Proteins and Protein Synthesis Flashcards
(126 cards)
1
Q
Stephen Hawkings
A
ALS- protein degradation disease
2
Q
Protein terminals
A
amino terminals- beginning
carboxyl terminals- end
3
Q
Digestion of dietary proteins
A
by proteolytic enzymes of the GI tract
4
Q
Cleavage of dietary proteins
A
in small intestine by pancreatic proteases
5
Q
Membrane proteins: functions
A
transport proteins, channels, enzymes, signal proteins, hormone receptors, second messengers, structure proteins
6
Q
Central dogma of molecular biology
A
DNA–transcription–>RNA–translation–>Protein
transcription–>splicing–>translation
DNA and transcription: nucleus
RNA, translation, and Protein: cytosol
7
Q
Most abundant and funtionally diverse molecules in living systems?
A
proteins!
8
Q
All physiological processes are dependent on?
A
proteins!
9
Q
Enzymes, peptide hormones, collagen, hemoglobin, antibodies (Igs), etc., are?
A
proteins!
10
Q
Biologically occurring short chains of amino acid monomers linked by peptide bonds are?
A
peptides
11
Q
Dipeptides
A
shortest peptides consisting of 2 amino acids joined by a single peptide bond
12
Q
Peptide bonds
A
R-OH H-N-R
R-O H–H -N-R
13
Q
What determines shape (form) of a protein?
A
interactions between amino acids
14
Q
Structure of amino acids
A
possess amino group, acid (carboxyl group), and side chain;
at pH7 both amino and carboxyl groups are ionized;
R is one of 20 different side chains
15
Q
Families of amino acids
A
acidic, basic, uncharged polar, nonpolar;
group according to side chain;
16
Q
Nonpolar side chains
A
do NOT gain or lose e-
do NOT participate in hydrogen or ionic bonds
in aqueous solution, side chains cluster together in interior of protein (hydrophobic effect)
proline’s side chain and alpha-amino N form ring structure
17
Q
Glyceine
A
nonpolar side chain
18
Q
Alanine
A
nonpolar side chain
19
Q
Valine
A
nonpolar side chain
20
Q
Leucine
A
nonpolar side chain
21
Q
Isoleucine
A
nonpolar side chain
22
Q
Phenylalanine
A
nonpolar side chain
23
Q
Tryptophan
A
nonpolar side chain
24
Q
Methionine
A
nonpolar side chain;
has sulfide group;
first codon in ALL eukaryotic proteins (mRNA)
25
Proline
nonpolar side chain;
side chain & amino group form ring structure,
-->has secondary amino group called imino acid
26
Cysteine
nonpolar side chain;
has sulfide group
-->participate in disulfide bonds between proteins;
can lose proton at alkaline pH;
27
Uncharged polar side chains
zero net charge at physiologic pH (7.4);
tyrosine can lose proton at alkaline pH;
serine, threonine, and tyrosine contain polar hydroxyl group (participates in H-bond formation);
28
Serine
uncharged polar side chain;
| contain polar hydroxyl group that participate in H-bond formation
29
Threonine
uncharged polar side chain;
| contain polar hydroxyl group that participate in H-bond formation
30
Tyrosine
uncharged polar side chain;
can lose proton at alkaline pH;
contain polar hydroxyl group that participate in H-bond formation
31
Asparagine
uncharged polar side chain
32
Glutamine
uncharged polar side chain
33
Acidic (negative) side chains
are proton DONORS;
| are fully ionized (COO-) at physiological pH (7.4)
34
Aspartic acid
acidic (negative) side chain
35
Glutamic acid
acidic (negative) side chain
36
Basic (positive) side chains
are proton ACCEPTORS;
are fully ionized AND positively charged at pH 7.4;
histidine's side chain can be positively charged OR neutral depending on environments pH
37
Histidine
basic (positive) side chain;
positively charged or neutral depending on environments pH;
has important function as a BUFFER
38
Lysine
basic (positive) side chain
39
Arginine
basic (positive) side chain
40
What distinguishes one amino acid from another?
side chain
41
alpha-amino acids
found in proteins EXCEPT
| triiodothyronine & thyroxine (thyroid hormones)
42
beta & gamma amino acids
important functions:
- taurine in bile acids
- GABA is an inhibitory neurotransmitter
43
Precursors of important molecules in physiology are?
amino acids
44
Hydroxylation of typtophan yields?
serotonin (neurotransmitter and paracrine hormone)
45
Acetylation and methylation of serotonin yields?
melatonin (hormone that influences reproductive activity)
46
Hydroxylation of tyrosine yields?
dopa-- is then decarboxylated to the neurotransmitter dopamine
47
Decarboxylation of histidine yields?
