzyme cannot
completely synthesize all of the nucleotides.
Ligase- This enzyme is in charge of "gluing" together Okazaki fragments, an area
that DNA Pol I is unable to synthesize.
Telomerase- Catalyzes the lengthening of telomeres; the enzyme includes a
molecule of RNA that serves as a template for new telomere segments.
Nuclease- This enzyme is in charge of excising, or cutting out, unwanted or
defective segments of nucleotides in a DNA sequence.

Origins of replication, multiple origins in eukaryotes-
Eukaryotes often have multiple origins of replication on each linear chromosome
that initiate at different times (replication timing), with up to 100,000 present in a
single human cell. Having many origins of replication helps to speed the
duplication of their (usually) much larger store of genetic material. The segment
of DNA that is copied starting from each unique replication origin is called a
replicon.
Replicating the ends of DNA molecules
leading strand is replicated until the end.
lagging strand cannot be completed because 1) not enough space for RNA
primer, or 2)if there is enough room then the RNA would bind to make okizaki
fragments, but then the rna would be remove. leaving it short
Telomerase extend the ends of the DNA allowing for complete replication of the
original DNA

Repair of DNA (BIO)

Repair during replication
DNA polymerase has proof-reading activity (also called 3' 5'
exonuclease activity). If a wrong nucleotide gets incorporated, the
polymerase will "back-up" and replace it with the correct one.
The special polymerase that replaces the RNA primers with DNA also
have 5' 3' activity. This allows the polymerase to clear away short
stretches of incorrect nucleotides (RNA or incorrect DNA) and replace it
with the right ones (DNA). This process is also called repair.
Repair of mutations
if during replication there is damage that is recognize then DNA poly gamma/
epsilon will do 3 to 5 exonuclease activity
Mismatch repair: enzymes recognize incorrectly paired base-pairs and cuts out
the stretch of DNA containing the mismatch. Then polymerase re-adds the
correct nucleotides in.
During mismatch repair, the repair enzyme must decide what strand of DNA to
cut since DNA contains 2 strands. To do this, the enzyme cuts the DNA strand
 that do not have methylations. The original (old) DNA has methylations, but the
newly synthesized DNA do not have them until shortly after replication. Thus,
there is a window of time when mismatch repair enzymes can know what strand
to cut if mismatch is encountered.
Base-excision repair: a damaged base gets cut out. Then the base's sugar
phosphate backbone gets cut out. And then, several more nucleotides next to the
base get cut out. Finally, polymerase remakes the cut out nucleotides.
Nucleotide-excision repair: damaged nucleotide(s) gets cut out and then
polymerase replaces it. This is like mismatch-repair, but it's not for mismatch. It's
for damages like thymine dimers, and other damages that changes normal
nucleotides into abnormal nucleotides.
Nick translation: this is basically 5' 3' exonuclease activity coupled to
polymerase activity. The polymerase here chugs along, chews off the
bad nucleotides and then replaces them with new nucleotides. This is
what happens when RNA primers are replaced with DNA.
SOS response in E. Coli: during replication, when there's just too much DNA
damage for normal repair to handle, the SOS repair system comes along.
Instead of correcting any DNA damages during replication, the polymerase
replicates over the damaged DNA as if it were normal. By using the damaged
DNA as a template error rates are high, but it's still better than not replicating at
all.
homologous recombination and end joining

Genetic Code (BIO)

Central Dogma: DNA RNA protein
DNA: resides in the nucleus. It codes information in genes.
Transcription: Inside the nucleus, the DNA genes get transcribed into RNA
(messenger RNAs or mRNAs).
RNA: The mRNAs get transported out of the nucleus into the cytoplasm. mRNAs
are working copies of the gene.
Translation: ribosomes read off the mRNAs to make proteins.
Protein: synthesized by ribosomes. They are the end product of what's encoded
in the genes and they perform all the functions in the cell.
ribosomal subunits assembled in nucleolus
The triplet code
3 dna nucleotides code for specific amino acids
Codonanticodon relationship

Codon: The mRNA is a sequence of nucleotides, but it codes for a sequence of
amino acids. To do this, every 3 nucleotide codes for an amino acid. These
triplets of nucleotides are called codons. A single mRNA contains many codons.
Codons are continuous, non-overlapping and degenerate.
Continuous because one codon follows right after another. There're no
nucleotides in between.
Non-overlapping because the 3 nucleotides that consist of one codon
never serve as part of another codon.
Degenerate because more than one codons code for a given amino acid.
Anticodon: the 3 bases on the "tip" of the tRNA. A single tRNA contains a single
anticodon at the "tip" and the corresponding amino acid at the "tail". Anticodons
are complementary to their corresponding codon.
The codon-anticodon relationship: During translation, codons pair with
anticodons so that the correct amino acids can be linked to a given codon.

Degenerate code, wobble pairing
Degenerate code- different codons can code for the same amino acid
unambiguous coding- one codon may code for only one amino acid
RNA pairing (G-C and A-U). wobble pairing is when the nucleotides do not follow
this rule (G-U and (A-C)
Missense, nonsense codons
Missense codon: mutated codon that results in a different amino acid.
Nonsense codon: mutated codon that results in something other than an amino
acid. For example, a stop codon.
Initiation, termination codons
Initiation codon (AUG): signals the start of translation. Lies just downstream of
the Shine Dalgarno sequence (Kozak sequence for eukaryotes).
Termination codon (UAG,UGA,UAA): signals the end of translation. Unlike other
codons, tRNA are not involved. Instead a protein called "release factor" comes
along and terminates translation
Messenger RNA (mRNA)
mRNA stands for messenger RNA. It's the product of transcription and the
template for translation.
The 5' cap is a modified nucleotide linked in a special way to the mRNA. This
protects the 5' end from exonuclease degradation.
 The poly-A tail protects the 3' end of the mRNA from exonuclease degradation.
Eukaryotic mRNA: 5' cap - nucleotides - 3' polyA.
Prokaryotic mRNAs don't have the 5' cap or polyA tail.

Transcription (BIO)
Transfer RNA (tRNA); ribosomal RNA (rRNA)
Both tRNA (transfer RNA) and rRNA (ribosomal RNA) are products of
transcription. However, they do not serve as the template of translation. tRNA is
responsible for bringing in the correct amino acid during translation. rRNA makes
up the ribosome, which is the enzyme responsible for translation.
tRNA is made of nucleotides, many of which is modified for structural and
functional reasons. At the 3' end of the tRNA, the amino acid is attached to the
3'OH via an ester linkage.
tRNA structure: clover leaf structure with anticodon at the tip, and the amino acid
at the 3' tail.
rRNA is made of nucleotides, many of which is modified for structural and
functional reasons.
rRNA is highly structured because it contains the active site for catalysis. The
rRNA of the large ribosomal subunit is responsible for catalyzing peptide bond
formation, and can do this even without ribosomal proteins.

Mechanism of transcription
Chain Initiation: RNA polymerase binds to the promoter (TATA box) of the double
stranded DNA (closed complex). The double stranded DNA template opens up
(open complex).
Chain elongation: nucleoside triphosphates (AUGCs) adds corresponding to the
DNA template. No primer is required. RNA elongates as the RNA polymerase
moves down the DNA template. RNA is made from the 5' to 3' direction.
Chain termination: there are 2 ways that transcription can terminate.
Intrinsic termination: specific sequences called a termination site creates
a stem-loop structure on the RNA that causes the RNA to slip off the
template.
Rho () dependent termination: a protein called the factor travels along
the synthesized RNA and bumps off the polymerase.
occurs in the nucleus
mRNA processing in eukaryotes, introns, exons
karyotic structure
5 UTR (untranslated region)
directly upstream of coding region. used to control translation
the 5 UTR or a portion of it is sometimes translated into a protein
product. This product can then regulate the translation of the main
coding sequence of the mRNA. In many other organisms,
however, the 5 UTR is completely untranslated, instead forming
complex secondary structure to regulate translation
Coding sequence
Where translation begins and ends
 Contains the amino acid sequences for protein synthesis during
translation
Varies in length
3 UTR (untranslated region)
Contains crucial information for mRNA stability
3'-UTR often contains regulatory regions that post-transcriptionally
influence gene expression.
Processing is only required for eukaryotes
Capping
Addition of a 5, 7-methyl guanosine cap
Occurs during transcription
Is recognized by the translation machinery
Nucleases prevent RNA chain degradation
Polyadenylation
A poly-A tail is added at the 3 end
Enhances the stability of eukaryotic mRNA
Regulates transport to cytoplasmic compartment
Splicing
Removes the introns
Introns are not expressed in proteins (are an intervening
sequence)
Exons are encoding sequences and they are reserved
alternative splicing- single gene can code for multiple proteins
depending on what exons are included in mrna.
constitutive splicing- Splicing is usually constitutive, which means
that all exons are joined together in the order in which they occur
in the heterogeneous nuclear RNA
Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear
RNAs (snRNAs)
Ribozymes
Ribonucleic acid enzyme
Catalyzes biochemical reactions
Found in the ribosomes
Joins amino acids together, forming protein chains
Play a crucial role in RNA splicing, in viral replication and in RNA
biosynthesis transfers
Spliceosomes
Large splicing machines
Found within the nucleus of eukaryotic cells
Made of 5 small snRNAs and protein factors
Removes/cuts introns from pre-mRNA
snRNA
Small nuclear RNA
Found in the nucleus of eukaryotic cells
Couples with snRNPs, which recognizes both the 5 and 3 splice sites of
introns
snRNPs
Small nuclear ribonucleoproteins
Found in the nucleus of eukaryotic cells
 A combination of small RNAs and protein factors
Essential in the removal of introns as well

Functional and evolutionary importance of introns
While introns do not encode protein products, they are integral to gene
expression regulation. Some introns themselves encode functional RNAs through
further processing after splicing to generate noncoding RNA molecules.
Alternative splicing is widely used to generate multiple proteins from a single
gene. Furthermore, some introns play essential roles in a wide range of gene
expression regulatory functions such as non-sense mediated decay and mRNA
export.

Translation (BIO)
Roles of mRNA, tRNA, rRNA
mRNA (messenger RNA): contains codons that code for the peptide sequence.
tRNA (transfer RNA): contains the anticodon on the "tip" and the corresponding
amino acid on the "tail". Link the correct amino acid to its corresponding mRNA
codon through codon-anticodon interaction.
rRNA (ribosomal RNA): forms the ribosome. Catalyzes the formation of the
peptide bond.
Role and structure of ribosomes
Ribosome is the enzyme that catalyzes protein synthesis.
Ribosome has 2 subunits - the large and the small.
The large subunit is responsible for the peptidyl transfer reaction.
The small subunit is responsible for the recognizing mRNA and binds to the
Shine-Dalgarno (RBS) sequence on the mRNA (Kozak sequence for
eukaryotes).
Both subunits are needed for translation to occur and they come together in a
hamburger fashion that sandwiches the mRNA and tRNAs in between.
Initiation, termination co-factors
occurs in the cytoplasm
Initiation
The initiation complex near the initiation codon (AUG methionine) is
necessary for translation to begin. It includes mRNA, initiator tRNA and
ribosomes.
The small subunit of the ribosome binds to the 5 end of the mRNA
Upon encountering the start codon AUG, the large subunit joins the small
subunit along with initiator tRNA. Start codon also codes for methionine.
tRNA binds to the P site on the large subunit of the ribosome
Elongation
Amino acids are added by forming peptide bonds (creating a growing
polypeptide chain)
Protein synthesis occurs from the N-terminus to the C-terminus
mRNA codons are read from the 5 end to the 3 end
tRNA reads the anticodon
 Aminoacyl-tRNA (tRNA covalently bound to amino acid) pairs with the
next codon in the A site ( acceptor for the growing protein) with the help of
elongation factor and GTP (a form of energy)
Ongoing amino acids are linked with peptide bonds
rRNA gets released from the P(the ribosomal site most frequently
occupied by peptidyl-tRNA, i.e. the tRNA carrying the growing peptide
chain) site and ribosomes move one codon downstream (remember, a
codon has three nucleotides), shifting the latest tRNA to the P site
Termination
Translation stops when a stop codon is reached (UAA, UAG, UGA)
No tRNA molecule has an anticodon for stop codons
The protein release factor recognizes the stop codons instead
Upon the binding of release factors, the polypeptide chain is released
from the ribosome
The ribosome detaches back to its small and large subunit

Post-translational modification of proteins
The polypeptide chain, the product of translation, undergoes post-translational
modification before becoming the final protein product
Allows for the extension of functions of the protein by undergoing different
processes
Addition of functional groups
Glycosylation (addition of carbohydrates)
Acetylation (addition of acetyl group)
Methylation (addition of methyl group)
Sulfation (addition of sulfate group to a tyrosine)
Change of the chemical nature of the amino acids
Change of the overall structure
Removal of the amino end of the protein
Phosphorylation
Activates or inactivates proteins
Most proteins are cleaved as part of their post translational modification process

Eukaryotic Chromosome Organization (BIO)

Chromosomal proteins
Histones- responsible for the compact packing and winding of chromosomal DNA
All other proteins- responsible for various roles such as regulatory and enzymatic
Single copy vs. repetitive DNA
Single copy DNA
Present in less than 10% per genome in prokaryotes
Present in between 30-85% per genome in eukaryotes
Holds great measure of the organisms genetic information
 Protein synthesis and gene expression (regulation)
Most protein-coding genes are single copy DNA
May be translated
Long base sequences
Low rate of mutation
Repetitive DNA
In mammals and insects, repetitive DNA is concentrated at the
centromeres (region that join two sister chromatids)
Not translated
Short base sequences
Higher rate of mutation
Moderate repetitive DNA
Transcribed by RNA Polymerase I or III
Contains protein-coding genes (ex. actin and myosin)
Moves around within the genome
Highly repetitive DNA sequence
Not transcribed
Does not contain any genes

Supercoiling
A form of DNA in which the double helix is further twisted about itself, forming a
tightly coiled structure
Heterochromatin vs. euchromatin
When stained euchromatins are the light-colored bands while heterochromatins
are the dark-colored bands.Darker staining indicates tighter DNA packaging
Heterochromatins are compactly coiled regions while euchromatins are loosely
coiled regions.
Euchromatin contains less DNA while heterochromatin contains more DNA.
Euchromatin is early replicative while heterochromatin is late replicative.
Euchromatin is found in eukaryotes, cells with nuclei, and prokaryotes, cells
without nuclei.
Heterochromatin is only found in eukaryotes.
The functions of euchromatin and heterochromatin are gene expression, gene
repression, and DNA transcription.
Telomeres, centromeres
Telomeres- the ends of the chromosomes
Centromere- a region of the chromosome (center or near ends), where sister
chromatids are attached and where spindle fibers attach to pull the chromatids
apart

Control of Gene Expression in Prokaryotes (BIO)

Operon Concept, Jacob-Monod Mode
Operons
Genomic unit containing cluster of genes under the control of a single
promoter
Consists of an operator and three protein-encoding genes associated with
it (promoter, repressor etc.)
Transcribed together into an mRNA strand
Repressor: reduces transcription
 Inducer: increases transcription
Either translated together or separately
Genes in an operon are either expressed together or not at all
Jacob-Monod model
the manufacture of proteins, such as the ones encoded within the lac
(lactose) operon, is prevented when a repressor, encoded by a regulatory
gene, binds to its operator, a specific site on the DNA next to the genes
encoding the proteins. It is now known that repressor bound to the
operator physically blocks RNA polymerase from binding to the promoter,
the site where transcription of the adjacent genes begins.

Gene repression in bacteria

Binds to the operator to suppress the expression by blocking the attachment of
RNA polymerase to the promoter
Transcription cant occur, so no mRNA is produced
An RNA-binding repressor binds to mRNA, inhibiting translation, so no protein
produced
Positive control in bacteria
positive control tested with expected results to access the validity of an
experiment (ecoli transformed with a positive plasmid to ensure that the bacteria
can grow)
auxotrouphs- inability of an organism to synthesize a particular organic
compound required for its growth. Cannot grow on minimal media

Control of Gene Expression in Eukaryotes (BIO)

Transcriptional regulation
Transcription factors (protein) bind to enhancers or silencers (DNA) to affect
transcription. Enhancers increase transcription when bound, while silencers
decrease it
 In eukaryotes, enhancers/silencers can be very far from the promoter, and can
be upstream or downstream
DNA loops back on itself so transcription factor can make contact with promoter
(intermediate proteins involved)
Eukaryotes lack the bacterial transcription regulation mechanisms such as the
operon and attenuation
DNA binding proteins, transcription factors
DNA-binding proteins bind to DNA
Transcription factors bind to DNA, so they have a DNA-binding domain
DNA-binding domains interact with the grooves in the double helix (major and
minor)
Advanced: Common DNA-binding domains include helix-turn-helix, zinc finger,
basic-region leucine zipper
Gene amplification and duplication
Gene amplification
The number of copies of a gene can increase in development
Duplication of a DNA region that contains a certain kind of gene
Can occur naturally or artificially
In response to signals from other cells or from the environment,
cancer cells can produce multiple copies of genes
Usually occurs during meiosis, when chromosomes cross over
and recombination occurs
Necessary for maintenance of the genome
This process is used in the polymerase chain reaction (PCR) for medical
and biological research purposes
The amplification of rRNA genes occurs during the development of ova
Gene duplication is also referred to as chromosomal duplication or gene
amplification
Post-transcriptional control, basic concept of splicing (introns, exons)
tRNA and rRNA modifications: some normal nucleotides are modified to control
the structure of these RNAs
mRNA modification
RNA splicing: introns cut out and exons kept to be expressed
Alternate splicing: different ways to cut RNA
5 capping and 3 poly-A tail: protect RNA from degradation so they last
longer
After modification, RNA transported out of nucleus for translation
RNA is later degraded (rate and timing of degradation controlled by the cell)
Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes
Failure of normal cellular controls:
Cancer cells continue to grow and divide in situations normal cells would
not, fail to respond to cell controls and signals that would halt growth
Avoid apoptosis that normally occurs when extensive DNA damage is
present
Stimulate angiogenesis- cause new blood vessels to grow to nourish the
cancer cell
Cancer cells are immortal while normal cells die after a certain number of
divisions
 Cancer cells can metastasize- break off and then grow in another location
Oncogenes- cause cancer when activated (SRC), harmless proto-oncogenes are
somehow activated into a oncogene
Tumor Suppressors: slow or control cell division (P53), cell becomes cancerous if
tumor suppressor no longer functions
Regulation of chromatin structure
Functions of chromatin
to package DNA into a smaller volume to fit in the cell
to reinforce the DNA macromolecule to allow mitosis
to prevent DNA damage
to control gene expression and DNA replication.
The structure of chromatin can be modified by various mechanisms, such as
methylation, acetylation and phosphorylation.
Such modifications change chromatins interaction with DNA and with
nuclear proteins
Methylation: the addition of a methyl group to amino acids. Makes DNA
heterochromatin
Acetylation: the addition of an acetyl group to amino acids, makes dna
euchromatin and open for translation
Phosphorylation: the addition of a phosphate group
Regulation involves:
Nucleosome
A repeating subunit of chromatin
Composed of:
Nucleosome core: contains an octamer of 2 copies each of
the core histones and 146 base pairs of DNA wrapped
around the octomer
Histones types include H2A, H2B, H3, and H3
Histone H1
Variable length linker DNA

Histones
Found in eukaryotes (in cell nuclei)
Crucial protein component of chromatin
Function to compact the DNA
Two H3 and H4 dimers are linked together, forming a tetramer that
binds DNA
Two H2A and H2B dimers are linked together with the tetramer,
forming the histone octamer
The modification of histones can affect transcription and gene
expression
Dna is wrapped around histone proteins. 8 wrapped histones
forms a nucleosome. Nucleosome wind into complexes called
chromatin. These are condensed in chromosomes.

DNA methylation
Addition of methyl group to cytosine
Converted to 5-methylcytosine
Done by the DNA methyltransferase (DNMT) enzyme
 Usually besides the guanine nucleotide, methylated cytosine molecules usually
are diagonal to each other
Blocks the promoter, so no transcription factors can bind for gene expression to
occur (works as a repressor)
Crucial role for cell differentiation and embryonic development
Hyper- or hypomethylation can cause cancer

Role of non-coding RNAs
Not translated into a protein
Includes tRNAs, rRNAs, and many more different types
Crucial role in cellular processes such as translation
Regulate RNA splicing, DNA replication, and gene regulation
Exact numbers unknown, but are abundant


Recombinant DNA and Biotechnology (BIO)

Gene cloning
Both plasmid and gene have same restriction sites so can be inserted into each
other
Plasmid must have origin of replication to clone, and must have antibiotic
resistance to isolate on antibiotic plate
Plasmids replicate independently of genomic DNA
Restriction enzymes
Also known as restriction endonucleases as they cut within the molecule
Cuts foreign double stranded DNA sequences into fragments
Host DNA is protected
Found in bacteria and archaea
Some cut fragments with sticky ends, which can hybridize
Some cut fragments with blunt ends, which cannot hybridize

Type 1 restriction enzyme- Type I enzymes cleave at sites remote from the
recognition site; they require both ATP and S-adenosyl-L-methionine to function.
Type 2 restriction enzyme- cleave within or at short specific distances from
recognition site and often require magnesium.
Type 3 restriction enzyme- cleave at sites a short distance from recognition site;
require ATP (but do not hydrolyse it); S-adenosyl-L-methionine stimulates
reaction but is not required
type 4 restriction enzyme- target modified DNA (e.g. methylated,
hydroxymethylated).
DNA libraries
Compilation of DNA fragments within a host organism for molecular cloning
Long strands of DNA are cut to be stored and replicated in the host
organism
Different types of DNA libraries
cDNA library
mRNA is purified and converted back to DNA by reverse
transcriptase
Beneficial in reverse genetics
Genomic library
Cloned genes signify the entire genome of an organism
Beneficial in genome projects and in other genetic engineering
research areas
Generation of cDNA
cDNA
Complementary DNA synthesized from mRNA
Messenger RNA is reversely transcribed in the nucleus that only has the
expressed gene of an organism
Involves reverse transcriptase and DNA polymerase
 Frequently used to clone eukaryotic genes in prokaryotes
best to use in laboratory setting because the introns have already been
removed
cDNA library
Consists of cloned cDNAs inserted into particular host cells
Positive aspect: can easily identify gene products
Negative aspect: lacks information about introns and other regulatory
elements
Lacks introns because mRNA in eukaryotic cells are already
spliced

Hybridization
(annealing) DNA strands base pair with each other
In gene cloning, hybridization is when sticky ends from a restriction fragment of a
gene base pairs with the sticky ends of a plasmid
Expressing cloned genes
Both plasmid and gene have same restriction sites so can be inserted into each
other
Plasmid must have origin of replication to clone, and must have antibiotic
resistance to isolate on antibiotic plate
Plasmids replicate independently of genomic DNA
Plasmids inserted into bacteria via transformation, allowing for expression
Polymerase chain reaction
Denaturing- separating DNA strands with heat (90C)
Annealing- cooling reaction to allow (excess) primers to anneal
Elongation: polymerase extends primers
Amplification of DNA after n cycles is 2^n

Gel electrophoresis and Southern blotting
gel electro-Gel electrophoresis works by using an electric current to pass DNA
samples through a gel. The gel acts like a sieve allowing smaller DNA molecules
to migrate through the gel quicker than larger molecules. The gel is then
visualised under UV light where DNA samples appear as bands. Bands which
have migrated further down the gel are smaller than those which have not moved
as far.
Dna is negatively charged. Moves toward the anode (anions move
towards anode
In Southern Blotting, used to verify presence of nucleotide sequence from
sources
dna digested, run on agarose gel, transferred onto nylon, and then
radiative probe is added. Binds to complementary dna segments, which
can then be detected on xray film (western blot for DNA)
DNA sequencing
Similar to the process of PCR
Denaturation
Breaks two strands apart
Annealing
 Primers bind to specific locations, then DNA polymerase follows
and elongates the strands
Replication
Replication of the new strand of DNA forms many copies

Now they just tag the complementary bases with fluorescents, and read the
fluorescents
Analyzing gene expression
Useful to detect:
Any viral infections in the cells
Ones susceptibility to cancer
Resistance to penicillin
mRNA quantification
Northern blotting
Determines the size and sequence information of mRNA
Use of radioactive labeled RNA
RT-qPCR
Reverse transcription followed by quantitative PCR
cDNA is created from mRNA then amplified
Protein quantification
Western blot
Identifies the type and size of the proteins
Location of the expression
Use of fluorescent protein marker


Determining gene function
BLASTN, BLASTN, and more analysis tools are available. These tools group and
interpret genes that are similar to certain proteins or related groups. Such tools
provide an easier way to determine the functions of genes in biology.
Another way to determine gene function is to observe a biological system without
a certain gene. Comparing the system that has the gene and that does not, one
can learn about the genes function and its effect.
Stem cells
Undifferentiated cells found in multicellular organisms
Have the ability to differentiate into other specialized cells
Can divide to produce more stem cells
In humans they are found in:
Bone marrow
Extracted by harvesting
Adipose tissue
Extracted by liposuction
Blood
Extracted by apheresis (blood draw)
Functions
Self-renewal
Differentiation into specialized cells
There is a lot of research being conducted around the world on stem cells as a
form of treatment for various diseases (refer to the diagram below).


