Chapter 3-Amino Acids, Peptides and Protein

3-d structure of a protein

tertiary structure

3-d structure is related to ___

function

tertiary structure determines function, what is an example?

the enzyme catalytic site which forms a pocket for a specific substrate

4 examples of tertiary structures

H-bonds, ionic bonds, hydrophobic interactions and disulfide bonds

quaternary structure involves more than 1 ___ subunit (aka monomer)

polypeptide

3 examples of quaternary structure

H-bonds, ionic bonds and hydrophobic interactions

in quaternary structure, the degree of subunit ___ affects function

association

found in RBCs; hemoprotein

hemoglobin

hemoglobin: ___ polypeptides of 2 classes; each subunit has a ___

adult HbA: alpha2beta2
fetal HbF: alpha2___2
4; heme; gamma

8 ___-handed alpha-helices in each alpha subunit

right

___ right-handed alpha-helices in each beta subunit

7

functions of hemoglobin
O2 and CO2 transport, buffer

what binds O2 as it relates to hemoglobin function?

Fe2+; His (F8); His (E7) --> specifically hinders CO binding

hemoglobin contains 4 subunits held by ___ bonds --> ___ structure

non-covalent; quaternary

___ and ___ hemoglobin structures are flexible

secondary; tertiary

___-form of hemoglobin binds O2, ___-form cannot

R; T

binding of first O2 takes the longest time...the rest get progressively faster. this is
b/c binding O2 changes conformation of other subunits, facilitating further
O2 binding
cooperative allosterism

T-conformation has a ___ O2 affinity; R-conformation has a ___ O2 affinity

low; high

sickle-cell anemia = ?
reduced O-carrying capacity of blood

myoglobin found in ___; hemo___; 1 polypeptide of ___ amino acids; ___ righthanded alpha-helices (A-H) with heme b/t helices ___ and ___
muscle; protein; 153; E; F

O2 bound to ___ is a reserve for when pO2 of tissues is low...it is then released for
___ synthesis
myoglobin; ATP

most abundant protein in the body

collagen

mature ___ composed of 3 alpha-chain subunits

tropocollagen

collagen consists of ___ subunits held together by ___-bonds

3; H

re: collagen, different tissues have different ___ ___ compositions, e.g. type I
collagen is ___ alpha-1 and ___ alpha-2 chain
amino acid; 2; 1

___ is the most abundant amino acid in collagen, with lots of proline and ___
glycine; lysine

amino acids definition

monomeric unit of peptides and proteins

most amino acids occur as?

L-alpha amino acids

ideal formula of amino acid has ___ charges and practical formula has ___ and ___
charges and the ___ from the carboxyl group shifts
zero; +; -; hydrogen

acronym to describe the essential amino acids is?

Phenylalanine
Valine
Threonine
Tryptophan
Isoleucine (Ile)
Methionine
Histidine
Arginine
Leucine
Lysine

essential amino acids ___ be synthesized by the body

cannot

adults can synthesize which 2 essential amino acids (children cannot)?

histidine and arginine

amino acid classification by nutritional criteria includes the ___ amino acids
non-essential

what are the 12 non-essential AAs?

Glycine; alanine; serine; aspartic acid; tyrosine; asparagine; cysteine; proline; hydroxyproline;
hydroxylysine; glutamic acid; glutamine

which 2 AAs are not required for protein synthesis since they are formed after
protein is synthesized?
hydroxyproline & hydroxylysine

amino acid classification by chemical criteria incorporates the use of ___ ___
properties (R-group)
side chain

AA classification by chemical criteria includes which 7 groups of amino acids?

Aliphatic, hydroxyl, sulfur, carboxyl/amide, basic, aromatic and pyrrolidine

5 aliphatic AAs
Gly, Ala, Val, Leu, Ile

5 hydroxyl AAs
Ser, Thr, Tyr, Hyl, Hyp

2 sulfur AAs
Cys, Met

3 carboxyl/amide AAs
Asp, Glu/Asn, Gln

4 basic AAs
Lys, Arg, His, Hyl

4 aromatic AAs
His, Phe, Tyr, Trp

2 pyrrolidine AAs
Pro, Hyp

which 4 AAs DON'T occur in proteins?

Homocysteine, ornithine, citruline and arginosuccinic acid

req'd for Met synthesis

functions with Vit B12
high levels associated with atherosclerosis
homocysteine

intermediates in biosynthesis of urea

ornithine, citrulline, arginosuccinic acid

precursor for biosynthesis of catecholamines

L-DOPA (3,4-dihydroxyphenylalanine)

what are the 3 most abundant catecholamines?

epinephrine (adrenaline), norepinephrine (noradrenaline) and dopamine

the most abundant catecholamines are all produced by which 2 AAs?