histamine (mediator of allergic reations)
48
Peptides of physiological relevance
oxytocin, antidiuretic hormone (ADH), creatine, bradykinin, angiotensin II
49
Oxytocin
peptide of physiological relevance
9 peptide long hormone;
produced in hypothalamus (uterine contractions and milk secretion)
50
Antidiuretic hormone (ADH)
peptide of physiological relevance
9 peptide long hormone;
produced in the hypothalamus (maintenance of water balance)
51
Creatine
peptide of physiological relevance
tripeptide;
involved in E production in muscle and cardiac cells
52
Bradykinin
peptide of physiological relevance
9 peptide long;
vasoactive substance
53
Angiotensin II
peptide of physiological relevance
| a potent vasoconstrictor
54
Polypeptide
long, continuous, unbranched peptide chain;
| peptides are distinguished from proteins based on size and contain 50 or less amino acids
55
Polypeptides of physiological relevance
gastrin, CCK, glucagon, atrial natriuretic peptide (ANP)
56
Gastrin
polypeptide of physiological relevance;
stomach hormone;
stimulates secretion of gastric glands
57
CCK (cholicystekinin)
polypeptide of physiological relevance;
| stimulates pancreas and liver secretion
58
Glucagon
polypeptide of physiological relevance;
| produced by alpha-cells of the pancreas
59
ANP (atrial natriuretic peptide)
polypeptide of physiological relevance;
produced in the heart (atria);
regulation of blood volume and pressure
60
Changing amino acids in proteins lead to?
non-functional protein or a misfolded protein
| changing amino acids is called a MUTATION in the DNA
61
Examples of mutations in DNA (changing AA's)
sickle cell anemia, Alzheimer disease, transport defects, enzyme deficiencies, etc
62
Types of mutations
silent, missense, nonsense, frame-shift, splice site
63
Silent mutation
codon containing changed base may code for SAME amino acid
| UCA->Ser UCU->Ser
64
Missense mutation
codon containing changed base may code for DIFFERENT amino acid
UCA->Ser CCA->Pro
65
Nonsense mutation
codon containing changed base may become a TERMINATION codon
| UCA->Ser UAA->Stop
66
Frame-shift mutation
alter reading frame
67
Splice site mutation
remove introns which changes nucleotide SO
| splice site will replace the intron
68
Sickle cell anemia
cause by single nucleotide substitution in gene for beta-globin
-->missense mutation changes Glu for Val;
cause tissue anoxia (lack O2) causing severe pain;
blood cells only last a few days;
change in single nucleotide causes long chains of fibers
-->changes RBC structure to sickle shape
69
Characteristics of genetic code
specificity, universality, degeneracy, nonoverlapping and commaless
70
Specificity
a particular codon always codes for same AA
71
Universality
genetic code is conserved from very early stages of evolution
72
Degeneracy
aka redundancy;
a given AA may have more than one triplet coding for it
-->Arg is coded by 6 different codons
73
Nonoverlapping & Commaless
genetic code is read from a fixed starting point as a continuous sequence of bases without any punctuation between codons
74
Genetic code
4 letter (U,C,A,G) with 64 combination possibilities that can be translated to 20 different amino acids
75
Start codon(s)
AUG
76
Stop codon(s)
UAA, UAG, UGA
77
Eukaryotes (AA's and Proteins)
have different compartments:
- DNA & transcription in nucleus
- RNA & translation in cytosol
- mRNA found in nucleus AND cytosol
78
Prokaryotes (AA's and Proteins)
DNA, transcription, RNA, translation, & protein all happen in same compartment
79
DNA complimentary base pairing
A-T
G-C
THYMINE used in DNA
80
RNA complimentary base pairing
A-U
G-C
URACIL used in RNA
81
Alternative splicing
enzyme snRNP can recognize and remove specific signal sequences in mRNA from the transcript;
can produce 5 alternative proteins from the same gene
-->may have different funtions
82
tRNA
transfer RNA;
resembles a clover;
have attachment site for a specific amino acid at its 3' end;
have anticodon that pairs with a specific codon on the mRNA
-->adapter combining amino acids with codons
83
Ribosomes
cell structure that makes proteins;
consist of 2 subunits:
60s & 40s in eukaryotes (50s & 30s in prokaryotes);
can be "free" in cytosol OR in close association with rER
84
Ribosome sites
A site, P site, E site
85
A site
binds an incoming aminoacyl-tRNA to codon occupying the site
86
P site
is occupied by peptidyl-tRNA which carries the chain of AA's that has already been synthesized
87
E site
occupied by the empty tRNA as it is about to EXIT the ribosome
88
RER-ribosomes
responsible for synthesizing proteins that are to be exported from the cell or to be placed in cell membranes (plasma membranes, ER membranes, lysosome membranes)
89
Cytosolic ribosomes
synthesize cytosolic proteins or those intended for the nucleus, mitochondria, or peroxisomes
90
Protein synthesis steps