Practical applications of DNA technology: medical applications, human gene
Medical applications
Diagnose genetic and infectious diseases
Sickle cell disease
Allow for early treatments in the next generations
HIV DNA in blood and/or tissue
Development of vaccines
Utilize a harmless variant of pathogens to stimulate the immune
system for defense in the future
Therapeutic hormones
Insulin for diabetes
 Human gene therapy
For those with genetic disorders
Insertion of a normal allele into the somatic cells of an affected
tissue
Forensic evidence
Blood type and tissue evidence can be identified by using
antibodies
Use of fingerprints
Environmental cleanup
Use of genetically engineered microbes
Extract heavy metals from the environments
Agriculture
Use of genetically modified organisms (GMOs)
Induces faster and bigger growth of crops
Safety and ethics of DNA technology
May generate new harmful pathogens
May lead to the development of antibiotic and fungal resistance
Experimental abuse on human subjects
Treatments are used for preferences, not for necessity
Pick specific traits in a child, such as eye or hair color
Genetically modified crops may be hazardous to humans and to the environment
Ethical questions
Who is qualified to receive such treatments?
How can genetic information be used?

Content Category 1C: Transmission of heritable information from generation to

generation and the processes that increase genetic diversity
The information necessary to direct life functions is contained within discrete nucleotide
sequences transmitted from generation to generation by mechanisms that, by nature of their
various processes, provide the raw materials for evolution by increasing genetic diversity.
Specific sequences of deoxyribonucleic acids store and transfer the heritable information
necessary for the continuation of life from one generation to the next. These sequences, called
genes being part of longer DNA molecules are organized, along with various proteins, into
biomolecular assemblies called chromosomes. Chromosomes pass from parents to offspring in
sexually-reproducing organisms. The processes of meiosis and fertilization maintain a species
chromosome count during the sexual life cycle. Because parents pass on discrete heritable
units that retain their separate identities in offspring, the laws of probability can be used to
predict the outcome of some, but not all, genetic crosses. The behavior of chromosomes during
meiosis and fertilization is responsible for most of the genetic variation that arises each
generation. Mechanisms that contribute to this genetic variation include independent assortment
of chromosomes, crossing over, and random fertilization. Other mechanisms, such as mutation,
random genetic drift, bottlenecks, and immigration, exist with the potential to affect the genetic
diversity of individuals and populations. Collectively, the genetic diversity that results from these
processes provides the raw material for evolution by natural selection. The content in this
category covers the mechanisms by which heritable information is transmitted from generation
to generation, and the evolutionary processes that generate and act upon genetic variation. The
topics and subtopics in this category are the following
Evidence that DNA is Genetic Material (BIO)

Mendelian Concepts (BIO)

Phenotype and genotype
Phenotype = what is observed
Genotype = the genetic makeup
Probability calculations- Use punnett squares and then multiply each possibility
together to find total
Pedigrees: squares = male, circle = female, shaded = positive phenotype, white
= wild type, dot = carrier
Gene= stretch of DNA that codes for a trait. In molecular biology, the gene codes for a
protein, which acts to bring about a trait
Locus = location (of a gene) on a chromosome
Allele: single and multiple
An allele is a variant of a gene. A gene may have a number of alleles. All alleles
of the same gene exist at the same locus
A cell holds 2 alleles of each gene (one from each parent)
Simple case: when a gene only has 2 alleles
For example, height in peas is governed by T and t, where TT and Tt are
tall and tt are short
Multiple alleles = gene has more than 2 alleles
For example, blood type is governed by 3 alleles: IA, IB, and i. Each cell
only has 2 alleles

Genotype Blood type (phenotype)

IAIA, IAi A

IBIB, IBi B

IAIB AB

ii O


Homozygosity and heterozygosity
Homozygous: when two alleles that an individual carries are the same
Heterozygous: when the two alleles that an individual carries are different
Wild-type : the normal allele or phenotype for an organism. The wild-type is usually the
most prevalent, although it doesnt have to be
Recessiveness : the weak allele (usually lowercase). The recessive allele is only
expressed if both copies are present. Only a single copy is needed for the dominant
allele.
Complete dominance
Homozygotes (AA) is complete dominance and Heterozygotes (Aa) show the
dominant phenotype
Co-dominance
 Heterozygotes (AB) show both A and B phenotypes
AB blood is a combination of A and B phenotypes
Incomplete dominance, leakage, penetrance, expressivity
Incomplete dominance: Heterozygotes (AB) show a phenotype in between A and
B
A cross between black and white chickens gives grey chickens
Leakage: gene flow from one species to another
Penetrance is the frequency that a genotype will result in the phenotype (95%
penetrance means 95% of those with the gene express it)
Expressivity is to what degree a penetrant gene is expressed. Constant
expressivity means every time the gene is expressed, it is the same (always red).
Variable expressivity means it can be different (pink or dark red)
Hybridization: viability
The process of two complementary, single-stranded DNA or RNA combining
together, producing a double-stranded molecule through base pairing
Interbreeding between individuals from genetically distinct populations
The two individuals are each carrying a different allele of the same gene
Depending on the temperature, the base pairing can be broken and the strands
will be separated
Gene pool = all of the alleles in a population

Meiosis and Other Factors Affecting Genetic Variability (BIO)

Significance of meiosis : meiosis introduces genetic variability by genetic recombination.
Genetic recombination is the product of independent assortment and crossing-over,
which introduces genetic variability

Occurs during prophase I of meiosis
Important differences between meiosis and mitosis


Mitosis Meiosis
 No tetrad Tetrad formation (pairing of
homologous chromosomes) and cross
over

Daughter cells identical to parent cell Daughter cells different from parent
cell

Diploid (2n) daughter cells Haploid (n) daughter cells

1 division involved 2 divisions involved

2 daughter cells 4 sperm cells or 1 egg (with polar

bodies)

Segregation of genes
Independent assortment
Independent assortment generates genetic variation
A cell has 2 copies of each somatic chromosome- one from mom, one
from dad (homologous chromosomes)
Independent assortment shuffles these chromosomes, and then places
only one copy of each into the gamete. (Different chromosomes from
different parents)
Mechanism of independent assortment:
During metaphase I of meiosis, homologous chromosomes pair up
along the metaphase line in random orientation (either moms or
dads on the right or left)
During anaphase I of meiosis, the homologous chromosomes are
pulled apart, one going into each daughter cell
Linkage
Because of independent assortment, genes on different chromosomes
are randomized. However, genes on the same chromosome are not
randomized this way
Genes on the same chromosome are linked to some extent
Crossing over is a mechanism that reduces linkage. However, crossing
over is only efficient when the genes are physically apart from each other
on the chromosome
When the genes are further apart on the chromosome, crossing over
makes them less linked
The physically closer the genes are on the chromosome, the more linked
they are, and the less likely they will be separated
Recombination : Introduction of genetic diversity into gametes during meiosis (via
independent assortment and crossing over)
Crossing over: occurs during prophase I at the chiasma, which formed
from synapses to connect tetrads
Single crossovers : results in genetic recombination. The chromatids
involved exchange alleles at a given locus (results in 2/4 recombinants)
Double crossovers
 Scenario 1: results in no genetic recombination. The chromatids
involved exchange alleles at first, but then exchange them back,
resulting in no net recombination. Called the 2-strand double
crossover (results in 0/4 recombinants)
Scenario 2: results in genetic recombination. The chromatids
exchange alleles during a crossover. Then, one of the crossover
chromatids exchanges with a different chromatid. Called 3-strand
double crossover (results in 2/4 recombinants)
Scenario 3: results in genetic recombination. The chromatids
exchange, then 2 different chromatids on the same chromosome
exchange. Called 4-strand double crossover (results in 4/4
recombinants)
Synaptonemal complex
A protein complex located in between homologues chromosomes
Thought to be involved in genetic pairing, synapsis and
recombination
However, research has shown that it is not involved in
recombination

Tetrad
Produced during meiosis through the process of synapsis
Chiasma between a pair of homologous chromosomes results in
the formation of four chromatids

Sex-linked characteristics
Very few genes on Y chromosome
Y chromosome is small and carries few genes of importance
All the sex-linked alleles are carried on the X chromosome
Sex determination
XX = female, XY = male
(SRY gene on the Y chromosome is what makes a person male)
Cytoplasmic/extranuclear inheritance
Cytoplasmic inheritance = inheritance of things other than genomic DNA
All cellular organelles, such as mitochondria, are inherited from the
mother
Mutation
General concept of mutation error in DNA sequence
Mutation = change in DNA sequence by means other than recombination
(error in DNA sequence)
Types of mutations: random, translation error, transcription error, base
substitution, inversion, addition, deletion, translocation, mispairing
Random mutation = random changes in DNA sequence. Can be due to
radiation, chemicals, replication error, etc
Transcription error = even if DNA is perfect, errors during transcription
can cause expression of mutant phenotype
Translation error = even if DNA is perfect, errors during translation can
cause expression of a mutant phenotype
 Base substitution = mutation involving a base changing into a different
base
Inversion = a chromosomal rearrangement in which a segment of a
chromosome is reversed end to end. An inversion occurs when a single
chromosome undergoes breakage and rearrangement within itself.
Addition = insertion = an extra base is added into the DNA sequence
Deletion = a base is taken out of the DNA sequence
Translocation = Translocations are chromosome mutations in which
chromosome segments, and the genes they contain, change positions
Frameshift: an addition or deletion causes each codon to now be different
Mispairing = A not paired with T, or G not paired with C
Advantageous vs. deleterious mutation
Advantageous = results in a benefit to the fitness of the organism
Deleterious = results in a harmful effect to the fitness of the organism

Inborn errors of metabolism = genetic diseases resulting in faulty metabolism
For example, PKU (Phenylketonuria) is an inborn error of metabolism
where people cant metabolize phenylalanine
Relationship of mutagens to carcinogens
Mutagen = causes mutation
Carcinogen = something that causes cancer
Carcinogens are almost always mutagens (Exception: some are direct
mitogens- increase mitosis)
Not all mutagens are carcinogens
Genetic drift
Genetic drift is the random changes in allele frequencies
Effect of genetic drift increases as population size decreases
Bottlenecks increase the effect of genetic drift
Synapsis or crossing-over mechanism for increasing genetic diversity
Synapsis: a mechanism that occurs during prophase I of meiosis (pairing of two
homologous chromosomes)
A replicated, homologous pair of chromosomes from each parent come together
(synapsis) and a section of the chromosomes is exchanged (crossing over)
Synapsis occurs before crossing over
Synapsis always occurs, while crossing over may or may not occur
As a result, daughter chromosomes contain genes from both parents, increasing
genetic diversity


Analytic Methods (BIO)

HardyWeinberg Principle
(P + Q)2 = 1 P2 + 2PQ + Q2 = 1
Five Assumptions of Hardy-Weinberg
Infinitely large population (no genetic drift)
No mutation
No migration
Random mating (no sexual selection)
No natural selection
Testcross (Backcross; concepts of parental, F1, and F2 generations)
Test Cross: to find out if you have AA or Aa, cross it with aa and see if you have
any recessive offspring
Back Cross: mating between offspring and parent = get more of parental
genotype
Parental generation = P
F1 generation = Filial 1 = children
F2 generation = Filial 2 = grandchildren
 Gene mapping: crossover frequencies
A way to determine the location of genes on chromosomes
Can identify the distance between genes and the frequency of
recombination
The closer the genes, the less likely they are going to be separated during
crossover and the more likely they will be passed on to the next generation
together
Provides useful information about the chance of the inheritance of
disorders

Biometry: statistical methods
Two basic rules of probability to solve problems in genetics:
Multiplication
Independent events in sequence
Questions with and
Addition
Mutually exclusive events
Questions with or
Nature of inheritance
Draw a test cross
Apply the chi-squared test
A method to determine the actual and the expected results
x2 = [(obs. exp.)2 / exp.]
obs. = observed data
exp. = expected data


Evolution (BIO)
Natural selection
Fitness concept
Fitness is defined as the ability to pass your genes on, or reproductive
success
Selection by differential reproduction
Individuals who reproduce more viable offspring are selected FOR
Individuals who reproduce less viable offspring are selected AGAINST
Concepts of natural and group selection
Natural selection = survival and reproduction of the fittest
Directional selection = selects for a trait on one extreme (trees compete
for sunlight, so selection favors taller trees)

Stabilization selection = selects for a trait that is moderate, and selects
against the extremes (moderate birth weight is ok)

Disruptive selection = selects for extremes (birds with small beaks can eat
seeds, large beaks can eat berries)

Group selection = natural selection acting on the group, not the individual
Explains why altruism exists
Altruism = sacrifice fitness of the individual for the benefit of the
group (family), which shares similar genes as the individual. When
the benefit outweighs the cost, the altruistic behavior is selected
for
Evolutionary success as increase in percent representation in the gene pool of
the next generation
If the frequency of an allele increased, thats evolutionary success for that
allele
If the frequency of alleles of an individual increased in a population, thats
evolutionary success for the individual


Speciation
Definition of species
Three conditions for biological species:
Able to interbreed
Able to produce fertile, viable offspring
Does this naturally
Polymorphism = different forms of alleles/traits (phenotypes)
Adaptation and specialization
Adaptation = genetic change in a population caused by natural selection
Adaptation is Darwins idea of existing diversity, not Lamarcks ideas that
we change ourselves and pass on that change
Specialization = adaptation of traits to better fill a niche
Inbreeding
Inbreeding is mating between relatives
Inbreeding increases the frequency of homozygotes, decreases
heterozygotes, and decreases genetic diversity
Inbreeding depression occurs because of the increase in frequency of
homozygous recessive detrimental alleles
Some species (naked mole rats) naturally inbreed because:
They stay in one small area and dont migrate much
Detrimental homozygous recessive alleles are eliminated because
of many generations of natural selection
Outbreeding
Outbreeding is mating with non-relatives, which increases heterozygosity
Bottlenecks
 A bottleneck is a severe reduction in population size. This can be caused,
for example, by a natural disaster that wipes out a majority of the
population
Genetic drift is the random changes in allele frequencies
Effect of genetic drift increases as population size decreases
Bottlenecks increase the effect of genetic drift
Evolutionary time as measured by gradual random changes in genome
Random genetic mutations (drift) that are not acted on by natural selection
(neutral) occur at a constant rate
By measuring the amount of these neutral mutations, you can find out how much
time has passed
You can compare genome differences between two species to find out how long
ago they have diverged

also called a molecular clock

Content Category 1D: Principles of bioenergetics and fuel molecule metabolism

Living things harness energy from fuel molecules in a controlled manner in order to sustain all
of the processes responsible for maintaining life. Cell maintenance and growth is energetically
costly. Cells harness the energy stored in fuel molecules, such as carbohydrates and fatty acids,
and convert it into smaller units of chemical potential known as adenosine triphosphate (ATP).
The hydrolysis of ATP provides a ready source of energy for cells that can be coupled to other
chemical processes in order to make them thermodynamically favorable. Fuel molecule
mobilization, transport, and storage are regulated according to the needs of the organism. The
content in this category covers the principles of bioenergetics and fuel molecule catabolism.
Details of oxidative phosphorylation including the role of chemiosmotic coupling and biological
electron transfer reactions are covered, as are the general features of fatty acid and glucose
metabolism. Additionally, regulation of these metabolic pathways, fuel molecule mobilization,
transport, and storage are covered. The topics and subtopics in this category are the following:

Principles of Bioenergetics (BC, GC)

Bioenergetics/thermodynamics
Free energy/Keq
Equilibrium constant
There are 2 ways of getting Keq
From an equation, Keq = [C]c[D]d/[A]a[B]b
From thermodynamics, G = -RT ln (Keq)
Derivation: G = 0 at equilibrium.
 G = G + RT ln Q
0 = G + RT ln Qat equilibrium
G = -RT ln Keq
At equilibrium:
G = 0
rforward = rbackward
Q = Keq
kdissociation=K-1/K1. Kbinding= K1/K-1. Equilibrium constant K=1/(kd)
Keq is a ratio of kforward over kbackward

K G reaction favored spontaneity

nonspontaneou
<< 1 + reverse
s

1 0 n/a n/a

>> 1 forward spontaneous

Concentration
Le Chteliers Principle
When a system at equilibrium is subjected to change in
concentration, temperature, volume, or pressure, then the system
readjusts itself to (partially) counteract the effect of the applied
change and a new equilibrium is established.
Endothermic/exothermic reactions
Endothermic- energy must be put into the system for the reaction to go
forward. Exothermic- releases energy from the reaction
Free energy: G
Equation 1: G = H TS
Energy is converted into work at a uniform temperature and
pressure throughout a system
G is the change in free energy of a system
negative means spontaneous when pressure and volume
are the same
H is the change in enthalpy
T is the absolute temperature
S is the change in entropy
Equation 2: G= -RTlnK
G is the change in standard free energy
R is the gas constant
T is the temperature
K is the equilibrium constant
Spontaneous reactions and G
if delta g is negative then the reaction is spontaneous
Phosphoryl group transfers and ATP
ATP hydrolysis G << 0
 atp is cleaved into ADP and Pi releases a large amount of energy and is
able to be combined with endothermic reactions to push them forward
ATP group transfers
Phosphoryl groups (PO3) are derivatives of phosphoric acid (a strong
acid)
The nucleophilic attack by water on a phosphate monoester
produces inorganic phosphate
Different derivatives are used for various reactions
For example, inorganic phosphate groups (Pi) are used during
glycolysis
When ATP is depleted during exercise, phosphate is transferred
from phosphocreatine to ADP to replenish ATP
Phosphate diester is used in the backbone of DNA
Biological oxidation-reduction
Half-reactions
A half reaction is either the oxidation or reduction reaction component of a
redox reaction. A half reaction is obtained by considering the change in
oxidation states of individual substances involved in the redox reaction.
Soluble electron carriers
Electrons are transferred from one electron carrier to another
energy level decreases energy is released
Electron transport chain (ETC): a series of compounds that
transfer electrons from an electron donor to an electron acceptor
(via redox reactions), which then transfers protons across a
membrane
Ubiquinone (Q)
Lipid-soluble electron carrier
Reduced to ubiquinol (QH2)
The process: NADH + H+ Complex I Q ( complex II
succinate) complex III cytochrome c complex IV
O2
located in the membrane of the mitochondria
Cytochrome c
A water-soluble electron carrier located within the intermembrane
space
Pigments that contain iron (Fe)
The process: QH2 + 2 cytochrome c [Fe(III)] + 2 H+ (in)
Q + 2 cytochrome c [(Fe(II)] + 4 H+ (out)
Quinone
A lipid-soluble carrier that shuttles electrons between large
macromolecular complexes embedded in the membrane
Flavoproteins
Proteins that contain a nucleic acid derivative of riboflavin
FAD = flavin adenine dinucleotide
FMN = flavin mononucleotide
Respiratory enzymes catalyze redox reactions
Involved in bioluminescence, photosynthesis, DNA repair, apoptosis, and
many other processes
 Electron transfer flavoprotein (ETF) function as a specific
electron acceptor for primary dehydrogenases
Transfers the electrons to terminal respiratory systems

Carbohydrates (BC, OC)

Description
general chemical formula (CH2O)n
Nomenclature and classification, common names
nomenclature
Carbohydrate = Sugars, monosaccharides, disaccharides,
polysaccharides
Prefix:
Deoxy = it has an -H in place of an -OH at a certain
position.
D/L = absolute configuration = assigned based on the
chirality of the carbon atom furthest from the carbonyl
group.
/ = anomeric configuration.
Suffix: all sugars end in -ose.
classification
aldose = sugars with an aldehyde group.
ketose = sugars with a ketone group.

pyranose = sugars in a 6 membered ring structure = hexagon

shaped. For example, glucopyranose = glucose in a 6 membered
ring.
furanose = sugars in a 5 membered ring structure = pentagon
shaped. For example, fructofuranose = fructose in a 5 membered
ring.
#ose = sugar with # carbon atoms. For example, hexose = sugar
with 6 carbons. Another example: aldopentose = a five-carbon
sugar with an aldehyde group.
In order to be classified as a carbohydrate, a molecule must have:
at least a 3 carbon backbone.
an aldehyde or ketone group.
at least 2 hydroxyl groups.
 Beta is when the anomeric OH sticks up

Alpha is when the anomeric OH sticks down

A alpha or beta bond is dependent on if the bond sticks up or
down from carbon 1
common names

The simplest, smallest carbohydrates are glyceraldehyde and
dihydroxyacetone.

The 3 common monosaccharides are glucose, fructose, and
galactose. Glucose is our blood sugar and the product of
photosynthesis. Fructose is the sugar in fruits, and it is sweeter
than glucose. Galactose is one of the monomers that make up
lactose, which is the sugar in milk; it is less sweet than glucose.


The sugar that make up RNA is ribose, and for DNA it is

deoxyribose (More precisely it's 2'-deoxyribose because the
difference is at the 2 carbon).
Sucrose is a disaccharide made from -glucose and -fructose
joined at the hydroxyl groups on the anomeric carbons (making
acetals). Sucrose is table sugar, the sugar we buy in stores.

Lactose is a disaccharide made from -galactose and /-glucose

joined by a 1-4 linkage.

Starch = glucose molecules joined by 1-4 linkage.



Glycogen = same as starch, but with additional 1-6 linkages for

branching.

Absolute configuration

The chiral carbon furthest from the carbonyl group determines the
absolute configuration L or D of the sugar.
If in the fischer projection, the OH group on the chiral carbon furthest from
the carbonyl is pointing left, then it's L. If it's pointing right, then it's D.
Note: L and D are enantiomers, not epimers. So, every chiral carbon
center inverts. It's just that you assign L and D based on the chiral carbon
furthest from the carbonyl.
epimers- only one chiral center is changed
Absolute configuration S= L sugar. Absolute configuration R= D sugar
Cyclic structure and conformations of hexoses

Fructose forms a furanose when carbon 5 attacks the carbonyl carbon.

Glucose forms a pyranose when carbon 5 attacks the carbonyl carbon.

Convert a Fischer projection to Haworth (cyclic) form
-OH groups that are pointing Left on the Fischer becomes Up on
the Haworth.
-OH groups that are pointing Right on the Fischer becomes Down
on the Haworth.
The -OH group on the anomeric carbon (the Fischer carbonyl) can
be either up (beta) or down (alpha).
The CH2OH group on the absolute configuration carbon (carbon 5)
points up for D, and down for L.

In the planar conformation, everything is eclipsed.
In the chair conformation, everything is staggered.
All the conformations in between are partially eclipsed.
The Boat conformation has Flagpole interactions because axial
groups attached to the head and tail of the boat clash.
The Twist-boat conformation lessens these Flagpole interactions
in addition to reducing the number of eclipsed interactions.
Epimers and anomers

Epimers = different configuration in just one chiral carbon.

Anomers = different configuration in the chiral, anomeric carbon when the
molecule is in the cyclic form.
Anomers are simply special types of epimers.
Epimers are simply special types of diastereomers.
Don't confuse with enantiomers (D/L configuration), in which everything
changes configuration.

Hydrolysis of the glycoside linkage
Glycoside linkage = acetal linkage = linkage involving the hydroxyl group of the
anomeric carbon.
Glycoside linkage can also mean the linkage between the sugar and the base in
nucleotides.
Examples of glycosidic linkages = starch, glycogen, nucleotide.
Hydrolysis of the glycosidic bond has the same mechanism as hydrolysis of the
acetal bond.

glycoside + H2O + catalyst hydrolysis.
Catalysts include: Amylase for starch and glycosylase for nucleotide.
Monosaccharides
most basic form of carb.
Disaccharides
A disaccharide is a sugar (a carbohydrate) composed of two monosaccharides. It
is formed when two sugars are joined together and a molecule of water is
removed.
Polysaccharides
Polysaccharides are polymeric carbohydrate molecules composed of long chains
of monosaccharide units bound together by glycosidic linkages and on hydrolysis
give the constituent monosaccharides or oligosaccharides.

