Proteins Flashcards
(161 cards)
1
Q
A
1
Q
DNA
A
- software
- nucleotides chemically similar
2
Q
proteins
A
- hardware
- amino acids chemically distinct
3
Q
building blocks of proteins
A
amino acids
4
Q
general structure of amino acids
A
- amino group
- R side chain
- carboxyl group
5
Q
zwitterionic form of the general structure of amino acids
A
- NH+
- COO-
6
Q
no. of common amino acids
A
20
7
Q
variation in R groups
A
- size
- shape
- charge
- polarity
- solubility
8
Q
groups of different amino acids
A
- polar, uncharged
- nonpolar, hydrophobic
- electrically charged
9
Q
R group of polar, uncharged amino acids
A
- OH
- amide
- sulfhydryl/thiol groups
- can H-bond with water
10
Q
where are polar, uncharged amino acids found
A
surface of globular proteins
11
Q
where are polar, uncharged amino acids soluble
A
aqueous solutions
12
Q
what are the polar, uncharged amino acids
A
- serine
- threonine
- cysteine
- asparagine
- glutamine
13
Q
R group of non-polar, hydrophobic amino acids
A
- aliphatic
- aromatic
14
Q
where are non-polar, hydrophobic amino acids found
A
interior of globular proteins
15
Q
core of non-polar, hydrophobic amino acids
A
insoluble core
16
Q
what are the non-polar, hydrophobic amino acids:
aliphatic
A
- glycine
- alanine
- proline
- valine
- leucine
- isoleucine
- methionine
17
Q
what are the non-polar, hydrophobic amino acids:
aromatic
A
- phenylalanine
- tyrosine
- tryptophan
18
Q
what are the negatively charged R groups
A
- aspartate
- glutamate
19
Q
what are the postively charged amino acids
A
- lysine
- arginine
- histidine
20
Q
- formed by dehydration synthesis
- allows free rotation of attached atoms
- various shapes of the polypeptide
A
peptide bond
21
Q
how are peptide bonds formed
A
by dehydration synthesis
22
Q
unbranched chain of amino acids
A
polypeptide chain
23
Q
how many amino acid chains are there to be considered as a polypeptide chain
A
> 10 amino acids
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may consist of one or more polypeptide chains
protein
25
directionality of polypeptide chains
N-terminus to C-terminus
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levels of protein structure
1. amino acid residues
2. α Helix
3. polypeptide chain
4. assembled subunits
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sequence of amino acids linked together by peptide bonds, forming a polypeptide
primary structure
28
local regions of the resulting polypeptide can then be coiled into an α helix
secondary structure
29
- regions of secondary structure associate with each other in a specific manner
- describes the final folding of the polypeptide
tertiary structure
30
association of two or more polypeptides as they interact to form the final, functional protein
quaternary structure
31
aa sequence ->
3D structure (non-covalent bonds) -> cellular function
32
where did the mutation happen in sickle cell anemia
codon 6 of beta-globin
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organization in secondary structure
localized organization
34
stabilizes the secondary structure
hydrogen bonds
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where does the hydrogen bond stabilize in secondary structure
1. between 2 peptide bonds
2. between peptide bond and side chain
3. between 2 side chains
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- spiral
- each turn has 3.6 amino aicds
- symbolized by barrel/rod/coiled ribbons
- most common secondary structure
α-helix
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amount of amino acids in each turn of α-helix
3.6 aa
38
symbolizes α-helix
barrel/rod/coiled ribbons
39
stabilizes α-helix
almost linear hydrogen bonds
40
where is the hydrogen bond in α-helix
between NH and CO groups
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linkages in α-helix
disulfide linkages (S-S) (cysteine aa)
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eg. of α-helix
α-keratin in hair
43
most common type of secondary structure
α-helix
44
- 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
β pleated sheet
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how are β pleated sheet arranged
regularly sheet/pleated
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where do hydrogen bonds form in β pleated sheet
between neighboring chains within a sheet
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symbolizes β pleated sheet
arrow
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purpose of β pleated sheet
strength and stability of structural proteins
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eg. of β pleated sheet
silk fibroin
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- U-shaped
- reverses direction of peptide chain
- for building compact globular protein
- usually glysine (small R side chain) or proline (with built-in bend)
β-turn or β-bend
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shape of β-turn or β-bend
U-shaped
52
what do β-turns do
reverses direction of peptide chain
53
no. of amino acids in β-turn
~4 aa
54
purpose of β-turn or β-bend
building compact gobular protein
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amino acids that are usually associated with β-turns
1. glysine (small side chain)
2. proline (with built-in bend)
