Biochem Block 1: Protein Structure (Fulop)

Front 1

The peptide backbone of the primary protein structure allows some flexibility that creates secondary structures due to ____________

Back 1

the bonds of the alpha carbon

Front 2

Because of resonance, the double bond nature of the ____________ in the primary structure of proteins does not allow rotation

Back 2

peptide bonds

Front 3

Secondary structures are held together by __________________ within the protein backbone

Back 3

hydrogen bonds

Front 4

What is the most common secondary structure?

Back 4

alpha helix

Front 5

What is the main secondary structure in transmembrane domains? Why?

Back 5

alpha helices. You can incorporate hydrophobic amino acids and their hydrophobic R groups will be pointing away from the helix, allowing them to span the hydrophobic transmembrane region

Front 6

Side groups point away from the helix to minimize _________

Back 6

steric hindrance

Front 7

Strands of antiparallel beta sheets are connected by _____________

Back 7

BETA TURNS

Front 8

Beta turns are turns formed from ___ amino acids and are stabilized by ____________

Back 8

4 amino acids

a single hydrogen bond

Front 9

What are the 3 main domains of transmembrane proteins? Give an example of a transmembrane protein

Back 9

ligand binding domain extracellularly

transmembrane domain consisting of alpha helices formed by hydrophobic amino acids

cytoplasmic domain

transmembrane protein: G-protein coupled receptor

Front 10

What are two types of proteins that have a quarternary structure?

Back 10

globular proteins and fibrous proteins

Front 11

Globular protein--a quarternary structure--is tertiary protein subunits held together by __________ bonds

Back 11

non-covalent (sometimes disulfide) bonds

Front 12

Fibrous protein--a quarternary protein--are protein chains held together by __________ bonds

Back 12

covalent

Front 13

Describe the structure of type II collagen. What is the overall structure called?

Back 13

-3 identical protein chains held together by covalent bonds and non-covalent interactions

-homotrimer

Front 14

Describe the structure of a G-protein. What is the overall structure classified as?

Back 14

-3 DIFFERENT protein chains held together by noncovalent interactions

-heterotrimer

Front 15

what is a heterotrimer?

Back 15

a protein composed of 3 different subunits

Front 16

describe the structure of hemoglobin. What is this structure classified as?

Back 16

-2 alpha and 2 beta chains held together by noncovalent interactions

-a2b2 tetramers

Front 17

Globular proteins tend to be _________ in water.

Back 17

soluble

Front 18

Fibrous proteins tend to be _____________ in water.

Back 18

insoluble

Front 19

Collagens, elastin and fibrillin are all ____________.

Back 19

fibrous proteins

Front 20

Blood transport proteins, enzymes and antibodies are all___________________

Back 20

globular proteins

Front 21

What are the benefits of quarternary structure (3)?

Back 21

-stable (collagen due to covalent bonds between 3 units)
-cooperativity (hemoglobin)
-regulate overall activity of protein (in g proteins, the alpha subunit cannot perform its function until it dissociates from the beta and gamma subunits)

Front 22

Myoglobin is the main ____________ molecule in skeletal and heart muscle. Its 8 alpha helices form a pocket in which a prosthetic __________ group binds oxygen

Back 22

-oxygen storage molecule
-heme iron (Fe2+)

Front 23

In alpha helices, you will not find the amino acid _________

Back 23

proline

Front 24

Which amino acids will you find in a transmembrane alpha helix?

Back 24

leucine, isoleucine, valine, phenylalanine, tryptophan, cysteine and methionine. all hydrophobic

NOT PROLINE--although it is hydrophobic it breaks the alpha helix

Front 25

Hemoglobin is the major __________ molecule in red blood cells. It can bind _____ oxygen molecules

Back 25

oxygen transport

-4

Front 26

Hemoglobin subunits don't bind O2 in the _______ state. They bind in the ________ state.

Back 26

-T (taut)

-R (relaxed)

Front 27

Under low O2 conditions, hemoglobin ___________ O2 and myoglobin __________.

Back 27

-hemoglobin releases

-myoglobin picks it up

Front 28

Fetal hemoglobin has a _________ oxygen binding capability than adult hemoglobin

Back 28

higher

Front 29

Igs (immunoglobulins) are composed of __________________________ held together by _________

Back 29

two heavy and two light chains held together by noncovalent interactions and disulfide bonds

Front 30

The __________ region of the Igs forms the antigen binding site that recognizes the foreign invader

Back 30

variable

Front 31

The ___________ region of the ___________ chain binds macrophages and facilitates clearance

Back 31

-constant region

-heavy chain

Front 32

Protein folding occurs in what organelle?

Back 32

the ER

Front 33

What determines a protein's primary structure?

Back 33

primary structure (the amino acid sequence)

Front 34

Some proteins require __________ to help them fold

Back 34

accessory proteins (chaperonins)

Front 35

What does hsp70 do?

Back 35

-binds to elongating protein chain to prevent premature folding

Front 36

What does hsp60 do?

Back 36

it's a chamber that folds proteins using ATP

Front 37

What are the 4 ways proteins can be denatured?

Back 37

-oxidative damage
-pH
-temp
-solvents

Front 38

The myoglobin binding curve is described as ____________. Hemoglobin?

Back 38

myoglobin - hyperbolic
hemoglobin - sigmoidal

Front 39

A ____________ deficiency causes intracellular proteins to become denatured by oxygen radicals, causing dark spots in red blood cells called ___________ due to the accumulation of damaged proteins.

Back 39

G6PD, Heinz bodies

Front 40

What is the abbreviation describing the normal conformation of prion protein? Misfolded?

Back 40

Normal: PrPC

Misfolded: PrPSC