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BIO130—sec 1 MR > week 2 > Flashcards

week 2 Flashcards

1
Q

what is the primary sequence of a protein?

A

The a.a. sequence, most simple

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2
Q

what is the secondary structure of a protein?

A

local folding i.e. alpha helix, beta sheet

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3
Q

what is the tertiary structure of a protein?

A

long-range folding, 3D structure, overall shape

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4
Q

what is the quaternary structure of a protein?

A

multi-metric organization

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5
Q

what proteins have a quaternary structure?

A

proteins that have more than one polypeptide chain

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6
Q

what part of the amino acid structure is variable and determines the type of amino acid?

A

The R group (side chain)

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7
Q

what are the four major categories of amino acids?

A

acidic, basic, (both important to overall structure) uncharged polar (H-bond in water), nonpolar (often found in interior of protein and lipid bilayer)

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8
Q

why is cysteine a unique amino acid?

A

due to -SH grp, it can form disulphide bonds (disulphide bridges)

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9
Q

To form a peptide bond, what groups react?

A

The carboxyl group on one a.a. and the amino group on another a.a

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10
Q

What type of reaction forms a peptide bond

A

condensation reaction (releases water)

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11
Q

what does ‘residue’ refer to?

A

a.a. w/n peptide chain (what is left over after loss of H2O)

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12
Q

How many H-bonds are there in a alpha helix for each residue?

A

n+4

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13
Q

where are some common places that alpha helices are found?

A

skin, hair, cell membranes (lipid bilayer)

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14
Q

approximately how many residues long is an alpha helix?

A

10

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15
Q

what kind of bonding is associated with an alpha helix?

A

local H-bonding

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16
Q

Where does H-bonding occur in a beta sheet?

A

between the carbonyl oxygen of one a.a. and the amide hydrogen of an a.a. in a NEIGHBOURING strand

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17
Q

Are R groups involved in structure of beta sheet

A

no

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18
Q

how many beta strands does a beta sheet usually contain

A

4-5 (can contain up to 10)

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19
Q

why can alpha helices and beta sheets form from many types of a.a. sequences?

A

R-grps are not involved

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20
Q

what is the difference in bonding between an alpha helix and a beta sheet

A

alpha helix forms bonds between a.a. four residues away, beta sheet forms bonds b/w neighbouring strands

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21
Q

What are the two types of beta sheet?

A

parallel and anti-parallel

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22
Q

In beta sheet diagrams, where do the arrows point

A

towards the carboxyl end of protein/strand

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23
Q

which type of beta sheet needs more a.a. between strands?

A

parallel

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24
Q

which atoms are hydrogen bonded in secondary structures?

A

carbonyl oxygen & amide hydrogen—in peptide backbone, not R grp

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25
Q

What kind of secondary structure is a coiled coil?

A

amphipathic alpha helix

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26
Q

amphipathic

A

has both hydrophobic and hydrophilic parts

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27
Q

why are coiled coils amphipathic?

A

non-polar a.a. forma stripe down the helix

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28
Q

where are coiled coils found?

A

alpha-keratin of skin, hair and also myosin motor proteins

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29
Q

where does the hydrophilic end of a coiled coil face?

A

aqueous environment

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30
Q

what level of protein structure are alpha helix, beta sheet, and coiled coil?

A

secondary structure

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31
Q

what holds together the tertiary structure of a protein?

A

hydrophobic interactions, non-covalent bonds, covalent disulphide bonds

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32
Q

what conformation do proteins generally fold into?

A

The most energetically favourable conformation

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33
Q

what do chaperone proteins do?

A

help make the protein folding process more efficient and reliable.

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34
Q

are electrostatic interactions involved in tert. structure?

A

yes

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35
Q

Protein domains are a portion of a protein that has its own ________________

A

tertiary structure

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36
Q

protein domains function in a __________________ manner

A

semi-independent

37
Q

how many protein domains do eukaryotic proteins often have

A

2 or more

38
Q

how are protein domains connected

A

intrinsically disordered sequences (allow flexibility, conformation can change)

39
Q

what are protein domains specialized for?

A

different functions

40
Q

What are protein domains important for?

A

the evolution of proteins

41
Q

what do kinases do?

A

they phosphorylate proteins (add on a phosphate grp)

42
Q

How many protein domains does Src protein kinase have? List them

A

Three: kinase domain, SH3, SH2 (regulates)

43
Q

what similarities to members of the same protein family share?

A

similar aa sequences and tertiary structures

44
Q

what have members of the same protein family evolved to have differently?

