BILD1: Midterm 1 Notes

Ch.1Evolution & Foundations of Biology

The cell
-smallest unit of organization that can perform all
required activities
-eukaryotic: membrane-enclosed, larger
-prokaryotic: lack nucleus/membrane-enclosed
organelles
-all deal with 1) containment 2) information 3)
specificity
Domains of life
1) bacteria:most diverse and widespread prokaryotes
2) archaea: prokaryotes in extreme environments
3) eukarya:
plantae: photosynthetic
animalia: ingest other organisms
fungi: absorb outside nutrients
protists: unicellular eukaryotes
Levels of biological
1) biosphere: all life on earth
organization
2) ecosystem: all living and nonliving in a certain area
3) communities: sets of populations, organisms
inhabiting a certain ecosystem ex) trees, animals,
fungi
4) populations: all individuals of species living within a
certain area ex) population of deer
5) organisms: individual living things
6) organ: body part w/ certain function ex) leaf
7) tissues: group of cells working together for a
function
8) cells: lifes unit of structure and function
9) organelle: functional part inside cell ex) chloroplast
10) molecules: chemical structure of two or more
atoms ex) chlorophyll molecule
Emergent property
-complexity increases as you go up levels of biology
due to arrangement/interaction of parts
Structure x function Ex) hummingbirds anatomy
Ex) endorphin receptors and proteins at the molecular
lvl
Ex) morphine and endorphin
-molecular mimic: importance of shape because thats
how biological molecules recognize/respond to each
other
Ch.2 Chemical Context of Life
Covalent bond
-sharing of pair of valence electrons b/w two atoms
-strong, stable, more permanent
-molecule: two atoms held together by covalent

Noncovalent bond

Polar covalent bond

Water

Ionic bonding
Hydrophilic/hydropho
bic
Dispersions of lipids
in H2O/hydrophobic
effect

Emergent property

bonds
-H-bonds: noncovalent b/w H atom and
electronegative atom
-ionic: anions and cations attracted to each other
-Van der Waals: weak, reversible, dont share
electrons
-oppositely charged regions of neighbors are
attracted to each other
-cohesive
-versatile as solvent
-expands upon freezing
-ability to moderate temperature
-polar covalent bonds: oppositely charged regions of
neighbors are attracted to each other
-hydration shell: sphere of water molecules that
surround each dissolved ion
-ionic bonds are weaker in liquid than dry salt crystal
-can form b/w ions even if electron is not transferred
-ionic compound: salt formed by ionic bonds
-hydrophilic: water loving ex) cotton
-hydrophobic: nonionic, nonpolar, water hating ex) oil
-hydrophobic bonds: H2O forces hydrophobic
groups together to minimize disruption
-each lipid molecule forces H2O molecules to very
ordered
-therefore, clusters are formed where entropy
increase and less H2O are ordered
-micelles: all hydrophobic groups have tails facing
inward, away from H2O
-compound has different chemical/physical properties
from its elements

Ch.3 Carbon & Molecular Diversity of Life

Lifes molecular
-organic compound: carbon-based molecule
diversity is based on
-macromolecule: carbohydrates/proteins/nucleic
carbon properties
acids are all very large
Valences of major
-valence: # of covalent bonds that an atom can form
elements of organics
(basically # of e- required to complete valence shell)
Biologically important -hydroxyl: -OH
chemical groups
-carbonyl: -C=O
-carboxyl: -COOH
-amino: -NH2
-sulfhydryl: -SH
-phosphate: -OPO32-methyl: -CH3

