HUBI 2001 - Chapter 1 Gibbs Energy

Protein folding is a ___________________ process

spontaneous

When Gibbs energy is less than 0

spontaneous

When Gibbs energy is greater than 0

non-spontaneous

When Gibbs energy is = 0

the system is at equilibrium.

Synonym for spontaneous

exergonic

Synonym for non-spontaneous

endergonic

Interactions between charged species

Ionic

Weakest intermolecular force

Van der Waals

Van der Waals interactions are always ______________

attractive

For clathrates, the ___________ the surface area the __________ the entropy

bigger, lower

Species that loses a proton

Acid

Species that gains a proton

Base

Central carbon in an amino acid

Alpha Carbon

A ______________ group contains a carbon, two oxygens and a hydrogen (COOH)

carboxyl

An _____________ group contains a nitrogen and two hydrogen (NH2)

amino

an enzyme that breaks down proteins and peptides.

protease

Lysine at pH=7

Positive

Arginine at pH=7

Positive

Histidine at pH=7

Neutral

Aspartate at pH=7

Negative

Glutamate at pH=7

Negative

Approximate pKa for carboxyl groups

2

Approximate pKa for amino groups

9.5

Approximate pKa for aspartate, glutamate

4

Approximate pKa for lysine, arginine

11.5

Approximate pKa for histidine

6

When pH is less than pKa it is…

Protonated

When pH is greater than pKa it is…

Deprotonated

Protein folding is stabilized by ____________ interactions

Non covalent

The terminal with the amino

N

The terminal with the carboxyl

C

Ionizable Amino Acids

DEKRHCY

Alpha helices are stabilized by this weak force

Hydrogen bonding

Alpha helices have __________ residues per turn

3.6

There are _____________ residues between each hydrogen bond of an alpha helix

4

another molecule that binds to a
specific site on the protein)

Ligand

Psi for right-handed alpha helix

-60

Phi for right-handed alpha helix

-50

Psi for beta stand structures

+135

Phi for beta strand structures

-135

Anti-parallel (left) and parallel (right) beta sheets are what placed on the Ramachandran chart

Top left

Right handed alpha helix is where on the Ramachandran chart

Middle Left

Left handed alpha helix is where on the Ramachandran chart

High middle right

Long skinny sidechains fit better in…

Alpha helices

Chunky sidechains fit better in…

Beta sheets

A proteins function is determined by its…..

Structure

Which protein provides support

Fibrous

The helices in alpha keratin are held together by…

Hydrophobic Interactions

Stabilization of protofibril and protofilament comes from…

Disulfide bonds

Disulfide bonds are _______x stronger than hydrogen bonds

100

Wool and skin are ~____% cysteine

4

Hair and feathers are ~______cysteine

11

Nails and claws are ~_____%cysteine

18

The quaternary structure in alpha keratin is stabilized by what type of non-covalent interaction

Disulfide

Fibroin is stabilized by which non-covalent interaction?

Hydrogen bonding

Hydroxyproline is modified ___________ translation of protein

after

is caused by a serious deficiency of vitamin C (ascorbic acid) in the diet, which is essential for the synthesis of collagen needed for connective tissues, skin, bone, and cartilage

Scurvy

Secondary structure of collagen is a…

Left-handed helix

a complex composed of three distinct subunits, where at least one subunit differs from the other

Heterotrimer

Quaternary structure of collagen is a…

Right-handed triple helix

For globular proteins the hydrophobic residues are on the…

inside

For globular proteins the hydrophillic residues are on the…

outside

one polypeptide chain in a protein with
more than 1 chain

subunit

a compact unit of protein
structure that is usually capable of folding
stably as an independent entity in solution

domain

some proteins, called ___________ proteins,
contain permanently associated chemical
components in addition to amino acids

conjugated

beta-mercaptoethanol breaks __________ bonds

disulfide

urea breaks ____________ bonds

non-covalent

Conversion of an irregular,
flexible arrangement of the protein chain
to a regular, relatively rigid, well defined
3D structure

Protein folding

The only interaction that favors protein folding

Hydrophobic

the information required to fold the
protein into its tertiary structure is contained in
the

primary sequence

proteins present in cells that
help other proteins fold

Chaperones 

plaques destroy nerve
cells and lead to loss of
thought and memory

Amyloid

Proteins that can misfold and cause
infectious disease

Prions

Myoglobin is used for binding and…

storage

Hemoglobin is used for binding and…

transport

Immunoglobulins are used for binding and…

recognition

Iron forms 2 perpendicular bonds. 1 is to the ___________ and the other is to the __________

nitrogen, oxygen

Fe²⁺ and Fe³⁺ is called ________ meaning it cant bind oxygen

ferric

The overall 3D arrangement of secondary
structure elements that characterizes a
single domain is called a

Fold

The 3D structure of globins is mostly stabilized by ______________ and other non-covalent interactions

hydrogen bonds

Myoglobin is a…

monomer

Hemoglobin is a

tetramer

The R-state of Hemoglobin is stabilized by

oxygen bonding

The ________ is (more stable) when oxygen isnt bound

T-state

The T-state is stabalized by

ionic interactions

A_______ protein is one
whose conformation is
changed when it binds a
ligand

allosteric