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway (BIO, BC)

Glycolysis (aerobic), substrates and products

Feeder pathways: glycogen, starch metabolism
glycogen cleaved by glycogen phosphorylase to produce monomers of
glucose-1-phosphate, which is then converted to glucose 6-phosphate by
phosphoglucomutase.
starch broken down into glucose
Fermentation (anaerobic glycolysis)
A metabolic, anaerobic process that converts sugars to acids, gases and/or
alcohols. occurs in cytoplasm
Occurs in bacteria, yeast and oxygen-starved muscle cells to produce energy
(ATP)
Regenerates the NAD supply to keep glycolysis going
Glycolysis uses up NAD to produce NADH
Glycolysis is common to all fermentation pathways:
C6H12O6 + 2 NAD+ + 2 ADP + 2 Pi 2 CH3COCOO + 2
NADH + 2 ATP + 2 H2O +
Glycolysis fermentation

Fermentation is a redox reaction that reduces the pyruvate to oxidize NADH into
NAD. The resultant product is 1 NAD per pyruvate

Two types of fermentation (refer to the diagram):
Alcohol fermentation
Pyruvate is reduced to ethanol

Lactic acid fermentation
Pyruvate is reduced to lactate


Gluconeogenesis (BC)

Pentose phosphate pathway (BC)
G6P + 2NADP+ + H2O = Ribose 5 P + CO2 + 2H+ + 2NADPH

Net molecular and energetic results of respiration processes


should really be 2.5 ATP/ NADH and 1.5ATP/FADH2 (4 H+=1

ATP)because energy must be expended to bring ADP into the matrix,
which isnt included.
30 for eukaryotes (use g3p shuttle) and 32 for prokaryotes (use
malate aspartate shuttle)

Principles of Metabolic Regulation (BC)

Regulation of metabolic pathways (BIO, BC)
Maintenance of a dynamic steady state
Feedback inhibition
A molecule (inhibitor) binds to an enzyme and decreases its
activity
Inactivates or activates enzymes in the pathway
Isozymes
Different enzymes that catalyze same reaction
Enzymes
Increase or decrease enzyme concentrations for metabolic
reactions
Rapid/short effect vs. slow/long effects
Rapid effect: example- right after exercise
Regulating body temperature (sweating, breathing, etc.)
nervous system is usually rapid response
Slow effect: example- during puberty
 The synthesis of certain required proteins throughout a
longer period of time
usually by hormones

Regulation of glycolysis and gluconeogenesis
High blood glucose leads to a release of insulin leading to the turning on
glycolysis
low blood glucose leads to the release of glucagon which turns off glycolysis and
turns on gluconeogenesis
Metabolism of glycogen
glycogen phosphorylase breaks the 1,4 bond while inserted a Pi forming a G1P.
Phospho gluco mutase then converts it to G6P
Regulation of glycogen synthesis and breakdown
Allosteric and hormonal control
Glycogen
A polysaccharide of glucose
A readily available store of energy
A large and branched polymer
Synthesis of glycogen
Uridine diphosphate glucose (UDP-glucose)
An activated form of glucose is required
Immediate precursor
Glucose-1-phophate + uridine triphosphate (UTP)
UDP-glucose + 2 Pi. UDP- glucose then binds onto
nonreducing end of glycogen
glycogen synthase active when high blood glucose leads to
elevated g6p
alpha 1,4 linear linkage, and alpha 1,6 branch linkage
Breakdown
Produces energy by breaking the glycosidic bonds
Release of glucose-1-phosphate from glycogen
Glycogen phosphorylase breaks the 1,4 glycosidic linkages
Glycogen + Pi glycogen (the remaining glycogen)
+ glucose-1-phosphate
Remodeling of the glycogen substrate to permit further
degradation
Phosphoglucomutase converts glucose-1-phosphate to glucose 6-
phosphate for further metabolism
Glucose is used for:
Glycolysis in the muscles and in the brain
Free glucose is found in the liver and kidneys
Production of NADPH and ribose derivatives via the pentose
phosphate pathway
Regulation
Hormones allow for the regulation of glycogen metabolism
glycogen synthase and glycogen phosphorylase is reciprocally
regulated

Analysis of metabolic control
 A technique of examining how the control of influxes and concentrations of
metabolites in a metabolic pathway is distributed between different enzymes
Flux control coefficients
J (pathway flux): system scale variable
Vi (steady-state rate of reaction i): local parameter for one reaction
How much flux occurs through a pathway depends on the rate of the
particular reaction = the slope of the tangent

Concentration control coefficients

S: metabolite concentrations
Vi: the steady-state rate of reaction I

Citric Acid Cycle (BIO, BC)
Acetyl-CoA production (BC)
PDH complex


Regulation of the cycle
protein kinase bounds to E1 when NADH and acetyl-CoA concentrations rise.
When E1 is phosphorylated the enzyme 1 is shut of. Protein phosphatase can
remove phosphate group to turn back on E1.
 Net molecular and energetic results of respiration processes

produce 2 acetyl coa and 2 NADH per glucose molecule

Metabolism of Fatty Acids and Proteins (BIO, BC)

Description of fatty acids (BC)
composed of a carboxylic acid attached to a hydrocarbon chain
Digestion, mobilization, and transport of fats
Digestion
Lipase breaks down fats (triacylglycerol, TAG) to fatty acids and
monoglycerides by hydrolyzing them
found in mouth, stomach, and pancreas
Emulsification
Breaks down fat globules into emulsion droplets
Increases the surface area over which digestion can occur
Colipase
Amphipathic protein (hydrophobic and hydrophilic)
Binds lipase at the surface of the emulsion droplets
Mobilization/transportation
Bile salts and phospholipids form micelles
Amphipathic (has both hydrophobic and hydrophilic groups)
Found in the small intestine
Prevents the emulsion droplets from regrouping
Micelles
Lipid molecules that are smaller than emulsion droplets
Have fat soluble vitamins and cholesterol
Transport poorly soluble monoglycerides and fatty acids to the
surface of the enterocyte to get absorbed
They do not get absorbed
Enterocytes
 Enterocytes, or intestinal absorptive cells, are simple columnar
epithelial cells found in the small intestine.
Monoglycerides + fatty acids reform into
triacylglycerides with cholesterol + fat soluble vitamins
become chylomicrons
Chylomicrons
Lipoproteins
Transport lipids in the circulation by entering lymphatic
capillaries
Released by exocytosis at the basolateral surface of
the enterocytes to the bodys cells lipoprotein
lipase in capillary endothelial cells hydrolyzes them
into monoglycerides and fatty acids diffused into
cells

Oxidation of fatty acids
Fatty acids are broken down into acetyl-CoA in the mitochondria
Fatty acids go through beta-oxidation which is divided into two stages
1) Carnitine shuttle
Fatty acid activation occurs in the cytosol -> Oxidation occurs in
the inner mitochondria -> transport must occur
Carnitine palmitoyltransferase I, located on the outer
mitochondria, transfers the acyl-coA to the hydroxyl group of
carnitine, producing acylcarntine
Carnitine-acylcarnitine translocase shuttles acylcarnitine into the
inner mitochondria -> converted back to acyl coA by carnitine
acyltransferase II found in the inner mitochondria -> carnitine
shuttles back to the cytosol
2) Fatty acid catabolism (beta-oxidation)
Fatty acyl CoA dehydrogeanse catalyzes long chain fatty acid into
trans-delta-2-enoyl CoA (double bond between second and third
carbon is created) as FAD (work as an electron acceptor) is
reduced as FADH2
Enoyl CoA hydratase catalyzes trans-delta-2-enyl CoA into L-B-
hydroxyacyl CoA which is dehydrogenated into B-ketoacyl CoA by
B-hydroxyacyl CoA dehydrogenases as NAD is used as an
electron acceptor
Thiolase breaks the bond between C2 and C3 of B-ketoacyl CoA
into acetyl CoA and fatty acyl CoA until all the carbons are broken
into acetyl CoA
Saturated fatty acids
No double bonds
Goes through dehydrogenation, hydration, oxidation, and thiolysis
as it cleaves into acetyl-CoA
Refer to the diagram below
Unsaturated fatty acids
Double bonds
 Odd numbered double bonds handled by the isomerase
Even numbered double bonds by reductase (creates odd-
numbered double bond which is then handled by the isomerase)
Must have odd number to ensure that when it is cleaved the
molecule will be three carbons long
Ketone bodies (BC)

acetone is a byproduct that is removed from the body. Acetoacetate and b
hydroxybutyrate are transferred throughout the body. Can be converted
back into acetyl coa for energy
Anabolism of fats (BIO)
Anabolism: the biosynthesis of complex molecules from simpler forms
Increases cellular size/complexity
Requires ATP
Endergonic reaction
Acetyl-CoA fatty acids
Involves the condensation of two acetates
Occurs in mitochondria
The precursors for this reaction involve intermediates from the citric acid
cycle and from glycolysis
Malonyl-CoA
Fatty acid synthases
Oxidizing agent: acetyl-CoA
Reducing agent: NADPH
Acetyl-CoA can be synthesized into:
Fatty acids
Triglycerides
Phospholipids
Cholesterol

Non-template synthesis: biosynthesis of lipids and polysaccharides (BIO)
Lipids
Glycerol 1-phosphate + 2 acyl coenzyme A phosphatidic acid
Acyl coenzyme A: derivatives of fatty acids with 16 18 carbon
atoms
Phosphatidic acid diglyceride
Catalyzed by phosphatase
 Loss of the phosphate group
Diglyceride + acyl coenzyme A triglyceride
Third acyl coenzyme A

Polysaccharides
Conversion of glucose 6-phopshate glucose 1-phosphate
Glucose 1-phosphate + UTP UDP-glucose + PPi
UDP-glucose + glucose (n) glucose (n+1) + UDP
Glucose is added to the terminal glucose of a polysaccharide
chain
Glycogen in animals
In the liver: used for plasma glucose
In the adrenal cortex: for plasma glucose
In skeletal tissue, cardiac muscle and intestinal wall: for
themselves (for energy)
Catalyzed by glycogen synthetase
ADP-glucose + glucose (n) glucose (n+1) + ADP
Starch in plants
Catalyzed by amylose synthetase
ADP is used instead of UDP for starch synthesis
 Other plants use GDP or CDP-glucose

Metabolism of proteins (BIO)
Proteins
Make up the cellular structures for muscle tissues/tendons
Transport oxygen to hemoglobin
Catalyze biochemical reactions
Regulate reactions
Protein amino acids
Hydrochloric acid (HCl) and proteases in the gastrointestinal tract break
peptide bonds
Amino acids go through different processes for various uses in the body
Deamination: removal of an amino group
Amino acid keto acid
A keto acid may become pyruvic acid, acetyl-CoA, etc.
Some reactions are reversible, providing amino acids if
needed
Amination: addition of NH2
Transamination: transfer of NH2 from one to another or to an alpha-keto
acid
Catalyzed by aminotransferases
These resultant products enter the citric acid cycle as
intermediates
Glutamic acids NH2 group gets removed and is converted back
to alpha-ketoglutaric acid in the liver; toxic ammonia (NH3)
accumulates as a result
The ammonia enters the urea cycle
NH3 + CO2 urea
Urea is excreted with the urine from our body
If this cycle doesnt occur properly, ammonia will
accumulate in the blood and can result in death

Oxidative Phosphorylation (BIO, BC

Electron transport chain and oxidative phosphorylation, substrates and products, general
features of the pathway
 Complex 1 (NADH dehydrogenase)- converts NADH to NAD+ releasing 4H+ into
the IMS and Q to QH2 in the inner membrane
Complex 2 (succinate dehydrogenase)- converts succinate to fummerate,
releasing 2e- to convert Q to QH2
Complex 3 (ubiquinone cytochrome c oxidoreductase)- pushes 4H+ into the IMS,
QH2 converted to Q and 2 cytochrome C molecules in the IMS are reduced
Complex 4 (cytochrome C oxidase) cytochrome C is oxidized and the 2 electrons
flow into the matrix where it reacts with O2to form water. This reaction also
pushes 2H+ into the IMS.
Electron transfer in mitochondria
NADH, NADPH
NADH: the reduced form of nicotinamide adenine dinucleotide (NAD)
Works as an electron donor
Found in mitochondria
Required to generate the proton gradient
often used when breaking down compounds
NADPH: the reducing agent in anabolism. Drives redox reactions
Conversion of NADP+ to NADPH. The flow of H+ ions across the
chloroplast in plants occurs
often used when making molecules
Flavoproteins
Proteins that contain a nucleic acid derivative of riboflavin
Function as a specific electron acceptor for primary dehydrogenases
example-FADH2
Cytochromes
Water-soluble, mobile (some immobile) electron carriers
Pigments that contain iron
Different types: complex III and complex IV

ATP synthase, chemiosmotic coupling
Proton motive force
ATP synthase uses the proton gradient built up in order to create ATP.
uses 3 electrons flowing through ATP synthase to form an ATP from ADP
Chemiosmosis is the movement of ions across a selectively permeable
membrane, down their electrochemical gradient. More specifically, it
relates to the generation of ATP by the movement of hydrogen ions
across a membrane during cellular respiration or photosynthesis.
Net molecular and energetic results of respiration processes
every NADH that goes through electron transport creates 2.5 ATP, and every
FADH2 forms 1.5 ATP (3 H+ for synthase and 1 H+ to move phosphate into the
matrix
Regulation of oxidative phosphorylation
Magnitude of the proton motor force (PMF)
PMF
Proton and voltage gradient across the membrane
Proton concentration and electrical potential difference
Generated by an electron transport chain
Hydrogen ions are pumped out across the membrane
there is a lower concentration of positively charged
 protons inside, so it is slightly negative on the inside of
the membrane
Affected by the pH gradient
The higher the PMF, the slower the rate of electron transport. Inversely,
the lower the PMF, the faster the rate of electron transport
The magnitude of the PMF depends on the energy charge of the cell
Concentration of intramitochondrial ADP
Phosphate group acceptor
An increased level of ADP induces cellular respiration (oxygen consumption)

Mitochondria, apoptosis, oxidative stress (BC)
Apoptosis
Programmed cell death
Plays a critical role in embryonic development
Homeostasis, host defense of postnatal tissues, surveillance,
remodeling, etc.
Insufficient apoptosis can cause carcinogenesis, leading to the growth of
cancer
Excessive apoptosis can cause stroke and heart failure
The mitochondrial pathway of apoptosis occurs intrinsically
Affected by extracellular and intracellular stimuli
e.g. Radiation, physical stress, DNA damage, oxidative stress
Nitric oxide initiates and inhibits apoptosis
Small mitochondria-derived activators of caspases (SMACs)
Mitochondrial proteins that are released into the cytosol
bind to Inhibitors of apoptosis proteins (IAPs), which work to
cease apoptotic processes, allowing for apoptosis to occur
Cytochrome c is also released for the regulation of apoptosis
Binds to the apoptotic protease activating factor-1 (APAF-
1) and ATP binds to procaspase-9 a complex called
apoptosome is created
Oxidative stress
Oxidative stress is essentially an imbalance between the production of
free radicals and the ability of the body to counteract or detoxify their
harmful effects through neutralization by antioxidants.
Free radicals will take electrons from other species, destabilizing them,
and causing damage.

Hormonal Regulation and Integration of Metabolism (BC)

Higher level integration of hormone structure and function
Pineal gland
Melatonin: plays a crucial role in the sleep-wake cycle; helps one fall
asleep
Thymus gland
Thymus hormone: stimulates T-cell development
Thyroid gland
Thyroid hormones: regulate metabolism
Calcitonin: causes calcium to be stored in bones
 Parathyroid gland
Parathyroid hormone (PTH): withdraws calcium from the bones and
releases the calcium into the bloodstream
Adrenal glands
Gluccocorticoids: increase gluconeogenesis, which increases blood
sugar. These are usually secreted to deal with stress.
e.g. Cortisol, cortisone
Mineralocorticoids: regulate salt balance through sodium ions.
Cortical sex hormones: effects secondary sex traits in women
Epinephrine and norepinephrine: fight or flight response
Pancreas
Glucagon: when we are hungry and our blood sugar is low, glucagon is
secreted to inhibit uptake and use of glucose by the cells
Insulin: after we eat food, our blood sugar is high. Insulin stimulates the
uptake of glucose (or sugar) by the cells
Ovaries
Estrogen: develops secondary sex traits.
Progesterone: develops the endometrium (mucous membrane that lines
the inside of the uterus)

Tissue specific metabolism
Liver
Center for processing and distribution
Process nutrients (carbohydrates, fats and proteins)
Converts necessary molecules and distributes them to proper
locations in need
Glucose fatty acids
Synthesizes fats
Detoxification of foreign compounds such as drugs, preservatives and
food additives
takes lactate from muscle, converts it into pyruvate, and re-releases it
part of cori cycle
liver takes lactate and converts it into pyruvate for the muscles to
use
Adipose tissue
Stores and distributes fat supplies
15% of body mass
Found under skin, in abdominal cavity, etc.
Metabolically active
Regulated by hormones
Hydrolyzes triacylglycerol free fatty acids are released
Epinephrine stimulates this reaction, while insulin inhibits it
Muscle
Mechanical movements
50 90% of the bodys oxygen is supplied to the muscles
ATP generator
converts pyruvate into lactate
Cardiac muscle stores energy using phosphocreatine
Brain
 Ion pumps electrical signals are produced
Consumes energy (glucose, cannot use fat or amino acids)
Blood
Carrier of hormones, ions, nutrients, etc.

Hormonal regulation of fuel metabolism
Glucose level
Homeostasis promotes the uptake of glucose into cells and to used by
tissues; this lowers the glucose level in the blood
Intracellular glycogen stores promote gluconeogenesis to maintain the
normal level
Hormonal regulation
Insulin promotes glucose uptake
Stimulated by high blood glucose, amino acids (usually
right after a meal)
Stimulates fatty acid, cholesterol and protein synthesis
Epinephrine inhibits insulin, preventing glucose uptake
Epinephrine stimulates glucagon
Glucagon releases stored energy by synthesizing glucose
Glucose inhibits glucagon


Obesity and regulation of body mass

Obesity
When an excess amount of body fat accumulates in ones body, causing
overall negative effects
Increased health problems
Reduced life expectancy
The result of consuming more calories in the diet than energy being used
Body mass index (BMI)
Compares weight and height and calculates which categories one is in
BMI = mass (kg) / [height (m)]2
Categories include:
Underweight = 18.5 or less
Normal weight = 18.5 24.9
Overweight = 25 29.9
Obesity = 30 or greater
Regulation of body mass
Balance between food intake and expenditure
Exercise more to burn excess fuel consumed to prevent it from
being stored in the body


Foundational Concept 2
Highly-organized assemblies of molecules, cells, and organs interact to carry out the
functions of living organisms.

Cells are the basic unit of structure in all living things. Mechanisms of cell division provide not
only for the growth and maintenance of organisms, but also for the continuation of the species
through asexual and sexual reproduction. The unique micro-environment to which a cell is
exposed during development and division determines the fate of the cell by impacting gene
expression and ultimately the cells collection and distribution of macromolecules, and its
arrangement of subcellular organelles. In multicellular organisms, the processes necessary to
maintain life are executed by groups of cells that are organized into specialized structures with
specialized functions both of which result from the unique properties of the cells component
molecules.

Category 2A: Assemblies of molecules, cells, and groups of cells within single cellular
and multicellular organisms
The processes necessary to maintain life are executed by assemblies of molecules, cells, and
groups of cells, all of which are organized into highly-specific structures as determined by the
unique properties of their component molecules. The processes necessary to maintain life
require that cells create and maintain internal environments within the cytoplasm and within
certain organelles that are different from their external environments. Cell membranes separate
the internal environment of the cell from the external environment. The specialized structure of
the membrane, as described in the fluid mosaic model, allows the cell to be selectively
permeable and dynamic, with homeostasis maintained by the constant movement of molecules
across the membranes through a combination of active and passive processes driven by
several forces, including electrochemical gradients. Eukaryotic cells also maintain internal
membranes that partition the cell into specialized regions. These internal membranes facilitate
cellular processes by minimizing conflicting interactions and increasing surface area where
chemical reactions can occur. Membrane-bound organelles localize different processes or
enzymatic reactions in time and space. Through interactions between proteins bound to the
membranes of adjacent cells, or between membranebound proteins and elements of the
extracellular matrix, cells of multicellular organisms organize into tissues, organs, and organ
systems. Certain membrane-associated proteins also play key roles in providing identification of
tissues or recent events in the cells history for purposes of recognition of self versus foreign
molecules. The content in this category covers the composition, structure, and function of cell
membranes; the structure and function of the membrane-bound organelles of eukaryotic cells;
and the structure and function of the major cytoskeletal elements. It covers the energetics of
and mechanisms by which molecules, or groups of molecules, move across cell membranes. It
also covers how cellcell junctions and the extracellular matrix interact to form tissues with
specialized functions. Epithelial tissue and connective tissue are covered in this category. The
topics and subtopics in this category are the following

Plasma Membrane (BIO, BC)

General function in cell containment
Cell containment is crucial in evolution of life.
Cells boundaries between inside and outside have to be made for
structure and functions.
All of the membranes of the cells are composed of lipid bilayer membrane
Molecules/ions/nutrients/waste/hormones pass through the membrane in
many ways including osmosis, passive transport, active transport,
sodium-potassium pump, cell signaling, exocytosis, endocytosis, and
many more . small nonpolar can pass through by diffusion
Fluid mosaic model: describes the membranes as proteins floating in lipids
Composition of membranes
Lipid components (BIO, BC, OC)
Phospholipids (and phosphatids)
Lipid bilayer membranes are the lowest in energy state and can
reseal and are capable of self repair if a small portion of the
membrane is removed
Interior: hydrophobic = scared of water
Hydrophilic molecules such as ions, carbohydrates, and
amino acids are not soluble (creating membrane barrier to
the passage)
Nonpolar molecules like CO2 or O2, or steroid
hormones can cross very easily
Water is passed through specialized protein
channels

Waxes
Waxes are similar to fats except that waxes are composed of only
one long-chain fatty acid bonded to a long-chain alcohol group
attached. Because of their long, nonpolar carbon chains, waxes
are extremely hydrophobic (meaning they lack an affinity for
water). Both plants and animals use this waterproofing
characteristic as part of their composition.
Protein components
 Integral membrane proteins are embedded, Peripheral membrane
proteins stuck on integral membrane proteins (temporary)
Fluid mosaic model
cell membrane as a two-dimensional liquid in which phospholipid and
protein molecules diffuse easily
hydrophobic allowing for diffusion of small nonpolar molecules
Membrane dynamics
Extracellular
Outside of the cell
Intracellular
Inside the cell
Uncatalyzed movements:
Trans bilayer diffusion
Also known as flip-flop
Very slow movement
Movement of the outer leaflet into the inner leaflet, or vice versa
Does not happen that often
Lateral diffusion
Movement of phospholipids from side to side
Fast movement
Catalyzed movements:
Flippase
Requires energy
Fast movement
Flips of the outer leaflet to the inside
Floppase
Requires energy
Fast movement
Movement of the inner leaflet to the outer leaflet
Scramblase
Does not require energy
Fast movement
Movement of the inner leaflet to the outer leaflet and the outer
leaflet to the inner leaflet

Solute transport across membranes
Thermodynamic considerations
passive transport- thermodynamically favorable because driven by
concentration gradient. no energy is required
active transport- requires energy to power transporter to bring molecules
across membrane
facilitated diffusion- passive, same as simple diffusion but uses protein
transporter.
primary active transporter- cells move through against concentration
gradient through direct hydrolysis of atp
secondary active transport- employ energy stored in existing concetration
to move molecules against concentration gradients. generally ATP
consumed in order to create concentration gradient
Osmosis
 Colligative properties; osmotic pressure (GC)
In chemistry, colligative properties are properties of solutions that
depend upon the ratio of the number of solute particles to the
number of solvent molecules in a solution, and not on the type of
chemical species present.
The osmotic pressure of a solution is the pressure difference
needed to stop the flow of solvent across a semipermeable
membrane.

Passive transport
Passive transport: any thermodynamically favorable movement of a
solute across a membrane (down the gradient)
No energy is required due to the concentration gradient driving the
movement of the solute
Simple diffusion: the solute diffuses through the membrane
without any help from a protein
e.g. Steroid hormones
Facilitated diffusion: diffusion of solutes across membrane down a
gradient when the membrane is impermeable to those solutes
through channel/carrier proteins
Selective permeability: only some things are allowed to
pass through the proteins
Channel proteins: narrow tunnels (ion channels) that allow
specific ions to pass through
K+ channel: only potassium flows through down the
gradient
Voltage-gated ion channels: channels open in
response to electric potential changes across the
membrane
Ligand-gated ion channels: opens in response to
the binding of a specific molecule, such as a
neurotransmitter
 Carrier proteins: no tunnels; bind to the molecule that needs to
be transported conformation change move the molecule
to the other side of the membrane
Uniports: transport only one molecule across the
membrane at a time
Symports: carry two substances in the same direction
Antiports: carry two substances in the opposite directions

Simple vs. facilitated diffusion

The rate of simple diffusion is limited by the surface area of
the membrane and the size of the driving force
The rate of facilitated diffusion depends on the number of
integral membrane proteins
Saturation kinetics: increasing the driving force for
facilitated diffusion will increase the rate of diffusion (only to
a certain point). When all transport proteins are saturated,
there will be no further increase in flux.

