Biochemistry Exam 2 Whaley Fall 2022

Protein structure and function

the function of a protein is due to its structure

4 levels of protein structure

primary, secondary, tertiary, quaternary

primary structure

the amino acid sequence of a single polypeptide subunit

ex: met-gly-asp-phe

secondary structure

short domains or motifs of 3d structure

ex: alpha helix and beta sheet

Tertiary Structure

The 3D structure of a single polypeptide unit

Quaternary structure

the arrangement of polypeptide subunits relative to each other in a multi-subunit protein

the primary structure of human myoglobin

154 Amino Acids long

myoglobin

muscle protein; almost all myoglobin has a bound O2 molecule

Fetal Hemoglobin

Oxygen is released from mom's hemoglobin to baby's hemoglobin which then goes to baby's myoglobin

enzymes

catalysts that function in living organisms; most enzymes are proteins but some examples of RNA molecules having catalytic activity; alters the rxn mechanism to lower Ea

When delta G rxn is negative

the reaction is spontaneous as it is written

The effect of a catalyst on reaction rate

Ea for catalyzed reactions is much lower; this results in a dramatic increase in reaction rate

Vmax

A characteristic of a given enzyme at a defined concentration [E]; the higher the enzyme concentration, the greater Vmax will be

At high [S]

all of the enzyme molecules have a bound substrate molecule; The enzyme is working at full capacity

3 assumptions for Michaelis menten model

1. Rapid equilibrium formation of ES complex

2. We are dealing with initial rates only so that [P] is small

3. The value of K-2 is small and negligible

Increasing [E] increases....

the rate of the reaction (Assuming constant [S])

Side Chains of amino acids

charge on the Side chain is affected by the pH of the aqueous solution; side chains facilitate intra-peptide interactions that cause protein folding

Protein synthesis and folding

proteins are synthesized by ribosomes; however, they go from a randomly coiled structure to a properly folded structure to have the right activity

Salt bridges

actual proteins have many salt bridges that promote protein folding

Formation of a disulfide bridge

limits the number of possible folded structures

histidine importance

the imidazole ring side chain has a pKa value (6.0) that is in an intermediate range; histidine has a key role in the catalytic actions of many enzymes

How can pI value be estimated?

Take the average of pKa2 and PKa3

hydrogen bonding

also contributes to the correct folding of a protein

The alpha helix

proceeds from N terminus to C terminus in a clockwise fashion; stabilized by hydrogen bonds between the carbonyl groups of one turn and the amide N-H groups in the next turn

Zwitterion form of glycine

dominant form in aqueous solution at neutral pH (net charge is 0); water soluble, so can travel in the bloodstream; remember that the uncharged form of glycine DOES NOT represent the actual form in aq. solution.

Glycine in acidic environment (stomach: ph=2)

Dominant form of glycine in acidic conditions has a charge of +1. In an electrophoresis experiment, this form will migrate towards the negative electrode

Glycine in an alkaline environment (pH=12)

Dominant form of glycine in alkaline conditions has a charge of -1. In an electrophoresis experiment, this form will migrate towards the positive electrode.

How many amino acid residues per turn are there in the alpha helix?

3.6

isoelectric point

the pH at which glycine exhibits no migration in an electric field; glycine has a net charge of 0 at the isoelectric point

Aspartic acid at pH=7.0

net charge of -1

Lysine at pH=7.0

has a net charge of +1

Lineweaver-Burk form of the Michaelis Menten equation

1/V= Km/Vmax (1/[S]) + 1/Vmax

Enzyme inhibitors

diminish the activity of an enzyme; many modern medications are enzyme inhibitors

Enzyme-Substrate recognition: Lock and Key model

Substrate binds to enzyme like a key goes in a lock

Enzyme-Substrate recognition: Induced Fit Model

enzyme must undergo a change in conformation (shape) to allow the substrate to bind

competitive inhibitors

tend to be structural similar to the substrate; the inhibitor prevents the substrate from binding to the enzyme; changes the value of Km but does not change the value of Vmax

NSAIDs (non-steroidal anti-inflammatory drugs)

