URI CMB 311 Exam 1 (Review)

Place these molecular bonds in the correct order, from strongest to weakest: covalent, ionic, van der Waals, hydrogen

Covalent > Ionic > Hydrogen > Van der Waals

Why does water have such high freezing and boiling points?

Water is capable of forming extensive hydrogen bonding networks. Each water molecule can donate and accept H-bonds.

What is the basis for the hydrophobic effect?

Water molecules form ordered shells around non-polar (hydrophobic) groups, resulting in decreased entropy. The hydrophobic effect is largely entropic in nature.

What functional groups are likely to engage in hydrophobic interactions?

Non-polar groups containing only C-H, such as methyl, ethyl, or other hydrocarbon groups, or aromatic groups such as phenyl rings

Name a functional group that can act as a hydrogen bond acceptor but not a donor.

Carbonyl groups can accept H-bonds but cannot donate H-bonds, since they have no hydrogens

Give examples of functional groups that are likely to participate in hydrogen bonding.

-NH2 (amino), -C=O (carbonyl), -COOH (carboxyl), -OH (hydroxyl), etc

What functional groups can be ionized (at neutral pH)?

-NH3+ (amino), -COOH (carboxyl), imidazole

Name a functional group that is hydrophobic.

-CH3, etc (see question 4)

Name four functional groups that are hydrophillic.

-NH2 (amino), -C=O (carbonyl), -COOH (carboxyl), -OH (hydroxyl), etc (see question 6)

Given the pKa of 4.76 for acetic acid, what is the ratio of [CH3COO-] to [CH3COOH] at pH 4.76?

Given the Henderson-Hasselbalch equation, an acid is half dissociated at its pKa, therefore the answer is 1.

Given the pKa of 4.76 of an imidazole group is around 6.0, what is the net charge of imidazole at pH 8.0?

Two units above the pKa essentially all of the imidazole will be deprotonated, therefore it will be neutral (0)

What is the [H+] (or [H3O+]) in a solution with a pH of 5?

pH=-log10[H+], therefore [H+]=10^-pH, therefore [H+]=10^-5 M

Which amino acids have a net negative charge at neutral pH?

Aspartic acid (Asp, D) and glutamic acid (Glu, E)

What functional group is found in the side chain of Arginine?

Guanidinium

What amino acids have a carboxyl group as part of their side chains?

Aspartic acid (Asp, D) and glutamic acid (Glu, E)

What interactions stabilize the alpha-helix?

Hydrogen bonding between backbone carbonyl oxygens and amino group nitrogens

What interactions stabilize the beta-sheet?

Hydrogen bonding between backbone carbonyl oxygens and amino group nitrogens

How many amino acids are there per turn of the alpha-helix?

About 4 amino acids per turn, or 3.6 to be precise

Is the alpha-helix right-handed or left-handed?

Right handed, although left-handed helices do exist

What was the conclusion if Afinsen's experiments with the refolding of ribonuclease A?

All the information needed for a protein to fold into its native, active conformation is contained in the amino acid sequence

What do Ramachandran plots show?

Ramachandran plots show the allowable and favorable combinations of phi and psi bond angles in a polypeptide backbone

What is the primary driving force behind protein folding?

Hydrophobic interactions

What is the significance of the following expression used to describe protein-ligand binding?

q = [L]/([L] + Kd)

It indicates that the Kd is the ligand concentration at which one half of the binding sites are filled

Describe the O2 binding behavior of Mb and Hb in terms of cooperativity and the shapes of their binding curves.

Mb binds non-cooperatively, while Hb binds cooperatively

Based on the previous question/graph, describe the behavior or proteins A and B in the curves (A on top, B on bottom)

Protein A binds the ligand L non-cooperatively, whereas Protein B binds the ligand L cooperatively

Based on the binding curves from the previous question, give reasonable estimates of the Kd of proteins A and B for L?

The Kd of Protein A for L is about 5 uM and the Kd of Protein B for L is about 25 uL

What purification method separates proteins based on their charge?