Active transport: the movement of solutes against a gradient
Requires energy input, always involves a protein
Primary active transport: ATP hydrolysis is coupled to transport molecules
Secondary active transport: ATP is first used to create a gradient, then
potential energy is used to transport the molecules (indirectly use ATP)
Sodium/potassium pump
 Transporter transports 3 NA out of the cell and 2 K into the cell.
This unbalance creates a charge difference allowing the firing of
action potentials
Membrane channels : ion channels to help ions cross the membrane
Membrane potential: the resting potential of the cell membrane is negative because of
the sodium-potassium pump
Membrane receptors
Many hormones cant cross the plasma membrane, so they bind to membrane
receptors on the outside
Receptor binding triggers the production of second messengers
Second messengers cause a change inside the cell (through a protein kinase
cascade)
Cell Signaling Pathways:
Contract signaling- physical contact triggers a change inside cell
Chemical signaling- chemical binding to receptor triggers a change inside
cell
Nerves use neurotransmitters
Endocrine system uses hormones
Electric Signaling- change in membrane potential triggers change in cell
Action potential along neurons propagates and cause release of
neurotransmitters into synapse
Action potential along muscle cell membrane causes contraction
Exocytosis and endocytosis
exo = going out, endo = taking in (both use energy)
Intercellular junctions (BIO)
Gap Junctions: connects two cells and allows stuff to flow between the cells
(neurons, and cardiac muscles)
Tight Junctions: stitches/glues two cells together, and does not allow stuff to flow
between the cells. A series of cells with tight junctions also effectively forms an
impermeable barrier ( bladder, kidney, intestine)
Desmosomes: connects two cells together by linking their cytoskeleton (strongest
of bonds). They are organized for mechanical strength, not an impermeable
barrier. LIke a tunnel to transfer between the two cells (skin, intestine)

Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells (BIO)
Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of
organelles, mitotic division
Eukaryotes have membrane-bound organelles (ER, Golgi, lysosomes,
mitochondria), prokaryotes dont
Eukaryotes divide by mitosis (all chromosomes line up), while prokaryotes do
binary fission (no chromosomes, just a circular ring of DNA, no need for complex
mitosis)

Nucleus
Compartmentalization, storage of genetic information
Compartmentalization: nuclear membrane / nuclear envelope surrounds
the nucleus
Genetic information is stored inside nucleus as DNA
 Nucleolus: location and function
Location is a region inside nucleus
Function is to transcribe rRNA
Nuclear envelope, nuclear pores
Nuclear Envelope is a double membrane system made of an outer and
inner membrane (also called nuclear membrane)
Nuclear Pores are holes in the nuclear envelope where things can pass
through. Transcription occurs in the nucleus and mRNA must pass out.
Transcription factors and other things must pass into the nucleus to
access DNA to be transcribed

Mitochondria
Site of ATP Production: an apparatus called the ATP Synthase makes ATP from
ADP by utilizing the proton gradient as the driving force (H+ concentration higher
in intermembrane space than matrix)
Inner and outer membrane structure (BIO, BC)
Inner membrane surrounds matrix
Folds of inner membrane make up the cristae
Between inner and outer membrane is intermembrane space, which is
high in H+
Outer membrane separates the mitochondria from the cytoplasm
Self-replication
Mitochondria replicate independently from the cell
Mitochondria does not share genome with host
Mitochondria has own ribosomes, which are different from the hosts
ribosomes in both sequence and structure
All these serve to support endosymbiosis theory
Lysosomes: membrane-bound vesicles containing hydrolytic enzymes
Digests things like food and viral/bacterial particles
Things you want to digest gets into a vacuole by endocytosis or phagocytosis,
and then the vacuole fuses with the lysosome (Anything inside gets digested by
the hydrolytic enzymes)
Endoplasmic reticulum
Rough and smooth components
Rough ER has ribosomes and deals with protein processing, folding,
modification, and export (protein made in cytoplasm) (eukaryotic
ribosomes larger than prokaryotic)
Smooth ER deals with biosynthesis of lipids and steroids, and metabolism
of carbohydrates and drugs
In the muscles, the SER or SR stores and regulates calcium
Rough endoplasmic reticulum site of ribosomes- the ribosomes attach to the
outside of rough ER and synthesize protein into the lumen
Double membrane structure
hydrophilic heads stick out and hydrophobic tails are inside
Role in membrane biosynthesis
SER makes lipids of the plasma membrane
 RER makes transmembrane proteins, carries them on its membrane,
RER membrane forms vesicles and bud off, fuses with plasma
membrane, transmembrane proteins now on plasma membrane
Role in biosynthesis of secreted proteins
Transmembrane proteins (consists of mostly alpha helices) , or proteins
that are to be secreted (need RER vesicle) have a signal sequence right
at the beginning
When ribosome starts making those proteins, they make the signal
sequence first
Signal sequence recruits a signal recognition particle that drags it to the
RER
Ribosome now on the RER continues making the protein, but snakes it to
the lumen
Signal sequence is clipped off
Golgi apparatus: general structure and role in packaging and secretion
Stack of membranous sacs
Modifies and/or secretes macromolecules for the cell
RER makes protein modified in the Golgi which then buds off Golgi and secreted
out of cell by exocytosis
Glycoprotein = protein with attached saccharides
Golgi can glycosylate (add polysaccharide to) proteins
Glycosylation affects proteins structure, function, and protects from degradation
Peroxisomes: organelles that collect peroxides
has a single membrane
metabolizes lipids and toxins using hydrogen peroxide

Cytoskeleton (BIO)
General function in cell support and movement
Provides structural support, allows movement of cell and its appendages (cilia
and flagella) and transport of substances within the cell
Animal cells have an internal cytoskeleton composed of 3 types of proteins:
microtubules, intermediate filaments, microfilaments
Microfilaments: composition and role in cleavage and contractility
Made of actin
Responsible for cytokinesis (physical process of cell division): supports cell
shape by bearing tension
Microtubules: composition and role in support and transport
Made of tubulin
Responsible for mitotic spindle, cilia/flagella, intracellular transport of organelles
and vesicles, supports cell shape by bearing compression
Intermediate filaments, role in support
Varied composition
Supports cell shape by bearing tension
Composition and function of cilia and flagella
Made of microtubules (9+2 arrangement = 9 microtubules surrounding 2).
Microtubules bound to neighbors by the contractile protein dynein
Cilia and Flagella attached to plasma membrane via basal body
 Cilia- small hairs on the cell surface which move fluids past the cell surface
(locomotion, sensory, or sweeping mucus)
Flagella- large tail that moves cell by wiggling (locomotion)
Centrioles, microtubule organizing centers
Microtubules Organizing Center- located near nucleus and anchored to
microtubules
Centrioles are inside microtubule organization center, and each centriole is
composed of a ring of nine microtubule triplets
Centriole involved in pulling chromatids apart

Tissues Formed from Eukaryotic Cells (BIO)

Epithelial cells
Squamous = flat
Cuboidal = cube
Columnar = column shaped
Simple epithelium = single cell layer = good for absorption, secretion, filtration,
diffusion
Simple squamous = endothelium, capillary wall, alveolar wall
Simple cuboidal = gland ducts,, kidney tubules
Simple columnar = stomach, gut
Stratified epithelium = two or more cell layers = good for protection against
abrasion
Stratified squamous = skin
Stratified cuboidal/columnar = not common


Connective tissue cells
Connective tissue structure = cells + extracellular matrix
Cells: secrete the extracellular matrix (ground substance and fibers)
Ground substance- glue that holds the matrix together
Fibers- mostly collagen, gives the matrix strength
Connective tissue cells and tissue types: bone, fat, tendons, ligaments, cartilage,
blood
Osteoblasts make bone
Fibroblasts make connective tissue (fats, tendons, ligaments, beneath
epithelia)
Chondroblasts make cartilage
Hematopoietic stem cells make blood
Nomenclature:
-blast = stem cell actively producing matrix
-ctye = mature cell, doing housekeeping
Fiber Types:
Collagen- the most common fiber type, very strong, present in large
amounts in dense connective tissue
Elastic fibers = can stretch
Reticular fibers = can branch and form nets. Found in loose connective
tissue
Loose vs Dense
 Loose = loose fibers, lots of fluff (ground substance, cells) = anything that
you dont associate with being fibrous = fat, padding around organs
Dense = dense fibers predominantly collagen = genuinely fibrous, little
fluff (ground substance, cells) = tendon, ligament
Cartilage = chondrocytes + matrix = elastic, flexible, used as padding in spinal
discs, ends of bones, ear
Extracellular Matrix = secreted by cells = ground substance (glue) and fibers
connective tissue- reticular connective tissue, adipose tissue, cartilage, bone,
and blood

Content Category 2B: The structure, growth, physiology, and genetics of prokaryotes and
viruses
The highly-organized assembly of molecules that is the cell represents the fundamental unit of
structure, function, and organization in all living organisms. In the hierarchy of biological
organization, the cell is the simplest collection of matter capable of carrying out the processes
that distinguish living organisms. As such, cells have the ability to undergo metabolism; maintain
homeostasis, including ionic gradients; the capacity to grow; move in response to their local
environments; respond to stimuli; reproduce; and adapt to their environment in successive
generations. Life at cellular levels arises from structural order and its dynamic modulation. It
does so in response to signals, thereby reflecting properties that result from individual and
interactive features of molecular assemblies, their compartmentalization, and their interaction
with environmental signals at many spatial and temporal scales. The content in this category
covers the classification, structure, growth, physiology, and genetics of prokaryotes, and the
characteristics that distinguish them from eukaryotes. Viruses are also covered here. The topics
and subtopics in this category are the following:

Cell Theory (BIO)

cell theory is a scientific theory which describes the properties of cells. These cells are
the basic unit of structure in all organisms and also the basic unit of reproduction.
Transformation: incorporation into bacterial genome of DNA fragments from external
medium
Lysed bacteria spills DNA fragments into the environment
Another bacteria can take in this DNA and incorporate it into its own genome
Conjugation
transfer of genetic material between bacterial cells by direct cell to cell contact or
by bridge like connection (specifically the F-plasmid/ F-factor)

Transposons (also present in eukaryotic cells)
A DNA sequence
Genetic components with the ability to insert or remove themselves from
the genome. Can be moved from one part to another. Cas also
incorporate plasmid dna into the genome
Can created or reverse mutations
Can be inserted within a coding region of a gene; that gene may
be disrupted
Can change the size of the genome
Found in both prokaryotes and eukaryotes
Types of transposons:
Class I (copy and paste)
Transcription from DNA RNA
Reverse transcription: RNA DNA via reverse
transcriptase
Copied DNA is inserted into a new location in the genome
Class II (cut and paste)
Transposases (enzymes) bind to a non-specific or a specific site in
the DNA
Transposases cut at the site, making sticky ends, then cut out the
DNA transposon
With the help of DNA polymerase and ligase, the space is filled
out and ligated together
Types of bacteria
bacillus (rod)
Probably most dangerous of the three
Bacillus anthrasis- causes anthrax a potentially fatal disease
Clostridium botulium- causes botulism in incorrectly canned food
Clostridium tetani- causes tetanus or lockjaw
 Clostridium perfringes- causes gas gangrene
Coccus (sphere)
Streptococcus pyogenes caused rheumatic fever and most strep throat
infections
Staphlococcus aureus- normally a harmless occupant of a persons skin is
a major cause of infections in hospital based infections (MRSA)
Neiseria gonnorea- causes gonnorea
spirillus (spiral)
Most spirillium are harmless...with one notable exception:
Treponemia palladin- causes syphillus
Gram negative


Virus Structure (BIO)

General structural characteristics (nucleic acid and protein, enveloped and
nonenveloped)
 Nucleic acid can be DNA or RNA, single stranded or double stranded
Protein coat covers the nucleic acid
Some viruses have an envelope derived from the hosts cell membrane, while
others lack it (nonenveloped)
Enveloped viruses bud off the hosts membrane (only infect animal cells)
Nonenveloped viruses cause the host to burst to release viral particles
Lack organelles and nucleus
Lack organelles, nucleus: genetic material is simply packed inside a protein coat
Structural aspects of typical bacteriophage

Head stores genetic material
Sheath provides passageway for genetic material to be injected into host
bacteria
Tail fibers attach to host bacteria
Genomic content RNA or DNA
RNA viruses that can use RNA dependent RNA polymerase to convert their
genome into DNA inside host cells are called retroviruses ()
Size relative to bacteria and eukaryotic cells
Size relative to bacteria and eukaryotic cells: viruses are roughly 100 times
smaller than bacteria, and 1000 times smaller than eukaryotic cells

Viral Life Cycle (BIO)

Self-replicating biological units that must reproduce within specific host cell
Depend on hosts replication organelles to replicate
Host ribosomes will make necessary protein coats and polymerases that
replicate the viral genetic material
Retroviruses contain their own reverse polymerase to convert RNA to DNA
before the hosts polymerases take over (RNA specific RNA polymerase)
Generalized phage and animal virus life cycles
Attachment to host, penetration of cell membrane or cell wall, and entry of viral
genetic material
Use of host synthetic mechanism to replicate viral components: Host ribosomes
synthesize the necessary enzymes, hosts ATP provides energy, host provides
raw materials such as nucleotides and amino acids
Self-assembly and release of new viral particles:The coat proteins and viral
genetic material will assemble into viral particles all by themselves
Transduction: transfer of genetic material by viruses
Virus infects cell: host DNA degraded into fragments, viral DNA takes over control
Host DNA fragment gets packed into virus progeny by accident
Virus progeny infects another cell, injects previous hosts DNA fragment
Fragment enters cell, find its homologous counterpart, and crossover
Retrovirus life cycle: integration into host DNA, reverse transcriptase, HIV
Retrovirus enters the host
 Viral reverse transcriptase converts the viral RNA genome into double-stranded
DNA
Virally encoded enzyme called integrase adds in the viral DNA into the hosts
genome at a random place
When host replicates, the viral DNA gets replicated too
Types of viruses
lysogenic infects cell, integrates into DNA, and then sites dormant before it re-
emerges and takes over the host genetic and protein synthesizing machinery
lytic virus- infect cell, immediately takes over cell machinery to replicate, and then
kill cell by lysing and releasing new viruses
Bacteriophage- only attacks bacteria
attenuated virus- virus weakened so not as virulent (flu shot)
Prions and viroids: subviral particles
prions do not have nucleic acid. They are misfolded protein that propagate by
transmitting a misfolded protein stain. converts proteins into tightly packed beta
sheets, making them incredibly stable
Viroids are the smallest infectious pathogens known, consisting solely of short
strands of circular, single-stranded RNA without protein coats. They are mostly
plant pathogens, some of which are of economical importance

Content Category 2C: Processes of cell division, differentiation, and specialization

The ability of organisms to reproduce their own kind is the characteristic that best distinguishes
living things. In sexually reproducing organisms, the continuity of life is based on the processes
of cell division and meiosis. The process of cell division is an integral part of the cell cycle. The
progress of eukaryotic cells through the cell cycle is regulated by a complex molecular control
system. Malfunctions in this system can result in unabated cellular division, and ultimately the
development of cancer. In the embryonic development of multicellular organisms, a fertilized
egg gives rise to cells that differentiate into many different types of cells, each with a different
structure, corresponding function, and location within the organism. During development,
spatialtemporal gradients in the interactions between gene expression and various stimuli
result in the structural and functional divergence of cells into specialized structure, organs, and
tissues. The interaction of stimuli and genes is also explained by the progression of stem cells
to terminal cells. The content in this category covers the cell cycle; the causes, genetics, and
basic properties of cancer; the processes of meiosis and gametogenesis; and the mechanisms
governing cell specialization and differentiation. The topics and subtopics in this category are
the following:

Mitosis (BIO)
Mitotic process: prophase, metaphase, anaphase, telophase, interphase
Mitosis
Prophase: Prepare (condense chromatin into chromosomes, break down
nuclear membrane, assemble mitotic spindle, centriole pairs move toward
opposite poles of the cell)
Metaphase: Middle (chromosomes line up in the middle)
Anaphase: Apart (sister chromatids pulled apart to opposite sides of the
cell)
 Telophase: de-condense chromosomes, reform nuclear membrane, break
down mitotic spindle, cytokinesis
Interphase
G0 = no DNA replication or cell division (eg. Nerves, muscles, and other
cells that dont divide much spend the majority of their life in G0)
G1 = Growth = make organelles, increase cell size
S = DNA replication, centrioles replicated
G2 = Growth = make organelles, increase cell size
Mitotic structures
Centrioles, asters, spindles
Responsible for pulling apart the sister chromatids

Chromatids, centromeres, kinetochores

Sister chromatids are duplicated copies of the chromosome
Chromatids are joined at the centromere
A protein at the centromere called the kinetochore is where spindle fibers
attach to pull the chromatids apart
Nuclear membrane breakdown and reorganization
For most eukaryotes, the nuclear membrane breaks down at the
beginning of mitosis, and reforms at the end of mitosis around each other
the two newly formed nuclei
Mechanisms of chromosome movement
Chromatids move apart during anaphase by the spindle fibers
Microtubules cause the chromosome movement
Phases of cell cycle: G0, G1, S, G2, M
G0 = no more DNA replication or cell division (eg. Nerves and muscles)
 G1 = Growth = make organelles, increase cell size
S = DNA replication, centrioles replicated
G2 = Growth = make organelles, increase cell size
M = Mitosis
Growth arrest
Too much genomic mutation/damage causes a cell to arrest in M phase
Contact Inhibition: normal epithelial cells stop growing when it gets crowded such
that it touches adjacent cells
Lack of food can cause growth arrest
Control of cell cycle
There are various mechanisms that control the cell cycle:
DNA damage checkpoint
Occurs before the cell enters S phase, known as G1 checkpoint
If the damage of DNA is detected at this checkpoint, this cell
cannot enter the S phase (progress through the cell cycle) until
the damage is repaired
If there is excessive damage on DNA and no repair can be done,
the programmed cell death (apoptosis) occurs
Occurs after S phase, known as G2 checkpoint
If the damage of DNA is detected at this checkpoint, this cell
cannot enter the G2 phase and onto mitosis phase
Where the condition of DNAs are checked
Spindle checkpoint
M checkpoint when spindle fibers fail to attach to kinetochores, the cell
is arrested in metaphase until all the kinetochore is attached correctly
When spindle alignment occur improperly, cytokinesis is stopped until
alignment is corrected

Loss of cell cycle controls in cancer cells
A malignant tumor (neoplasm)
Benign neoplasms are non-cancerous
Cancer cell cycle
In normal cells, there are various mechanisms that regulate the cell cycle
to either continue or stop the cycle at certain point
Also any errors and damages are corrected and repaired
This proper regulatory mechanism helps suppressing growth of
tumors
However, cancer cells genetic mutations occurs causing this regulatory
mechanism to fail or cells fail (resist) to respond to these signals (like
contact inhibition) and results in uncontrolled cell proliferation
Cancer cells go through the cell cycle again and again
Cancer cells evade programmed cell death (apoptosis) even when
cells have numerous abnormalities and should be dead

Biosignaling (BC)
Oncogenes, Apoptosis
 Oncogenes- cause cancer when activated (SRC), harmless proto-oncogenes are
somehow activated into a oncogene
Tumor Suppressors: slow or control cell division (P53), cell becomes cancerous if
tumor suppressor no longer functions
Cancer cells continue to grow and divide in situations normal cells would not, fail
to respond to cell controls and signals that would halt growth
Avoid apoptosis that normally occurs when extensive DNA damage is present
Stimulate angiogenesis- cause new blood vessels to grow to nourish the cancer
cell
Cancer cells are immortal while normal cells die after a certain number of
divisions
Cancer cells can metastasize- break off and then grow in another location

Reproductive System (BIO)

Gametogenesis by meiosis

Male = spermatogenesis = occurs in the seminiferous tubules
Spermatogonium (2n) = stem cell. Mitosis of spermatogonium can either
create more spermatogonium or create spermatocyte
Spermatogonium (2n) mitosis primary spermatocyte (2n). Occurs after
puberty
Primary spermatocyte (2n) meiosis I secondary spermatocyte (n)
Secondary spermatocyte (n) meiosis II spermatid (n)
 Spermatid (n) mature sperm (n). Sperm = spermatozoa
Female = oogenesis = occurs in ovaries, then fallopian tubes
Oogonium (2n) = stem cell
Oogonium (2n) mitosis primary oocyte
Primary oocyte (2n) arrests at prophase I (occurs before birth). One
comes out of arrest every month (between puberty and menopause)
Primary oocyte (2n) meiosis I secondary oocyte (n). Ruptures from
ovary follicle into fallopian tube
Secondary oocyte (n) arrests at metaphase II. Comes out of rest if
fertilization occurs
Secondary oocyte (n) meiosis II ovum (n)

Ovum and sperm
Differences in formation

Male and Female Gametogenesis Side by Side

Male Female Difference

Spermatogonium Oogonium (2n) Spermatogonium renews its

(2n) population by mitosis
throughout life. Oogonium
stops renewing its population
sometime before birth

Primary Primary Oocyte Primary oocyte arrests at

Spermatocyte prophase I

Secondary Secondary Secondary oocyte arrests at

Spermatocyte Oocyte metaphase II

Sperm Ovum Between the secondary

spermatocyte and the sperm,
theres the spermatid

Differences in morphology
Sperm = motile = flagella
Egg = non-motile = round
Relative contribution to next generation
Sperm contributed DNA only (the egg actively destroys sperm
mitochondria)
Egg contributes DNA + everything else (mitochondria, organelles,
epigenetics)
Reproductive sequence: fertilization; implantation; development; birth
Fertilization: sperm + egg= zygote
Implantation:
Zygote
Morula (solid ball)
 Blastula (sea urchins) or blastocyst (mammals)
Blastocyst is the one that implants in the endometrium
Development:
Zygote- sperm+egg
Blastocyst- after a few days of division the zygote turns into a ball of cells
(inner cells with an outer shell)
Blastocyst buries into uterine wall, get nutrients
Week 5= embryonic period major systems and structures start develop
Fetus- end of week 10 and at advanced stage of development. Called a
fetus until birth
dysgenesis- abnormal organ development during embryonic growth and
development
Birth:
Switch from getting oxygen from moms blood to breathing
Switch from getting nutrients from moms bloods to suckling
Fetal circulation (which bypasses lungs and liver) switched to normal
circulation (by closing off ducts and openings)

Embryogenesis (BIO)
Stages of early development (order and general features of each)
Fertilization
Sperm meets egg
Acrosomal reaction causes sperm to penetrate egg
Cortical reaction causes egg to prevent additional sperm from penetrating
Egg completes meiosis II
Sperm and egg nuclei fuse
Cleavage
Normal mitotic cell divisions: cell grows then divides, grows again, then
divides
Cleavage = mitotic divisions without cell growth, Stays within the zona
pellucida (glycoprotein layer from the original egg)- eventually called a
morula when it has divided enough.
compaction- the cells in the morula start compacting together. The cells
on the outside start becoming something else (trophoblast) and the cells
inside (embryoblast). This is called differentiation

Blastula formation
Fertilization produces zygote
Cleavage produces a solid ball called the Morula
Morula hollows out into the blastula or blastocyst
Blastula occurs in non-mammals
Blastocyst occurs in mammals

Blastocyst implants
Blastocyst travel to endometrium
Endometrial lining is proliferating and form valleys called crypt.
The egg rest in the crypt. This leads to apposition (the cell from
the endometrium and egg are in contact)
trophoblasts start to multiply and invade into the endometrial
tissue (it gets stuck so it is called adhesion). At the same time the
endometrium is dividing and tying down the egg)
Trophoblasts start to fuse and get bigger (multinucleated cell) and
grow into endometrium (syncytiotrophoblasts). Cells that dont
grow into endometrium are cytotrophoblasts
Syncytiotrophoblasts continue to grow- forming finger like
projections called villi.
Uterine blood vessels start to get merge together and get bigger
cytotrophoblasts creep into the villa, and start developing fetal
blood vessels. The uterine blood is close enough so that nutrients
can diffuse into the fetal blood and waste can transfer into the
uterine blood. The structure grows and forms the placenta

The inner cells divide more


Gastrulation
First cell movements
Cells from the surface migrate inwards
Gastrulation occurs slightly different for different animals. Some by
invagination, some by migration, some by splitting
In mammals, cells start migrating inward at primitive streak
Formation of primary germ layers (endoderm, mesoderm, ectoderm)
The cells that migrate inwards form the endoderm
The cells that remain outside form the ectoderm
The cells in the middle form the mesoderm

Neurulation
Ectoderm turns into brain, spinal cord, and peripheral nervous system
Ectoderm does so by folding into a tube
notochord starts forming in mesoderm, inducing a change in the ectoderm
to start forming the neural plate.
The plate cells start diving into mesoderm, forming a tunnel (called
neural tube).
Some cells from the ectoderm are going into the mesoderm
(neural crest cells)

Major structures arising out of primary germ layers
Endoderm = innermost layer = guts, lungs, and digestive internal organs (liver,
pancreas)
Mesoderm = middle layer = muscle, blood, and bone tissues, and internal organs
(kidney and gonads)
Ectoderm = outermost layer = skin and nerves (including brain), eyes, nose,
mouth


Neural crest
A group of embryonic cells
Migratory
Transient
Multipotent
Generate various types of differentiated cells (derivatives)
Including neurons and glial cells of the sensory,
sympathetic, and parasympathetic nervous system,
medulla cells of the adrenal gland, and many of the
skeletal and connective tissue components of the head
They are pinched off as neural tube is formed
Cranial neural crest migrates into the brachial arches and
the face
To form the bones and cartilage of the face and
neck
Produce pigment and cranial nerves
Vagal neural crest and sacral neural crest
Form parasympathetic nerves of the gut
Cardiac neural crest
Make decision between the aorta and the
pulmonary artery
Neural crest of the trunk
Make the sympathetic neurons
Also form the medulla portion of the adrenal gland

Environmentgene interaction in development
Environment-gene interaction
Studies the relationship between genes and environmental factors when
there are continuous phenotypic differences
 Provide gainful information for medical uses such as diseases and
environmental risk factors
Individuals with different genes are affected differently by same
environmental factors different disease phenotype
This kind of study is medically significant
Genetic information can help prevent disease by reducing
exposure to environmental risks

Mechanisms of Development (BIO)

Cell specialization
Determination
Determination = irreversible commitment to become a certain cell type
Differentiation = becoming a cell type and adopting its specialized functions
Epidermal cells produce keratin to protect skin against abrasion
Myocyte produce actin and myosin to make muscles contract
Neurons make neurotransmitters to transmit electrochemical impulses
Tissue types
Epithelial: skin, lining of organs
Connective: blood, bone, tendons, ligaments, cartilage
Nervous: brain, spinal cord, nerves
Muscle: skeletal, smooth, and cardiac muscle
Cellcell communication in development
Induction: one group of cells changing the behavior of an adjacent group of cells
Inducer = the one that sends the signal for the other to change
Responder = the one that gets the signal and changes
For example, the optic vesicle is able to induce the ectoderm to develop
into lens
Another example: induction of wing feathers in the chick by the dermal
mesenchyme
Induction mechanisms: physical touching of cells (juxtracine) or by releasing
chemicals (paracrine)
Cell migration
Also known as gastrulation or cell movement
Occurs differently for various animals
During development of embryo:
The blastula, simple spherical ball of cells are organized into a multi-
layered organism
Many of the cells at or near the surface of the embryo move (migrate)
inwards
Germ layers are formed depending on the cells migration (location)
The cells that migrate inward form the endoderm
The cells that remain outside form the ectoderm
The cells in the middle form the mesoderm
Refer to the diagram below
Pluripotency: stem cells
Pluripotency
The ability to produce certain distinct biological responses
Induced pluripotent stem cells
Also given a term true stem cells
 Type of pluripotent stem cell that can be generated directly from adult
cells
This discovery hold great promise in regenerative medicine field due to
the characteristics of indefinite propagation of cells which can become
almost all cell type in the body
Gene regulation in development
Differential gene transcription:
Modification of DNA (methylations) can shut off or turn on genes
Modification of histones (methylations, acetylations) the wrap the DNA
can shut off or turn on genes
To make or not to make transcription factors can regulate what genes get
transcribed
Differential RNA processing:
Selecting what RNA make it outside the nucleus to be translated
Alternative splicing of RNA
Translation regulation
Some mRNA are made to last longer than others (more proteins
translated off of it), and some are made to be rapidly degraded (less
proteins translated off of it)
Selective inhibition of translation of stored RNA in the oocyte- gets
translated only when needed after fertilization
(for prokaryotes- translation and transcription occur almost simultaneous)
Post-translational regulation
Some proteins are inactive until modified by certain enzymes
Active proteins can be selectively marked for degradation by ubiquitin
Programmed cell death
Apoptosis = programmed cell death
During apoptosis, strong proteases are activated and they digest the cell from
within. In mammals, the proteases are called caspases
Spaces between our fingers are created by apoptosis
The tail of a tadpole undergoes apoptosis when it morphs into a frog
Existence of regenerative capacity in various species
Some animals are capable of regeneration, the ability to regrow or grow new
parts of their bodies
Salamanders and newts can regenerate entire body parts
Great for escape technique
Mice can regenerate toes with enough nail left
Planarians (flat worms) can grow into a new worm when cut into pieces
Sharks regrow lost teeth
They grow about 24,000 teeth in a lifetime
Spiders can regrow missing legs or parts of legs
Humans grow scar tissues after amputation

Senescence and aging
Senescence = biological aging
Aging: declining ability to respond
As cells mature, they naturally stop dividing and enter the period of
senescence
 Can also occur prematurely due to oncogenes involved in cancer
development
Gradual deterioration of function of life forms
Normal diploid cells cease to divide
Cause suffering, disease, and death

Foundational Concept 3
Complex systems of tissues and organs sense the internal and external environments of
multicellular organisms, and through integrated functioning, maintain a stable internal
environment within an ever-changing external environment.

