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BIO 107 - Cell and Mol. Bio > IB: Proteins > Flashcards

IB: Proteins Flashcards

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1
Q

made of long unbranched chain of these amino acids

A

Protein

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2
Q

a linear chain of amino acids

A

polypeptides

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3
Q

repeating sequence of atoms along the core of the polypeptide chains

A

Polypeptide backbone

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4
Q

give amino acids its unique properties

A

side chains

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5
Q

involved in protein folding

A

weak covalent bonds

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6
Q

Types if if weak noncovalent bonds on protein folding

A

-Hydrogen bonds
-electrostatic attrations
- Van der Waals

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7
Q

contains all the information needed for specifying the three-dimensional shape of a protein

A

amino acid sequence

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8
Q

assist in protein folding

A

Molecular chaperones

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9
Q

Common folding patterns

A
  • α helix
  • β-sheet
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10
Q

Types of folding that leads to α-helix and β-sheet folding patterns?

A

Hydrogen bonding between N-H and C=O groups

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11
Q

Types of β-sheet structures

A
  • Parallel chains
  • antiparallel chains
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12
Q

form from neighboring segments of the polypeptide backbone that run in the same orientation

A

parallel chains

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13
Q

-from a
polypeptide backbone that folds
back and forth upon itself
-each section of the chain running in the direction opposite of that of its immediate neighbors

A

Antiparallel chains

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14
Q

Formation of α-helix

A
  • when single polypeptide chain twist around on it self to form rigid cylinder
    -Hydrogen bonds between every 4th peptide
    -coiled-coil form
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15
Q

4 levels of protein structure

A
  • Primary structure
  • secondary structure
  • tertiary structure
  • Quaternary structure
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16
Q

amino acid sequence

A

primary structure

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17
Q

hydrogen
bonding of the peptide
backbone; α helices and β sheets

A

Secondary structure

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18
Q

full 3D
organization of a polypeptide chain

A

tertiary structure

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19
Q

protein
molecule formed as a complex of more than one polypeptide chain

A

Quaternary structure

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20
Q

How are protein classified?

A

Based on their tertiary structure

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21
Q

used to see structure of protein

A

X-ray crystallography

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22
Q

the basic units of proteins that can fold,
function, and evolve independently

A

Protein domains

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23
Q

process of
creating new combination of gene functional domains

A

domain shuffling

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24
Q

subset of protein domains, mobile during evolution

A

protein modules

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25
Q

only in humans, the reason why humans cant receive blood from other organisms

A

MHC (Major Histocompatibility Complex)

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26
Q

allow proteins to bind to each other to produce
structures in the cell

A

Weak noncovalent bonds

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27
Q

any region of a protein’s surface that can interact with another molecule

A

binding site

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28
Q

forming a symmetric complex of two protein subunits (dimer)

A

“Head-to-head” arrangement

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29
Q

two identical α-globin
subunits and two identical β-globin subunits, symmetrically arranged

A

Hemoglobin

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30
Q

long helical structure produced from many molecules of the protein actin

A

actin filament

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31
Q

a long chain comprised of identical protein molecule

A

Filaments

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32
Q

Why is alpha helix common?

A

All subunits are identical
- can only fit together in one way

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33
Q

Types of protein molecule shapes

A

-Fibrous protein
-Elongated protein

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34
Q

elongated three-dimensional structure

A

fibrous protein

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35
Q

example of fibrous protein

A
  • keratin filaments
  • a(alpha) keratin
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36
Q

ropelike structures;
important component of the cytoskeleton

A

intermediate filaments

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37
Q

consists of three long polypeptide chains
- each containing that nonpolar amino acid glycine at every 3rd position

A

collagen

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38
Q

Another abundant protein in ECM
- highly disordered polypeptide

A

Elastin

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39
Q

causes of disordered polypeptide chain

A
  • To form specific binding sites for other protein
  • Trigger cell signaling
  • Restrict diffusion
  • Serves as tether to hold two domains
40
Q

act as atomic staple
stabilize monomeric and multisubunit proteins

A

S-S bonds (Disulfide bonds)

41
Q

Advantages of subunits

A

-requires only small amount of genetic information
- assembly and disassembly
- error in synthesis can be avoided easily

42
Q

example of subunit

A

capsid of viruses

43
Q

made of identical protein subunits that enclose and protect viral nucleic acid

A

Capsid of viruses

44
Q

Guide construction but take no part in the final assembled structure

A

Assembly factors

45
Q

self propagating, stable β-sheet aggregates

A

amyloid fibrils

46
Q

What dangers does amyloid cause?