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small side chain
glysine
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with built-in bend
proline
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- important constituents of the connective tissue matrix
- stabilized by the associateion of 3 α helices to form a right-handed collagen triple helix
collagen helix
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imporance of collagen helix
constituents in connective tissue matrix
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stabilizes collagen helix
3 α helices
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what is formed by the 3 α helices
right-handed collagen triple helix
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- the 3d/overall conformation of a polypeptide chain
- stabilized by hydrophobic interactions
- highest level of organization of large proteins
teritary structure
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stabilizes tertiary structures
hydrophobic interactions
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Two general shapes of tertiary structures
1. fibrous proteins
2. globular proteins
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- polypeptide chains are arranged or coiled around a single dimension often in parallel bundles
- for exteral protection and support, form, shape
fibrous proteins
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how are fibrous proteins arranged
around a single dimension often in parallel bundles
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eg. of fibrous proteins
1. keratin
2. collagen
68
functions of fibrous proteins
1. external support
2. support, form, shape
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external support
- hair
- feather
- skin
- nail
- horn
70
support, form, shape
- tendons
- cartilage
- bone
- deeper layers of skin
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fiber used to make silk cloth
protein fibroin
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consists of layers of antiparallel beta sheets rich in ala and gly residues
fibroin
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- polypeptide chains are tightly folded into compact 3D structure
- more complex than fibrous proteins
globular proteins
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how are globular proteins folded
compact 3D structure
75
eg. of globular proteins
- enzymes
- globin proteins
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location of amino acids in globular proteins
1. exterior
2. interior
3. both interior and exterior
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exterior aa
hydrophilic/polar aa
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interior aa
hydrophobic/nonpolar aa
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amino acids that are both interior and exterior
1. pro
2. ser
3. ala
4. tyr
5. thr
6. cys
7. gly
80
forces that stabilize the tertiary structure of globular proteins
1. hydrogen bonds
2. ionic interactions
3. hydrophobic interactions
4. covalent cross linkages
81
hydrogen bond in tertiary structure of globular proteins
between R groups of aa residues in adjacent loop of chain
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ionic interactions in tertiary structure of globular proteins
- oppositely charged R groups
- R group and water
- R group and ions
83
eg. of covalent cross linkages in tertiary structure of globular proteins
disulfide bonds
84
general principle of secondary structure
determined by short range sequences of R groups
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general principle of tertiary structure
conferred by longer range aspects of aa sequence
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determines the formation of bends in polypeptide chain
precise location of aa
87
quaternary structure:
the number of relationships of sub-units in a __ protein
multimeric
88
biological functions of proteins
1. enzyme
2. transport
3. storage
4. contractile or motile
5. structural
6. defense
7. regulatory proteins
8. allosteric proteins
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eg. enzyme
- ribonuclease
- spliceosome
- replisome
90
eg. transport protein
- hemoglobin
- myoglobin
- lipoprotein
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eg. storage protein
- gliadin (wheat)
- ovalbumin (egg)
- casein (milk)
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eg. contractile or motile protein
- actin
- myosin
- tubulin
93
eg. structural protein
- keratin
- fibroin
- collagen
- elastin
- proteoglycans
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eg. defense proteins
- antibodies
- fibrinogen
- snake venom
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eg. regulatory proteins
- insulin
- growth hormone
- repressors
- transcription factors
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eg. allosteric proteins
have 2 or more slightly diff. conformations which can havve alternative functions
97
apoenzyme+cofactor
holoenzyme
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protein portion
apoenzyme
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non-protein portion
cofactor
100
- where substrate binds to
