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BIO107 - Cell and Molecular Biology > Proteins > Flashcards

Proteins Flashcards

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1
Q
A
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1
Q

DNA

A
  • software
  • nucleotides chemically similar
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2
Q

proteins

A
  • hardware
  • amino acids chemically distinct
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3
Q

building blocks of proteins

A

amino acids

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4
Q

general structure of amino acids

A
  • amino group
  • R side chain
  • carboxyl group
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5
Q

zwitterionic form of the general structure of amino acids

A
  • NH+
  • COO-
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6
Q

no. of common amino acids

A

20

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7
Q

variation in R groups

A
  • size
  • shape
  • charge
  • polarity
  • solubility
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8
Q

groups of different amino acids

A
  1. polar, uncharged
  2. nonpolar, hydrophobic
  3. electrically charged
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9
Q

R group of polar, uncharged amino acids

A
  1. OH
  2. amide
  3. sulfhydryl/thiol groups
  4. can H-bond with water
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10
Q

where are polar, uncharged amino acids found

A

surface of globular proteins

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11
Q

where are polar, uncharged amino acids soluble

A

aqueous solutions

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12
Q

what are the polar, uncharged amino acids

A
  1. serine
  2. threonine
  3. cysteine
  4. asparagine
  5. glutamine
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13
Q

R group of non-polar, hydrophobic amino acids

A
  • aliphatic
  • aromatic
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14
Q

where are non-polar, hydrophobic amino acids found

A

interior of globular proteins

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15
Q

core of non-polar, hydrophobic amino acids

A

insoluble core

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16
Q

what are the non-polar, hydrophobic amino acids:

aliphatic

A
  1. glycine
  2. alanine
  3. proline
  4. valine
  5. leucine
  6. isoleucine
  7. methionine
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17
Q

what are the non-polar, hydrophobic amino acids:

aromatic

A
  1. phenylalanine
  2. tyrosine
  3. tryptophan
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18
Q

what are the negatively charged R groups

A
  1. aspartate
  2. glutamate
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19
Q

what are the postively charged amino acids

A
  1. lysine
  2. arginine
  3. histidine
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20
Q
  • formed by dehydration synthesis
  • allows free rotation of attached atoms
  • various shapes of the polypeptide
A

peptide bond

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21
Q

how are peptide bonds formed

A

by dehydration synthesis

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22
Q

unbranched chain of amino acids

A

polypeptide chain

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23
Q

how many amino acid chains are there to be considered as a polypeptide chain

A

> 10 amino acids

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24
Q

may consist of one or more polypeptide chains

A

protein

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25
Q

directionality of polypeptide chains

A

N-terminus to C-terminus

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26
Q

levels of protein structure

A
  1. amino acid residues
  2. α Helix
  3. polypeptide chain
  4. assembled subunits
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27
Q

sequence of amino acids linked together by peptide bonds, forming a polypeptide

A

primary structure

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28
Q

local regions of the resulting polypeptide can then be coiled into an α helix

A

secondary structure

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29
Q
  • regions of secondary structure associate with each other in a specific manner
  • describes the final folding of the polypeptide
A

tertiary structure

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30
Q

association of two or more polypeptides as they interact to form the final, functional protein

A

quaternary structure

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31
Q

aa sequence ->

A

3D structure (non-covalent bonds) -> cellular function

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32
Q

where did the mutation happen in sickle cell anemia

A

codon 6 of beta-globin

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33
Q

organization in secondary structure

A

localized organization

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34
Q

stabilizes the secondary structure

A

hydrogen bonds

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35
Q

where does the hydrogen bond stabilize in secondary structure

A
  1. between 2 peptide bonds
  2. between peptide bond and side chain
  3. between 2 side chains
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36
Q
  • spiral
  • each turn has 3.6 amino aicds
  • symbolized by barrel/rod/coiled ribbons
  • most common secondary structure
A