Ion exchange chromatography

What purification method separates proteins based on their size?

Size exclusion chromatography

SDS-PAGE (SDS-polyacrylamide gel electrophoresis) separates proteins based on what property?

Molecular weight

What method would you use to remove mitochondria and ribosomes from a cell extract?

Ultracentrifugation

What method best takes advantage of specific protein-ligand interactions?

Affinity chromatography

What is the sequence of the polypeptide that yields the following products?

CNBR:

ELVISFSTREM

MEYWDEM

LIYLEG

KGAGM

Trypsin:

GAGMELVISFSTR

MEYWDEMK

EMLIYLEG

Chymotrypsin:

DEMKGAGMEKVISF

STREMLIY

LEG

MEYW

MEYWDEMKGAGMELVISFSTREMLIY

What is the sequence of the polypeptide that yields the following products?

Trypsin:

VGAHAGEYGAEATE

AAWGK

VLSPAK

TNVK

Chymotrypsin:

GAEATE

GKVGAHAGEY

VLSPAKTNVKAAW

VLSPAKTNVKAAWGKVGAHAGEYGAEATE

What is the mathematical relationship between the ΔG of a reaction and the reaction quotient Q?

ΔG = ΔG*' + RT ln Q, where ΔG*' is the change in Gibbs free energy under standard conditions (1M reactants and products), R is the gas constant (8.315 x 10-3 kJ mol-1 K-1) and T is temperature. Q is the reaction quotient ([reactants]/[products])

How does the ΔG at the start of a reaction compare to the ΔG at equilibrium?

ΔG at the start of the reaction depends on the concentration of the reactants depends on the concentration of the reactants and products and the Keq, while ΔG at equilibrium is 0

What is the difference between the ΔG of a reaction and the ΔG*' of a reaction?

ΔG depends on the concentrations of the reactants at any point in a reaction, whereas ΔG*' is under standard conditions (1M reactants and products)

Enzyme act by affecting what thermodynamic parameter?

ΔG+ (the activation-energy of the reaction)

What effect do enzymes have on the equilibrium of a reaction?

None

What effect do enzymes have on the ΔG*' of a reaction?

None

Define the term Km in terms of rate constants for an enzyme reaction.

KM = (k-1 + k2)/k1 (the ratio of the rate constants for the breakdown of the ES complex over the

rate constant for the formation of the ES complex.

Define KM in terms of substrate concentration and reaction velocity.

KM = [S] at 1/2 Vmax (the substrate concentration sufficient to yield one have maximum velocity)

What is the Michaelis-Menten equation?

V0 = Vmax[S]/(KM + [S])

For the enzyme catalyzed reaction S

[P] vs t is used to determine values for V0

What equation defines a Lineweaver-Burk plot?

1/V0=(Km/Vmax)*1/[S] + 1/Vmax

What defines the slope of a Lineweaver-Burk plot?

Km/Vmax

What are the axes on a Lineweaver-Burk plot?

1/V0 vs 1/[S]

What catalytic mechanism does hexokinase use?

Proximity and orientation

Draw the transition state for the hexokinase reaction.

This would just be glucose-P-ADP with the P in a trigonal bipyramid configuration

Ribonuclease A (RNase A) uses what mechanism of catalysis?

Acid-base catalysis

What role does His12 of RNase A play in catalysis?

His12 acts as a base and removes a proton from a substrate -OH group

What role does His119 of RNase A play in catalysis?

His119 acts as an acid and adds a proton to the RNA to cleave the phosphodiester bond

What catalytic mechanism(s) does chymotrypsin use?

Chymotrypsin uses both acid-base catalysis and covalent catalysis

What three amino acid residues make up the catalytic triad of chymotrypsin?

Asp102-His57-Ser195

What covalent bond is formed during the chymotrypsin reaction?

A covalent bond is formed between the Ser195 O- and the substrate carbonyl carbon