Content Category 3A: Structure and functions of the nervous and endocrine systems and
ways in which these systems coordinate the organ systems.
The nervous and endocrine systems work together to detect external and internal signals,
transmit and integrate information, and maintain homeostasis. They do all of this by producing
appropriate responses to internal and external cues and stressors. The integration of these
systems both with one another, and with the other organ systems, ultimately results in the
successful and adaptive behaviors that allow for the propagation of the species.

Animals have evolved a nervous system that senses and processes internal and external
information that is used to facilitate and enhance survival, growth, and reproduction. The
nervous system interfaces with sensory and internal body systems to coordinate physiological
and behavioral responses ranging from simple movements and small metabolic changes to long
-distance migrations and social interactions. The physiological processes for nerve signal
generation and propagation involve specialized membranes with associated proteins that
respond to ligands and/or electrical field changes, signaling molecules and, by extension, the
establishment and replenishment of ionic electrochemical gradients requiring ATP.

The endocrine system of animals has evolved to produce chemical signals that function
internally to regulate stress responses, reproduction, development, energy metabolism, growth,
and various individual and interactive behaviors. The integrated contributions of the nervous and
endocrine systems to bodily functions are exemplified by the process whereby the signaling of
neurons regulates hormone release, and by the targeting of membrane or nuclear receptors on
neurons by circulating hormones.
The content in this category covers the structure, function, and basic aspects of nervous and
endocrine systems, and their integration. The structure and function of nerve cells is also
included in this category. The topics and subtopics in this category are the following

Nervous System: Structure and Function (BIO)

Major Functions
High level control and integration of body systems
Adaptive capability to external influences
Sensory input
Sensory = afferent
Nerve impulses conveyed to CNS
Motor output
Motor = efferent
Nerve impulses from CNS to effector organs
Integrative and cognitive abilities
Organization of vertebrate nervous system

CNS = Central Nervous System = Brain and Spinal Cord
PNS = Peripheral Nervous System = Everything else
Sensory = Afferent = nerves carry signal toward CNS
Motor = Efferent = nerves carry signal toward effector organs
Somatic Nervous System = Voluntary = controls skeletal muscles
Autonomic Nervous System = Involuntary = effects visceral organs
Sympathetic division = fight or flight
Parasympathetic division = rest
Sensor and effector neurons
Sensor = senses, carries sensory signals from the body to the CNS
Effector = causes an effect = carries motor signals from the CNS to the body
Sympathetic and parasympathetic nervous systems: antagonistic control
Sympathetic = prepares body for activity = fight or flight
Increases heart rate, blood pressure, breathing rate
More blood flow to muscles, less to digestive system
Pupil dilation
Break down glycogen to release glucose into blood
 Parasympathetic = prepares body to rest
Decrease heart rate, blood pressure, breathing rate
Less blood to muscles, more to digestive system
Pupil constriction
Synthesizes glycogen for storage from glucose
Reflexes
Feedback loop, reflex arc
Feedback Loop = positive feedback (reinforce initial event), negative
feedback (counteracts initial event), or reflex arc (usually a type of
negative feedback)
Positive Feedback = blood clotting platelets activated at wound
site attract more platelet activation and clumping
Negative Feedback = drop in blood pressure causes ADH release,
which increases it. Conversely increase in blood pressure causes
a drop in ADH
Reflex Arc = withdrawal from a painful stimulus = negative
feedback
Reflex Arc = knee jerk = tapping the knee tendon causes sudden
stretching of the muscle, which lead to contraction of that muscle
that creates the knee jerk = negative feedback
Reflex Arc = receptorsensory neuron integration center
motor neuron effector
Receptor = site of stimulus
Sensory neuron = carries impulse from receptor to integration
center
Integration center = connects sensory to motor neuron via
synapse inside the CNS
Monosynaptic = no interneuron, direct synapse of sensory
to motor
Polysynaptic = interneuron(s) present
Motor neuron = carries impulse towards effector
Effector = site of response of the stimulus
Examples of reflexes: knee-jerk, withdrawal from pain
Effects on flexor and extensor muscles:
During knee-jerk, in addition to contracting the extensor, the reflex
relaxes the flexor
Golgi tendon reflex: sudden contraction of the quads (extensor)
causes a negative feedback that relaxes the quads and contracts
the hamstrings (flexor)
Role of spinal cord and supraspinal circuits
The spinal cord
Part of Central nervous system (CNS)
Cylindrical shape bundle of nerve fibers
Important cable that connects nerves between brain and rest of
the body and provides synapses for the reflex arc
Controls most of functions of the body and the mind
Supraspinal circuits
 Involves input from the brain or brainstem to process a stimuli,
unlike most reflex arcs (

Integration with endocrine system: feedback control
Feedback control
Feedback loop = chain/loop of cause and effect
Feedback mechanism controls and maintains endocrine system for
proper body functions by synthesizing, releasing, and inhibiting hormones
(chemical messengers)
Some areas of control include:
Stress
Injury
Growth/development
Reproduction
Energy metabolism
Water/electrolyte balance
Birth/lactation
Absorption of nutrients
There are positive and negative feedback loop
Positive reinforce initial event
Not very common as negative feedback control
For example, during birth uterus contraction leads to
release of hormone oxytocin, causing to release more
oxytocin until the baby is born and no more contraction is
required.
Negative counteracts initial event
For example, high blood glucose level causes pancreases
to release insulin, which causes liver to take up glucose
from the blood decreasing the blood glucose level.

Nerve Cells (BIO)
Cell body: site of nucleus, organelles
Contains nucleus and organelles like any other cell
Has well-developed RER and golgi (makes lots of proteins)
Dendrites: branched extensions of cell body
Receptive region of the nerve = gets input
Branching helps to increase surface area for reception
Axon: structure and function
Axon = conducting region of the nerve
Axon terminals = secretory regions of nerve
Other names for axon terminal = synaptic knob = bouton
take information away from cell body
Myelin sheath, Schwann cells, insulation of axon
Myelin Sheath- covers the axon intermittently, with gaps called Nodes of Ranvier
Purpose of myelin sheath is to speed up conduction by insulating the nerve in
intervals. Intermittent insulation causes action potential to jump from one node of
Ranvier to the next
Schwann Cells- makes myelin sheath in the peripheral nervous system by
wrapping around the axon
Oligodendrocytes- the CNS analog of Schwann cells, makes myelin sheath
around CNS axons
Insulation of axon = achieved by myelin sheath. Insulation occurs in intervals,
which causes action potential to jump from one node of Ranvier to the next
Myelin Sheath is a good insulator because it is fatty and does not contain any
channels
Nodes of Ranvier: propagation of nerve impulse along axon
Action potential jumps from one node of Ranvier to the next
This jumping of action potential speeds up conduction in the axon
Synapse: site of impulse propagation between cells
Synapse- conduction from one cell to another
Axodendritic Synapse- axon terminal of one neuron (presynaptic) dendrite of
another neuron (post synaptic)
Axosomatic Synapse- axon terminal of one neuron (presynaptic) cell body of
another neuron (postsynaptic)
Axoaxonic Synapse (rare)- axon terminal of one neuron (presynaptic) axon
hillock of another (postsynaptic)
Synaptic activity: transmitter molecules

transmitter molecules
Transmitter molecules = neurotransmitters
 Action potential release of neurotransmitters by presynaptic axon
terminal picked up by receptor of postsynaptic neuron
Release of neurotransmitter = exocytosis of vesicles containing
neurotransmitters. Triggered by calcium influx where action potential
reaches axon terminal
Neurotransmitter reception = diffusion of neurotransmitter across the
synaptic cleft, binds to receptor, opens up ion channels that cause a
change in membrane potential of the postsynaptic neuron (graded
potential). If this graded potential is large enough, it will trigger a full-
fledge, all-or-nothing action potential in the postsynaptic neuron
Neurotransmitters are quickly eliminated (destroyed by enzymes,
reuptake by presynaptic terminal, or diffuse away) so they dont
overstimulate postsynaptic neuron
Neurotransmitter molecules include:
Acetylcholine (ACh) (most common neurotransmitter for
preganglionic neurons in total ANS and postganglionic in the
parasympathetic branch. also used for somatic system)
Norepinephrine (NE) (also called noradrenaline- common
neurotransmitter for postganglionic neurons in sympathetic
nervous system)
epinephrine (also called adrenaline common neurotransmitter for
postganglionic neurons in sympathetic nervous system
Dopamine
Serotonin
Histamine
ATP
Resting potential: electrochemical gradient
Na+/K+ Pump: 3Na+ out, 2K+ in = net negative to the inside, net positive outside
K+ Leakage- the resting cell membrane has channels that allow K+ to leak out,
but dont allow Na+ to leak in = even more negative inside, more positive outside
Resting potential is -70mV
Electrochemical gradient = combination of electrical and chemical gradient = both
electrical potential and ion concentration gradient across the membrane
Action potential

Stages of an action potential
Resting: cell at rest, sodium-potassium pump maintaining resting potential
(-70 mV). Lots of sodium outside, lots of potassium inside. Ion channels
closed so the established ion gradient wont leak
Depolarization: sodium channels open, positive sodium rushes inside,
membrane potential shoots up to +30 mV. Lots of sodium inside, lots of
potassium inside
Repolarization: potassium channels open, sodium channels close,
positive potassium rushes outside, membrane potential drops back down.
Lots of sodium inside, lots of potassium outside (opposite of resting state)
Hyperpolarization: potassium channels dont close fast enough, so
membrane potential drops lower than resting potential (too much
potassium outside so super negative inside)
Refractory Period: sodium-potassium pump works to re-establish the
original resting state (more potassium inside, sodium outside). Until this is
done, the neuron cant generate another action potential
Absolute refractory period- sodium channels have been
inactivated, and nothing can activate them until they return to
normal
Relative refractory period- can transmit another action potential
but depolarization required is greater, since the membrane is
hyperpolarized (hasnt returned to -70 yet)
Threshold, all-or-none
When a stimulus (graded potential) depolarizes above a threshold value,
an action potential occurs
Action potentials are all-or-none, meaning that if it occurs, all action
potentials have the same magnitude
Sodium/potassium pump
3 Na+ out, 2 K+ in = net positive out
 Causes membrane to be more negative on the inside = negative
membrane potential
Excitatory and inhibitory nerve fibers: summation, frequency of firing
Excitatory = stimulates an action potential to occur
Excitatory Synapse = receptor binding causes postsynaptic potential to be more
positive (depolarization) = if it gets above threshold, action potential results
Inhibitory = inhibits an action potential from occurring
Inhibitory Synapse = receptor binding causes postsynaptic potential to be more
negative (hyperpolarization) = makes it more difficult to reach threshold
Summation = two or more nerves firing at the same time
Temporal Summation- signals pile on top of each other, so you take a
summation of a time period all at once
Spatial Summation- signals from all areas are summed at a given time
Frequency = Firing, then quickly firing again
If first fire is subthreshold, will fire again before previous depolarization
dies, and the new depolarization will be even higher than the first time
Glial cells, neuroglia
Supportive cells in the central nervous system (CNS)
Supportive do NOT conduct electrical impulses
Instead, surround and provide support for and insulation between
neurons
Most abundant cell types in the CNS
Different types of glial cells include:
Astrocytes
Star shaped cell
Provide physical and nutritional support
form majority of structure that forms the spinal cord and
brain
glial scaring- form tissue (similar to scar tissue) that
surrounds an injury cite
blood brain barrier
Clean debris (clean out synapeses by removing
neurotransmitters allowing to reset the synapses)
Transport nutrients to neurons
Hold neurons in place
Digest parts of dead neurons
Regulate content of extracellular space (maintain
homeostasis in the cns.
can release lactate into the cns to give neurons an energy
source if necessary
Satellite cells
Provide insulation to neurons in the peripheral nervous system
(PNS)
glial cells that cover the surface of nerve cell bodies in sensory,
sympathetic and parasympathetic ganglia
Microglia
smaller than the other glia (other called macroglia)
when active they swell up and bloob up
 when resting they are sampling the outer liquid with branch
processes. When find something they dont like they retract
the processes and swell up. They are looking for infection
on inflammation
active glia act like macrophage.
if see bacteria can release cytotoxic factor to kill bacteria.
Eats the debris
Antigen presentation- places antigens of the surface,
leading to immune system cells (lymphocytes) reacting to
the antigen and leading to more inflammation
Digest parts of dead neurons
Ependymal cells
make up the lining for the ependyma (hold in the cerebrospinal
fluid)
Produce cerebrospinal fluid
Schwann cells
derive from neural crest cells
Insulation
Found in PNS
Oligodendrocytes
Myelinated axons of neurons
Each have many extending processes, each extension can form
one segment of myelin on an axon, but each oligodendrocytes can
myelinate many
Found in CNS

Electrochemistry (GC)
Concentration cell: Direction of electron flow, Nernst Equation
Concentration cell
A special type of galvanic cell
Contains two half-cells connected by a conductive material
Composed of an electrodes within a solution containing cathode and
anode in each
Anode: the species that has the highest oxidation potential
Cathode: the species that has the highest reduction potential
Spontaneous oxidation-reduction (redox) reaction occurs as a result,
current is generated and energy is delivered
Remember OILRIG Oxidation is losing electron and reduction is
gaining electrons
Oxidation half reaction
At anode
Loss of electrons
Increase in charge
The overall reaction: Zn + Cu2+ Zn2+ + Cu
Oxidation: Cu2+ + 2e Cu
Reduction half reaction
At cathode
 Gain of electrons
Decrease in charge
The overall reaction: Zn + Cu2+ Zn2+ + Cu
Reduction: Zn Zn2+ + 2e
Direction of electron flow
Electron (negatively charged particle) will flow to the cathode to reach the
equilibrium of the ion gradient
When concentration of ions in the half-cells equal, the current will stop
Nernst equation
Help determine the cell potential
Ecell = E0cell (0.0592/n)logQ
E0cell = Standard cell potential
Ecell = The half-cell reduction potentiation at standard
temperature (298K)
Q = Reaction quotient
E0cell = E0cathode E0anode

Biosignaling (BC)
Gated ion channels
Voltage-gated channels
Group of transmembrane ion channels
Open/close by change in membrane potential across the membrane
Various ion channels include:
Voltage-gated sodium channels
Voltage-gated calcium channels
Voltage-gated potassium channels
Ligand-gated channels
Group of transmembrane ion channel proteins
Open when specific ligand molecule bind to the receptor protein
Binding of ligand causes conformational change of the protein leading ion
flux across the membrane occurs
Ligand can be neurotransmitter
Receptor enzymes
Also known as enzyme-linked receptor and catalytic receptor
Transmembrane receptor
Extracellular ligand binds (on the cytoplasmic side of the membrane) and
activates intracellular enzymatic activity
Upon binding of ligand, conformation change of the protein occurs
Kinase = covalently attaches phosphate groups to proteins -> modify with
phosphate on the side chain hydroxyl of serine, threonine, or tyrosine
Regulated by modification of proteins with phosphates
hill coefficient- measures degree of cooperative binding- n>1 positively
cooperative binding, c<1 negative cooperative binding, n=1
noncooperative binding
There are three types of receptor enzymes:
Receptor serine-threonine kinase
Receptor tyrosine kinases
Tyrosine-kinase associated receptors
 G protein-coupled receptors
Found only in eukaryotes
Large integral membrane proteins
Single polypeptide folded into a globular shape
Ligands bind and activate the receptor causes conformational
change that activate G protein transmits the extracellular signal to
inside of the cell
Ligand = can be cyclic AMP, peptides, and large proteins
G proteins can bind GTP (guanosine triphosphate) and GDP (guanosine
diphosphate)
GTP = active
GDP = inactive
GDP binds to the alpha subunit and the G protein-GDP
complex binds to nearby GPCR
When ligand binds to GPCR, GPCR activates G protein
and GTP replaces GDP bound to the alpha subunit -> the
subunits are dissociated into GTP-bound alpha subunit
and a beta-gamma dimer
GTP is hydrolyzed back to GDP when no lingered needed
to be activated

Lipids (BC, OC)

Description; structure
Steroids
The main feature of steroids is the ring system of three cyclohexanes and
one cyclopentane
There are a variety of functional groups that may be attached. The main
feature, as in all lipids, is the large number of carbon-hydrogens which
make steroids non-polar.

Terpenes and terpenoids
Terpenes are hydrocarbons, whereas terpenoids contain additional
functional groups.
Terpenes are derived biosynthetically from units of isoprene,
which has the molecular formula C5H8. The basic molecular
formulae of terpenes are multiples of that, (C5H8)n where n is the
number of linked isoprene units.

 Monoterpenes are formed from two terpenes put togehter
sesquiterpene is 3 terpenes put together
diterpene is 4 (2 monoterpenes)
combine enough together to form steroids

Endocrine System: Hormones and Their Sources (BIO)

Function of endocrine system: specific chemical control at cell, tissue, and organ level
Glands makes hormones which are released into the blood stream specific
control of all target cells of that hormone
Hypothalamus is the control center for the brain- creates ADH and oxytocin
Pituitary- master gland. Right below the hypothalamus
thyroid gland- located in neck- regulate metabolism with T3 and T4
parathyroid- (4 spots on back of thyroid)- regulates calcium with PTH
Adrenal- right above kidneys- adjacent to the kidneys (renal)
outer- cortex- steroids (cortisol (stress hormone and anti inflammatory)
and aldosterone (regulation of blood volume))
inner- medulla- catecholamines (epi and norepi)
Gonads- ovaries and testes- release sex hormones- main purpose is to develop
sexual differences
Pancreas- upper part of the abdomen- control blood sugar with insulin and
glucagon
Definitions of endocrine gland, hormone
Endo = within, cine = to secrete
Endocrine glands secrete hormones into surrounding tissue fluids
Endocrine vs Exocrine, Autocrine, Paracrine
Endocrine: hormone, no duct, acts long distances, bloodstream
Exocrine: non-hormone secretions into ducts
Autocrine: local chemicals, act short distances on themselves
Paracrine: local chemicals, act short distances on other cells
Hormone = chemicals that regulate metabolism and functions of other cells
Major endocrine glands: names, locations, products

Hormones
Gland Locations Effect of hormone
produced

Hypothalamu Above the Simulates pituitary to

GnRH
s brainstem release FSH (follicle
(Gonadotropi
(releases stimulating hormone)
n releasing
hormones/fac and LH (luteinizing
hormone)
tors that hormone)
simulates
CRF (Corticotrophin releasing hormone),
pituitary to
TRH (thyroid releasing hormone)
release its
ADH Increases water
hormones) reabsorption in kidney
(antidiuretic
which increases blood
hormone,
pressure to conserve
Vasopressin)
water

Inhibits prolactin
Dopamine
release

Stimulates uterine
contraction during
Oxytocin labor and milk
secretion during
suckling

Stimulates ovary
follicles to mature and
FSH
testes to produce
sperm

Stimulates ovulation
LH and testes to produce

Pituitary Near the testosterone

gland brain ACTH Stimulates adrenal

(adrenocortic cortex to release
otropic glucocorticoid and
Hormone) mineralocorticoids

Stimulates growth of
Growth
muscle, bones, and
hormone
burns fat

Near the
Pineal gland center of the Melatonin Regulates sleep
brain

Thyroid gland Neck area Thyroid Increases metabolism

 hormone (requires iodine)

Increases blood
calcium by bone
reabsorption, dietary
Parathyroid Parathyroid
calcium absorption,
gland hormone
and calcium
reabsorption in
kidneys

Epinephrine Fight or flight

and response from
At the top and
norepinephrin sympathetic nervous
Adrenal behind the
e system
kidneys
Glucocorticoi
Increases blood sugar
ds (cortisol)

Decreases blood
sugar, stimulates
Insulin
glucose by uptake into

Back of the cells

Pancreas
abdomen Increase blood sugar,
stimulate
Glucagon
gluconeogenesis,
breaks down glycogen

Ovary and Estrogen and Regulate reproductive

Pelvic area
testis testosterone systems/respo

Major types of hormones
Hypothalamus: releases hormones for the pituitary, ADH and oxytocin
Releasing hormones/factors stimulates pituitary to release its hormone
GnRH = Gonadotropin Releasing Hormone = stimulates pituitary to
release FSH and LH
CRF = Corticotropin Releasing Factor
TRH = Thyroid Releasing Hormone
Dopamine = inhibits prolactin release
GHRH = Growth Hormone Releasing Hormone
ADH = Antidiuretic Hormone = Vasopressin = increase water reabsorption
in kidney = conserve water, increase blood pressure
Oxytocin = stimulates uterine contractions during labor, also milk
secretion during suckling
Pituitary: Makes FLAT PEG, stores ADH and oxytocin
FSH = Follicle Stimulating Hormone = stimulate ovary follicles to mature,
testes to produce sperm. Lowest during pregnance
LH = Luteinizing Hormone = LH surge triggers ovulation, stimulate testes
to produce testosterone
ACTH = AdrenoCorticoTropic Hormone = stimulates adrenal cortex to
release glucocorticoids and mineralcorticoids
TSH = Thyroid Stimulation Hormone = stimulate thyroid to release thyroid
hormones
PRL = Prolactin = stimulates breasts to produce milk
E = Endorphins
GH = Growth Hormone = stimulates growth of muscle, bone, burns fat
Pineal: makes melatonin with makes you sleepy at night
Thyroid
Thyroid Hormones: increase metabolism, requires iodine
Calcitonin: turns blood Ca2+ into bone, lowers blood Ca2+
 Parathyroid: makes Parathyroid Hormone (PTH), which increases blood Ca2+ by
bone reabsorption, dietary calcium absorption, and calcium reabsorption in
kidneys
Thymus: Thymus Hormones (thymo-, thymic), stimulates T cells to develop
Adrenal
Epinephrine and norepinephrine = fight or flight response
Mineralocorticoids = aldosterone = increase Na+ and water retention,
raises blood pressure. secrete potassium
Glucocorticoids = cortisol = stress hormone = increase blood sugar
Androgens = testosterone
Pancreas
Glucagon = increases blood sugar (break down glycogen, stimulate
gluconeogenesis)
Insulin = lower blood sugar (stimulates glucose uptake by cells)
Ovary: make estrogen (and a small amount of testosterone)
Testes: make testosterone
Hormone concentration metabolism and negative feedback
Metabolism- liver, kidney, blood, sweat
Negative Feedback loops
Neuroendrocrinology relation between neurons and hormonal systems
Endocrine system is little slower than nervous system because it requires
hormones to travel throughout the body in the bloodstream
Two systems work closely together to regulate physiological processes in the
human body
Hypothalamus and pituitary gland are interconnected with both systems
Hypothalamus controls/innervates pituitary glands
Hypothalamus: regulates homeostasis, reproduction, metabolism,
food consumptions, energy utilization, blood pressure, and more

Endocrine System: Mechanisms of Hormone Action (BIO)