A
  • Alzheimers disease and other neurodegenerative illness
47
Q

may be released from dead cells and accumulate as amyloid

A

Protein aggregates

48
Q

caused by a misfolded, aggregate form of a particular protein called PrP (prion protein)

A

Prion diseases

49
Q

What does misfolded protein do?

A

convert normal PrP into abnormal conformation

50
Q

acts like a vesicle containing peptide and hormones

A

specialized “secretory granules” that consist of amyloid fibrils

51
Q

Protein functions

A
  • Contractile
  • Hormonal
  • Protection
  • Transport
  • Enzyme
  • Storage
  • Structural
  • Receptor
52
Q

each protein molecule can usually bind just one or a few molecules out of many thousands

A

Specificity

53
Q

the substance that is bound by the protein

A

Ligand

54
Q

Noncovalent bonds in proteins

A
  • Hydrogen bonds
  • Electrostatic attractions
  • Van der Waals
55
Q

the region of protein that associates with a ligand

A

Binding site

56
Q

Determines the chemistry of protein

A

Surface Conformation

57
Q

Types of Surface conformation

A
  1. Interaction of neighboring parts of polypeptide chain
  2. Clustering of neighboring polar amino acid chains
58
Q

Types of Interfaces (Protein binding)

A
  1. Surface string interaction
  2. Helix-helix
  3. Surface-surface
59
Q

Most common interface

A

Surface-surface

60
Q

binds tightly to a particular target molecule (antigen), inactivating directly or making it for destruction

A

antibody or immunoglobulins

61
Q

Shape of antibody molecules

A

Y-shaped

62
Q

cause the chemical transformations that make and break covalent bonds in cells

A

Enzymes

63
Q

speed up reactions, act as catalysts

A

Enzymes

64
Q

the maximum rate of reaction divided by the enzyme concentration

A

Turnover number

65
Q

unstable intermediate state

A

Transition state

66
Q

the free energy required to attain the transition state

A

Activation energy

67
Q

adds a molecule of water to a single bond between two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to break

A

Hydrolysis

68
Q

Add Extra Functions to Proteins

A

Tightly Bound Small Molecules

69
Q

key light-sensitive protein expressed exclusively in rod photoreceptor cells of the retina

A

Rhodopsin

70
Q

tightly related to rhodopsin, helps it to carry reaction

A

Retinal

71
Q

Gives red color in blood

A

heme group

72
Q
  • a large protein assembly
  • allows the product of enzyme A to be passed directly to enzyme B, and so on
A

multienzyme complex

73
Q

the factor that limits the reaction rate is the frequency wuth which the enzymes collides with its substrate

A

Diffusion-limited

74
Q

a product produced late in a reaction pathways inhibits an enzyme that acts earlier in the pathway

A

feedback inhibition

75
Q

prevent an enzyme from
acting

A

Negative regulation

76
Q

regulatory molecule stimulates the enzyme’s activity rather than shutting the enzyme down

A

Positive regulation

77
Q

have at least two binding sites on their surface

A

Allosteric enzymes

78
Q

Two binding site of allosteric enzymes

A
  • Active site
  • Regulatory site
79
Q

that recognizes the
substrates

A

Active site

80
Q

that recognizes a regulatory molecule

A

Regulatory site

81
Q

interaction between separated sites on a protein

A

conformational change

82
Q

can occur in multimeric proteins, where each subunit of the protein has its own ligand binding site

A

cooperative allosteric
transition

83
Q

Contains a Large Collection of Protein Kinases and Protein Phosphatases

A

Eukaryotic cell

84
Q

transfer of the terminal phosphate group of an ATP molecule to the hydroxyl group

A

Protein phosphorylation

85
Q

phosphorylates

A

Protein kinase

86
Q

phosphate removal,
dephosphorylate

A

Protein phosphates

87
Q
  • phosphate is part of guanine nucleotide GTP
  • addition and removal of phosphate
A

GTP-binding proteins

88
Q

generate forces responsible for muscle contraction and the crawling and swimming of cells

A

Motor proteins

89
Q

major function of motor proteins

A

Move other molecules, reversible

90
Q

coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein

A

unidirectional conformation changes

91
Q

function to export
hydrophobic molecules from the cytoplasm

A

ABC transporters

92
Q

are made up of individual proteins that collaborate to perform specific task

A

Protein machines

93
Q

proteins binding sites for multiple other proteins

A

Scaffold proteins

94
Q

What does scaffold proteins serve?

A
  • both to link together specific sets of interacting proteins
  • Position them at specific locations (inside a cell)
95
Q

Computer based bioinformatics tools

A

Proteomics

96
Q

protein is represented by a box or dot in two-dimensional network

A

Protein interaction map

BIO 107 - Cell and Mol. Bio (5 decks)

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