phenylalanine & tyrosine

when the 4 groups on a carbon are different

chiral carbon

3 non-alpha amino acids

Beta-alanine, taurine (2-aminoethylsulfonate) and GABA (gamma-aminobutryic acid)

part of pantothenic acid (Vit B5)

beta-alanine

resp. for integrity and function of retina

part of a bile acid (taurocholic acid)
taurine

inhibitory neurotransmitter from glutamate

GABA

when the 4 groups on a carbon are different

chiral carbon

there is more ___ charge at low pH and more ___ charge at high pH
+; -

a pH with lots of protons would favor the ___ form at the bottom of the ratio and
would be ___ 1 and for a higher pH it would be the opposite
uncharged; less than

if R-groups are hydrocarbons then they are ___ and can form ___ bonds
hydrophobic; hydrophobic

if R-groups are polar (COOH, NH3, OH) then they are ___ and can form ___
bonds (salt bridge) or ___ bonds
hydrophilic; ionic; hydrogen

if r-groups are aromatic then they possess strong ___ absorption; this is used for
quantitation of ___ in solution
UV; protein

if r-groups are -OH then they become esterified by ___

PO4

phosphorylation alters ___ function; major role is in phosphorylation ___

protein; cascade

if r-groups are -SH (usually Cys) then they are oxidized to form ___ bonds
disulfide

if a compound has hydrogen it's in ___ form and w/o hydrogen it's ___
reduced; oxidized

b/t COOH and NH3

in vivo, catalyzed by enzymes
aka peptide bond
amide bond

usually formed b/t 2 cysteines

involved in redox reactions
antioxidants
general 3D protein structure
disulfide bond

if r-groups are -OH or -NH2 they can form ___ by covalently bonding
carbohydrates via ___ bonds
glycoproteins; glycosidic

HbA1c stands for?

Hemoglobin adult 1 carbohydrate attached

glycohemoglobin is ___ or ___ hemoglobin

glycosylated; glycated

less than/equal to 10 amino acids

peptide

more than 10 AAs

polypeptide

many AAs
may be comprised of multiple polypeptides
protein

N-terminal aka? C-terminal aka?

amino terminal and carboxy terminal

intracellular antioxidant; will prevent oxidation of other compounds, thus it must

reduce other compounds while it is being oxidized
glutathione (GSH)

tripeptide of glutathione
Glu Cys Gly; Cys contains S so can possibly form disulfide bond

tripeptide form hypothalamus, stimulates pituitary

thyrotropin-releasing hormone (TRH)

pain neurotransmitter; 11 AA peptide in gut, SC and brain

substance P

vasodilating; derived form proteolytic cleavage

kinins (bradykinin and kallidin)

analgesic action like opiates

opiopeptides

3 types of opiopeptides are?

enkaphalins, beta-endorphin and dynorphin

Leu and Met are part of which sub-group?

enkaphalins

30 AA polypeptide derived from lipotropin about 60x stronger than opium

beta-endorphin

an opiopeptide in the SC
dynorphin

specific amino acid sequence

primary structure

in primary structure:
connected by ___ bond (covalent amide bond) which can be hydrolyzed by
___ or boiling
dictated by ___ in genes
dictates subsequent ___
peptide; proteases; codons; organization

4 types of secondary structure

alpha helix,beta pleated sheet,beta bending and random coil

alpha helix and beta pleated sheet are examples of ___ bonding
hydrogen

3 steps of collagen synthesis

1.translation of mRNA into pro-alpha chain in fibroblasts
2.hydroxylation of pro-alpha chains
proline by prolyl hydroxyls
lysine by lysyl hydroxylase
3.three hydroxylated pro-alpha-chains H-bond to form pro-collagen (hydroxyproline, hydroxylysine,
glycine)
4. secretion of pro collagen out of cell by exocytosis
5. cleavage of N and C-terminal segments by procollagne peptidases -->tropocollagens
6. oxidation of some lysine's to lysyl aldehydes by lysyl oxidase

both reactions in the collagen synthesis 2nd step require which 3 components?
vit C, iron, O2

genetic mutation where Gly is replaced by Cys; easy bone bending and fracture,
humpback (twisted spine); delayed wound healing
osteogenesis imperfecta

step 6 of collagen synthesis requires which 3 components?

Cu, vit B6, O2

re: step 6 of collagen synthesis, the ___ functional group leads to cross linking of
tropocollagen-->collagen fibrils (the ___ structure)
aldehyde; quaternary

due to deficiency of lysyl oxidase; deformed spine; bone demineralization; joint

dislocation; aortic aneurysms
lathyrism

protein classification based on which 4 factors?