Competitive inhibitors of cyclo-oxygenase

non-competitive inhibitors

can bind to the free enzyme (E) and to the ES complex

uncompetitve inhibition

very rare type of inhibition; the inhibitor binds only to the ES complex and NOT to the free enzymes

irreversible inhibition

form covalent bonds with the enzyme or bind to the enzyme in a manner that permanently denatures the enzyme; lots of toxins follow this inhibition

Hg2+ and Pb2+

Both very toxic due to their ability to denature proteins; enzyme no longer fits the substrate

Isaac Newton

spent years in an insane asylum due to mercury poisoning (which was detected in a hair strain)

Gas in the 1960's and 1970's

contained tetraethyl lead

oxidoreductases

catalyze oxidation-reduction reactions which involve the transfer of electrons from one chemical species to another

in biochemistry, electrons are often transferred in the form of

H. (Hydrogen atoms)

Transferases

transfer molecular groups from a donor molecule to an acceptor molecule; groups include amino, carboxyl, carbonyl, methyl, phosphoryl, and acyl groups; example: Transminase- transfers an amine group from a donor to an acceptor

hydrolases

catalyze the cleavage of bonds by the addition of water molecules; include esterases, phosphatases, and proteases

lyases

catalyze reactions in which groups (H2O, CO2, and NH3) are removed by elimination to form a double bond, or they are added to a double bond. Example: decarboxylates, hydralases, dehydratases, deaminases, and synthases

isomerases

catalyze intermolecular rearrangements and interconversions of one isomer (of substrate) into another isomer. Examples: aldoses and ketoses acting on sugar molecules

Ligases

Join two smaller molecules together. Example: DNA ligase would join two molecules of DNA together to make one larger molecule of DNA

Does protein synthesis use L or D amino acids?

Only L-amino acids are used in ribosome-directed protein synthesis (translation)

3 main parts of an amino acid

amino group, carboxyl group, side chain

R vs S configuration

R: clockwise

S: counterclockwise

Non-polar amino acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

polar amino acids

Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

Acidic amino acids

aspartic acid, glutamic acid

basic amino acids

lysine, arginine, histidine

aromatic amino acids

phenylalanine, tyrosine, tryptophan

Cyclic amino acid

Proline

what is special about serine and threonine?

can both be H-bond donors or acceptors

what is special about glutamine and asparagine?

Both have amide side chains; amide derivative of glutamic acid and aspartic acid

Sulfur containing amino acids

cysteine and methionine

what is special about cysteine?

Can form a disulfide bridge, can act as a weak acid

Glycine

Gly, G

Proline

Pro, P

Alanine

Ala, A

Valine

Val, V

Leucine

Leu, L

Isoleucine

Ile, I

Phenylalanine

Phe, F

Tyrosine

Tyr, Y

Tryptophan

Trp, W

Methionine

Met, M

Serine

Ser, S

Threonine

Thr, T

Cysteine

Cys, C

Asperagine

Asn, N

Glutamine

Gln, Q

Aspartic Acid

Asp, D

Glutamic Acid

Glu, E

Lysine

Lys, K

Arginine

Arg, R

Histidine

His, H

Condensation and Hydrolysis of peptide bonds

Condensation is removing water, hydrolysis is adding water

phi and psi peptide torsion angles and free rotation

there is free rotation about the bonds defined by the angles phi and psi; the bond defined by angle omega has a partial double bond character and therefore has restricted orientation (go look at diagram)

Two structural motifs of peptide secondary structure

alpha helix; beta pleated sheet

alpha helix is stabilized by

hydrogen bonds

standard form of beta sheet structures

from N terminus to C terminus

beta barrel

complex structure baed on anti-parallel strands

beta meander

based on anti-parallel strands

beta-alpha-beta motif

an alpha helix between two parallel beta strands

Greek key

based on anti-parallel strands

leucine zipper motif

Involved in proteins that bind to DNA

Glutathione

an important antioxidant

zinc finger motif

common in proteins that bind other proteins, DNA, or RNA

ATP binding domain

present in enzymes that catalyze reactions that use ATP as a reactant; the ATP binding pockets are where ATP is hydrolyzed into ADP or AMP

Amino acid interactions that stabilize protein structures

electrostatic interactions; hydrogen bonding

Oxidation of two cysteine molecule can form

cystine

9 functions of proteins

catalysis, structure, movement, defense, regulation, transport, storage, stress response, toxins

Michaelis-Menten equation

v = (vmax [S])/(Km + [S])