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BIOCHEM LEC > MOD 2 L2 > Flashcards

MOD 2 L2 Flashcards

1
Q

how many species of tRNA

A

20

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2
Q

proteins can be described in four ways

A

▫ Primary
▫ Secondary
▫ Tertiary
▫ Quaternary structure

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3
Q

the sequence of the amino acids in the chain and the disulfide links.

A

PRIMARY

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4
Q

arrangement of amino acids

A

SEQUENCE

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5
Q

peptide bond

A

PRIMARY

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6
Q

structure formed by hydrogen bonding. Examples are α-helix and β-pleated sheet.

A

SECONDARY

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7
Q

complete 3-D conformation

A

TERTIARY

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8
Q

association of two or more peptide chains to form protein.

A

QUATERNARY

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9
Q

not all amino acids undergo this structure. only hemoglobins

A

QUATERNARY

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10
Q

linear sequence of amino acids

A

PRIMARY

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11
Q

units of secondary structure
α-helix β-sheet β-turns loops

A

SECONDARY STRUCTURE

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12
Q

associations of secondary structure
α-α, β-α-β, greek key, helix-loop-helix

A

SUPERSECONDARY STRUCURE

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13
Q

units of tertiary structure
all alpha, all beta, α/β, αβ

A

DOMAIN STRUCTURE
FOLDS OR MODULES

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14
Q

associations of domain structures
multidomain (mosaic) or single domain

A

TERTIARY STRUCTURE

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15
Q

association of tertiary structure
two or more polypeptides each polypeptide a subunit

A

QUATERNARY STRUCTURE

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16
Q

The primary structure of a protein is its linear sequence of amino acids and the location of any ____

A

DISULFIDE BRIDGE

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17
Q

The primary structure of a protein is defined by the

A

sequence of amino acids

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18
Q

the sequence of amino acids forms the

A

PROTEIN

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19
Q

each component amino
acid

A

“residue” or “moiety”

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20
Q

number of amino acids

A

number of residues

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21
Q

describes the way that the chain of amino acids folds itself due to intramolecular hydrogen bonding.

A

SECONDARY STRUCTURE

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22
Q

Two common secondary structures

A

α-helix
β-sheet

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23
Q

how long is the typical α-helix

A

11 amino acids long

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24
Q

how many residues/turn in α-helix

A

3.6

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25
Q

Amino acids such as A, D, E, I, L and M (small aminoa acids) favor the formation of

A

α-helices

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26
Q

favor disruption of the helix (producing a bend)

A

G & P

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27
Q

The ____ is important as it introduces additional folding of the polypeptide backbone to allow the formation of globular proteins.

A

DISRUPTION OF THE HELIX

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28
Q

1 complete rotation

A

0.54 nm
3.6 residues

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29
Q

Cα-N bond is termed

A

phi angle

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30
Q

phi Φ angle

A

-57º

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31
Q

CO-Cα bond is termed

A

psi angle

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32
Q

psi ψ angle

A

-47º

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33
Q

fibrous protein whose structure is nearly entirely α-helical

A

KERATIN

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34
Q

a globular, flexible molecule whose structure is approximately 80% α-helical.

A

HEMOGLOBIN

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35
Q

responsible for the formation of H-bonding

A

BETA PLEATED SHEET

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36
Q
  • Composed of 2 or more different regions of stretches of at least 5-10 amino acids.
  • Stabilized by H-bonding between amide N’s and carbonyl C’s.
  • H-bonding residues are present in adjacently opposed stretches of the polypeptide backbone.
A

BETA PLEATED SHEET

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37
Q

same direction

A

PARALLEL

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38
Q

different direction

A

anti-parallel

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39
Q

When the H-bonds are formed between the polypeptide backbones of separate polypeptide chain, they are termed

A

INTERCHAIN BONDS

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40
Q

The H-bonds of a β-sheet formed by a single polypeptide chain folding back on itself are termed

A

INTRACHAIN BONDS

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41
Q

Found in both fibrous and globular proteins

A

β-sheet protein

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42
Q

composed of twisted β-pleated sheet fibrils whose 3D structure is identical to that of silk fibrils.

A

AMYLOID PROTEIN

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43
Q

are regions that contain residues beyond the minimum number necessary to connect adjacent regions of secondary structure.

A

LOOPS

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44
Q

refer to short segments of amino acids that join two units of secondary structure

A

TURNS & BENDS

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45
Q

involves 4 aminoacyl residues, in which the 1st residue is H-bonded to the 4th, resulting in a 180° turn.

A

β turn

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46
Q

are often present in β turns

A

PROLINE & GLYCINE

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47
Q

Also known as Structural motifs

A

SUPERSECONDARY STRUCTURES OR FOLDS

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48
Q
  • maintains the three dimensional shape of the protein (give shape to the secondary structure).
  • The amino acid chain (in the helical, pleated or random coil form) links itself in places to form the unique twisted or folded shape of the protein.
A

TERTIARY STRUCTURE

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49
Q

ways to stabilize its tertiary shape

disulfide bridges formed when two cysteine molecules combine in which the –SH groups are oxidized

A

COVALENT BONDING

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50
Q

ways to stabilize its tertiary shape

between polar groups on the side chain.