Sex
hormones/steroids
4 main biological
molecules
Lipids
Fats

Phospholipid

Steroid
Dehydration reaction
Hydrolysis
Carbohydrates

Sugars

-functional group: affects biological molecules

function in a characteristic way
-show similar compounds that differ only in
functional groups
-chemical groups affect shape of molecule
1) protein
2) lipids: fat, phospholipid, steroid
3) nucleic acid
4) carbs
-covalent, hydrophobic
-made of one glycerol and three fatty acids, joined
together by ester linkage (bond b/w hydroxyl and
carboxyl group)
-fatty acid: long carbon skeleton with nonpolar C-H
bonds
-unsaturated: has one nor more double bonds w/ one
less H on each double bonded C (kink)
-saturated: no double bonds b/w carbon atoms, thus
it is saturated with H atoms
-important for energy storage and cell membrane
-hydrophilic head w/ two hydrophobic tails
-differ based on fatty acids and groups attached to
phosphate head
-important for cell membranes
-lipids of four-ring carbon skeleton
-differ based on chemical group attached to ring s
-cholesterol: common part of animal cell membranes
-monomers are connected by covalently bonding and
losing a H2O molecule
-H2O is added to break apart polymer
ex) digestion: enzymes attack polymers and speed
hydrolysis
-polymers of sugars
-monosaccharides: simplest carbohydrate
-disaccharides: two monosaccharides covalently
bonded by glycosidic linkage (dehydration rxn)
-polysaccharides: polymers made of many sugars
joined by dehydration rxns
important for storage, protection
-monosaccharide: simple sugar ex) glucose
-vary in length of carbon skeletons and location of
carbonyl groups
-most names of sugars end in ose and are six to
seven carbons long
-cells extract energy from glucose in series of rxns

Storage
polysaccharides

Structural
polysaccharides

Nucleic acid

Nucleotide polymers

DNA

tRNA
Proteins

Polypeptide

and carbon skeletons are material for synthesis of

amino acids
-starch: polymer of glucose in plants joined by one to
four linkages, stores energy which can be extracted
w/ hydrolysis (alpha form)
-glycogen: polymer of glucose in animals, more
branched than starch
-cellulose: polymer of glucose with one to four
linkages in B form, never branched
-enzymes that digest starch cant hydrolyze cellulose
due to different form
-chitin: carbohydrate to build exoskeletons, similar to
cellulose except with nitrogen
-polymers made of monomers called nucleotides
-store, transmit, express hereditary info
-nucleotide:
1) N-base
pyrimidine: six membered ring of carbon and
nitrogen atoms (C,T,U)
purines: six membered ring + five membered
ring (G,A)
2) pentose
deoxyribose: for DNA, lacks oxygen on 2nd
carbon
ribose: for RNA
3) phosphate group attached to 5
-one end has P attached to 5 carbon
-other end has OH on 3 carbon
-sequence of four bases is very specific for amino
acid
-sugar phosphate backbones of anti-parallel
nucleotide strands are on outside of helix
-nitrogen bases attached to each other by hydrogen
bonds
-roughly L-shaped
-GCAU
-RNA is more variable in shape than DNA
-molecule of polypeptides folded and coiled
-polypeptides: amino acid polymers
-amino acid: organic molecules w/ amino group,
carboxyl group, H, and R group (side chain) which
differs w/ each amino acid
-amino acids joined by dehydration rxn creating
covalent bond
-formed starting at N-terminus

Primary structure
Secondary structure

Tertiary structure

Quaternary structure
Sickle cell disease
Overview of protein
functions

-chemical nature is determined by type and

sequence of side chains
-protein is the twisted, folded, unique chain of
polypeptides (polypeptide =/= protein)
-sequence of amino acids determined by inherited
genetic information, NOT random linking of amino
aicds
-coiled/folded polypeptide chains as result of H bonds
-O atoms = partial (-), H atoms = partial (+)
-a helix: coil held by H bond b/w every amino acid
-B pleated sheet: B strands connected by H bonds
b/w two parallel polypeptide backbone sections
-3D shape stabilized by interactions b/w R groups
-helixes held by H bonds, ionic bonds, and disulfide
bridges
-hydrophobic interactions
-overall protein structure, one functional
macromolecule of two or more polypeptide chains
-replacement of valine w/ glutamic acid
-side chains are important!
-Receptor
response of cell to chemical stimuli
ex) receptors built into nerve cell membrane
detect signaling molecules
-Enzymatic
acceleration of chemical rxns
ex) digestive enzymes catalyze hydrolysis
-Storage
storage of amino acids
ex) casein is major source of aa for baby
mammals
-Structure
support
ex) keratin for hair
-Transport
ex) hemoglobin transports oxygen from lungs
to other parts of the body
-Defensive
protection against disease
ex) antibodies inactivate viruses
-Contractile/Motor
movement
ex) undulations of cilia/flagella
-Hormonal

