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Biochemestry unit one > exam 1exam chapter 3 and 4 > Flashcards

exam 1exam chapter 3 and 4 Flashcards

1
Q

non polar, aliphatic R groups

A

glycine
alanine
proline
valine
leucine
isoleucine
methionine

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2
Q

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

A

glycine

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3
Q

R group is CH3 (methyl group)

A

alanine

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4
Q

Extended aliphatic chains and can be branched

A

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

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5
Q

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

A

proline pro p

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6
Q

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

A

methionine Met M

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7
Q

aromatic R group

A

phenylalanine
tyrosine
tryptophan

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8
Q

Can be phosphorylated on hydroxyl groups

A

Tyrosine, Serine, and Threonine

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9
Q

polar, uncharged R groups

A

Serine
Threonine
Cysteine
Asparagine
Glutamine

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10
Q

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

A

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

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11
Q

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

A

Cysteine (C, Cys)

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12
Q

positive charged R group

A

Lysine
Arginine
Histidine

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13
Q

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

A

phenylalanine
tyrosine
tryptophan

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14
Q

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

A

Lysine
Arginine
Histidine

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15
Q

negatively charged R group

A

Aspartate
Glutamate

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16
Q

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

A

histidine

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17
Q

Found in collagen, the principle component of
connective tissue.

A

Hydroxyproline and hydroxylysine

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18
Q

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

A

Proline and lysine

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19
Q

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

A

Hydrophobic effect

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20
Q

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

A

Hydrogen bonds

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21
Q

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

A

London dispersion

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22
Q

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

A

Electrostatic interactions

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23
Q

a resonance hybrid of two canonical structures

A

peptide bond

24
Q

spherical proteins that are folded into a three-dimensional structure

A

globular protein

25
Q

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.

A

peptide bond

26
Q

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

A

quaternary structure

27
Q

Loss of structural integrity with accompanying loss of activity is called

A

denaturation

28
Q

are composed of different motifs
folded together.

A

Globular proteins

29
Q

is the main protein in silk from moths and
spiders

A

Fibroin

30
Q

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

A

collagen

31
Q

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

A

crosslink

32
Q

occur frequently whenever strands in beta sheets change the direction

A

beta turns

33
Q

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

A

Proline

glycine

34
Q

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

A

hydrogen bond

35
Q

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

A

antiparallel

36
Q

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

A

parallel

37
Q

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

A

Beta sheet

38
Q

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

A

proline

39
Q

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

A

Glycine

40
Q

Small hydrophobic residues such as Ala and Leu are

A

strong helix formers

41
Q

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

A

alpha helix

42
Q

stabilized by hydrogen bonds between nearby residues

A

alpha helix

43
Q

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

A

beta sheets

44
Q

secondary structure

A

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

45
Q

Tertiary structure

A

α-keratine
collagen
silk fibroin

46
Q

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

A

protein folding

47
Q

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

A

Intrinsically disordered proteins

48
Q

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

A

silk fibroin

49
Q

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

A

α-keratine

50
Q

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

A

collagen

51
Q

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.

A

beta turns

52
Q

is a common secondary structure motif found in proteins.

A

beta sheet

53
Q

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.

A

α-helix

54
Q

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

A

Edman degradation

55
Q

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

A

Monomer

56
Q

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

A

Oligomer

Biochemestry unit one (6 decks)

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