Function,conjugation,shape and solubility

which 4 contractile proteins are resp. for contraction & relaxation?

actin, myosin, tropomyosin, troponins

globular actin polymerizes into actin ___

filaments

G-actin =? F-actin=?
globular actin; actin filaments

f-actin is wrapped with a dimer of rope-shaped ___ and is attached by ___

troponins-->thin filament of the ___
tropomyosin; 3; sarcomere

___ is the thick filament

myosin

found in lung, large aa., skin and other CT

many random coils (2 degree structure) --> elasticity and extensibility
pralines are hydroxylated (as in collagen)
some lysine's oxidized to aldehydes (as in collagen)
elastin

___ formed from condensation of ___ lysine aldehydes plus ___ unmodified lysine->marker of elastin metabolism/turnover (i.e. emphysema); comes out of ___
desmosine; 3; 1; urine

due to lack of ATP; actin cannot be released; the actin-myosin complex remains
contractd
rigor mortis

whenever you see ATP there's going to be ___ involved

Mg2+

albumins are ___, e.g. serum albumin

globulins are ___ ___ solutions with low water solubility, e.g. antibodies
glutelins are ___ or ___ soluble, e.g. gluten
basic proteins are ___ or ___ soluble, e.g. histones
water-soluble; dilute salt; acid or base; acid or salt

most proteins, when classified according to shape, belong to this class

globular

elongated proteins, generally structural e.g. actin, myosin, collagen, elastin, keratin,
etc.
fibrous

no attachment of non-protein component

simple proteins

apoprotein + prosthetic group

conjugated (complex) proteins

5 conjugated proteins
hemo Hb, cytochromes, glyco antibodies, glycophorin, lipo chylomicrons, LDL, HDL, VLDL
phospho casein metallo some hemoproteins (Fe), IGFBP-5 protease

9 types of proteins based on function

enzymes; structural proteins; contraction; transport; hormones; protection; storage; receptor; crossmembrane transporter

2 protein sub-classifications based on conjugation

simple & conjugated

2 sub-classes of protein based on shape

globular & fibrous

Part 2
1. All proteins in humans are polymers made up of ____ different __________.
1. 20 different amino acids.

What types of functions to structural proteins provide? Give 2 examples.

They provide structural components. Eg. Collagen in tendons and cartilage and Keratin in hair, skin,
wool, and nails.

What types of functions to contractile proteins provide? Give 2 examples.

They provide movement of the muscles. Eg. Myosin and actin control muscle fibres.

What types of functions to transport proteins provide? Give 2 examples.

They carry essential substances throughout the body. Eg. Hemoglobin transports oxygen and

lipoproteins transport lipids.

What types of functions to storage proteins provide? Give 2 examples.

They store nutrients. Eg. Casein stores protein in milk and Ferritin stores iron in the spleen and liver.

1. What types of functions to hormone proteins provide? Give 2 examples.

2. Hormones can be either protein based or _______ based.
1. The regulare body metabolism and nervous system. Eg. Insulin regulates blood glucose levels and
growth hormone regulates the body's growth.
2. steroid.

What types of functions to enzyme proteins provide? Give 2 examples.

They catalyze biochemical reactions in cells. Eg. Sucrose catalyses the hydrolysis of sucrose. Trypsin
catalysez the hydrolysis of protein.

What types of functions to protection proteins provide? Give 2 examples.

They recognize and destroy foreign objects. Eg. Immunoglobulins stimulate immune responses.

1. What are the functional groups in amino acids (AAs)?

2. What three things are bonded to a central carbon atom in the 20 AAs
found in proteins?
3. AAs with this structure are called _______.
4. The unique characteristics of these 20 AAs are due to the side chain (Rgroup) which occupies _______________.
1. an amino group (NH) and a carboxylic acid group (COOH)
2. an amino group (NH) and a carboxylic acid group (COOH) and a hydrogen
3. amino acids
4. the 4th bond to the central carbon atom

What is a zwitterion and what is its charge?

A molecule with a positive and a negative charge on the same structure. It has a net charge of zero.
*** All amino acids are examples of zwitterions.

1. How are atoms combined in proteins?

2. What is important to remember about them?
3. What is the nature of the side chain in the AA? Why is this important?
1. The carboxyl and amino groups are combined in peptide linkage.
2. They are not available for chemical reaction, except for H-bonding
3. It dictates the AAs role in the protein and is useful to classify AA according to the properties of the
chain.

1. With the exception of ___________, all AAs are (1, 2, or 3) amines?

2. What are primary amines?
1. Proline. 1.
2. Primary amines arise when one of three hydrogen atoms in ammonia is replaced by an alkyl.

Non-polar AAs:
1. The NP side chain (does/does not) bind, give off protons, or participate in
H or ionic bonds.
2. What makes these AAs hydrophobic?
1. The NP side chain does NOT bind, give off protons, or participate in H or ionic bonds.
2. The HCs are NP and, therefore, not soluble in water. *** These AAs can be thought of as lipid-like.
Therefore, they are soluble in lipids.

Non-polar AAs:
1. What happens with the side chains in proteins that are in aqueous solution
and why?
2. What happens with the side chains in lipid cell membranes and why?
1. The side chains cluster together in the interior of the protein. This is due to the hydrophobicity of the
non-polar R-groups.
2. When in a lipid cell membrane, the non-polar R groups are then found on the surface of the protein

Polar AAs:
1. Why are they hydrophilic?
3. Which 3 AAs contain a polar hydroxyl group that can participate in Hbonding?
4. Which 3 AAs exhibit some degree of polarity in the R groups.
1. B/c the EN atoms in the side chains form H-bonds with water.
3. The first 3: Serine, threonine, and tyrosine.
4. The last 3: Asparagine, cysteine, and glutamine.

