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Proteins and Protein Synthesis Flashcards

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Biology 101 flashcards
1
Q

Stephen Hawkings

A

ALS- protein degradation disease

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2
Q

Protein terminals

A

amino terminals- beginning

carboxyl terminals- end

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3
Q

Digestion of dietary proteins

A

by proteolytic enzymes of the GI tract

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4
Q

Cleavage of dietary proteins

A

in small intestine by pancreatic proteases

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5
Q

Membrane proteins: functions

A

transport proteins, channels, enzymes, signal proteins, hormone receptors, second messengers, structure proteins

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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

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7
Q

Most abundant and funtionally diverse molecules in living systems?

A

proteins!

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8
Q

All physiological processes are dependent on?

A

proteins!

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9
Q

Enzymes, peptide hormones, collagen, hemoglobin, antibodies (Igs), etc., are?

A

proteins!

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10
Q

Biologically occurring short chains of amino acid monomers linked by peptide bonds are?

A

peptides

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11
Q

Dipeptides

A

shortest peptides consisting of 2 amino acids joined by a single peptide bond

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12
Q

Peptide bonds

A

R-OH H-N-R

R-O H–H -N-R

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13
Q

What determines shape (form) of a protein?

A

interactions between amino acids

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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

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15
Q

Families of amino acids

A

acidic, basic, uncharged polar, nonpolar;

group according to side chain;

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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

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17
Q

Glyceine

A

nonpolar side chain

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18
Q

Alanine

A

nonpolar side chain

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19
Q

Valine

A

nonpolar side chain

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20
Q

Leucine

A

nonpolar side chain

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21
Q

Isoleucine

A

nonpolar side chain

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22
Q

Phenylalanine

A

nonpolar side chain

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23
Q

Tryptophan

A

nonpolar side chain

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24
Q

Methionine

A

nonpolar side chain;
has sulfide group;
first codon in ALL eukaryotic proteins (mRNA)

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25
Q

Proline

A

nonpolar side chain;
side chain & amino group form ring structure,
–>has secondary amino group called imino acid

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26
Q

Cysteine

A

nonpolar side chain;
has sulfide group
–>participate in disulfide bonds between proteins;
can lose proton at alkaline pH;

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27
Q

Uncharged polar side chains

A

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);

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28
Q

Serine

A

uncharged polar side chain;

contain polar hydroxyl group that participate in H-bond formation

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29
Q

Threonine

A

uncharged polar side chain;

contain polar hydroxyl group that participate in H-bond formation

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30
Q

Tyrosine

A

uncharged polar side chain;
can lose proton at alkaline pH;
contain polar hydroxyl group that participate in H-bond formation

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31
Q

Asparagine

A

uncharged polar side chain

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32
Q

Glutamine

A

uncharged polar side chain

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33
Q

Acidic (negative) side chains

A

are proton DONORS;

are fully ionized (COO-) at physiological pH (7.4)

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34
Q

Aspartic acid

A

acidic (negative) side chain

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35
Q

Glutamic acid

A

acidic (negative) side chain

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36
Q

Basic (positive) side chains

A

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

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37
Q

Histidine

A

basic (positive) side chain;
positively charged or neutral depending on environments pH;
has important function as a BUFFER

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38
Q

Lysine

A

basic (positive) side chain

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39
Q

Arginine

A

basic (positive) side chain

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40
Q

What distinguishes one amino acid from another?

A

side chain

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41
Q

alpha-amino acids

A

found in proteins EXCEPT

triiodothyronine & thyroxine (thyroid hormones)

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42
Q

beta & gamma amino acids

A

important functions:

  • taurine in bile acids
  • GABA is an inhibitory neurotransmitter
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43
Q

Precursors of important molecules in physiology are?

A

amino acids

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44
Q

Hydroxylation of typtophan yields?

A

serotonin (neurotransmitter and paracrine hormone)

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45
Q

Acetylation and methylation of serotonin yields?

A

melatonin (hormone that influences reproductive activity)

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46
Q

Hydroxylation of tyrosine yields?

A

dopa– is then decarboxylated to the neurotransmitter dopamine

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47
Q

Decarboxylation of histidine yields?