α-helix

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37
Q

amount of amino acids in each turn of α-helix

A

3.6 aa

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38
Q

symbolizes α-helix

A

barrel/rod/coiled ribbons

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39
Q

stabilizes α-helix

A

almost linear hydrogen bonds

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40
Q

where is the hydrogen bond in α-helix

A

between NH and CO groups

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41
Q

linkages in α-helix

A

disulfide linkages (S-S) (cysteine aa)

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42
Q

eg. of α-helix

A

α-keratin in hair

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43
Q

most common type of secondary structure

A

α-helix

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44
Q
  • peptide planes are arranged like a regularly sheet/pleated
  • h-bonds can only form between neighboring chains within a sheet
  • symbolized by arrow
  • strength and stability in structural proteins
A

β pleated sheet

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45
Q

how are β pleated sheet arranged

A

regularly sheet/pleated

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46
Q

where do hydrogen bonds form in β pleated sheet

A

between neighboring chains within a sheet

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47
Q

symbolizes β pleated sheet

A

arrow

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48
Q

purpose of β pleated sheet

A

strength and stability of structural proteins

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49
Q

eg. of β pleated sheet

A

silk fibroin

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50
Q
  • U-shaped
  • reverses direction of peptide chain
  • for building compact globular protein
  • usually glysine (small R side chain) or proline (with built-in bend)
A

β-turn or β-bend

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51
Q

shape of β-turn or β-bend

A

U-shaped

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52
Q

what do β-turns do

A

reverses direction of peptide chain

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53
Q

no. of amino acids in β-turn

A

~4 aa

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54
Q

purpose of β-turn or β-bend

A

building compact gobular protein

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55
Q

amino acids that are usually associated with β-turns

A
  1. glysine (small side chain)
  2. proline (with built-in bend)
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56
Q

small side chain

A

glysine

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57
Q

with built-in bend

A

proline

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58
Q
  • important constituents of the connective tissue matrix
  • stabilized by the associateion of 3 α helices to form a right-handed collagen triple helix
A

collagen helix

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59
Q

imporance of collagen helix

A

constituents in connective tissue matrix

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60
Q

stabilizes collagen helix

A

3 α helices

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61
Q

what is formed by the 3 α helices

A

right-handed collagen triple helix

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62
Q
  • the 3d/overall conformation of a polypeptide chain
  • stabilized by hydrophobic interactions
  • highest level of organization of large proteins
A

teritary structure

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63
Q

stabilizes tertiary structures

A

hydrophobic interactions

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64
Q

Two general shapes of tertiary structures

A
  1. fibrous proteins
  2. globular proteins
65
Q
  • polypeptide chains are arranged or coiled around a single dimension often in parallel bundles
  • for exteral protection and support, form, shape
A

fibrous proteins

66
Q

how are fibrous proteins arranged

A

around a single dimension often in parallel bundles

67
Q

eg. of fibrous proteins

A
  1. keratin
  2. collagen
68
Q

functions of fibrous proteins

A
  1. external support
  2. support, form, shape
69
Q

external support

A
  • hair
  • feather
  • skin
  • nail
  • horn
70
Q

support, form, shape

A
  • tendons
  • cartilage
  • bone
  • deeper layers of skin
71
Q

fiber used to make silk cloth

A

protein fibroin

72
Q

consists of layers of antiparallel beta sheets rich in ala and gly residues

A

fibroin

73
Q
  • polypeptide chains are tightly folded into compact 3D structure
  • more complex than fibrous proteins
A

globular proteins

74
Q

how are globular proteins folded

A

compact 3D structure

75
Q

eg. of globular proteins

A
  • enzymes
  • globin proteins
76
Q

location of amino acids in globular proteins

A
  1. exterior
  2. interior
  3. both interior and exterior
77
Q

exterior aa

A

hydrophilic/polar aa

78
Q

interior aa

A

hydrophobic/nonpolar aa

79
Q

amino acids that are both interior and exterior

A
  1. pro
  2. ser
  3. ala
  4. tyr
  5. thr
  6. cys
  7. gly
80
Q

forces that stabilize the tertiary structure of globular proteins

A
  1. hydrogen bonds
  2. ionic interactions
  3. hydrophobic interactions
  4. covalent cross linkages
81
Q