A

HYDROGEN BONDING

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51
Q

ways to stabilize its tertiary shape

(ionic bonds) formed between –NH3+ and –COO- groups

A

SALT BRIDGES

52
Q
  • Binding of a substrate or other ligands.
  • Anchor a protein to a membrane.
  • Interact with a regulatory molecule that modulates its function.
A

FUNCTIONS OF DOMAIN

53
Q

FUNCTIONS OF DOMAIN

Binding of a ____ or other ____.

A

substrate, ligands

54
Q

FUNCTIONS OF DOMAIN

Anchor a ____ to a ___

A

protein, membrane

55
Q

FUNCTIONS OF DOMAIN

Interact with a ____ that modulates its function

A

REGULATORY MOLECULE

56
Q

These tend to form ball-like structures where hydrophobic parts are towards the center and hydrophilic are towards the edges, which makes them water soluble.

A

GLOBULAR

57
Q

The proteins form long fibers and mostly consist of repeated sequences of amino acids which are insoluble in water.

A

FIBROUS

58
Q
  • Favor protein folding
  • Between oppositely charged R-groups such as K or R and D or E.
A

CHARGE-CHARGE

59
Q
  • Interaction of ionized R-groups of amino acids with the dipole of the water molecule.
A

CHARGE-DIPOLE

60
Q
  • The slight dipole moment that exist in the polar R-groups of amino acid also influences their interaction with water.
  • Majority of the amino acids found on the exterior surfaces of globular proteins contain charged or polar R-groups.
A

DIPOLE-DIPOLE

61
Q

involve the interactions among induced dipoles that arise from fluctuations in the charge densities that occur between adjacent uncharged non-bonded atoms.

A

ATTRACTIVE VAN DER WAALS FORCES

62
Q

involve the interactions that occur when uncharged non-bonded atoms come very close together but do not induce dipoles.

A

REPULSIVE VAN DE WAALS

63
Q

only proteins with more than one chain have a

A

QUATERNARY STRUCTURE

64
Q

Many proteins are not

A

SINGLE STRANDS

65
Q

proteins with multiple polypeptide chains; can be composed of multiple identical polypeptide chains or multiple distinct polypeptide chains.

A

OLIGOMERIC PROTEINS

66
Q

oligo means

A

FEW

67
Q

proteins with identical subunits

A

HOMOOLIGOMERS

68
Q

proteins containing several distinct polypeptide chains.

A

HETEROOLIGOMERS

69
Q
  • The oxygen carrying protein of the blood.
  • Contains two α and two β subunits arranged with a quaternary structure in the form, α2β2
A

HEMOGLOBIN

70
Q

hemoglobin is a ____ protein

A

HETEROOLIGOMERIC

71
Q

Protein fold and unfold in

time

A

milliseconds

72
Q

participate the first time the protein is folded, but not in subsequent folding

A

RIBOSOMES

73
Q

Information needed for correct protein folding is contained in the

A

PRIMARY STRUCTURE

74
Q

Native conformation of a protein is ____ favored

A

THERMODYNAMICALLY

75
Q

Folding is

A

MODULAR

76
Q

assist folding

A

AUXILLARY PROTEINS

77
Q
  • Specialized group of protein required for the proper folding of many species of proteins.
  • PCB (Polypeptide chain-binding) protein.
  • Acts as catalysts by increasing the rates of the final stage in the folding process.
A

CHAPERONES

78
Q
  • Do not convey steric information.
  • Do not form part of the final structure.
  • Suppress non-productive interactions by binding to transiently exposed portions of the polypeptide chain.
  • First identified as heat shock proteins (Hsp).
  • Hsp expression is elevated when cells are grown at higher-than-normal temperatures.
  • Use an ATP-dependent mechanism.
A

CHAPERONES

79
Q

chaperones are first identified as

A

HEAT SHOCK PROTEINS

80
Q

HSP expresion is elevated when cells are grown at

A

higher than normal temp

81
Q

TYPES OF CHAPERONES

  • thought to bind and stabilize the nascent polypeptide chain as it is being extruded from the ribosome.
  • also involved in “pulling” newly synthesized polypeptide into ER lumen.
  • bind short sequences of
    hydrophobic amino acids thus,
    shielding them from solvent.
A

HSP70 (cytoplasm, ER,
chloroplasts, mitochondria)

82
Q

TYPES OF CHAPERONE

forms large 28-subunit
complexes called GroEL

A

HSP60 (mitochondria,
chloroplasts)

83
Q

provides a sheltered environment in which a polypeptide can fold until all hydrophobic regions are buried in its interior, thus eliminating aggregation.

A

CHAPERONINS

84
Q

Facilitates formation of disulfide bonds that stabilize a protein’s native conformation.