A

histamine (mediator of allergic reations)

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48
Q

Peptides of physiological relevance

A

oxytocin, antidiuretic hormone (ADH), creatine, bradykinin, angiotensin II

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49
Q

Oxytocin

A

peptide of physiological relevance
9 peptide long hormone;
produced in hypothalamus (uterine contractions and milk secretion)

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50
Q

Antidiuretic hormone (ADH)

A

peptide of physiological relevance
9 peptide long hormone;
produced in the hypothalamus (maintenance of water balance)

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51
Q

Creatine

A

peptide of physiological relevance
tripeptide;
involved in E production in muscle and cardiac cells

52
Q

Bradykinin

A

peptide of physiological relevance
9 peptide long;
vasoactive substance

53
Q

Angiotensin II

A

peptide of physiological relevance

a potent vasoconstrictor

54
Q

Polypeptide

A

long, continuous, unbranched peptide chain;

peptides are distinguished from proteins based on size and contain 50 or less amino acids

55
Q

Polypeptides of physiological relevance

A

gastrin, CCK, glucagon, atrial natriuretic peptide (ANP)

56
Q

Gastrin

A

polypeptide of physiological relevance;
stomach hormone;
stimulates secretion of gastric glands

57
Q

CCK (cholicystekinin)

A

polypeptide of physiological relevance;

stimulates pancreas and liver secretion

58
Q

Glucagon

A

polypeptide of physiological relevance;

produced by alpha-cells of the pancreas

59
Q

ANP (atrial natriuretic peptide)

A

polypeptide of physiological relevance;
produced in the heart (atria);
regulation of blood volume and pressure

60
Q

Changing amino acids in proteins lead to?

A

non-functional protein or a misfolded protein

changing amino acids is called a MUTATION in the DNA

61
Q

Examples of mutations in DNA (changing AA’s)

A

sickle cell anemia, Alzheimer disease, transport defects, enzyme deficiencies, etc

62
Q

Types of mutations

A

silent, missense, nonsense, frame-shift, splice site

63
Q

Silent mutation

A

codon containing changed base may code for SAME amino acid

UCA->Ser UCU->Ser

64
Q

Missense mutation

A

codon containing changed base may code for DIFFERENT amino acid
UCA->Ser CCA->Pro

65
Q

Nonsense mutation

A

codon containing changed base may become a TERMINATION codon

UCA->Ser UAA->Stop

66
Q

Frame-shift mutation

A

alter reading frame

67
Q

Splice site mutation

A

remove introns which changes nucleotide SO

splice site will replace the intron

68
Q

Sickle cell anemia

A

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
Q

Characteristics of genetic code

A

specificity, universality, degeneracy, nonoverlapping and commaless

70
Q

Specificity

A

a particular codon always codes for same AA

71
Q

Universality

A

genetic code is conserved from very early stages of evolution

72
Q

Degeneracy

A

aka redundancy;
a given AA may have more than one triplet coding for it
–>Arg is coded by 6 different codons

73
Q

Nonoverlapping & Commaless

A

genetic code is read from a fixed starting point as a continuous sequence of bases without any punctuation between codons

74
Q

Genetic code

A

4 letter (U,C,A,G) with 64 combination possibilities that can be translated to 20 different amino acids

75
Q

Start codon(s)

A

AUG

76
Q

Stop codon(s)

A

UAA, UAG, UGA

77
Q

Eukaryotes (AA’s and Proteins)

A

have different compartments:

  • DNA & transcription in nucleus
  • RNA & translation in cytosol
  • mRNA found in nucleus AND cytosol
78
Q

Prokaryotes (AA’s and Proteins)

A

DNA, transcription, RNA, translation, & protein all happen in same compartment

79
Q

DNA complimentary base pairing

A

A-T
G-C
THYMINE used in DNA

80
Q

RNA complimentary base pairing

A

A-U
G-C
URACIL used in RNA

81
Q

Alternative splicing

A

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
Q

tRNA

A

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
Q

Ribosomes

A

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
Q

Ribosome sites

A

A site, P site, E site

85
Q

A site

A

binds an incoming aminoacyl-tRNA to codon occupying the site

86
Q

P site

A

is occupied by peptidyl-tRNA which carries the chain of AA’s that has already been synthesized

87
Q

E site

A

occupied by the empty tRNA as it is about to EXIT the ribosome

88
Q

RER-ribosomes

A

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
Q

Cytosolic ribosomes

A

synthesize cytosolic proteins or those intended for the nucleus, mitochondria, or peroxisomes

