Biochemistry exam 1

Is there any freedom of rotation around a peptide bond?

no

A peptide bond has a -- bond character and -- structures are possible.

double, resonance

This is what is left in a peptide if side chains are eliminated.

protein backbone

This atom in the backbone carbonyl can H bond with these atoms in the amine group.

O, H

In an alpha helix, the H in NH3+ in amino acid number -- interacts with the O- in amino acid number --.

1, 5

This plot shows what phi and psy angles are possible in amino acid residues in peptides.

Ramachandran

In a Ramachandran plot, the -- areas represent more favorable angles.

darker

What is the stabilizing force of an alpha helix?

H bonding between backbone amino hydrogen and carbonyl oxygen.

How many AAs per turn of an alpha helix?

3\.6

This amino acid is not found in alpha helices because its lack of rotation is destabilizing

proline

This amino acid is rare in alpha helices because it rotates too much

glycine

Alpha helices can be ---, with one side having hydrophobic residues and one having hydrophilic

amphipathic

An alpha helix orients itself with its --- side on the outside

hydrophilic

What is the minimum number of AAs needed for a beta sheet to form a turn?

4

Name for beta sheet with amino-amino orientation

parallel

Name for beta sheet with amino-carboxyl orientation

antiparallel

Beta sheets are held together by:

H bonding

Side chains in beta sheets go -- -- -- in an alternating sequence.

up and down

Side chains in beta sheets do not --- like in an alpha helix.

interact

A beta sheet or alpha helix conformation can be predicted based on -- sequence

AA

These two amino acids are the most likely ones to be present in a tight beta turn

proline and glycine

Collagen is this kind of structure

triple helix

Keratin is this kind of structure

alpha helix

Triple helix has -- AAs per turn

3

Every 3rd AA in collagen is almost always -- but is sometimes --.

glycine, proline

This is a modified form of proline that strengthens it for incorporation into collagen.

4-hydroxyproline

This enzyme adds hydroxy groups to proline to make it 4-hydroxyproline.

Prolyl hydroxylase

Collagen has lots of covalent -- linking.

cross

Silk fibroin has this structure:

beta sheets

What is the name for a region of a protein that can undergo movement as a single entity?

domain

These proteins help other proteins fold.

chaperone

This provides the energy chaperone proteins need to function.

ATP hydrolysis

Misfolded proteins may --- and cause health problems.

aggregate

Myoglobin is in __.

muscles

Hemoglobin is in __.

blood

Myoglobin (Mb) allows O2 to diffuse to __.

muscles

Hemoglobin can transport some -- and -- back to the lungs.

CO2, H+

Myoglobin is made of alpha helices and a ---- group.

prosthetic

A non AA compound needed for a protein to function

prosthetic group

The prosthetic group in myoglobin

heme

This prosthetic group in myoglobin binds O2

heme

The -- angle is the angle between the alpha C and N.

phi

The -- angle is the angle between the alpha C and carboxyl C.

psy

In myoglobin, 2 of these amino acids play crucial role in O2 binding.

histidine

In myoglobin, one histidine binds -- and the other helps form -- binding site.

Fe, O2

Myoglobin does not have this type of structure.

quaternary

Hemoglobin has 4 subunits, so it is called a:

tetramer

Each of hemoglobin’s subunits has a -- prosthetic group

heme

Each hemoglobin binds -- O2 molecules.

4

Heme maintains iron in this oxidative state.

2+

Saturation of myoglobin has a --- curve.

hyperbolic

Saturation of hemoglobin has a -- curve.

sigmoidal

Myoglobin binds oxygen at a -- concentration than hemoglobin.

lower

Hemoglobin has -- binding of O2 molecules.

cooperative

About --% of O2 molecules bound to hemoglobin are dumped off to myoglobin.

66

When O2 binds hemoglobin, it induces a conformational change in --.

porphyrin

Porphyrin is a component of -- in hemoglobin.

heme

Binding of O2 to heme make subsequent binding easier by making porphyrin more ---.

planar

Hemoglobin is -- because other molecules can bind to it (not on its binding site) and change its conformation and binding affinity to O2.

allosteric

This negatively charged molecule decreases binding affinity to O2 by binding hemoglobin.

2,3-BPG

2,3-BPG works by stabilizing -- and -- residues in Hb.

histidine, lysine

CO2 and H+ in tissues bind to terminal -- groups in Hb, which decreases O2 affinity. This is called the --- Effect.

amino, Bohr

Bohr Effect works by protonating ---, causing it to H bond with ----.

His 146, Asp 94

Fetal hemoglobin needs to have a --- affinity for O2 than maternal hemoglobin.

greater

Fetal hemoglobin has 2 alpha subunit and 2 -- subunits.

gamma

Fetal hemoglobin has a lower affinity for:

2,3-BPG

In sickle cell anemia, AA 6 of B subunit is changed from a -- to a --.

glutamate, valine

In sickle cell anemia, these AAs polymerize and cause aggregation.

valine

Sickle cell anemia causes cells to rupture before -- parasites can complete their life cycle.

malarial

This is a class of enzymes that joins 2 substrates into 1.

Ligase

Lots of ---- chemistry occurs at enzyme active sites.

acid-base

Hemoglobin has more -- interactions than myoglobin because these are important to maintain quaternary structure.

nonpolar

Would a change in blood pH from 7 to 6 increase or decrease hemoglobin’s O2 affinity?

decrease

Hemoglobin has a higher affinity for -- than for O2.

CO

Most peptide bonds are -- because of steric hindrance.

trans

This constant measures the affinity of a protein to a ligand.

Kd

\--- AAs are on the surface of heme subunits and hold them together.

hydrophobic

alpha and beta subunits of hemoglobin look similar but have differences in --.

sequence

Muscles make more -- at high altitudes.

2,3-BPG

This is a synthetic hormone that increases RBC production.

erythropoeitin

There are this many binding sites for 2,3-BPG per hemoglobin molecule.

1

The buffering region of a buffer is plus or minus -- pH unit from --.

1, pKa

Ratio of base to acid in blood

20:1

Blood is better at buffering against acid because most --- waste is acid.

metabolic

pKa of blood

6\.1

Multicellular organisms overwhelmingly use -- amino acids, but bacteria use --.

L, D

Two adjacent cysteine AAs can form a covalent bond and make:

cystine

\-log\[H+\]=

pH

-log[Ka]=

pKa

The lower the pKa, the -- the acid.

stronger

When relative concentrations of acid and conjugate base are equal, pH=

pKa

Henderson-Hasselbalch equation

pH=pKa+log[A]/[HA]

When oxygen binds to myoglobin, the two open coordination bonds of Fe2+ are occupied by one -- molecule and one atom from a --.

O2, histidine

Heme in hemoglobin and myoglobin is -- bound.

noncovalently

Hemoglobin contains 4 subunits that interact --.

noncovalently

The heterocyclic ring that holds Fe2+ in heme is called:

porphyrin

Enzyme that transfers electrons

oxidoreductase

Enzyme that catalyzes the transfer of groups

Transferase

Enzyme that catalyzes hydrolysis reactions

hydrolases

Enzyme that cleaves bonds (especially C-C, C-O, C-N) by elimination and leaves double bonds or rings

lyase