initiation, elongation, termination
91
Protein synthesis: initiation
assembly of components of the translation system before peptide bond formation occurs
92
Protein synthesis: elongation
addition of AA's to carboxyl end of the growing chain;
ribosome moves from 5' end to 3' end of mRNA;
STEP 1:
binding aminoacyl-tRNA to A-binding domain
STEP 2:
generation of peptid bound in P-binding domain
STEP 3:
movement of mRNA through small subunit 3NT
93
Protein synthesis: termination
occurs when one of three termination codons moves to A-binding domain
94
Fate of newly generated protein
```
transport into ER;
placement of membrane proteins in plasma membrane;
protein folding;
transport from ER to golgi;
glycosylation of newly made proteins;
```
95
Golgi apparatus function
transport proteins to other organelles
96
Signal sequences in proteins
recognize "delivery address"
| N-terminal, C-terminal, and internal signals
97
N-terminal sequences
import proteins into ER
OR
import proteins into mitochondria
98
C-terminal sequences
retain proteins in lumen of ER
99
Internal signals
import proteins into nucleus
OR
import proteins into peroxisomes
100
Protein transport into ER
ER synthesizes 3 kinds of protein:
-lysosomal proteins, secretory proteins, membrane proteins
N-terminal sequences import proteins into ER
101
Characteristics of signal sequences
10-36 amino acid length;
at least one basic amino acid;
10-13 hydrophobic amino acids;
small amino acids in cleavage site
102
Signal Recognition Particle (SRP)
bind to protein (still attached to ribosome) after recognition of specific signal;
protein synthesis is stopped
103
SRP/Ribosomal complex
binds to SRP-receptor (docking protein) in ER membrane
104
In an E-dependent process (GTP)
ribosome/protein complex will be placed in translocation protein;
at same time, SRP will be released and translation continued
105
Once protein is in ER lumen...
signal sequence has to be removed
106
Type 1 topographic arrangement of membrane proteins
C-terminus is in cytosol
107
Type 2 topographic arrangement of membrane proteins
N-terminus is in cytosol
108
Structure of proteins
Primary- bases
Secondary- alpha-helix
Tertiary- folding
Quarternary- large scale (cofactors)
109
Folding patterns in secondary structure
alpha-helix
beta-sheet
beta-bends: turns, also called proline kinks
110
alpha-helix folding pattern
H-bonds between carboxyl and amino groups;
distance of 4 amino acids;
makes spiral structure;
all side chains are outside the helix
111
beta-sheet folding pattern
linking amino acids in 2 different polypeptide chains;
PARALLEL: carboxyl & amino terminus at same end of sheet;
ANTIPARALLEL: carboxyl & amino terminus at opposite end of sheet;
side chains are above and below sheet
112
beta-bend folding pattern
reverse direction of polypeptide chain helping form compact, globular shape;
connects alpha-helix & beta-sheets together;
prolines are critical for protein structure and function
113
Vesicular transport
if proteins aren't needed in rER, are sent to gogli
- go via transport through vesicles (COP2)
- in golgi, sugars added to proteins, will then go to plasma membrane
114
Envelope proteins (COP)
fusion with target membrane;
hydrolysis of GTP to GDP;
clathrin coated vesicles
-clathrin also present in receptor-mediated endocytosis
115
SNARE
soluble NSF attachment protein (SNAP) receptors:
| receptors that recognize envelope proteins (COP)
116
SNARE examples
synaptobrevin:
responsible for fusion of synaptic vesicles with the plasma membrane;
neurotransmitters are in vesicles, SNARE catches the transmitter;
ex. botox
117
Protein transport into nucleus
nuclear transport signal (NLS)
118
Golgi apparatus consists of
cis-Golgi, medial-Golgi (trans-Golgi area), trans-Golgi net
119
cis-Golgi
protein phosphorylation
120
medial-Golgi (trans-Golgi area)
modification of the N-attached sugar chains of glycoproteins;
O-glycosylation: sugar chains will be attached to OH groups of Ser/Thr
121
trans-Golgi net
proteins will be packed in vesicles and sent to specific delivery address
122
Protein folding
chaperons, folding cyclus
123
Chaperons
heat stable proteins;
high activity at high temps;
are ATP-ases;
like "quality control", will make sure protein has right shape
124
Folding cyclus
requires ATP;
chaperon is bound to ADP;
ADP/chaperon-complex has high affinity for unfolded proteins;
after binding, ADP is released;
after protein folding and ATP binding the complex dissociates, the correct folded protein is released
125
N-glycosylation
starts in ER;
attachment of sugar to asparagine's amino group;
recognition sequence is: Asn - X - Ser/Thr;
further processing in golgi
126
O-glycosylation
starts in golgi;
attachment of sugar to OH group of Ser/Thr;
important for functional conformation of a protein;
sugar chains in proteins are important for sorting