90
Q

Protein synthesis steps

A

initiation, elongation, termination

91
Q

Protein synthesis: initiation

A

assembly of components of the translation system before peptide bond formation occurs

92
Q

Protein synthesis: elongation

A

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
Q

Protein synthesis: termination

A

occurs when one of three termination codons moves to A-binding domain

94
Q

Fate of newly generated protein

A 
transport into ER;
placement of membrane proteins in plasma membrane;
protein folding;
transport from ER to golgi;
glycosylation of newly made proteins;
95
Q

Golgi apparatus function

A

transport proteins to other organelles

96
Q

Signal sequences in proteins

A

recognize “delivery address”

N-terminal, C-terminal, and internal signals

97
Q

N-terminal sequences

A

import proteins into ER
OR
import proteins into mitochondria

98
Q

C-terminal sequences

A

retain proteins in lumen of ER

99
Q

Internal signals

A

import proteins into nucleus
OR
import proteins into peroxisomes

100
Q

Protein transport into ER

A

ER synthesizes 3 kinds of protein:
-lysosomal proteins, secretory proteins, membrane proteins
N-terminal sequences import proteins into ER

101
Q

Characteristics of signal sequences

A

10-36 amino acid length;
at least one basic amino acid;
10-13 hydrophobic amino acids;
small amino acids in cleavage site

102
Q

Signal Recognition Particle (SRP)

A

bind to protein (still attached to ribosome) after recognition of specific signal;
protein synthesis is stopped

103
Q

SRP/Ribosomal complex

A

binds to SRP-receptor (docking protein) in ER membrane

104
Q

In an E-dependent process (GTP)

A

ribosome/protein complex will be placed in translocation protein;
at same time, SRP will be released and translation continued

105
Q

Once protein is in ER lumen…

A

signal sequence has to be removed

106
Q

Type 1 topographic arrangement of membrane proteins

A

C-terminus is in cytosol

107
Q

Type 2 topographic arrangement of membrane proteins

A

N-terminus is in cytosol

108
Q

Structure of proteins

A

Primary- bases
Secondary- alpha-helix
Tertiary- folding
Quarternary- large scale (cofactors)

109
Q

Folding patterns in secondary structure

A

alpha-helix
beta-sheet
beta-bends: turns, also called proline kinks

110
Q

alpha-helix folding pattern

A

H-bonds between carboxyl and amino groups;
distance of 4 amino acids;
makes spiral structure;
all side chains are outside the helix

111
Q

beta-sheet folding pattern

A

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
Q

beta-bend folding pattern

A

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
Q

Vesicular transport

A

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
Q

Envelope proteins (COP)

A

fusion with target membrane;
hydrolysis of GTP to GDP;
clathrin coated vesicles
-clathrin also present in receptor-mediated endocytosis

115
Q

SNARE

A

soluble NSF attachment protein (SNAP) receptors:

receptors that recognize envelope proteins (COP)

116
Q

SNARE examples

A

synaptobrevin:
responsible for fusion of synaptic vesicles with the plasma membrane;
neurotransmitters are in vesicles, SNARE catches the transmitter;
ex. botox

117
Q

Protein transport into nucleus

A

nuclear transport signal (NLS)

118
Q

Golgi apparatus consists of

A

cis-Golgi, medial-Golgi (trans-Golgi area), trans-Golgi net

119
Q

cis-Golgi

A

protein phosphorylation

120
Q

medial-Golgi (trans-Golgi area)

A

modification of the N-attached sugar chains of glycoproteins;
O-glycosylation: sugar chains will be attached to OH groups of Ser/Thr

121
Q

trans-Golgi net

A

proteins will be packed in vesicles and sent to specific delivery address

122
Q

Protein folding

A

chaperons, folding cyclus

123
Q

Chaperons

A

heat stable proteins;
high activity at high temps;
are ATP-ases;
like “quality control”, will make sure protein has right shape

124
Q

Folding cyclus

A

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
Q

N-glycosylation

A

starts in ER;
attachment of sugar to asparagine’s amino group;
recognition sequence is: Asn - X - Ser/Thr;
further processing in golgi

126
Q

O-glycosylation

A

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

Cell Bio (4 decks)

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