hydrogen bond in tertiary structure of globular proteins

A

between R groups of aa residues in adjacent loop of chain

82
Q

ionic interactions in tertiary structure of globular proteins

A
  • oppositely charged R groups
  • R group and water
  • R group and ions
83
Q

eg. of covalent cross linkages in tertiary structure of globular proteins

A

disulfide bonds

84
Q

general principle of secondary structure

A

determined by short range sequences of R groups

85
Q

general principle of tertiary structure

A

conferred by longer range aspects of aa sequence

86
Q

determines the formation of bends in polypeptide chain

A

precise location of aa

87
Q

quaternary structure:
the number of relationships of sub-units in a __ protein

A

multimeric

88
Q

biological functions of proteins

A
  1. enzyme
  2. transport
  3. storage
  4. contractile or motile
  5. structural
  6. defense
  7. regulatory proteins
  8. allosteric proteins
89
Q

eg. enzyme

A
  • ribonuclease
  • spliceosome
  • replisome
90
Q

eg. transport protein

A
  • hemoglobin
  • myoglobin
  • lipoprotein
91
Q

eg. storage protein

A
  • gliadin (wheat)
  • ovalbumin (egg)
  • casein (milk)
92
Q

eg. contractile or motile protein

A
  • actin
  • myosin
  • tubulin
93
Q

eg. structural protein

A
  • keratin
  • fibroin
  • collagen
  • elastin
  • proteoglycans
94
Q

eg. defense proteins

A
  • antibodies
  • fibrinogen
  • snake venom
95
Q

eg. regulatory proteins

A
  • insulin
  • growth hormone
  • repressors
  • transcription factors
96
Q

eg. allosteric proteins

A

have 2 or more slightly diff. conformations which can havve alternative functions

97
Q

apoenzyme+cofactor

A

holoenzyme

98
Q

protein portion

A

apoenzyme

99
Q

non-protein portion

A

cofactor

100
Q
  • where substrate binds to
  • formed by aa whose side chains have two principal roles
A

active site of enzyme

101
Q

two principal roles of aa side chains that form the active site

A
  1. contact residue
  2. catalytic residue
102
Q
  • attract and orient the substrate in a specific way
  • determines substrate specificity
A

contact residue

103
Q

what does the contact residue determine

A

substrate specificity

104
Q
  • participate in the formation of temporary bonds with substrate
  • triggers catalytic change/events
A

catalytic residue

105
Q

what does the catalytic residue trigger

A

catalytic change/events

106
Q

enzymes that exist in alternative conformations

A

allosteric enzymes

107
Q

two binding sites of allosteric enzymes

A
  1. active site
  2. allosteric/effector site
108
Q

site for substrate

A

active site

109
Q

site for regulatory molecule

A

allosteric/effector site

110
Q

where are allosteric enzymes involved in

A
  • cell signaling
  • regulation of metabolism
111
Q

multiple forms of an enzyme

A

isozymes or isoenzymes

112
Q

isozymes have same __, different __

A

same reaction, different aa sequence

113
Q

example of isozyme

A

lactate dehydrogenase

114
Q

protein structure determines its interaction with other molecules

A
  1. protein-protein interaction
  2. protein-RNA
  3. protein-DNA
  4. protein-drug or chemical
115
Q
  • regular combination of secondary structure that has a particular topology
  • organized into a characteristic 3D structure
A

motif

116
Q

Motifs of DNA-binding proteins that regulate transcription

A
  1. zinc finger
  2. helix-turn-helix
  3. leucine zipper
  4. helix-loop-helix
  5. copper fist
117
Q

fingerlike projection consisting of ~30aa

A

zinc finger

118
Q

two types of zinc finger

A
  1. 2 cys + 2 his (C2H2 finger)
  2. 4 cys (C4 finger)
119
Q

coordinate a single zinc ion

A

2 cys + 2 his (C2H2 finger)

120
Q

regulatory protein transcription

A

4 cys (C4 finger)