What does the side chain of cysteine contain? Why is this important?
It contains a sulphydryl group (-SH). It is an important component of the active site of many enzymes.
For example, in proteins, the -SH groups of two cysteines can become oxidized to form a covalent
cross-link called a disulphide bond (S-S).

Acidic AAs:
1. What do they contain?
2. They can ionize as a (strong/weak) acid).
3. Which two amino acids are proton donors?
1. a carboxylic acid group (COOH)
2. weak
3. aspartic acid and glutamic acid. They become aspartate and glutamate.

Basic AAs:
1. What do these AAs contain?
2. ____________ is only weakly basic in comparison to the other two.
1. An amino group that can ionize as a weak base, by accepting proton(s).

2. Histidine.

1. The -carbon of each AA is attached to _____________, except for glycine. This

makes it a ________.
2. Why is glycine an exception?
1. 4 different chemical groups. Chiral carbon.
2. B/c its -carbon has two hydrogen substituents.

1. AAs that have an asymmetric centre at the -carbon can exist in two forms.
What are they? This makes them ___________.
2. How are they drawn and identified?
3. Which is most dominant in biological systems?
1. D & L. Stereoisomers of each other.
2. Drawn using Fisher Projections. But for the L isomer, the amino group (NH) is on the left and for
the D group, it's on the right
3. L-amino acids. D amino acids are in nature, but not in proteins.

1. What is the isoelectric point (pI)?

2. What happens when the pH is different from the pI?
3. In a solution that is more acidic than the pI, what happens with the -COO
group?
4. What about in a solution more basic than the PI?
1. The point at which an AA exists as a zwitterion (+ and - charge).
2. The zwitterion accepts or donates H.
3. It acts as a base and acceps an H, giving an overall positive charge to the amino acid.
4. The HN group acts as an acid and loses an H, giving the AA an overall negative charge.

When the conjugate base and acid are present in equal concentrations, their ratio is
_____, the log is _____, and so the pH = ______.
2. A buffer has maximum buffering capacity at its _______, when the acidic
and basic forms are present in ______ concentrations.
3. Each AA has 2 pKa's, referred to as ________ and ______.
4. An AA has minimal buffering capacity when the pH = _____ and it has
maximal buffering capacity at each of its ______.
1. one, zero, pKa.
2. pKa, equal
3. pKa and pKa
4. pI. pKa's (i.e. when [base]=[acid]

Of the 20 AAs, which are considered essential, meaning not produceable by the
body?
mnemonic device: PVT TIM HALL
PVT: Phenylalanine (Phe), Valine, Threonine
TIM: Tryptophan, Isoleucine, Methionine
HALL: Histidine, Argine, Leucine, Lycine

1. How are the characteristics of a protein determined?

2. What is a peptide bond?
3. Two amino acids linked together by a peptide bond, form a ____________.
4. In a peptide, the AA on the left with the free NH group is called the
_________, while the one on the right with the free COO group is called the
________.
1. By which AAs make up that protein.
2. An amide bond that forms when the COO group of one AA reacts with the NH group of the next
AA. terminal
3. dipeptide
4. N-terminal AA , the C-terminal AA.

1. As a consequence of resonance contributors, the peptide bond has ~40%

________ character. What does this mean for it's structure and function?
1. double bond the peptide bond is shorter than a regular chemical bond, making it rigid and planar.
This characteristic prevents free rotation about the bond.

1. The peptide bond is generally a _____ bond due to the steric hinderance of the Rgroups when in the __________.
2. The C=O and the NH groups of the peptide bond are polar and are
involved in _______ bonds.
1. trans, cis position
2. hydrogen

How do you name peptides?

2. What would be the name for a tripeptide consisting of alanine, glycine, and
serine be named?
1. Each AA beginning from the N-terminal is named in order with its 3-letter abbreviated name.
2. Ala-Gly-Ser

1. When is a polypeptide (PP) chain called a protein?

2. What are the levels of protein structures?
1. When there are more than 50 AAs.
2. Primary (1), secondary (2), tertiary (3), and quaternary.

1. How is a 1 protein structure determined?

1. Simply by the order of the amino acids held together by peptide bonds.

1. How is a 2 protein structure determined?

2. What are the most common secondary protein structures?
1. The secondary structure of a protein describes the way the AAs next to or near each other along the
polypeptide are arranged in space.
2. Alpha-helix, beta-pleated sheet, and the triple helix. Each type looks at: (a) the H-bonding between
the H atom of an amino group and the polypeptide chain and (b) the oxygen atom of the carbonyl group
in another part of the chain.