A

different functions (but related)

45
Q

most proteins belong to families with similar structural _____________

A

domains

46
Q

protein families are groups of proteins with common

A

evolutionary origin

47
Q

domains are added if useful through

A

natural selection

48
Q

how many subunits does hemoglobin have? Name them.

A

4: 2 alpha, 2 beta

49
Q

each subunit of hemoglobin is a separate ____________

A

polypeptide

50
Q

sickle cell anemia is caused by ______________ in hemoglobin

A

mutation in the beta subunit

51
Q

hemoglobin is an example of a protein with ____________ structure

A

quaternary (it has more than one pp chain)

52
Q

multi protein complexes can be:

A

many identical subunits, mixtures of different proteins and DNA/RNA, dynamic assemblies of proteins to form molecular machines

53
Q

what is an example of a multiprotein complex with identical subunits

A

actin filaments

54
Q

what is an example of a multiprotein complex with different proteins and DNA/RNA

A

viruses and ribosomes

55
Q

what is an example of a molecular machine

A

machines for DNA replication initiation or for transcription

56
Q

what is scaffold?

A

an entity (usually protein but can be RNA) that binds proteins and gets them in close enough proximity that they can interact

57
Q

pros and cons of AI being used to predict protein structure

A

very powerful, speeding up the study of proteins, not perfect

58
Q

what is proteomics

A

large scale study of proteins (looking at interactome): identity and structure of proteins, protein-protein interactions, abundance and turnover, location in cell or tissue

59
Q

what stabilizes the positive charge in some side chains?

A

resonance: causes greater basicity (basic side chains have a positive charge)

60
Q

when are both amino and carboxyl grps ionized

A

at a neutral pH (7)

61
Q

what is the result of the alpha carbon being asymmetric?

A

Allows for L and D isomers

62
Q

what atoms are involved in a peptide bond

A

C, N (bond is b/w them), carbonyl O, amine H

63
Q

is there rotation around the C-N bond

A

no, the four atoms in a peptide bond form a rigid planar unit

64
Q

why are long chains of aa flexible

A

single bonds b/w Cs allow for rotation

65
Q

what charge do acidic side chains have?

A

negative

66
Q

what groups do uncharged polar side chains have on their end

A

either -NH2 or -OH

67
Q

nonpolar side chain primary consist of __________

A

hydrocarbons

68
Q

every molecule of a protein has the exact same _________

A

amino acid sequence

69
Q

The polypeptide backbone is formed from a repeating sequence of what core atoms?

A

N-C-C

70
Q

what gives each aa its unique properties

A

side chains

71
Q

why is the folding process energetically favourable?

A

it releases heat

72
Q

how can a protein be denatured/unfolded?

A

with solvents that disrupt the noncovalent interactions holding the chain together

73
Q

renaturation

A

when a protein refolds spontaneously (will often happen under right conditions)

74
Q

can proteins fold into their correct conformation w/o the help of chaperone proteins?

A

yes

75
Q

isolation chambers

A

formed by chaperone proteins, where a single polypeptide chain can fold w/o the risk of forming aggregates in the crowded conditions of the cytoplasm

76
Q

amyloid structures

A

beta sheets stacked together in long rows with their aa side chains interdigitated (like the teeth of a zipper), sometimes formed from misfolded proteins

77
Q

what disorders are amyloid structures thought to contribute to?

A

neurodegenerative disorders e.g. Alzheimer’s and Huntington’s disease

78
Q

what can misfolded prions do?

A

convert properly folded version of a protein to the abnormal conformation

79
Q

why are prions considered infectious

A

they can spread from an affected individual to a normal individual

80
Q

the modular unit from which many larger proteins are constructed is called

A

protein domain

81
Q

Binding site

A

any region on a protein’s surface that interacts with another molecules through sets of noncovalent bonds

82
Q

what happens when a binding site recognizes the surface of a second protein?

A

the tight binding of the two folded pp chains (subunits) at this site will create a larger protein

83
Q

Dimer

A

a symmetrical complex of two protein subunits formed from the folding of two identical pp chains

84
Q

what holds dimers together?

A

interactions b/w two identical binding sites

85
Q

pp chain folded up into a compact shape like a ball with an irregular surface is called

A

globular protein

86
Q

fibrous proteins

A

span a large distance, relatively simple elongated 3-D structure

87
Q

gel-like, formed from fibrous proteins, helps bind cells together to form tissues

A

extracellular matrix

88
Q

how are extracellular proteins stabilized?

A

covalent cross linkages

89
Q

what happens inside the nucleolus

A

ribosomal RNAs are transcribed and ribosomal subunits are assembled

BIO130—sec 1 MR (5 decks)

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