Cellular mechanisms of hormone action
Water Soluble Hormones
Cant cross plasma membrane
Bind to membrane receptors on the outside of cells
Secondary messengers then replay signal inside cell
Lipid Soluble Hormones
Able to cross plasma membrane
Directly activate genes
cAMP pathway:
Amino acid hormone binds membrane receptor
G protein activated
Adenylate cyclase activated
cAMP made
Protein kinase cascade
Phospholipid pathway:
Amino acid hormone binds membrane receptor
G protein activated
Phospholipase C activated
 Membrane phospholipid split into DAG and IP3
DAG triggers protein kinase cascade
IP3 releases Ca2+ from ER
Steroid pathway:
Steroid hormone (and thyroid hormone even though its amino acid
based) goes inside the cell
Hormone binds receptor inside cell (cytoplasm or nucleus)
Hormone-receptor complex (transcription factor) turns on certain genes
inside nucleus
Transport of hormones: blood supply
Hormones travel long distances via blood and lymph
Specificity of hormones: target tissue
Specificity depends on the target cells having the receptors for the hormone, and
non-target cells lacking receptors
Cells can either upregulate or downregulate the receptors they express
Integration with nervous system: feedback control
The nervous system can modulate and override normal control of hormones
based on the status of the body. For example, the bodys blood normal glucose
level is set higher when youre under stress
Hormones can modulate the nervous system. For example, low estrogen levels
during menses gives you a bad mood
Normal control of hormones:
Humoral: glands directly respond to chemical levels in the blood
(parathyroid respond to low blood calcium)
Neural: glands release hormones when stimulated by nerves (fight or
flight response)
Hormonal: glands release hormones when stimulated by other hormones
(tropic hormones)
Regulation by second messengers
The nervous system
Modulates and overrides normal control of hormones based on the bodys
state
Control through hypothalamus
ex: Blood glucose level will set higher under stress
Endocrine system is slower than the nervous system
Due to signaling process of carrying hormones through the
circulation system
Hormones can modulate the nervous system
The nervous system can modulate and override normal control of
hormones based on the status of the body. For example, the bodys blood
normal glucose level is set higher when youre under stress
Hormones can modulate the nervous system. For example, low estrogen
levels during menses gives you a bad mood
Normal control of hormones:
Humoral: glands directly respond to chemical levels in the blood
(parathyroid respond to low blood calcium)
Neural: glands release hormones when stimulated by nerves (fight
or flight response)
 Hormonal: glands release hormones when stimulated by other
hormones (tropic hormones)
Control of hormones
Synthesis and release of most hormones are regulated by negative
feedback
Humoral
Glands directly respond to blood level of ions and nutrients
ex: Parathyroid respond to low blood calcium
Neural
Glands release hormones when stimulated by nervous impulse or
action potential
Fight or flight response
Hormonal
Glands release hormones when stimulated by other hormones
from another gland
Hypothalamus produces releasing/inhibiting hormones

Category 3B: Structure and integrative functions of the main organ systems
Animals use a number of highly-organized and integrated organ systems to carry out the
necessary functions associated with maintaining life processes. Within the body, no
organ system is an island. Interactions and coordination between organ systems allow
organisms to engage in the processes necessary to sustain life. For example, the organs
and structures of the circulatory system carry out a number of functions, such as
transporting:

nutrients absorbed in the digestive system;

gases absorbed from the respiratory system and muscle tissue;
hormones secreted from the endocrine system; and
blood cells produced in bone marrow to and from cells in the body to help fight
disease.
The content in this category covers the structure and function of the major organ
systems of the body including the respiratory, circulatory , lymphatic, immune, digestive,
excretory, reproductive, muscle, skeletal , and skin systems. Also covered in this
category is the integration of these systems and their control and coordination by the
endocrine and nervous systems. The topics and subtopics in this category are the
following

Respiratory System (BIO)

General function
Gas exchange, thermoregulation
In lungs: oxygen diffuses to blood. Carbon dioxide diffuses out of blood
Mechanism of gas exchange follows Henrys law: there is an equilibrium
concentration of oxygen that should be dissolved in blood
When blood reaches the lungs, it has less than the equilibrium
concentration of oxygen because the body used the oxygen up.
Therefore, oxygen diffuses into the blood
The CO2 in blood that reaches the lungs is higher than the equilibrium
concentration because the body that releases it. Therefore, CO2 diffuses
out of the blood
Thermoregulation: breathing causes you to lose heat (you breath out
warm, moist air)
Protection against disease: particulate matter
Nostril hair filters out particles
Mucus lining of respiratory tract traps pathogens and particles
Cilia on mucus lining of respiratory tract sweeps pathogen and particles
out, where you either spit it our or swallow it into stomach acid
Macrophages reside in alveoli
Structure of lungs and alveoli
Lungs
Pair of organs (left and right) with spongy structure filled with air
Right has a an upper lobe, middle lobe, and lower lobe
Left has upper and lower lobes and a cardiac notch for the heart
Located on the chest
Covered by tissue layer called pleura
RIbs surround the lung, and they sit on the diaphragm (the lungs and the
heart form the throax)
Trachea
Conduct inhaled air into the lungs through its tubular branches
Passageway that must remain open to permit air flow
Rings of cartilage prevent its collapse
Branches into two primary bronchi, each supplies one lung
Each bronchus branches repeatedly to supply the entire lung
Respiratory zone: parts that participate in actual gas exchanges
Alveolus (alveoli for plural)
Where gases diffuse
At the end of each alveolar duct
The wall is only one cell thick, except where capillaries pass
across its outer surface.
 Alveolar ducts
The duct leading to the alveoli and its walls are entirely made of
alveoli
Respiratory bronchiole
A tube made of smooth muscle (similar to terminal bronchioles)
but the respiratory bronchioles has a few alveoli scattered in its
walls, which allows it to perform gas exchange
Very small about 1mm wide
Contain no cartilage
The walls are made of smooth muscle which allows their diameter
to be regulated to adjust airflow into the system
Terminal bronchioles: smallest and final branches of the
conduction zone
Smooth muscles of the walls is too thick to allow adequate
diffusion of gases, so no gas exchange occurs; only for
ventilation

Breathing mechanisms

 Diaphragm, rib cage, differential pressure
Diaphragm = muscle that pulls downward when contracting, which
increases chest volume, decreases pressure, and sucks air into lungs
Rib cage = expands outward during breath intake. Intercostal muscles
help this expansion. At rest, the rib cage maintains lung volume, prevents
lung from collapsing, forms a cage around lungs for protection
Differential Pressure = difference between intrapulmonary (inside lung)
and intrapleural (outside lung) pressure
Intrapulmonary pressure = atmospheric pressure (lung is open to
the outside, so has same pressure as outside)
Intrapleural pressure = less than atmospheric pressure = sucks on
the lungs, prevents lung from collapsing. During breath intake,
intrapleural pressure decreases even further, causing the lung to
expand
Negative pressure mechanism in breathing is just sucking. You breathe in
by establishing negative pressure in the lung (sucking)
Mouth-to-mouth is positive pressure
Resiliency and surface tension effects
Lung is elastic: it recoils as soon as you relax after taking a breath. If not
for the rib cage, the lung would collapse even further
Surface tension causes the lung to collapse. Surfactants produced in the
alveoli decreases surface tension, and helps alveoli stay open
Thermoregulation: nasal and tracheal capillary beds; evaporation, panting
Breathing causes significant heat loss
Nose important for warming, humidifying, and filtering inhaled air
Trachea passageway that must remain open to permit air flow
Branches into two primary bronchi, each supplies one lung
Each bronchus branches repeatedly to supply the entire lung
Evaporation at the capillary beds (moist)
Mechanism to lose heat
Panting increases respiratory rate
Loses carbon dioxide from the body, so loses heat
Ex: Dogs depend on panting for dissipation of excess heat
because they cannot sweat


Particulate filtration: nasal hairs, mucus/cilia system in lungs
Nasal hairs are found anterior to nasal passage (nose)
They filter foreign particles from entering the nasal cavity and collecting
moisture
The airways is lined with sticky mucus that trap any particles like dust, pollutants,
bacteria, and more
Cilia, small hairs, weeps mucus from the nasal cavity into the back of the throat
to be swallowed into the stomach
We produce 2 to 4 cups of mucus per day
Alveolar gas exchange
diffusion
Main mechanism of gas and solute exchange
Molecules will move from higher concentration to lower concentration
(down the gradient)
Larger the surface area, the faster the speed of diffusion
Partial pressure (P)
Oxygen
Lower in the alveoli when compared to the external environment
 Allows diffusion of oxygen into the alveoli.Oxygen uptaken by
pulmonary capillaries
Carbon dioxide
Higher in the capillaries than in the alveoli
Allows for diffusion into the alveoli to be exhaled
Henrys Law
Says that when gas is in contact with the surface of a liquid, the amount
of the gas will go into the solution is proportional to the partial pressure of
that gas
Concentration (c) = P/KH
KH: constant with the dimensions of pressure divided by
concentration
P: partial pressure of the solute in the gas

pH control
The pH of blood can be controlled by respiration system
Increase in carbon dioxide concentration leads to decrease in the pH of
blood because carbon dioxide becomes carbonic acid in an aqueous
environment
When decrease in blood pH is recognized by central chemoreceptors
Central chemoreceptors are found on the ventrolateral surface of
medulla oblongata
Chemoreceptor = sensory receptor that detects the levels of
carbon dioxide in the blood
Respiratory center in the medulla sends nervous impulse to the external
intercostal muscles and the diaphragm to increase breathing rate and the
volume of the lungs during inhalation

Regulation by nervous control
Proper regulation of the rate of breathing is essential
Respiratory control center
Although breathing can be voluntarily controlled for short periods of time,
it is normally an involuntary process directed by this control center in the
medulla of the brain stem
The stimuli affects ventilation rate that are both mechanical and chemical
Chemical stimuli:
CO2 + H2O H2CO3 H+ + HCO3
Ventilation rate are increase PCO2 (partial pressure of gas CO2),
decreased pH, and decrease PO2, which are monitored by special
autonomic sensory receptors
Mechanical stimuli
Affect ventilation rate include physical stretching of the lungs and
irritants
Bronchoconstriction: contraction of smooth muscle (of wall of
bronchi and large bronchioles)
Irritant receptors: trigger coughing and/or bronchoconstriction
when an irritation chemical is detected

 CO2 sensitivity
An increase in carbon dioxide concentration leads to a decrease in the pH
of blood due to the production of H+ ions from carbonic acid.
In response to a decrease in blood pH, the respiratory center (in the
medulla) sends nervous impulses to the external intercostal muscles and
the diaphragm, via the intercostal nerve and the phrenic nerve
respectively to increase breathing rate and the volume of the lungs during
inhalation.
Central chemoreceptors, located on the ventrolateral surface of medulla
oblongata, detect changes in pH of cerebrospinal fluid.
Peripheral chemoreceptors act mostly to detect variation of the oxygen in
the arterial blood, in addition to detecting arterial carbon dioxide and pH.

Circulatory System (BIO)

Functions: circulation of oxygen, nutrients, hormones, ions and fluids, removal of
metabolic waste
Functions (circulation of oxygen, nutrients, hormones, ions, and fluids; removal of
metabolic waste)
Oxygen delivery to tissues
Diffuses into the blood in alveolar (lung) capillaries
Binds to hemoglobin in red blood cells
Gets transported to tissues
Used in cellular respiration
Carbon dioxide delivered out
Cellular respiration makes CO2: carbonic anhydrase converts it to
bicarbonate
CO2 gets transported by blood: dissolved CO2, dissolved bicarbonate ion
(major), bound to hemoglobin and plasma proteins
Diffuses out of the alveolar capillaries
Exhaled out
Nutrients
Nutrients absorbed (either by diffusion or active transport) into blood
stream in the small intestines
Nutrients can also be released into the blood stream by cells. For
example, glucagon causes glucose to be released into the blood stream
Nutrients can be taken up by cells. For example, insulin causes cells to
take in glucose from blood
Hormones released by endocrine glands, circulate the blood in order to reach
their target cells
Fluids and ions circulate the blood and are regulated by how much reabsorption
of water and salt occurs in the kidney
Urea = metabolic waste, travels in the blood to the kidneys, where it is filtered out
and passed in urine
Role in thermoregulation
Vasoconstriction conserves heat. When its cold, vasoconstriction occurs in the
arterioles that feed the skin. Less blood flows near the surface of the skin, less
heat loss
 Vasodilation cools you down. When its hot, vasodilation occurs in the arterioles
that feed the skin. More skin blood flow, more heat lost to the surroundings
Four-chambered heart: structure and function

Deoxygenated blood returns to the heart: superior/inferior vena cava
right atrium
Deoxygenated blood gets pumped to the lungs right atrium right
ventricle pulmonary artery lungs
Blood arrives at lungs and gets oxygenated
Oxygenated blood returns to the heart: lungs pulmonary vein left
atrium
Oxygenated blood gets pumped to the body: left atrium left
ventricle aorta
SA node is main pacemaker of heart. If that damaged than AV node
Endothelial cells
`Also can be called as endothelium
Thin layer of simple squamous cells
Simple = single layer of cells
Squamous = flat shaped
Line the interior surface of blood vessels direct contact with blood
 Found in all circulatory system including arteries, veins, and capillaries
These function to:
Provide barrier
Semi-permeable barrier between the vessel lumen and tissues
near by
Fluid filtration
Form new blood vessels
Control blood pressure by vasoconstriction and vasodilation
Systolic and diastolic pressure
Blood pressure = pressure blood exert on walls of blood vessel
Systolic pressure = blood pressure when blood is being pumped (ventricles are
contracting). pressure during and immediately after a heartbeat
Diastolic pressure = blood pressure when blood is not being pumped (ventricles
are relaxing). Blood pressure between heartbeats
Pulmonary and systemic circulation
Pulmonary circulation = heart lungs heart = oxygenates blood
Systemic circulation = heart body heart = delivers oxygenated
blood to body
Pulmonary circulation = shorter than systemic circulation = less resistance = less
blood pressure
Systemic circulation: vasodilation when oxygen levels are low more
blood flow to oxygen starved tissue
Pulmonary circulation: vasoconstriction when oxygen levels are low
less blood flow to low oxygen/blocked alveoli more blood flow to good
alveoli where gas exchange can occur
Arterial and venous systems (arteries, arterioles, venules, veins)

Structural and functional differences
Blood flows from artery arteriole capillary venule vein
Artery
Elastic artery
Aorta and its major branches
Major function = provide elastic pipe for blood straight out
of heart
Lots of elastic tissue
Layers: endothelium, smooth muscle, connective tissue
Not active in vasoconstriction
Muscular (distributing arteries)
Major function = distribute blood to specific organs
Lots of muscle
Layers: endothelium, lots of smooth muscle, connective
tissue
Some activity in vasoconstriction
Arteriole
 Ranges from being like a smaller version of the artery, to being a
larger version of the capillary with smooth muscles spiraling
around it
Major function = controls blood flow to the capillaries
Active in vasoconstriction- arterioles allow body to control which
tissues get more blood
Arteriole is most important site for vasoconstriction
Capillary
Layer: single cell thick endothelium
Major function: blood-tissue solute exchange
Not active in vasoconstriction
Venule
Ranges from being like a large capillary to being like a small vein
Major function: merge of capillaries to be conducted to veins
No vasoconstriction
Vein
Layers: endothelium, smooth muscle, connective tissue
Major function: returns blood back to the heart
Has valves to prevent the backflow of blood
Breathing, skeletal muscles, and smooth muscle adaptations help
blood flow through the vein at low pressure
Vasoconstriction can occur in the vein
For MCAT, only veins have valves, not arteries (although there is a single
aortic valve where it came from the heart)
Thickness: artery > vein > arteriole > venule > capillary
Differences between arteries and veins
Arteries are thicker, more muscular than veins
Veins have valves, arteries dont
Arteries carry blood away from the heart (oxygenated except for
pulmonary artery). Veins carry blood back into the heart
(deoxygenated except for pulmonary vein)
Differences between artery and arteriole
Arterioles are smaller
Vasoconstriction occurs predominantly at the arterioles
Pressure and flow characteristics
Blood pressure of arteries > arterioles > capillaries > venules > veins
Blood pressure is highest in the arteries (specifically aorta) because heart
pumps directly into the aorta
Blood pressure is lowest in the veins (specifically the vena cava) because
flow resistance brings the pressure down
Blood pressure is lower when you elevate a blood vessel (P = gh)
Blood pressure can be regulated by vasoconstriction (increase bp),
vasodilation (decrease bp) and hormones (ADH, aldosterone, renin,
adrenaline all increase bp)
Blood flows from artery arteriole capillary venule vein
Blood squirts from arteries, flows from veins, and oozes from capillaries
Elasticity of arteries causes blood to flow even when the heart is resting
between pumps (this is why diastolic bp is not zero)
Adaptations that help blood flow through the vein at low pressure:
 Respiratory pump: when you inhale, your stomach squeezes on
the veins, and your chest sucks on it
Muscular pump: skeletal muscle squeezes on the veins when you
exercise
When scared, smooth muscles around veins constrict and
squeezes blood
Capillary beds
Mechanisms of gas and solute exchange
Diffusion is the major mechanism of gas and solute exchange, whether it
is diffusion as a free molecule, or bound to carrier proteins
Continuous capillary
No pores on endothelial cells. May have clefts at cell boundaries
Exchange may occur through the clefts, or by vesicle trafficking
through endothelial cells
Found in skin and muscles
Blood-brain Barrier = sealing of clefts by tight junctions
Fenestrated capillary
Small pore, large enough for molecules, but not blood cells to leak
through
Found in small intestines to facilitate nutrient absorption
Found in endocrine organs to allow passage of hormones
Found in kidneys to allow blood filtration
Sinusoidal capillary
Large pores, large enough for blood cells to leak through
Found in lymphoid tissues, liver, spleen, bone marrow
Large pores facilitate lymphocyte travel to tissues
Large pores also facilitate blood cell modifications
Mechanism of heat exchange
Radiation- your body gives off IR signal
Conduction- you touch something cold, or take a hot bath
Evaporative cooling- you sweat, and it cools you as it evaporates
Source of peripheral resistance
Blood viscosity: blood cells and plasma proteins give blood a higher
resistance to flow compared to water. Diseases that increase the amount
of blood cells increase resistance
Total blood vessel length: more blood vessels you have, the more
resistance to flow. Overweight = more blood vessels to service the fat
cells = more resistance
Blood vessel diameter = vasoconstriction increases resistance,
vasodilation decreases it. Obstruction from plaques inside blood vessels
also increases resistance
Composition of blood

Plasma, chemicals, blood cells
 Plasma
It constitutes more than half of the blood's volume and consists
mostly of water that contains dissolved salts (electrolytes) and
proteins. The major protein in plasma is albumin.
Blood Cells
Red blood cells (RBC or erythrocytes)
Contain hemoglobin, transports O2 and CO2
No nucleus, which gives it a biconcave disk shape
Most abundant cell in blood
White blood cells (WBC or leukocytes)
Larger than RBCs
Lobed or irregular shaped nuclei
Fights off pathogens
Platelets
Technically not cells, but cell fragments
Responsible for clotting blood
Erythrocyte production and destruction; spleen, bone marrow
Bone marrow = makes RBCs from stem cells
Spleen = destroys aged and damaged RBCs
Other sites for RBC destruction include the liver and bone marrow
Components of hemoglobin from destroyed RBC gets recycled
Iron = recycled
Heme bilirubin bile excreted in feces
Protein (globin) = broken down into amino acids
Regulation of plasma volume
Blood osmolarity (like molarity)
Higher blood osmolarity water goes into blood higher blood
volume
Lower blood osmolarity water goes into tissues lower blood
volume
ADH (vasopressin): water reabsorption in kidney
Aldosterone: salt reabsorption, leads to water reabsorption
in kidney
Coagulation, clotting mechanisms
Platelets contains enzymes and chemicals needed in the clotting process
Liver produces clotting factors (eg. fibrinogen), which circulates in blood plasma
Coagulation = liquid blood gel
Clotting mechanism:
Platelet plug formation: wound + platelets platelets clump at wound,
release chemicals, activates clotting factors
Coagulation: series of clotting factors/enzyme activation that ends in
fibrinogen fibrin (fiber mesh that seals the clot)
Retraction and repair: clot contracts, gets compact, but after the wounded
blood vessel repairs itself, the clot dissolves
Oxygen transport by blood
Hemoglobin, hematocrit
Hemoglobin = (heme + globin) x 4
Heme = chemical ligand binding iron
Globin = protein that surrounds heme
 4 subunits of the heme-globin complex form a tetramer called
hemoglobin
Hemoglobin can bind oxygen and carbon dioxide
Hematocrit = % volume of blood that is red blood cells, usually ~45%
Oxygen content
Each iron atom in hemoglobin can bind 1 oxygen
Hemoglobin has 4 subunits containing 4 iron atoms
Each RBC has hundreds of millions of hemoglobin molecules
Oxygen affinity
Hemoglobin has a sigmoidal oxygen binding curve. This is because
oxygen binding to one subunit changes it from Tense to Relaxed, making
it easier for additional oxygen to bind
Carbon monoxide binds hemoglobin tighter than oxygen
Fetal hemoglobin binds oxygen tighter than adult hemoglobin
Myoglobin binds oxygen tighter than hemoglobin

Carbon dioxide transport and level in blood
Carbon dioxide is more soluble in blood than is oxygen; about 5 to 7 percent of
all carbon dioxide is dissolved in the plasma.
Carbon dioxide has the ability to attach to hemoglobin molecules (forming
carbaminohemoglobin); it will be removed from the body once they become
dissociated from one another.
carbon dioxide is used as a pH balance
Nervous and endocrine control
epinephrine and norepinephrine released by neurons of sympathetic nervous
system and by adrenal medulla of endocrine can direct blood by causing
restriction of blood vessels.

Lymphatic System (BIO)

Structure of lymphatic system
A part of vascular (circulatory) system
Components:
Lymphatic vessels
Have thin walls
Permeable with valves
Allow diffusion
Prevent any backflow of fluids
Absorb fluid (lymph) from blood vessel capillaries into surrounding
tissues
 Lymph: clear, watery fluid consisting of lymphocytes (a
type of white blood cell)
Made up of smallest lymphatic vessels called lymph capillaries
Lymph nodes
Small oval structures
Found at intervals along the lymphatic system
In armpits, groin, chest, abdomen, and so on
Receive the fluid from lymphatic vessels
Filter and diffuse back into the circulation through veins
Lymphoid organs
Crucial in the immune system
Thymus gland
Considered primary lymphoid organs
Promote production of immune cells
Bone marrow
Soft tissue found inside bones
Produce blood cells
Spleen
Largest organ of the lymphatic system
Filter any damaged cells, debris, and bacteria/viruses
Tonsils
Found in the upper throat area
Protect digestive tracts and lungs from pathogens
Major functions
Equalization of fluid distribution
Interstitial fluid pressure > lymphatic pressure lymph vessel
flaps open interstitial fluid enters lymphatic capillaries
lymphatic circulation merges with veins
Interstitial fluid pressure < lymphatic pressure lymph vessel
flaps close prevents lymph from leaking back out
Transport of proteins and large glycerides
Fats get absorbed into the lacteals in the small intestine
Lacteal = lymphatic capillary in the small intestine
Plasma protein that leaked into the interstitial fluids get returned to the
blood via the lymphatic system
Production of lymphocytes involved in immune reactions
Technically, lymphocytes are produced in the bone marrow from blood
stem cells
However, lymphoid tissues provide a place where lymphocytes can
reside, proliferate, and differentiate
Lymphoid tissue is found in lymph nodes, thymus, and scattered
throughout various organs
Lymph tissue contains many lymphocytes that cleans/filters lymph
Thymus is the place where T cells mature
Return of materials to the blood
Cells and plasma proteins that leak out of the blood capillaries gets
collected by the lymphatic capillaries and returned to the vein

Immune System (BIO)