1. Explain the -helix structure of protein. (4 points)

2. What types of tissues have this structure?
1. Strong, spiral, tightly coiled like a telephone cord
2. Extensive H-bonding between each NH group and the O of a C=O group in the next turn of the
helix, 4 AAs down the chain.
3. Individually bonds are weak, but together they are strong (like a zipper and its individual links)
4. All side chains (R-groups) are located on the outside of the helix.
2. skin and hair

1. Explain the -Pleated Sheet structure of protein. (4 points)

2. What types of proteins have this structure?
1. PP chains are held together side by side by H-bonds between the peptide chains
2. Surfaces of the -sheet appear pleated
3. -sheet have 2 or more peptide strands that are almost fully extended and held together by H-bonds
4. H-bonds are perpendicular to the PP backbone
2. Silk

1. Explain the Triple Helix structure of protein. (1 point).

2. What is the most abundant protein and where is it found?
3. What does this protein have a high content of and how does it contribute to
the strength of the helix?
1. * The result of three polypeptides woven together like a braid.
2. Collagen. Found in connective tissue, blood vessels, skin, tendons, ligaments, the eye and cartilage.
3. Glycine, proline, alanine, and hydroxylproline and hydroxylysisine. The -OH groups present in their

hydroxyl forms in proline and lysine form H-bonds across the peptide chains giving strength to the
helix.

What happens when a diet is deficient in Vitamin C? (4 points)

1. Collagen fibrils are weakened b/c the enzymes needed to form hydroxylproline and hydroxylysisine
require Vitamin C.
2. Without the -OH groups to form hydroxylproline and hydroxylysisine, there is less H-bondng
between collagen fibrils.
3. As a person ages, additional cross-links form making collagen less elastic.
4. Bones, cartilage, and tendons become more brittle and wrinkles are seen as skin loses elasticity.

1. How is a 3 protein structure determined?

2. What does tertiary refer to?
3. PP chains > 200 AAs generally consist of ___ or more domains.
4. What are the different stablizing interactions of 3 protein structures?
1. It involves attractions and repulsions between the side chain groups of the AAs in the PP chain.
Segments twist and bend until the protein acquires a specific 3D shape.
2. Refers to both the folding of domains (the basic unit of structure and function) and the final
arrangement of domains in the polypeptide.
3. two
4. Hydrophobic, Hydrophilic, H-Bonds, Disulphide bonds, and Ionic Interactions (Salt Bridges)

Describe hydrophobic interactions. (3 points)

1. NP side chains are located in the centre of the PP chain.
2. Hydrophilic portions of the PP chain are located on the surface
3. Proteins located in NP (lipid) environments have the reverse arrangement (i.e. Polar parts on surface
and Hydrophilic parts in interior).

Describe hydrophobic interactions. (2 points)

1. Attractions between the external, aqueous envt and AAs that have polar or ionized side chains.
2. Polar side chains pull twd the outer surface of the protein and hydrogens bond with water.

Describe H-Bond interactions. (2 points)

1. H-bonds form between polar amino acids.

2. Eg. An H-bond can occur between the -OH group of serine adn the -NH group of glutamine.

Describe Ionic (salt bridge) interactions. (2 points)

1. Ionic bonds between side groups of basic and acidic amino acids, which have + and - charges.
2. The attraction of the oppositely charges side chains forms a strong bond called a salt bridge.

Describe Disulphide Bond interactions. (2 points)

1. Covalent linkage between the -SH group of each two cysteine AAs.
2. The cysteines may be separated by many AAs or may be located in different PP chains altogether.

Secondary and tertiary structures are like the bricks and mortar of protein
architecture.
1. Globular proteins have ______ shapes b/c of their secondary structures of
the PP chain fold over on top of each other.
2. Globular proteins perform much of the work of the cells including these 3
functions?
3. Heme proteins are specialized globular proteins. What 2 are the most
abundant in humans?
1. compact, sphirical
2. synthesis, transport and metabolism
3. myoglobin and hemoglobin. They serve to bind oxygen reversibly.

1. What is a porphyrin?
2. Explain the properties of Heme. (5 points)
1. Cyclic compounds that readily bind to metals, particularly Fe and Fe.
2.a) It's a porphyrin ring with Fe at centre.
b) Responsible for the red colour of blood.
c) Iron is held in centre of the heme molecule by bonds to the 4 nitrogens of the porphyrin ring
d) Fe can form 2 additional bonds: One on either side of the ring
e) Each heme group can bond one molecule of O

1. What are fibrous proteins?

2. What are the two types? Describe them.
1. Long, thin, fibre-like shapes of proteins that are involved in the structure and cells of tissues.
2. & -keratins

1. Describe -keratins. (2 points)

2. Describe -keratins. (2 points)
-keratins:
1. Make up hair, wool, skin and nails.
2. Within the fibril, the -helices are held together by disulphide (S-S) linkages btwn the R groups of
the many cystein AAs in hair. Several fibrils bind together to form a strand of hair.
-keratins:
1. Found in feathers and scales.
2. The proteins consist of large amounts of -pleated sheets.

1. What is the quaternary structure of protein?

2. How do they work? (3 points)
1. The spacial arrangement of the PP subunits (i.e. a single chain, or 2 or more chains that may/may not
be related).
2.a) Held together by non-covalent interactions (ie. hydrophobic, ionic, etc.). b) interactions that
stabilize the tertiary structure also stabilizes the quaternary. c) Subunits may work together or
independently of one another.