A

PROTEIN DISULFIDE ISOMERASE

85
Q

“rescue” unfold proteins

A

CHAPERONE

86
Q

reduces inappropriate disulfide bond

A

GLUTATHIONE

87
Q
  • Disruption of the normal structure of a protein, such that it loses biological activity.
  • Some proteins will return to their native structures under proper conditions; but extreme conditions, such as strong heating, usually cause irreversible change.
A

PROTEIN DENATURATION

88
Q

Changes in temperature & pH can denature ____ a protein so it no longer works.

A

UNFOLD

89
Q

facilitates proper folding

A

SECONDARY STRUCTURE

90
Q

group of enzyme that can catalyze interconversion from cis to trans

A

ISOMERASE

91
Q

Cis configuration is commonly found in

A

β-turns

92
Q

loss of biological activity

A

DENATURATION

93
Q

regain biological activity

A

RENATURATION

94
Q

regain biological activity

A

RENATURATION

95
Q

unfolding and disorganization of protein structure (not accompanied by hydrolysis of peptide bond)

A

PROTEIN DENATURATION

96
Q

what is being destroyed by the denaturants?

A

HYDROGEN BONDS

97
Q

PD AGENTS

hydrogen bonds are broken by increased translational and vibrational energy. (coagulation of egg white albumin on frying)

A

HEAT

98
Q

PD AGENT

Similar to heat
(sunburn)

A

ULTRAVIOLET RADIATION

99
Q

PD AGENT

salt formation; disruption of hydrogen bonds. (skin blisters and burns, protein precipitation.)

A

STRONG ACIDS OR BASES

100
Q

PD AGENTS

competition for hydrogen bonds.
(precipitation of soluble proteins.)

A

UREA

101
Q

PD AGENT

(e.g. ethanol & acetone) change in dielectric constant and hydration of ionic groups.
(disinfectant action and precipitation of protein.)

A

SOME ORGANIC SOLVENTS

102
Q

PD AGENT

shearing of hydrogen bonds.
(beating egg white albumin into a meringue.)

A

AGITATION

103
Q

Denatured proteins are often ____ and therefore precipitate from solution.

A

INSOLUBLE

104
Q

rare cases

A

reversible

105
Q

most proteins

A

PERMANENT

106
Q
  • Transmissible spongiform encephalopathies.
  • Fatal neurodegenarative diseases characterized by spongiform changes, Astrocytic gliomas, and neuronal loss resulting from the deposition of insoluble protein aggregates and neural cell.
  • Includes:
    a) Creutzfeldt-Jakob disease (Human)
    b) Scrapies (sheep)
    c) Alzheimer’s disease
    d) Bovine spongiform encephalopathy (Mad Cow Disease) in cattle
    e) Scurvy
A

PRION DISEASES

107
Q

PRION DISEASES

HUMAN

A

CREUTZFELDT-JAKOB DISEASE

108
Q

PRION DISEASE

SHEEP

A

SCRAPIES

109
Q

PRION DISEASE

CATTLE / COW

A

BOVINE SPONGIFORM ENCEPHALOPATHY / MAD COW DISEASE

110
Q
  • for cellular
  • The normal protein has its secondary structure dominated by alpha helices (probably 3 of them)
  • is easily soluble
  • is easily digested by proteases
  • is encoded by a gene designated (in humans) PRNP located on our chromosome 20.
A

PrPc

111
Q

gene designated in humans that is located in chromosome 20

A

PRNP

112
Q
  • for scrapie
  • The abnormal, disease-producing protein
  • Primary structures are identical but its secondary structure is dominated by beta conformation
  • is insoluble in all but the strongest solvents is highly resistant to digestion by proteases
  • When this comes in contact with PrPC, it converts the PrPC into more of itself
  • These molecules bind to each other forming aggregates.
A

PrPSc

113
Q

PrPc & PrPSc bind to each other and forms

A

AGGREGATES

114
Q
  • Refolding or misfolding of β - amyloid in human brain tissue.
  • Elevated levels of β - amyloid undergoes conformational transformation.
A

ALZHEIMER’S DISEASE

115
Q

Genetic defects that impair the synthesis of one polypeptide sub-units (β) of hemoglobin.

A

BETA - THALASSEMIA

116
Q

absence of one globulin, whether β or α

A

THALASSEMIA

117
Q
  • A small change in the sequence of the primary structure can have a significant impact on protein structure
  • a glutamic acid is replaced by a valine in the amino acid sequence
A

SICKLE CELL ANEMIA

118
Q

Substitution of one amino acid for another in hemoglobin causes

A

SICKLE CELL DISEASE

119
Q

a protein that causes alzheimer’s disease

A

APOLIPOPROTEIN E

120
Q

Blood sugar level is controlled by a protein called

A

INSULIN

121
Q
  • Causes the liver to uptake and store excess sugar as glycogen.
  • The cell membrane also contains proteins.
A

INSULIN

122
Q

INSULIN

help cells recognize other cells

A

RECEPTOR PROTEINS

123
Q

tags aged protein for degradation

A

UBIQUITIN

124
Q

degradation happens through

A

HYDROLYSIS

125
Q

Ribosome size

A

30s, 50s

BIOCHEM LEC (12 decks)

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