 Innate (non-specific) vs. adaptive(specific) immunity

Innate = first line of defense = kills anything that isnt right = not specific to a
particular pathogen/antigen
First line (keep out of the system)
Skin: natural flora, layer or keratin
Mucus membranes: traps pathogen in mucus, and cilia moves it
out
stomach acid
Second line
Fever/inflammation: WBCs (white blood cells) are more active at
higher temperature, and inflammation recruits WBCs to site of
infection by sending out chemical signals and making capillaries
more permeable
Phagocytes: engulf pathogen.
Natural killer cells: destroy infected cells
Antimicrobial proteins: tears (lyse bacteria), interferons (interfere
with virus replication), complement (punch holes in cell/pathogen
membrane)
Adaptive Immunity = highly specific for a particular pathogen/antigen
Antigen-presenting cells present foreign antigen on surface
Antigen is recognized by T and B cells
Cytotoxic T cells kill infected cells
Helper T cells activate macrophages, T and B cells
B cells produce antibodies (humoral immunity- extracellular fluid)
Antibodies bind to antigens and bring about:
Neutralization- pathogen cant adhere to host cell
Opsonization- makes it easier for phagocytosis
Complement Activation- kills infected cell by punching holes in cell
membrane
Memory cells are made that are much more efficient (does not need T cell
activation) in proliferating and making antibodies in case the same
infection strikes in the future, allow the body to mount a greater, and more
 sustained response against the same pathogen during secondary
response
Adaptive immune system cells
T-lymphocytes
Matures in Thymus
focus on infiltrated cells
Cytotoxic T cells recognize antigen on infected cells through MHC I
receptors, and signal for apoptosis. Attack the infiltrated cells. (CD8+
receptor binds to MHC I). Known as cell-mediated immunity
Helper T cells recognize antigen on antigen-presenting cells, and signal
for activation of B cells, T cells, and macrophages
dendritic cells digest virus/bacteria. present pieces on MHC II
complex. Helper t cell has receptor to bind to MHC II (just like B
cell it is specific to certain MHC II)
turn into effector or memory helper cell
memory- storage in case experience the same
infection
effector helper cell- release cytokines- enter other
activated immunological cells, making them more
active in immune respons. Bind to MHC II receptor
on the sister B cell for the same virus/ bacteria,
leading to differentiation
CD4 + receptors bind to MHC II
B-lymphocytes
Matures in Bone marrow
B cells form plasma cells and memory cells when exposed to antigen
Plasma cells = secrete antibody
Memory cells = stick around in case same antigen attacks in the future
Each B cell has antigen receptors. If they bind to a random virus epitope,
then they start replicating
humoral (stuff that is floating around, foreign)
memory cell- have the correct receptors for the original virus. If we
get the same virus again then these cells will be able to fight the
virus
effector cells (plasma cell)- turn into antibody factories. create
antibodies for the virus. The antibodies will bind to the virus,
tagging them for phagocytosis
Innate immune system cells
Phagocytes
Phagocytes are cells that protect the body by ingesting (phagocytosing)
harmful foreign particles, bacteria, and dead or dying cells.
The main difference between professional and non-professional
phagocytes is that the professional phagocytes have molecules
called receptors on their surfaces that can detect harmful objects,
such as bacteria, that are not normally found in the body
the professional phagocytes include many types of white blood
cells (such as neutrophils, monocytes, macrophages, mast cells,
and dendritic cells
 mast cells release histamine (nonspecific inflammatory response)
Macrophages
Macrophages = large, non-specific phagocytic cell of the immune system.
They frequently leave the bloodstream to crawl around tissues and
perform clean-up duties, such as ingesting dead cells or cellular debris
at an injury site, or pathogens
Tissues
Bone marrow
All blood cells arise from stem cells in the bone marrow
B lymphocytes differentiate in the bone marrow
Spleen
Provide a site for WBCs to reside and proliferate
Removes pathogens from blood
Removes old RBCs and platelets
Thymus: T lymphocytes differentiate in the thymus
Lymph nodes
Provide a site for WBCs to reside and proliferate
Removes pathogens from lymph
Residing lymphocytes monitor lymph for foreign antigens, and initiate an
immune response when exposed to foreign antigens
Concept of antigen and antibody (immunoglobulin)
Antibody = lock, Antigen = key. Each antibody is specific to the binding of an
antigen
Antibody is like a Y, the times of the fork bind antigen
The tips of the fork are called hypervariable regions because they are unique to
each antigen-specific antibody
The antibody consists of 2 light chains and 2 heavy chains linked together by
disulfide bonds
Antigen presentation
Pathogen enters Antigen-presenting-cell (APC)
Pieces of the pathogen gets displayed at the surface of APCs
T cell receptors recognize the presented antigen, and activates various immune
responses
Clonal selection
Response of lymphocytes to specific antigens attacking the body
Selection B cells (lymphocytes) activates only specific
antigens
B cells are found in the blood and lymphoid tissues
B cells are produced from lymphoid stem cells
Clonal thus, multiplication of antibodies occurs only in
particular cells
Crucial in the understanding of immunology
Mechanism:
B cells present specific antibody on the surface
Proper antigen forms a complex with the antibody on the cell activating
the cell for further development. Those that do not meet the specificity are
not activated.
Antigen-antibody interaction occurs and the complexes accumulate on
the surface of the cell
 The complexes are internalized and begin to swell and rapidly divide.
B cells differentiate into plasma cells and memory cells.
Plasma cells: produce specific antibody that provoke its formation
Memory cells: remain in circulation, but do not produce antibodies
Antigen-antibody recognition
is a specific chemical interaction between antibodies produced by B cells of the
white blood cells and antigens during immune reaction.In the blood, the antigens
are specifically and with high affinity bound by antibodies to form an antigen-
antibody complex. The immune complex is then transported to cellular systems
where it can be destroyed or deactivated.
Structure of antibody molecule

Recognition of self vs. non-self, autoimmune diseases
The bodys immune defenses normally coexist peacefully with cells that carry
distinctive self marker molecules. But when immune defenders encounter
foreign cells or organisms carrying markers that say nonself, they quickly
launch an attack.
Too little regulation can lead to autoimmune disease, where hyperactive immune
system targets the bodys own tissues
Major histocompatibility complex
allows immune system to differentiate self and non-self cells
Decides the compatibility of donors for organ transport
If not compatible, autoimmune disease will occur
Group of glycoproteins on the plasma membrane
Antigen presentation depends on:
Class I MHC proteins
Found on all nucleated cell surface (every cell except red
blood cells)
Function to protect from viral infection
Epitope is presented to on MHC 1 cytotoxic T-
lymphocytes (CTLs) trigger apoptosis
(programmed cell death)
Epitope: part of antigen that immune system
recognizes
Class II MHC proteins
Found only on specialized antigen-presenting cells like B
lymphocytes and macrophages
 Mediate specific immunity acquired and adaptive
immunity
Antigen-presenting cells (APCs) uptake an antigen
present fraction of antigen on the surface
coupled with MHC class II molecule helper T cell
recognizes the antigen immune response

Blood cell Lineage



NK- natural killer cells- innate immune system

Megakaryocytes- make platelets
dendritic cells- come from both
macrophage come from monocyte.
Monocytes circulate in blood, change into macrophage or dendritic cells when
enter tissue
Granulocytes are immune cells that can be identified by the presence of granules
in their cytoplasms, granules that may contain histamine, defensins, or other
immune proteins. innate immune system responds to any and every foreign
invader with the white blood cells called granulocytes as well as with
inflammation and other actions

Digestive System (BIO)

Ingestion
Saliva as lubrication and source of enzymes
Saliva dissolves food
Saliva contains mucin, a protein that lubricates the bolus
 Saliva contains amylase (found also in small intestine), which breaks
down polysaccharides (starch and glycogen)
Saliva also contains antibodies and lysozyme that kills pathogens
Ingestion; esophagus, transport function
Muscular tube that propels bolus (food) to the stomach by peristalsis
Peristalsis = squeezing stuff through a tube (esophagus/gut) by smooth
muscle
esophagus does not secrete digestive juices
Stomach
Storage and churning of food
Storage = stomach is a muscular bag that is elastic and can stretch to
store food
Churning = mechanical digestion = mixing food
Low pH, gastric juice, mucal protection against self-destruction
Parietal cells secrete HCl that cuases the pH to be very acidic
Gastric juice = HCl + pepsin + hormones = secreted by the stomach
(parietal and chief cells (secrete pepsin), and enteroendocrine cells)
Pepsin = protease that works best in acidic environment
most gastric enzymes work best at low phf
Goblet cells secrete mucus lining that protect the stomach from the acid
and self-digestion
Production of digestive enzymes, site of digestion
Chemical digestion: stomach produces pepsin, which digests proteins
(secreted in an inactive form, gets activated in acidic environment)
Pepsin is special in that it works best at very acidic pH
Mechanical digestion: stomach churns food
Structure (gross)
Banana shaped bag that can stretch
Inner membrane densely folded (rugae), so can accommodate stretching
Sealed off on the top by the cardiac (gastroesophageal) sphincter
Sealed off on the bottom by the pyloric sphincter
Liver
Structural relationship of liver within gastrointestinal system
Largest gland in body, spans both sides of the abdomen (though right
side much larger)
Ducts draining to duodenum and gall bladder
Production of bile
Bile is a liquid released by the liver. It contains cholesterol, bile salts, and
waste products such as bilirubin. Bile salts help your body break down
(digest) fats. Bile passes out of the liver through the bile ducts and is
stored in the gallbladder.
Role in blood glucose regulation, detoxification
Blood glucose regulation by liver:
Blood sugar too low: glucogenesis
Blood sugar too high: glycogenesis
Detoxification: metabolize alcohol (alcohol dehydrogenase), remove
blood ammonia, inactivate various other drugs/toxins
Bile
Storage in gall bladder
 Gall bladder stores excess, unused bile, and concentrated it. Secretes it
when needed
Function
Bile is an emulsifying agent (not an enzyme)
Bile breaks down large fat droplets into smaller microscopic droplets by
forming micelles
This increases the total surface area of the fat for lipase action
Pancreas
Production of enzymes
Pancreas is the major source for all the digestive enzymes
Amylase- digests starch
Various proteases
Lipase- digests fat
Ribonuclease- digests nucleic acids
Pancreas makes HCO3- to neutralize HCl from stomach
Transport of enzymes to small intestine
Digestive enzymes of pancreas = exocrine = flows into small intestine via
duct
Small Intestine
Absorption of food molecules and water
Small Intestine is major place for digestion and absorption
Folds, villi, and microvilli increase surface area for absorption
Absorbs digested food into circulation (fats into lacteals, all other into
capillaries)
Active transport occurs to absorb against the concentration gradient
Intestinal lumen (less glucose) enterocyte (more glucose):
Secondary active transport by Na+/K+ pump and Na+/Glucose
symport
passive/facilitated diffusion occurs to absorb down the concentration
gradient
Enterocyte (more glucose) extracellular fluid (less glucose):
Facilitated diffusion (then the glucose will go from the extracellular
fluid to blood)
Function and structure of villi
Villi = finger-like protrusions inside small intestine
Microvilli = same as villi but on the surface of a single absorptive cell
Production of enzymes, site of digestion
Small intestine is the major place for digestion and absorption
Pancreas is the major source for enzymes. However, the small intestine
does make some of its own enzymes, including protease and amylase
Neutralization of stomach acid
Pancreas makes bicarbonate ion to neutralize the HCl from the stomach
This neutralization facilitates enzymes in the small intestine, which would
be denatured by stomach pH
Structure (anatomic subdivisions)
Duodenum- first part small intestine, food broken down by enzymes and
bile
jejunum-second part- inside walls absorb food nutrients
 Ileum- absorbs bile acid to deliver back to liver, absorbs B12 which is used
to make nerve cells and red blood cells (longest part of small intestine)
Large Intestine
Absorption of water
Large intestine absorbs any remaining water that is not absorbed by small
intestine
Bacterial flora
Ferment undigested nutrients, make gas
Produce vitamin K (important for clotting)
Structure (gross)
Lobes/pockets along its length due to muscle tone. Unlike small intestine,
the large intestine has no folds or villi
Rectum:storage and elimination of waste, feces
Rectum stores feces
Anal sphincter ties the end of the rectum
During defecation, sphincter opens, feces are released through the anus
Muscular control
Peristalsis
involuntary movement of smooth muscles, squeezes food along digestive
tract
Endocrine control
Hormones
Gastrin: Secreted from the stomach and plays an important role in control
of gastric acid secretion.
Cholecystokinin: A small intestinal hormone that stimulates secretion of
pancreatic enzymes and bile.
Secretin: Another hormone secreted from small intestinal epithelial cells;
stimulates secretion of a bicarbonate-rich fluids from the pancreas and
liver.
Target tissues
Nervous Control: the enteric nervous system
the digestive system's own local nervous system
The myenteric plexus is located between the longitudinal and circular layers of
muscle in the tunica muscularis and, appropriately, exerts control primarily over
digestive tract motility.
The submucous plexus, as its name implies, is buried in the submucosa. Its
principal role is in sensing the environment within the lumen, regulating
gastrointestinal blood flow and controlling epithelial cell function. In regions
where these functions are minimal, such as the esophagus, the submucous
plexus is sparse and may actually be missing in sections.

Excretory System (BIO)

Roles in homeostasis
Blood pressure
If blood pressure too low:
Renin-angiotensin pathway: Kidney (JGA cells) release renin,
triggers formation of angiotensin II, which stimulates aldosterone
release, raising blood pressure
 Aldosterone (aka mineralocorticoid): Adrenal glands release
aldosterone, causes kidney (distal tubules) to reabsorb more Na+,
which causes more water reabsorption, secretes potassium
ADH (made in hypothalamus, stored in pituitary): causes more
water reabsorption in the kidney tubules, raising blood pressure.
High levels also cause vasoconstriction. Act on collecting duct
If blood pressure too high:
All the above hormones stop releasing
Heart releases ANP (atrial natriuretic peptide), which antagonizes
aldosterone and cause kidney to excrete more Na+ and more
water. ANP can also cause vasodilation
Osmoregulation
Blood plasma is mainly Na+ and Cl- (inside cells is mainly K+ and
hydrogen phosphate ions)
Blood osmolarity is determined predominantly by Na+ and Cl-
Blood osmolarity too low aldosterone, reabsorb Na+. Cl- follows
Kidneys tubules secretion and reabsorption regulates osmolarity
Other ions:
K+ is regulated by aldosterone
Aldosterone: reabsorb Na+, pee out K+
Calcium and phosphate regulated by PTH
PTH = parathyroid hormone = more Ca2+ reabsorption in kidney
tubules (also, bone breakdown to release calcium and
phosphates, and small intestine to absorb more calcium)
Acidbase balance
Buffer systems: Bicarbonate buffer system (blood and extracellular fluid),
Phosphate buffer system (inside cells)
CO2 + H2O H2CO3 H+ + HCO3-
Breathing out CO2 decreases acidity in blood
Kidney tubules:
Bicarbonate ion (HCO3-): peeing it out makes blood more acidic,
reabsorption makes blood more basic (Le Chateliers)
H+ secretion gets rid of acidity
Removal of soluble nitrogenous waste
Urine = concentrated urea in water, with some salt
Urea = harmless form of toxic ammonia = nitrogenous waste
Amino acids ammonia urea peed out
Kidney structure

o Cortex = outer shell of kidney, contains the convoluted tubules
o Medulla = inner part of kidney, contains loop of Henle
Nephron structure

afferent arteriole flows threw kidney, pressure pushes filtrate into bowman's
capsule. This flows into proximal tubule. Sodium, glucose, and a little water starts
to be actively transported back into the blood. From the tubule goes to the loop of
 henle. Descending part of loop permable to water, ascending part actively
transport out salt ions (NA, K, Cl) to make the medulla salty so that it will pull out
water (environment of the loop). From the loop goes to the distal convoluted
tubule where more ions are reabsorbed (and water if stimulated by aldosterone).
From there it goes into collecting duct which goes through the salty medulla, so
ADH controls how much water leaves back into the medulla.
Nephron = functional unit of kidney = glomerulus + Bowmans capsule + proximal
tubule + loop of Henle + distal tubule + collecting duct (shared by many nephron)
Glomerulus = ball of capillaries at beginning of nephron where blood filtration
takes place. Formed by efferent arterioles connected to capillaries. Can increase
glomerular filtration rate while decreasing renal blood flow by increasing
resistance in the efferent arterioles
Bowmans capsule = cup/capsule that surrounds the glomerulus, collects plasma
that is filtered from the capillaries in the golmerulus. efferent arteriole takes
blood away from the glomerulus
Proximal tubule = convoluted tubule on the side of the Bowmans capsule = the
major site for reabsorption (nutrient, salts and water) and secretion (except for
K+, the secretion of which is the job of distal convoluted tubule in response to
aldosterone)
Loop of Henle = U shaped loop that dips into the renal medulla = countercurrent
multiplier mechanism occurs here. Descending limb permeable to water but not
sodium, and ascending limb is the opposite
Distal tubule = convoluted tubule on the side of the collecting duct = hormone-
controlled (fine-tunes the work done by the proximal tubule) reabsorption of water
and sodium.
Aldosterone-increasing reabsorption of ions and water in the kidney, to
cause the conservation of sodium, secretion of potassium, increase in
water retention, and increase in blood pressure and blood volume
Collecting duct = the distal tubules of many nephrons drain here = ADH-
controlled reabsorption of water, hormone-controlled reabsorption/secretion of
salts
Formation of urine
Glomerular filtration
Powered by hydrostatic pressure
Both good stuff (nutrients), bad stuff (urea, creatinine, uric acid), ions
filtered out, as long as it is small enough
Good stuff to be reabsorbed, bad stuff to be peed out
Secretion and reabsorption of solutes
Proximal convoluted tubules reabsorb all the good stuff (nutrients) and
most of the ions. Bad stuff left in the filtrate (urea) to be peed out, also
actively excreted (NH4+, creatinine, organic acids)
Loop of Henle reabsorbs water and salt using the countercurrent
mechanism
Distal convoluted tubules selectively reabsorb or secrete stuff based on
hormonal control
Collecting duct reabsorb water to concentrate urine if ADH present. (Also
can secrete and reabsorb stuff based on hormonal control)
 Regulation of blood pH: secrete H+ when blood too acidic, pee out (dont
reabsorb) HCO3- when blood too basic
Concentration of urine
Distal convoluted tubule contains dilute solution of urea
Collecting duct concentrates it by water reabsorption (facilitated diffusion)
when ADH present
Water reabsorption in the collecting duct is possible because the loop of
Henle has a very high osmolarity (very concentrated) at the bottom
Counter-current multiplier mechanism
Countercurrent multiplier creates an osmotic gradient down the loop of
Henle, which is used by the collecting duct to concentrate urine
Countercurrent: Descending limb is impermeable to salt but has water
flowing out of filtrate / Ascending limb is impermeable to water but has
salt flowing out of filtrate
Gradient-producing power of each individual NaCl pump multiplies down
the length of the loop of Henle. The longer the loop of Henle, the greater
the osmotic gradient, and the more concentrated the urine
Urea Recycling: urea at the bottom of the collecting duct leaks out into the
interstitial fluid and back into the filtrate = contributes to the high
osmolarity at the bottom of the loop of Henle
Storage and elimination: ureter, bladder, urethra
Collecting ducts drain into the ureter
Ureters drain into bladder
Bladder stores urine: its special epithelium (transitional epithelium) can squish to
accommodate storage of large amounts of urine
Urine gets peed out of the bladder through the urethra
Osmoregulation: capillary reabsorption of H2O,amino acids, glucose, ions
Sodium Chloride reabsorbed into the system increases the osmolarity of blood in
comparison to the glomerular filtrate. This reabsorption process allows water
(H2O) to pass from the glomerular filtrate back into the circulatory system
glucose and amino acids have carrier molecules that release them back into the
circulatory system. If all carrier molecules used up then excess is set free into
urine
A complication of diabetes is the inability of the body to reabsorb glucose. If too
much glucose appears in the glomerular filtrate it increases the osmolarity of the
filtrate, causing water to be released into the urine rather than reabsorbed by the
circulatory system. Frequent urination and unexplained thirst are warning signs of
diabetes, due to water not being reabsorbed.

Muscular control: sphincter muscle
Cardiac sphincter (gastroesophageal sphincter): sphincter between esophagus
and stomach. Prevents backflow of food
Pyloric sphincter: between stomach and small intestine. Releases food into small
intestine a small amount at a time
Anal sphincter: at the end of rectum, ties end of rectum

Reproductive System (BIO)

 Male and female reproductive structures and their functions
Gonads
Male: testes
Makes sperm in the seminiferous tubules
Makes testosterone
External
Female: ovaries
Houses immature egg, which matures monthly after puberty
Makes estrogen
Internal
Genitalia
Male: testes, penis, and various ducts and glands
Sperm made in the seminiferous tubules
Stores in the epididymis
Travels through vas deferens ejaculatory duct urethra penis
Mnemonic: Seven Up = Seminiferous tubules, Epididymis, Vas
deferens, Ejaculatory duct, nothing, Urethra, Penis
Female: ovaries, fallopian tubes, uterus, vagina
Monthly cycle: primary oocyte matures into secondary oocyte
every month. To prepare for it, the endometrium thickens. If
fertilization doesnt occur, menses (monthly discharge) occur, and
the cycle begins again
GnRH = stimulates release of FSH and LH
FSH = follicle stimulating hormone = stimulates growth and
maturation of follicle
Follicle = houses oocyte and produces estrogen
Estrogen = normally inhibits LH and FSH, but causes LH to surge
when it reaches a certain threshold
Estrogen reaches this threshold surge of LH occurs
LH = luteinizing hormone = stimulates the outer cells of the follicle
= turns it into corpus luteum + maintains it
LH surge triggers primary oocyte secondary oocyte rupture of
follicle
Corpus luteum = makes estrogen and progesterone = maintains
endometrium
No fertilization LH falls corpus luteum dies estrogen and
progesterone fall endometrium dies (menses) cycle begins anew
with FSH and LH re-rising
Fertilization occurs implanted embryo releases hCG hCG mimics
LH to maintain corpus luteum estrogen and progesterone
maintained by corpus luteum placenta takes over the
responsibility of making estrogen and progesterone later on

Differences between male and female structures
Males: mostly external, shared passage with urinary duct

Female: mostly internal. Separate passage from urinary tract


Hormonal control of reproduction

Male and female sexual development

Male Sexual Female Sexual
Development Development

Gonad development Y chromosome has BOTH male and

(occurs by the 8th SRY gene producing female start genital
week of gestation) testes-differentiation development with
factor (TDF), which same structure of
lead to testes genital tubercle,
formation urogenital sinus,
urogenital fold, and
Testes have Sertolie labiosacral swelling
cells that produce MIH
(Mullarian Inhibiting
hormone) and Leydig
cells that produce
androgens
(testosterone)

Differentiation of Wolffian duct Mullarian ducts

internal genital organs develops from the develop from the
Mesonephric duct Paramesonephric
duct
MIH and testosterone
prevent spontaneous Wolffian ducts
development of spontaneously
female internal regress in absence of
genitalia androgens

Androgens give rise to Mullarian ducts persist

male internal genitalia and give rise to
including epididymis, female internal genital
vas deferens, and including oviducts,
 seminal vesicles uterus, cervix, and
cranial vagina (1/3)
MIH causes
regression of Lower vagina (2/3)
Mullarian ducts comes from urogenital
sinus

Differentiation of Androgens cause Urethral folds and

external genital urethral folds to fuse genital swellings
organs to allow enclosure of remain separate to
the urethral tube, form the Labia minora
forming the shaft of and majora
the penis
Genital tubercle forms
the clitoris
Genital swellings fuse
in the midline to allow
formation of the
scortum

Genital tubercle
expands to give rise
to the glands penis

*Testosterone is
converted into DHT by
5-alpha-reductase
which allow
differentiation of
external genitalia

Female reproductive cycle
Menstruation
The shedding of the uterus lining (endometrium) occurs with
bleeding
Occurs approximately once a month during puberty and stops at
menopause (and during pregnancy)
Follicular phase
Begins on the 1st day of menstrual bleeding
Development of follicles in the ovaries
The uterus lining is thick with fluids and nutrients for an embryo in
case egg has been fertilized
Estrogen and progesterone levels are low
Production of follicle stimulating hormone (FSH) causes the
growth of 3~30 follicles, which only one of these continues to grow
 Follicle produces estrogen, stimulating the luteinizing hormone
(LH) surge. When this surge occurs, this phase ends (which
results in release of the egg)
This phase lasts about 13-14 days, but varies in length
Ovulation
Follicle ruptures to release the egg
The egg can be fertilized up to 12 hours after this release
Luteal phase
Phase after ovulation
Lasts about 14 days (if fertilization did not occur) and ends before
follicular phase begins again
Corpus luteum forms from the ruptured follicle
Corpus luteum degenerates if no fertilization occurs
Progesterone level increases, thickening the endometrium and the
mucus in the cervix (making it difficult for bacteria and sperm to
enter the uterus)
Body temperature also increases slightly until follicular phase
begins
Estrogen level is high

Pregnancy, parturition, lactation
Pregnancy
Usually takes about 40 weeks
The mothers body nurtures a fetus (baby)
Symptoms include:
No menstrual periods
Mood swings
Breast changes
Tiredness
Nausea
Parturition
Also known as childbirth, labor, and delivery
Delivery of newborn infant from a mothers uterus
Involves:
Shortening and dilation of the cervix
Increased secretion of oxytocin
Dilate to about 4 inches wide
Birth of the infant
Head first
Expulsion of the placenta
Lactation
Secretion of milk from the mammary glands of the breast
Loss of placenta reduces the estrogen and progesterone
level in a mothers body causing milk secretion to occur
Involves:
Mammogenesis
Breast growth
Lactogenesis
Function change of the breasts
Galactopoiesis
 Maintain milk production
Involution
Termination of milk production
Hormones like prolactin are involved

Integration with nervous control
Reproductive hormones
GnRH (Gonadotropin-releasing hormone)
Produced in the hypothalamus
Released by pituitary where secretion of follicle stimulating
hormone (FSH) and luteinizing hormone (LH) is stimulated
In males, FSH allows sperm maturation
Binding of LH to Leydig cells stimulates
testosterone secretion
In females, stimulates production of estradiol and
progesterone
Progesterone stimulates the growth of
uterus lining in case of pregnancy
FSH stimulates the maturation/growth of
follicles
LH triggers ovulation, the release of an egg
from the ovary


Muscle System (BIO)

Important functions
Support: mobility
Support = muscles maintain your posture when you sit/stand, muscles
stabilize joints, help prevent dislocations
Mobility = you move because of skeletal muscles. Your guts move
because of smooth muscles. Your blood flows because of the pumping
action of the heart
Peripheral circulatory assistance
Heart's a muscle that pumps blood
Contraction of skeletal muscles around the deep veins help squeeze the
blood through those veins
Diaphragm contraction (breathing) sucks blood into the chest cavity and
also squeezes on abdominal veins
Thermoregulation (shivering reflex)
Muscles generate heat when you shiver in response to cold
Structure of three basic muscle types: striated, smooth, cardiac