1. How does protein denaturation occur? What happens?

2. What are some denaturing agents?
3. Is denaturation reversible? Explain.
1. The disruption of any of the bonds that stabilize the 2, 3, 4 of the protein. However, covalent
bonds of the primary structure are unaffected. When denatured, proteins lose their shape and ability to
be functional.
2.Heat, strong acids, bases, and heavy metals.
3. No. The protein is unable to retain its original structure.

1. What proteins sequester and deliver O to the cells?

2. Where are they found and what are they responsible for?
1. Myoglobin (Mb) and Hemoglobin (Hb)
2. Mb found in skeletal and striated muscle.
Hb found in erythrocytes. Responsble for movement of O between lungs and other tissue.

What is the maximum pO (partial pressure of oxygen) in arterial blood? What

about in air?
100mm Hg (mercury) and 150 mm Hg

1. What is myoglobin?
2. How many AAs in a single PP chain of myoglobin with about 3/4 of the
chain in the -helix secondary structure?
1. a) A storage protein. A globular heme protein present in heart and skeletal muscle.
b) functions as a reservoir for oxygen & as an oxygen carrier that increases the rate of transport of
oxygen within the muscle cell.
2. 153.

1. Hemoglobin is composed of ___ PP chains or subunits: ___ chains and __

chains, denoted as _____.
2. How are the chains held together?
3. Each subunit of Hb contains a heme group giving the molecule ___ heme
groups in total (compared to 1 for Mb).
4. Te complete quaternary structure of Hb can bind and transport ___
molecules of oygen. It can transport CO from tissues to lungs and carry O
from lungs to tissues.
1. 4. 2. 2. denoted as .
2. By non-covalent interactions.
3. four
4. four.

1. Like O, CO binds to heme groups. The affinity for CO is more than 10 x that
of O. What implications does this have if there was prolonged exposure of
Hb to CO.
What would be the treatment of choice?
1. It would be irreversible and lead to highly toxic levels of arboxyhemoglobin.
2. Hyperbaric O

1. What unique role does Hb play in the body and why is

1. It gather incomming O from lungs and releases it to tissues.

1. What is an enzyme?
2. How do enzymes affect the breakdown of proteins in our diet?
3. How are enzymes named? What is the exception?
1. A protein that is a catalyst. Large protein molecules that speed up the rates of chemical reactions
without themselves undergoing any change. They lower the AE required. less energy is reqd to
convert reactant molecules to products.
2. Enzymes speed up the breakdown of proteins. Without them they wouldn't break down quickly
enough to meet the body's needs.
3. Replace the end of the name of the reaction/reacting compound with -ase. Exception: Early enzymes
sometimes used the -in suffix, such as pepsin and trypsin which are used to break down proteins.

1. For the enzyme class oxidoreductases. What reaction is catalyzed?

2. For example, what do oxidases,
reductases, and dehydrogenases do?
1. Oxidation-reduction RXNs
2. Eg. Oxidases oxidize a substance. Reductases remove a substance. Dehydrogenases remove atoms,
to form a double bond.

1. For the enzyme class transferases. What reaction is catalyzed?

2. For example, what do transaminases and kinases do?
1. Transfer a group between two compounds. 2. Eg. Transaminases transfer amino groups (NH).
Kinases transfer phosphate groups (PO)

1. For the enzyme class Hydolases. What reaction is catalyzed?

2. For example, what do proteases, lipases, carbohydrases, phosphatases, and
nucleases do?
1. Hydrolysis RXNs
2. Eg. Proteases hydrolyze peptide bonds. Lipases hydrolyze ester bonds in lipids.
Carbohydrases hydrolyse glycosidic bonds in carbohydrates. Phosphatases hydrolyze phosphate-ester
bonds.
Nucleases hydrolyze nucleic acids.

1. For the enzyme class Lysases. What reaction is catalyzed?

2. For example, what do carboxylases and deaminases do?
1. Add or remove groups involving a double bond without hydrolysis.
2. Eg. Carboxylases add CO and Deaminases add NH

1. For the enzyme class Isomerases. What reaction is catalyzed?

2. For example, what do Isomerases and Epimerases do?
1. Rearrange atoms in a molecule to form an isomer.
2. Eg. Isomerases converts cis to trans or vice versa and epimerases convert D to L isomers or vice
versa

1. For the enzyme class Ligases. What reaction is catalyzed?

2. For example, what do synthetases do?
1. Form bonds between molecules using ATP.
2. Eg. Synthetases combine two molecules.

1. What are substrates?

2. What structure of an enzyme plays an important role in how the enzyme
catalyzes RXNs?
3. How do enzymes work? What models do they use?
1. Reacting molecules.
2. The tertiary structure.
3. They bind to a substrat via its active site. They use a lock and key & Induced fit models.

1. What is the 2-step reaction of an enzyme catalyzed reaction?

2. What happens?
3. What factors affect enzyme activity?
1. E + S --> ES --> E + P
2. Leaves the exzyme and produces a product (i.e. sucrase + sucrose -->sucrase-sucrose complex -->
sucrase + glucose + fructose
3. Temp., pH, substrate concentration, & competitive & non-competitive inhibition?