Ch.4 Tour of the Cell

Light microscope
Electron microscope
Scanning electron
microscope
Transmission electron
microscope
Discoveries
Membranes are fluid
mosaics
Peripheral proteins
Integral proteins
Ribosomes

Smooth ER

Rough ER

Golgi

Lysosome
Autophagy

coordination of organisms activities

ex) insulin regulars [blood sugar]

-visible light is passed thru and refracted by lenses

-focuses beam of e- thru specimen
-better b/c shorter wavelengths
-study topography by exciting e- on surface which
are then translated into electronic signal on screen
-study internal structure
-specimen is stained with heavy metal atoms,
increasing e- density in some parts
-fluorescent marker, super-resolution, confocal
-amphipathic: both hydrophobic and hydrophilic
-held togeteher mainly by hydrophobic interactions
-made of lipids, proteins, cholesterol, glycolipids,
glycoproteins
-made of ribosomal RNA & protein
-carries out protein synthesis
-free: suspended in cytosol make proteins that
function in cytosol
-bounded: attached outside ER/nuclear envelope,
make proteins to insert into membranes for export
-synthesis of lipids
-detoxifies by adding OH
-makes steroids
-stores Ca ions so muscles can contract
-makes secretory proteins
-adds carbohydrates to proteins to make
glycoproteins
-makes new membrane
-grows by adding phospholipids and proteins to its
own membrane
-consist of cisternae, flat membranous sacs
-cis face: receives vesicles from ER and fuses
-trans face: vesicles pinch off
-modifies ER products like proteins, phospholipids
-sorts and ships products in transport vesicles
-makes many polysaccharides
-membranous sac of hydrolytic enzymes
-work best in acidic level
-breaks down damaged organelles with phagocytosis
-lysosomes use hydrolytic enzymes to reduce cells

Vacuole

Mitochondria
Chloroplasts
Endosymbiont theory
Thylakoid
Granum
Stroma
Plastids
Peroxisome
Microtubule

Centrosome
Centriole
Flagella/cilia
Cilia
Microfilament

own organic material

-damage is surrounded by double membrane ->
lysosome fuses -> organic compounds are released
for reuse
ex) Tay Sachs: lipid digesting enzyme in lysosome is
missing
-large vesicles derived from ER and Golgi
-food vacuole: formed by phagocytosis
-contractile vacuole: pump excess water out of cell
-central vacuole: combo of smaller vacuoles, allows
cell to become larger as it absorbs water
-use oxygen to generate ATP by extracting energy
from sugars, fats
-sites of photosynthesis
-convert solar to chemical energy
-cell living in a cell
-mitochondria and chloroplast have two membranes,
contain ribosomes, DNA molecules, grow/reproduce
-flattened, interconnected sacs inside chloroplast
-each stack of thylakoids
-fluid outside thylakoid which contains chloroplast
DNA and ribosomes, enzymes
-family of closely related plant organelles which
includes chloroplast
-contains enzymes that remove H atosm and transfer
them to oxygen by making H2O2 hydrogen peroxide
-detoxify liver
-constructed from globular protein called tubulin
-made of alpha and beta tubulin
-shape and support cell, serve as tracks
-also involved in separation of chromosomes
-region near nucleus
-microtubule organizing center
-within centrosome is a pair
-nine sets of triplet microtubules in a ring
-microtubule containing extensions that project from
some cells
-large numbers
-oar-like
-signal-receiving antenna cilia is only one
-thin solid rod
-twisted double chain of actin subunits
-form structural networks
-bear tension
-help support cell shape

Tight junction

Gap junctions
(communication
junctions)
Intermediate
filaments
Collagen
Proteoglycans

-increase surface area

-plasma membranes are pressed against each other
-prevent leakage of extracellular fluid
-bound by proteins
ex) b/w skin cells
-provide cytoplasmic channels from one cell to an
adjacent cell
-consist of membrane proteins surrounding a pore
where aa, sugars, ions, mol pass thru
-specialized for tension
-more permanent fixture of cell
-reinforces shape, fixing organelles
-glycoprotein in ECM that forms strong fibers outside
cells
-small protein with many carbs woven with collagen