exam 1exam chapter 3 and 4

Question 1

non polar, aliphatic R groups

Answer 1

glycine
alanine
proline
valine
leucine
isoleucine
methionine

Question 2

R group ishydrogen, found in flexible
parts of proteins, not chiral, can be modified
by addition of a fatty acid (myristate – 14
Carbon)

Answer 2

glycine

Question 3

R group is CH3 (methyl group)

Answer 3

alanine

Question 4

Extended aliphatic chains and can be branched

Answer 4

Valine (V, Val)
Leucine (L, Leu)
Isoleucine (I, Ile)

Question 5

Only imino acid, affects protein folding, often found at bends in protein 3-D structures. Hydroxylation of___ important for the structure of collagen

Answer 5

proline pro p

Question 6

Contains sulfur, can interact and bind
with metal ions, often found in
metalloproteins

Answer 6

methionine Met M

Question 7

aromatic R group

Answer 7

phenylalanine
tyrosine
tryptophan

Question 8

Can be phosphorylated on hydroxyl groups

Answer 8

Tyrosine, Serine, and Threonine

Question 9

polar, uncharged R groups

Answer 9

Serine
Threonine
Cysteine
Asparagine
Glutamine

Question 10

Classified as amides
* Neither acidic or basic
* Forms H-bonds
* Asn can be modified with sugars to
form glycoproteins

Answer 10

Asparagine (N, Asn) and Glutamine (Q,
Gln)

Question 11

Sulfhydryl side chain (-SH) (gives the polarity)
* Can oxidize to form disulfide bonds that strengthen protein structure
* Disulfide bonds are covalent but reversible upon reduction

Answer 11

Cysteine (C, Cys)

Question 12

positive charged R group

Answer 12

Lysine
Arginine
Histidine

Question 13

UV absorbing at 250-300 nm – can be useful to
identify proteins in a mixture

Answer 13

phenylalanine
tyrosine
tryptophan

Question 14

Side chains gain a proton at
physiological pH (Positively
charged)

Answer 14

Lysine
Arginine
Histidine

Question 15

negatively charged R group

Answer 15

Aspartate
Glutamate

Question 16

is ionizable at physiological pH; therefore can act as a proton donor or acceptor depending on the pH surrounding.

Answer 16

histidine

Question 17

Found in collagen, the principle component of
connective tissue.

Answer 17

Hydroxyproline and hydroxylysine

Question 18

modified after incorporation ,Modifications essential for maintaining normal
connective tissues in tendons, cartilage,
bones, teeth, skin

Answer 18

Proline and lysine

Question 19

The release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy

Answer 19

Hydrophobic effect

Question 20

Interaction of N−H and C=O of the peptide bond leads to local regularstructures such as
alpha helices and beta sheets

Answer 20

Hydrogen bonds

Question 21

Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein

Answer 21

London dispersion

Question 22

long-range strong interactions between permanently charged groups
* Salt bridges, especially those buried in the hydrophobic environment, strongly stabilize the protein

Answer 22

Electrostatic interactions

Question 23

a resonance hybrid of two canonical structures

Answer 23

peptide bond

Question 24

spherical proteins that are folded into a three-dimensional structure

Answer 24

globular protein

Question 25

covalent chemical bond that forms between the carboxyl group (COOH) of one amino acid and the amino group (NH2) of another amino acid, resulting in the formation of a dipeptide.

Answer 25

peptide bond

Question 26

is formed by the assembly of individual polypeptides into a larger functional cluster.

Answer 26

quaternary structure

Question 27

Loss of structural integrity with accompanying loss of activity is called

Answer 27

denaturation

Question 28

are composed of different motifs folded together.

Answer 28

Globular proteins

Question 29

is the main protein in silk from moths and spiders

Answer 29

Fibroin

Question 30

superstructures are formed by cross-linking of collagen triple-helices to form collagen fibrils.

Answer 30

collagen

Question 31

are covalent bonds between Lys or HyLys, or His amino acid residues.

Answer 31

crosslink

Question 32

occur frequently whenever strands in beta sheets change the direction

Answer 32

beta turns

Question 33

__ in position 2 or__ in position 3 are common in beta turns

Answer 33

Proline glycine

Question 34

beta turn is stabilized by ____from a carbonyl oxygen to amide proton three residues down the sequence

Answer 34

hydrogen bond

Question 35

In ___ beta sheets, the H-bonded strands run in opposite directions

Answer 35

antiparallel

Question 36

In beta sheets, the H-bonded strands run in the same direction

Answer 36

parallel

Question 37

The ____ is a planarity of the peptide bond and tetrahedral geometry of the alpha carbon create a pleated sheet-like structure

Answer 37

Beta sheet

Question 38

acts as a helix breaker because the rotation around the N-Ca (φ-angle) bond is impossible

Answer 38

proline

Question 39

acts as a helix breaker because the tiny R group supports other conformations

Answer 39

Glycine

Question 40

Small hydrophobic residues such as Ala and Leu are

Answer 40

strong helix formers

Question 41

Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n + 4 amino acids

Answer 41

alpha helix

Question 42

stabilized by hydrogen bonds between nearby residues

Answer 42

alpha helix

Question 43

stabilized by hydrogen bonds between adjacent segments that may not be nearby

Answer 43

beta sheets

Question 44

secondary structure

Answer 44

α-helix β-sheet β-turns role of hydrogen bonding

Question 45

Tertiary structure

Answer 45

α-keratine collagen silk fibroin

Question 46

the process by which a protein molecule assumes its three-dimensional structure or conformation, typically referred to as its native state

Answer 46

protein folding

Question 47

are proteins or segments of proteins that lack a stable three-dimensional structure under physiological conditions

Answer 47

Intrinsically disordered proteins

Question 48

a natural protein fiber produced by certain insects, primarily silkworms, and spiders.

Answer 48

silk fibroin

Question 49

a fibrous structural protein found in the skin, hair, nails, feathers, and horns of vertebrates, including mammals, birds, reptiles, and amphibians

Answer 49

α-keratine

Question 50

the most abundant protein in the human body and is found in connective tissues such as tendons, ligaments, skin, cartilage, bones, and blood vessels

Answer 50

collagen

Question 51

are secondary structural elements found in proteins. They are characterized by a tight turn in the polypeptide chain that reverses the overall direction of the backbone.

Answer 51

beta turns

Question 52

is a common secondary structure motif found in proteins.

Answer 52

beta sheet

Question 53

a common secondary structure motif found in proteins. It is characterized by a right-handed coil or helix in which the backbone of the polypeptide chain forms hydrogen bonds between the carbonyl oxygen of one amino acid residue and the amide hydrogen of an amino acid residue four positions down the chain.

Answer 53

α-helix

Question 54

a chemical method used to determine the amino acid sequence of a peptide or protein

Answer 54

Edman degradation

Question 55

a monomer refers to a single unit of a protein chain, which is typically an individual amino acid

Answer 55

Monomer

Question 56

refers to a molecule composed of a few (usually a small number) of monomer units linked together.

Answer 56

Oligomer