1. How does temperature affect enzyme activity?

2. How does pH affect enzyme activity?
3. Specifically, how does pepsin work in the stomach?
1. Low temp = little activity. Increase temp = increased activity until OPTIMUM temp is reached. For
most enzymes this is body temp (37C). At 50 and above, the protein can become denatured and lose
its activity.
2. pH above or below the optimum causes a change in the 3D structure of the enzyme that disrupts the
active site. Enzymes in most cells have an optimum pH at physiological pH (~7.4). But stomach
enzymes have lower optimum pH.
3. Pepsin has optimum pH of 2. Btwn meals pH rises to btwn 4-5 and pepsin shows little activity. When

we eat, it triggers the release of HCl to stomach, lowering the pH.

How does substrate concentration affect enzyme activity?

When enzyme [ ] is kept constant, increasing the substrate [ ] increases the rate of the catalyzed rxn as
long as their are more enzyme molecules than substrate molucules. At some point, the substrate [ ]
saturates the enzyme. All availble enzyme molecules are then bonded to the substrate, the rate of
catalyzed reaction reaches its max 7 adding more substrate cannot increase the rate any further.

How does competitive inhibition affect enzyme activity?

Competitive inhibition: An inhibitor has a structutre so similar to the substrate that it competes for the
same active site as the substrate. If the [ ] of the inhibitor is substantial, there is a loss of enzyme
activity. Increasing the substrate [ ] displaces more of the inhibitor molecules. As more enzyme
molecules bind to substrate (ES), enzyme activity is regained.

How does enzyme inhibition affect enzyme activity?

They prevent the active site from binding with a substrate.

How does non-competitive inhibition affect enzyme activity?

Non-competitive inhibition: The inhibitor acts on a site that is not the active site. It doesn't resemble the
substrate and doesn't compete for the active site.
The binding causes the shape of the enzyme to be distorted, including the shape of the active site.
Inhibition occurs b/c substrate cannot fit/does not properly fit the active site no catalysis can occur.
B/c a non-competitive inhibitor isn't competing for the active site, te addition of more substrate does
not reverse this type of inhibition.
Examples include heavy metal ions that bond with AA R-groups.
Catalytic activity is restored when chemical reagents remove the inhibitors.

1. What are simple enzymes?

2. What are enzyme cofactors?
3. What is an apoenzyme?
4. What are coenzymes?
1. When their functional forms consist only of proteins with tertiary structures (eg. Trypsin and pepsin)
2. Non protein portions of enzymes required for carrying out a catalyzed reaction. They may be
metallic ions or organic compounds.
3. The protein (polypeptide) portion of the the enzyme.
4. Organic cofactors. I.e B vitamins. If tan enzyme requires a cofactor, neither the protein structure or
the cofactor aloe has catalytic activity.

1. What are proenzymes or zymogens? Give an example.

1. Enzymes that are manufactured by the body in inactive form. In order to make them active, a small
part of their PP chain must be removed.
The body does this as a protective mechanism so that it will activate the enzyme where it wants it to
work.

Eg. Trypsin is a protease (cleaves proteins). We want it to work in our stomachs on the proteins we eat.
If it worked outside the stomach in its active form, it would destroy our body's own proteins.

1. What is allosterism?
2. What can happen if a substance binds non-covalently & reversible to a site
other than the active site?
3. The substance that binds the allosteric enzyme is called ____________.
1. When enzyme regulation takes places by means of an event that occurs at a site other than the active
site, but will effect the active site. The enzyme regulated by it is called an allosteric enzyme.
2. It may inhibit enzyme action (AKA negative modulation) or stimulate enzyme action (AKA positive
modulation)
3. A regulator.

1. What are isoenzymes?

2. Different forms of the same enzyme are called ____ or ____.
1. Enzymes that perform the same function but have very different combinations of subunits in
different tissues. (i.e. different quaternary structures)
2. isozyme or isoenzyme.

1. Heme has only up to a ___________ protein structure.

tertiary

Part 3
zwitterion
dipolar ion; can act as either an acid or base; overall net zero charge, but molecule contains positively
and negatively charged regions

isoelectric point
characteristic pH at which the net electric charge is zero (pI)

side chain
R group of an amino acid; vary in structure, size and electric charge which influence the solubility of th
amino acid in water

sequence (of a protein)

order of amino acids in a polypeptide chain

peptide
two or more amino acids joined by a peptide bond

protein
polypeptide with a molecular weight above 10,000

dialysis
a procedure that separates proteins from small solutes by taking advantage of the proteins' larger size;
small molecules transfuse across a semipermeable membrane while protein cannot

conjugated protein
protein that contains permanently associated chemical components in addition to amino acids

prosthetic group
non-amino acid part of a conjugated protein

primary structure
description of all covalent bonds (mainly peptide bonds and disulfide bonds) linking amino acid
residues in a polypeptide chain