- formed by aa whose side chains have two principal roles
active site of enzyme
101
two principal roles of aa side chains that form the active site
1. contact residue
2. catalytic residue
102
- attract and orient the substrate in a specific way
- determines substrate specificity
contact residue
103
what does the contact residue determine
substrate specificity
104
- participate in the formation of temporary bonds with substrate
- triggers catalytic change/events
catalytic residue
105
what does the catalytic residue trigger
catalytic change/events
106
enzymes that exist in alternative conformations
allosteric enzymes
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two binding sites of allosteric enzymes
1. active site
2. allosteric/effector site
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site for substrate
active site
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site for regulatory molecule
allosteric/effector site
110
where are allosteric enzymes involved in
- cell signaling
- regulation of metabolism
111
multiple forms of an enzyme
isozymes or isoenzymes
112
isozymes have same __, different __
same reaction, different aa sequence
113
example of isozyme
lactate dehydrogenase
114
protein structure determines its interaction with other molecules
1. protein-protein interaction
2. protein-RNA
3. protein-DNA
4. protein-drug or chemical
115
- regular combination of secondary structure that has a particular topology
- organized into a characteristic 3D structure
motif
116
Motifs of DNA-binding proteins that regulate transcription
1. zinc finger
2. helix-turn-helix
3. leucine zipper
4. helix-loop-helix
5. copper fist
117
fingerlike projection consisting of ~30aa
zinc finger
118
two types of zinc finger
1. 2 cys + 2 his (C2H2 finger)
2. 4 cys (C4 finger)
119
coordinate a single zinc ion
2 cys + 2 his (C2H2 finger)
120
regulatory protein transcription
4 cys (C4 finger)
121
interacts with major groove of DNA
alpha helix
122
structure of zinc finger
- 2 beta strands
- 1 alpha helix
123
function of zinc finger
binding in the major groove of the DNA
124
- 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
helix-turn-helix
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structure of helix-turn-helix
- 2 alpha helixes
- 1 beta turn
126
two parts of helix-turn-helix motif
1. recognition helix
2. second helix
127
helix-turn-helix:
binds specific sequence in the major groove of the DNA
recognition helix
128
helix-turn-helix:
stabilizes the configuration
second helix
129
- contains a leucine every 7th aa
- amphiphatic helix
- form dimers (homo- or hetero-)
leucine zipper
130
there is leucine in every __ aa in leucine zipper
7th
131
each monomer in leucine zipper contain:
1. dimerization domain
2. DNA-binding domain
132
dimerization domain
C-terminal (leu-rich)
133
DNA-binding domain
N-terminal (rich in basic aa)
134
each monomer with dimerization domain and DNA-binding domain
helix-loop-helix
135
almost all in the DNA-binding domain are __ aa
basic
136
- first structure formed around 8 Cu ions which interact with cys residues on the protein
- knuckles contain basic aa that interact with DNA
copper fist
137
where does the copper fist motif interact
cys residues on protein
138
contain basic aa that interact with DNA in copper fist
knuckles
139
function of copper fist
- electron transfer
- redux reduction
- stabilization of protein
140
- small proteinaceous infectious particles
- no nucleic acid
- neurodegenerative disease in mammals
prions
141
post mortem brain with large vacuoles in the cortex and cerebellum
Spongiform Encephalopathy or Prion Disease
142
where prions were first discovered
scrapie in sheep
143
who first discovered prions
Stanley Prusiner (1892)
144
prion disease:
mink
transmissible mink encephalopathy
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prion disease:
muledeer, elk
chronic wasting disease
146
prion disease:
cows
bovine spongiform encephalopathy
147
prion disease:
humans
Creutzfeldt-Jakob disease
148
early stages of prion disease
1. loss of muscle control
2. personality changes
3. impaired memory, judgement, thinking
4. impaired vision
5. insomnia
6. depression
7. dementia/insanity
149
later stages of prion disease
1. involuntary muscle jerk
2. blindness
3. paralysis, wasting
4. coma
5. death, typically following pneumonia
150
visible end results at post mortem of prion disease
1. non-inflammatory lesions
2. vacuoles
3. amyloid protein deposits
4. astrogliosis
151
- first known prion disease
- geographically isolated tribes in the highlands of New Guinea
- by ingesting brain tissue of dead relatives for religious reasons
Kuru
152
a prion is a modified form of __
PrPc (prion protein cellular)
153
where are prions encoded
single exon of single copy located at chromosome 28
154
where are prions found
predominant on surface of neurons
155
function of prions
synaptic function
156
characteristic of prions
- non-immunogenic, protease-sensitive
- subviral agent
157
modified form of PrPc
PrPsc (prion protein scrapie)
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where does PrPsc accumulate
cytoplasmic vesicles of diseased indiv.
159
where PrPc is found
predominantly at alpha helix
160
where PrPsc is found
predominantly at beta-sheet (mostly globular)