Skeletal muscle = striated, voluntary, shaped like long fibers, multinucleated
Smooth muscle = nonstriated, involuntary, shaped like almonds (tapered ends),
one nucleus per cell
Cardiac muscle = striated, involuntary, branched, shaped like fibers cross-linked
to one another, typically one nucleus per cell
Striated- due to sarcomere structure (A bands dark, I bands light). Skeletal and
cardiac muscles have sarcomeres
Nonstriated = smooth muscles dont have sarcomeres so theyre not striated.
They still have myosin, actin, and use the sliding filament mechanism. They just
arent organized into sarcomeres
Muscle structure and control of contraction
T-tubule system
transverse tubule (T-tubule)
Tubular invagination of the sarcolemma
Perpendicular to the myofibrils
Contains lots of proteins like L-type calcium channels
Size depends on the muscle type and locations
In skeletal muscle cells:
T-tubules are located at the junction between the A and I
bands of the sarcomere
In cardiac muscle cells:
T-tubule is located at the Z line
Contraction
Functions to allow depolarization to rapidly penetrate to the interior of
the cell
Allows force production by muscle fibers
Calcium channels open allowing calcium ions to flow down
its electrochemical gradient into the cell activates adjacent
sarcoplasmic reticulum membrane (SR)
Crucial in skeletal and cardiac muscles
(intracellular calcium levels in muscle cell increase as a result of action
potential, causing release of Ca+2 from the sarcoplasmic reticulum
Contractile apparatus
Electrical impulses from stimulate proper muscle fibers to generate
tension
Muscle can lengthen, shorten, or remain the same length.
Brain regulate voluntary muscles
Spinal cord regulates reflexes
Brain non-consciously regulate involuntary muscles like smooth
muscles and heart
 Muscle itself can regulate movements as well
Structure
Myofibrils: long cylindrical strand of contractile proteins
Sarcomeres: contractile unit of a muscle
Composed of thick and thin filaments
Thick filaments: located at the center of the sarcomere and
overlap with the thin filaments
Comprised of myosin elongated protein that forms cross
bridge binding to the thin filament
Thin filaments: attached to Z disk and extend towards the center
of the sarcomere
Comprised of actin and troponin
Troponin is binding site for calcium ions myosin
head binds to the actin as a result
Z- disk: dark strip at the ends of one sarcomere
Sarcoplasmic reticulum
Specialized type of endoplasmic reticulum (ER) in myocytes (muscle
cells)
Consists of complex network of vesicles, tubules, and cisternae
Surrounds myofibrils
Stores and pumps calcium ions
Crucial for muscle contraction
SR is electrically responsive to depolarization
Depolarization causes release of calcium ions into the
cytosol
Ca2+ binds to troponin
Tropomyosin shifts
Myosin-binding sites on actin is exposed
Ca2+ ions return to the SR by calcium pumps in the
membrane when done with their part
Fiber type
Slow twitch (Type I)
More efficient generating ATP by oxidative metabolism
Contains a lot of myoglobin, mitochondria, and blood capillaries
Fibers are red
For continuous muscle contraction over a long time
Fire slowly fatigues slower
Great use for: endurance sports
Marathons
Bicycling for hours
Fast twitch (Type II)
Utilize anaerobic metabolism to generate ATP
For short strength or speed required movements of muscles
Fire quickly fatigues faster
Great use for: short bursts of activity
Sprinter
IIA types
Red fibers
Hybrid of type I and type II fibers
 Contains lots of myoglobin, mitochondria, and blood
capillaries
Uses both aerobic and anaerobic metabolism
Very fast and strong contraction
IIB types
White fibers
Contains little myoglobin and mitochondria
ATP production is slower
Anaerobic metabolism
Resistance training can turn these types into type IIA
Contractile velocity of different muscle types
Force that muscle generates depends on the length, volume, fiber type,
and shortening velocity of the muscle
Muscle volume (CSA)
CSA = V/l
V = volume
l = length
Physiological CSA
PCSA = m x cos / l x p
m = muscle mass
= fiber angle
l = fiber length
p = muscle density
Short fibers
Higher PCSA/unit muscle mass greater force production
faster in slower speed
Long fibers
Lower PCSA/unit muscle mass lower force production
shorten in faster speed
Type I fibers
Slow increase in force
Smaller diameter slower contraction
Low force production
Type IIA fibers
Fast contraction
Faster force production
Type IIB fibers
Fast contraction
Faster increase in force
Large force production
Faster fatigue maintaining that force is harder
Force-velocity relationship
Muscle changes length affecting the force generation
Force decreases with increasing shortening velocity
Speed of muscle changing lengths during contraction
Regulation of cardiac muscle contraction
Only smooth and cardiac muscles use gap junctions to contract (because need
to contract as a whole group)
Regulation from nervous and endocrine system
 Vague nerve
Parasympathetic outflow to the heart slows the heart
rate
Acetylcholine
Binds to muscarinic cholinergic receptors opens ligand-
gated ion channels hyperpolarizes the membrane
potential decreases heart rate
Norepinephrine from sympathetic neurons & epinephrine from adrenal
medulla
Binds to beta-adrenergic receptors at the pacemaker
tissue (myocardium) increase uptake of calcium ions
the heart rate and contractility
Process involves increasing intracellular calcium level within
cardiac myocytes
Calcium influx
Regulate myocardial contractility
Increase calcium influx increase heart rate
Depolarization occurs

Oxygen debt: fatigue
Known as excess post-exercise oxygen consumption (EPOC)
Increased intake of oxygen after strenuous activity
Oxygen supply is not produced fast enough for demand
aerobic breakdown of pyruvic acid cannot produce all the ATP
required for further energy demands
The body finds another way to provide ATP through anaerobic
pathways
Lactic acid pathway
Production of ATP through anaerobic glycolysis
Pyruvic acid lactic acid
Most of lactic acid is transported to liver to convert back to
glucose or glycogen
After exercise recovery occurs
Lactic acid carbon dioxide + H2O
Requires extra oxygen for:
Above catabolic reaction to occur
Replenish ATP, phosphocreatine and glycogen
Pay back all the oxygen borrowed from hemoglobin, myoglobin,
air in the lungs, and body fluids
Depending on the intensity of exercise, EPOC takes from as short as 30 seconds
to as long as more than 24 hours

Nervous control
Motor neurons
Nerve cell that directly or indirectly controls the contraction or relaxation
of muscles
 Neuron starts from the motor region in the cerebral cortex or brain
stem
Efferent neurons that carry information from spinal cord to the
muscles and cause movement
Composed of:
Dendrites: branch-like structure that receives electrochemical
signals other units of nervous system
Cell body: contains cellular components and genetic information
for cellular function
Located in the spinal cord
Axon: long fiber conducting electrical impulses to send signals
Projects outside the spinal cord to
Somatic motor neurons
Direct innervation on skeletal muscles
Begins in the central nervous system (CNS) axons to
skeletal muscles locomotion
located on dorsal root ganglion
Special visceral motor neurons
Also called as branchial motor neurons
Direct innervation on branchial muscles
Movements in neck and face
General visceral motor neurons
Indirect innervation on cardiac and smooth muscles of the viscera
Viscera: muscles of the arteries
Sends signals to ganglia of autonomic nervous system and
peripheral nervous system, which then directly innervates visceral
muscles
Upper motor neurons (UMNs)
located in the motor region of the cerebral cortex or the brain stem
Sends motor signals to the lower motor neurons
Lower motor neurons (LMNs)
Located in ventral horn of the spinal cord and anterior nerve roots
Voluntary movements are regulated on spinal lower motor
neurons
Or located in the cranial nerve nuclei of the brainstem and cranial
nerves with motor function
Cranial nerve regulate movements of the eyes and tongue,
such as swallowing, chewing, etc.
Link between upper motor neurons and muscles

Neuromuscular junction, motor end plates
The site for interaction between motor nerve axons and muscle fibers to
send and receive signals
Multiple active zones and junctional folds of NMJ promote high
level of transmitter release
calcium causes the muscle to contract. The muscle is connected
to other muscles by gap junction, allowing for ion flow. The muscle
 cells are in syncytium so when one muscle cell contracts they all
contract.
Process:
Action potential travels along axon and reach the end of the motor
neuron
Causes opening of voltage dependent calcium channels
Calcium ions enter the neurons and binds to sensor proteins on
synaptic vesicles
Vesicles fusion with plasma membrane is triggered
Vesicles containing acetylcholine are released into the synaptic
cleft
Motor end plates consist of nicotinic receptors that binds acetylcholine
Muscles have nicotinic acetylcholine receptors. When ach binds to
receptor, this allows Na ions to enter, ultimately letting Ca ion
enter as well. This is voltage gated Ca+2 release. Ca+2 is stored
in sarcoplasmic reticulum.
in skeletal muscles- change in membrane potential triggers
release of calcium from SR
In cardiac muscles- intracellular calcium triggers the release of
even more calcium from SR (calcium induced calcium released)


Sympathetic and parasympathetic innervation
Sympathetic innervations include:
Eye dilation of pupil
Heart increase of heart rate and force of contraction
Kidney increase of renin secretion
Lungs dilation of bronchioles
Digestive tract inhibition of peristalsis
Blood vessels dilation in skeletal muscle and constriction in
gastrointestinal organs
Penis promotion of tissue engorgement with blood
Parasympathetic innervations:
Eye constriction of pupil and forced focus by moving lens
Heart decrease in heart rate and constriction of coronary veins
Lungs constriction of bronchioles
Digestive tract increase in peristalsis and relaxation of
sphincters
Gall bladder expulsion of bile
Stomach stimulation of secretion of enzymes
Bladder contraction of smooth muscle of bladder and relaxation
of urethral sphincter
Genitalia clitoral erection

Voluntary and involuntary muscles

Voluntary Muscles Involuntary Muscles
 skeletal muscles (ie-biceps) cardiac and smooth muscles (ie-
heart)

contract consciously- can be contracted unconsciously- cannot

controlled be controlled

Under the control of the somatic under the control of the autonomic
nervous system nervous system (sympathetic and
parasympathetic)

skeletal muscles are anchored to smooth muscles are found within

bones by tendons the walls of organs and cardiac
muscles are only found in the
heart

skeletal muscles are striated smooth muscles are non-striated

while the cardiac muscles are
striated

have multinucleated cells smooth muscles have 1

nucleus/cell while cardiac muscle
have 1-2 nuclei/cell

contraction is strong and forceful smooth muscle contracts smoothly

and continuously while cardiac
muscles contracts strongly and
forcefully

dealing with the muscle invervation

Specialized Cell - Muscle Cell (BIO)
Structural characteristics of striated, smooth, and cardiac muscle

skeletal muscles- attached to tendon/ bone, fastest of muscles
cardiac muscle- heart, intermediate speed,
smooth- hollow organs and blood vessels, slowest of the muscles
Striated = skeletal muscles, voluntary, has stripes, multiple nuclei shared within
the same muscle fiber. Strong, but tire easily = shaped like long fibers.
Smooth = visceral, involuntary muscles, no stripes, single nucleus per cell. Weak,
but doesn't tire easily = shaped like almonds, tapered on both ends.
Cardiac = heart muscles, involuntary, has stripes, single nucleus per cell, strong
and doesn't tire easily = highly branched, shaped like fibers cross-linked to one
another.

Abundant mitochondria in red muscle cells: ATP source
Abundant mitochondria in red muscle cells (ATP source)
Red muscle = high endurance, but slow.
Aerobic respiration predominant.
Many mitochondria because red muscles undergo aerobic
respiration.
Equipped to receive abundant oxygen supply: many capillaries,
many myoglobin.
High endurace, doesn't tire easily.
White muscle = fast, but fatigue easily.
Anaerobic respiration (glycolysis) predominant.
Few mitochondria because white muscles undergo mainly
glycolysis.
Equipped for short bursts of glycolysis: stores high amounts of
glycogen.
Pink muscle = intermediate between red and white muscle.

Organization of contractile elements: actin and myosin filaments, crossbridges, sliding
filament model

Actin filament = thin filament = has troponin and tropomyosin on it.
Myosin filament = thick filament = has myosin heads on it.
Cross bridge = myosin head binds to actin.
Sliding filament model = Cross bridge forms, myosin head bends (power stroke),
causes actin to move (slide) in the direction of the power stroke (toward the M
line). When all the actin slide toward the M line, the muscle fiber contracts.
Something counter-intuitive about the sliding filament model: ATP is not directly
needed for the powerstroke. ATP binding is needed for detachment of myosin
head to actin (cocks myosin protein to high energy). ATP hydrolysis is needed for
powerstroke (unbend myosin head, and push the actin).
high calcium binds to troponin, moves tropomyosin out of the way, allow for
sliding. low calcium, troponin goes back to standard conformation, makes
tropomyosin block again.
Rigor mortis = no ATP after a person dies, myosin heads can't detach after power
stroke, muscle remain in contracted position.
So what is troponin and tropomyosin there for? Ans: tropomyosin on actin blocks
the myosin head from crawling up the actin However, troponin moves
tropomyosin out of the way at high Ca2+ levels (Ca2+ binds to troponin, and
troponin moves tropomyosin).
Sarcomeres: I and A bands, M and Z lines, H zone

I band = thinnest = thin filaments only = sides of the sarcomere.
H zone = fattest = thick filaments only = center of the sarcomere, spans the M
line.
A band = contains both thick and thin filaments, center of the sarcomere spans
the H zone.
M line = line of myosin in the middle of the sarcomere, linked by accessory
proteins.
Z line = zigzag line on the sides of the sarcomere, connects the filaments of
adjacent sarcomeres.
mnemonics
I = thin like the letter I.
H = fat like the letter H.
A = letter width in between I and H, so a mixture of thick and thin
filaments.
M = middle line = myosin (linked by accessory proteins).
Z = zigzag line
Moving from middle to the side of sarcomere = M HAIZ, the Muscle says
HAIZ.
under a microscope the I and H bands will contract


Presence of troponin and tropomyosin

Tropomyosin = long protein that spirals along actin, blocks myosin head from
cross-linking.
Troponin = binds tropomyosin, moves it out of the way when calcium is around.
(only present in skeletal and cardiac muscles)

Calcium regulation of contraction

Sarcoplasmic reticulum (SR) = smooth ER in muscle = stores calcium, releases
them in response to AP.
The SR is also called terminal cisternae where it meets T-tubules at the edges of
the sarcomere.
T-tubule = extension of the muscle cell membrane that runs deep into the cell, so
that action potential can reach there (found in skeletal and cardiac muscles)
Muscle contraction:
Nerve stimulates muscle.
Action potential runs along muscle cell membrane.
 Goes deep into the muscle cell via T-tubules.
Stimulates the SR (terminal cisternae) to release calcium.
Calcium causes muscle to contract via the sliding filament mechanism

Skeletal System (BIO)

Functions
Structural rigidity and support: bone forms the bodys framework
Calcium storage
Bones store calcium
When blood calcium is low, parathyroid hormones signal bone tissue to
break down and release calcium
Physical protection
Rib cage protects internal organs, skull protects brain, spine protects
spinal cord
Large bones also shelter bone marrow that contains stem cells that make
blood
Skeletal structure
Specialization of bone types; structures
Long bones: shaped like a rod (arm, leg, finger)
Short bones: shaped like a cube (wrist, ankle)
Flat bones: flat (sternum, shoulder blades, ribs, skull)
Irregular bones: complicated shapes (vertebrae, hip)
Joint structures
Joint = where bone meets bone
Joints can be mobile or non-mobile
Mobile joints (synovial) have a fluid-containing cavity to lubricate
movement of bones
Non-mobile joints connect bone to bone with cartilage or fiber
Ball and socket joint (allows most freedom of movement): shoulder, hip
Hinge joint: elbow
Gliding joint: wrist
Immobile joint: plates of the skull, rib-to-sternum
Endoskeleton versus exoskeleton
Endoskeleton = what we have, skeleton on the inside
Exoskeleton = what insects have, skeleton (chitin) on the outside
Bone structure
Calcium/protein matrix
Composed of inorganic and organic components
Bones hardness comes from inorganic components
Ex: Calcium, phosphate and hydroxide ions form
hydroxyapatite crystals
Bones flexibility comes from organic components
Ex: Collagen, glycoproteins and other peptides
Minerals are also stored in bone
Ex: Sodium, magnesium and potassium
Osteons (Haversian systems)
Bony matrix units
 Encircles a Haversian canal ( network in bone and contain
blood vessels), a central microscopic channel, which is
surrounded by lamellae, circles of bony matrix
Spaces between the matrix is called lacunae
Interconnected by canaliculi, which are
small canals for the exchange of nutrients
and wastes with the Haversian canals
Mature bone cells called osteocytes
Housed in lacunae
Osteocytes: maintenance of bone
These contain blood vessels, nerve fibers and lymph

Cellular composition of bone

Osteoclasts
Large cells with many nuclei (multinucleated)
Precursors circulate in the blood and bone marrow
Fusion of the precursors produce mature osteoclasts
Found on the surface of the bone and at sites of injured,
unnecessary, and old bone
Reabsorb (breakdown of) bone
Balance between osteoblasts and osteoclasts is crucial in skeletal
system
Osteoblasts
Cuboidal and columnar shape with central nucleus on the bone
surface
Responsible for forming new bone
Found in periosteum and endosteum, the growing portions of
bone
Do not divide
Synthesize and secrete the collagen matrix and calcium salts
Osteocytes
Inside of the bone (lacuna), surrounded by bone tissue
Have long branches
Maintain the mineral concentration of the matrix
 Secrete enzymes
Senses mechanical strain on the bone
Secrete growth factors and activate the lining cells or stimulate the
osteoblasts
Osteoprogenitor (osteogenic) cells
Found in deep layers of periosteum and the marrow
Only bone cells that can divide
Develop into osteoblasts by differentiating

Cartilage: structure and function

Cartilage = cells + extracellular matrix

Cartilage cells = chondrocytes
Extracellular matrix = secreted by cells, contains fiber meshwork that gives the
cartilage its characteristic properties (flexibility and resilience)
Functions:
Flexibility: ear, nose, epiglottis, end of ribs
Resilience, compressibility: ends of bones in joints, knee, between
vertebrae
Ligaments, tendons
Ligament = connect bone to bone, stabilize joints
Tendon = connect muscle to bone, anchors muscle
Endocrine control
The excretory system is controlled by the:
Hypothalamus
Produces antidiuretic hormone (ADH) and released by the
posterior pituitary
 ADH causes more water to be absorbed through aquaporin by the
kidneys before excreted when water level in the body is low
Adrenal cortex
Produce aldosterone, which increase the level of sodium and
potassium ions in the blood, causing more water to be resorbed to
retain water in the body

Skin System (BIO)

Structure

Layer differentiation, cell types, tissue types (epithelial, connective)
Epidermis = stratified squamous epithelial tissue = protection
Keratinocytes = cells that produce keratin = dominates the
epidermis
Keratinocytes start off like normal cells at the bottom of the
epidermis but gets flatter as you go up, and becomes dead,
keratin plates at surface of skin
Melanocytes = cells that make melanin, the skin pigment
Dendritic cells (Langerhans cells) = phagocytes that eat pathogen
and present foreign antigens to activate immune response
Does not have blood vessels. Get nutrients through osmosis from
blood from dermis.
Dermis = connective tissue = blood, nerve supply
Fibroblasts = make fiber and ground substance (glue) for the
extracellular matrix that makes up connective tissue
Hair follicles, sweat glands, and oil (sebum) glands
Blood vessels and nerves
Relative impermeability to water: due to layer of dead, keratin-packed cells
sealed with glycolipids
Keratin is water insoluble, and layers of dead, keratin-packed cells reside
on the skin surface
Glycolipids seal the space between the dead keratin-packed cells
Sebum (skin oil) contribute some, but oil glands are not present
everywhere (absent in palms and soles)
 Functions in homeostasis and osmoregulation
Heat homeostasis:
Too cold: hair stands up (goose bumps), vasoconstriction decreases
blood supply at skin (less heat loss)
Too hot: sweat (evaporative cooling), vasodilation increases blood supply
at skin (more heat loss)
Water homeostasis: insulates body against water loss
Osmoregulation: sweat excretes salts and nitrogenous wastes (urea, uric acid,
ammonia)
Some other functions of the skins:
Protect against UV radiation by making melanin (absorbs UV)
Make vitamin D upon exposure to sunlight
Act as blood reservoir. Vasoconstriction in skin moves blood to other
organs
Sense touch, pressure, pain, heat, cold
Protection
Functions in thermoregulation
Hair, erectile musculature
Hairs help insulate the body by trapping air in them
Hormally hair lies at an angle to the skin, with erectile muscle attached to
it
When cold, erectile muscles contract, and hair stands up- this erect
position helps trap more air, providing better insulation
Fat layer for insulation: fat in hypodermis act as insulation
Sweat glands, location in dermis: produce sweat, cools the body by evaporative
cooling, located in dermis
Vasoconstriction and vasodilation in surface capillaries
When cold: vasoconstriction of arterioles reduce blood supply to skin
capillaries. Leads to less heat loss at skin surface
When hot: vasodilation of arterioles increase blood supply to the skin
capillaries. Leads to more heat loss at skin surface
Physical protection
Nails, calluses, hair
Nail = hard keratin = tougher than soft keratin on skin
Calluses = extra thick layer of dead keratin-packed cells on surface of the
skin
Hair = hair keratin
Protection against abrasion, disease organisms
Keratin protects skin against abrasion
Tight seal made from keratin-packed cells and glycolipids form a barrier
against pathogens
Chemical protection: sweat is acidic, contains antibodies, and
antimicrobial agents. Sebum (skin oil) kills bacteria
Natural flora: good bacteria on the surface of skin dont cause harm to
you, but they fight off bad bacteria
Brain
Parts of the brain

Cerebrum
The cerebrum is the largest portion of the brain, and contains tools which
are responsible for most of the brain's function. It is divided into four
sections: the temporal lobe, the occipital lobe, parietal lobe and frontal
lobe. The cerebrum is divided into a right and left hemisphere which are
connected by axons that relay messages from one to the other. This
matter is made of nerve cells which carry signals between the organ and
the nerve cells which run through the body
Frontal Lobe
The frontal lobe is one of four lobes in the cerebral hemisphere. This lobe
controls a several elements including creative thought, problem solving,
intellect, judgment, behavior, attention, abstract thinking, physical
reactions, muscle movements, coordinated movements, smell and
personality.
Parietal Lobe
Located in the cerebral hemisphere, this lobe focuses on comprehension.
Visual functions, language, reading, internal stimuli, tactile sensation and
sensory comprehension will be monitored here
Sensory Cortex
The sensory cortex, located in the front portion of the parietal lobe,
receives information relayed from the spinal cord regarding the position of
various body parts and how they are moving. This middle area of the
brain can also be used to relay information from the sense of touch,
including pain or pressure which is affecting different portions of the body.
Motor Cortex
This helps the brain monitor and control movement throughout the body.
It is located in the top, middle portion of the brain.
Temporal Lobe:
The temporal lobe controls visual and auditory memories. It includes
areas that help manage some speech and hearing capabilities, behavioral
elements, and language. It is located in the cerebral hemisphere.
Wernicke's Area
 This portion of the temporal lobe is formed around the auditory cortex.
While scientists have a limited understanding of the function of this area,
it is known that it helps the body formulate or understand speech.
Occipital Lobe
The optical lobe is located in the cerebral hemisphere in the back of the
head. It helps to control vision.
Broca's Area
This area of the brain controls the facial neurons as well as the
understanding of speech and language. It is located in the triangular and
opercular section of the inferior frontal gyrus.
Cerebellum
This is commonly referred to as "the little brain," and is considered to be
older than the cerebrum on the evolutionary scale. The cerebellum
controls essential body functions such as balance, posture and
coordination, allowing humans to move properly and maintain their
structure.
Limbic System
The limbic system contains glands which help relay emotions. Many
hormonal responses that the body generates are initiated in this area. The
limbic system includes the amygdala, hippocampus, hypothalamus and
thalamus.
Amygdala
The amygdala helps the body responds to emotions, memories and fear.
It is a large portion of the telencephalon, located within the temporal lobe
which can be seen from the surface of the brain. This visible bulge is
known as the uncus.
Hippocampus
This portion of the brain is used for learning memory, specifically
converting temporary memories into permanent memories which can be
stored within the brain. The hippocampus also helps people analyze and
remember spatial relationships, allowing for accurate movements. This
portion of the brain is located in the cerebral hemisphere.
Hypothalamus
The hypothalamus region of the brain controls mood, thirst, hunger and
temperature. It also contains glands which control the hormonal
processes throughout the body.
Thalamus
The Thalamus is located in the center of the brain. It helps to control the
attention span, sensing pain and monitors input that moves in and out of
the brain to keep track of the sensations the body is feeling.
Brain Stem
All basic life functions originate in the brain stem, including heartbeat,
blood pressure and breathing. In humans, this area contains the medulla,
midbrain and pons. This is commonly referred to as the simplest part of
the brain, as most creatures on the evolutionary scale have some form of
brain creation that resembles the brain stem. The brain stem consists of
midbrain, pons and medulla.
 Midbrain
The midbrain, also known as the mesencephalon is made up of the
tegmentum and tectum. These parts of the brain help regulate body
movement, vision and hearing. The anterior portion of the midbrain
contains the cerebral peduncle which contains the axons that transfer
messages from the cerebral cortex down the brain stem, which allows
voluntary motor function to take place.
Pons
This portion of the metencephalon is located in the hindbrain, and links to
the cerebellum to help with posture and movement. It interprets
information that is used in sensory analysis or motor control. The pons
also creates the level of consciousness necessary for sleep
Medulla
The medulla or medulla oblongata is an essential portion of the brain
stem which maintains vital body functions such as the heart rate and
breathing.