secondary structure
the particularly stable arrangements of amino acid residues giving rise to recurring structural patterns

tertiary structure
all aspects of the three-dimensional folding of a polypeptide

quaternary structure
arrangement of polypeptide subunits in space when a protein has two or more subunits

electrophoresis
important technique for the separation of proteins based on the migration of charged proteins in an
electric field

concensus sequences
sequence that reflects the most common base or amino acid at each position when a series of related
nucleic acid or protein sequences are compared; contains much of the functional information in protein
sequences; parts of the sequence that have particularly good agreement often represent evolutionarily
conserved functional domains

cation-exchange chromatography
column matrix that contains negatively charged polymer beads that cause positively charged proteins to
migrate more slowly through the column

anion-exchange chromatography
column matrix that contains positively charged polymer beads that cause negatively charged proteins to
migrate more slowly through the column

isoelectric focusing
procedure used to determine the pI of a protein; proteins placed in pH gradient in presence of electric
field so that each protein migrates until it reach the pH that matches its pI

SDS-PAGE electrophoresis
electrophoresis that uses SDS (sodium dodecyl sulfate) to give each protein a similar charge-to-mass
ratio and unfolds protein so that proteins are separated almost exclusively on the basis of size in gel
electrophoresis

size exclusion chromatography

aka gel filtration; separates proteins according to size with larger column emerging from the column
sooner than small ones due to polymer beads with engineered pores

affinity chromatography
based on binding affinity; beads in column have a covalently attached chemical group (ligand) that
binds to the desired protein; protein eluted by adding solution with high concentration of salt or ligand

Part 4
3D (primary) structure of a protein is determined by its
amino acid sequence

The function of a protein depends on its

structure

How many stable structural forms does a protein usually have

one or a small number

the most important forces stabilizing the specific structures maintained by a given
protein
non-covalent interactions

the spatial arrangement of atoms in a protein, achieved by rotation around single

bonds
conformation

proteins in functional conformations

native proteins

the tendency of a protein to maintain its native conformation

stability

forces counteracting high entropy in unfolded state

disulfide (covalent, S---S) and weak (non-covalent, hydrogen bonds, hydrophobic and ionic
interactions)

Why aren't disulfide bonds common in most cells and where are they commonly
found in eukaryotes?
reducing environment, secreted extracellular proteins (hormones)

Solvation layer occurs due to

less water order due to less hydrophobic material in contact (surface area) =increased entropy

release of free energy from this counteracts loss of entropy due to folded
conformation
increased entropy in surrounding aqueous environment

Why is the C-N bond in a peptide bond shorter and more rigid than in a classic CN amine structure?
resonance between amide nitrogen and carbonyl oxygen, no rotation between C and N

what does each dihedral bond angle represent

phi-alpha carbon/nitrogen rotation
psi-alpha carbon/carbon rotation
omega-nitrogen/carbon rotation (usually 180)

why can't phi and psi both be 0

steric interferences

The secondary structure of a protein refers to

The path or shape of the main chain polypeptide atoms in a segment, without regard to side chains or
other segments

In an alpha helix, the typical phi and psi angles are ____ and _____ and there are
_____ amino acids and a length of ______ per turn of the helix?
-57, -47, 3.6, 5.4 angstroms

Why is the alpha helix such a stable conformation?

optimal use of hydrogen bonding (N-H and C-O)

which amino acid has the greatest tendency to form alpha helices
alanine

What effect does adjacent charged amino acids at charged ph's have on the
stabillity of the helix?
unstable/will not form

what amino acids are not compatible being close together in a chain due to
bulk/shape?
Asn, Thr, Ser, Cys

critical interactions occur between amino acid side chains ____ and sometimes
_____ residues away from each other. These interactions include
3, 4. Oppositely charged residues, aromatic hhydrophobic

Amino acids least like to form alpha helices are

proline and glycine

why is proline not favorable for an alpha helix?

n in (n---C alpha) bond is part of rigid ring, no rotation possible for bond

why is glycine not favorable for an alpha helix?

more conformational flexibility than other amino acids

Which terminus has which charge of the helix dipole?

carboxyl amino +

what five constraints affect the stability of an alpha helix?

1) individual residue's propensity to form helix
2) interactions between r groups, particularly those 3 or 4 residues apart

3) bulkiness of adjacent r groups

4) occurrence of pro and gly residues
5) interactions between charged residues with dipole of the helix at ends

Part 5
20 common amino acids: Lehninger book. Figures from other set, names fixed.

Arginine-ARG, R

Histidine-HIS, H

Lysine-LYS, K

Aspartate-ASP, D

Glutamate-GLU, E

Serine-SER, S

Threonine-THR, T

Asparagine-ASN, N

Glutamine-GLN, Q

Cysteine-CYS, C

Glycine-GLY, G

Proline-PRO, P

Alanine-ALA, A

Valine-VAL, V

Isoleucine-ILE, I

Leucine-LEU, L

Methionine-MET, M

Phenylalanine-PHE, F

Tyrosine-TYR, Y

Tryptophan-TRP, W