121
Q

interacts with major groove of DNA

A

alpha helix

122
Q

structure of zinc finger

A
  • 2 beta strands
  • 1 alpha helix
123
Q

function of zinc finger

A

binding in the major groove of the DNA

124
Q
  • 2 alpha helixes + 1 beta turn
  • recognition helix binds specific sequence in the major groove of the DNA while the second helix stabilizes the configuration
A

helix-turn-helix

125
Q

structure of helix-turn-helix

A
  • 2 alpha helixes
  • 1 beta turn
126
Q

two parts of helix-turn-helix motif

A
  1. recognition helix
  2. second helix
127
Q

helix-turn-helix:
binds specific sequence in the major groove of the DNA

A

recognition helix

128
Q

helix-turn-helix:
stabilizes the configuration

A

second helix

129
Q
  • contains a leucine every 7th aa
  • amphiphatic helix
  • form dimers (homo- or hetero-)
A

leucine zipper

130
Q

there is leucine in every __ aa in leucine zipper

A

7th

131
Q

each monomer in leucine zipper contain:

A
  1. dimerization domain
  2. DNA-binding domain
132
Q

dimerization domain

A

C-terminal (leu-rich)

133
Q

DNA-binding domain

A

N-terminal (rich in basic aa)

134
Q

each monomer with dimerization domain and DNA-binding domain

A

helix-loop-helix

135
Q

almost all in the DNA-binding domain are __ aa

A

basic

136
Q
  • first structure formed around 8 Cu ions which interact with cys residues on the protein
  • knuckles contain basic aa that interact with DNA
A

copper fist

137
Q

where does the copper fist motif interact

A

cys residues on protein

138
Q

contain basic aa that interact with DNA in copper fist

A

knuckles

139
Q

function of copper fist

A
  • electron transfer
  • redux reduction
  • stabilization of protein
140
Q
  • small proteinaceous infectious particles
  • no nucleic acid
  • neurodegenerative disease in mammals
A

prions

141
Q

post mortem brain with large vacuoles in the cortex and cerebellum

A

Spongiform Encephalopathy or Prion Disease

142
Q

where prions were first discovered

A

scrapie in sheep

143
Q

who first discovered prions

A

Stanley Prusiner (1892)

144
Q

prion disease:
mink

A

transmissible mink encephalopathy

145
Q

prion disease:
muledeer, elk

A

chronic wasting disease

146
Q

prion disease:
cows

A

bovine spongiform encephalopathy

147
Q

prion disease:
humans

A

Creutzfeldt-Jakob disease

148
Q

early stages of prion disease

A
  1. loss of muscle control
  2. personality changes
  3. impaired memory, judgement, thinking
  4. impaired vision
  5. insomnia
  6. depression
  7. dementia/insanity
149
Q

later stages of prion disease

A
  1. involuntary muscle jerk
  2. blindness
  3. paralysis, wasting
  4. coma
  5. death, typically following pneumonia
150
Q

visible end results at post mortem of prion disease

A
  1. non-inflammatory lesions
  2. vacuoles
  3. amyloid protein deposits
  4. astrogliosis
151
Q
  • first known prion disease
  • geographically isolated tribes in the highlands of New Guinea
  • by ingesting brain tissue of dead relatives for religious reasons
A

Kuru

152
Q

a prion is a modified form of __

A

PrPc (prion protein cellular)

153
Q

where are prions encoded

A

single exon of single copy located at chromosome 28

154
Q

where are prions found

A

predominant on surface of neurons

155
Q

function of prions

A

synaptic function

156
Q

characteristic of prions

A
  • non-immunogenic, protease-sensitive
  • subviral agent
157
Q

modified form of PrPc

A

PrPsc (prion protein scrapie)

158
Q

where does PrPsc accumulate

A

cytoplasmic vesicles of diseased indiv.

159
Q

where PrPc is found

A

predominantly at alpha helix

160
Q

where PrPsc is found

A

predominantly at beta-sheet (mostly globular)

BIO107 - Cell and Molecular Biology (18 decks)

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