Section 2 - Module 8 Flashcards
1
Q
What does nucleotide sequences specify?
A
Amino acid sequence
2
Q
What is a codon?
A
Found in mRNA, and are the three letters of nucleotide bases that make up a single amino acid
3
Q
Ala
A
Alanine
4
Q
A
A
Alanine
5
Q
Cys
A
Cysteine
6
Q
C
A
cysteine
7
Q
Asp
A
aspartic acids or aspartate
8
Q
D
A
aspartic acids or aspartate
9
Q
Glu
A
glutamic acid or glutamate
10
Q
E
A
glutamic acid or glutamate
11
Q
Phe
A
phenylaniline
12
Q
F
A
phenylaniline
13
Q
Gly
A
glycine
14
Q
G
A
glycine
15
Q
His
A
Histadine
16
Q
H
A
Histidine
17
Q
Ile
A
isoleucine
18
Q
I
A
isoleucine
19
Q
Lys
A
Lysine
20
Q
K
A
lysine
21
Q
Leu
A
Leucine
22
Q
L
A
Leucine
23
Q
Met
A
Methionine
24
Q
M
A
Methionine
25
Asn
asparagine
26
N
asparagine
27
Pro
proline
28
P
proline
29
Gln
Glutamine
30
Q
glutamine
31
Arg
arginine
32
R
Arginine
33
Ser
serine
34
S
serine
35
Thr
Threonine
36
T
Threonine
37
Val
valine
38
V
valine
39
Trp
tryptophan
40
W
tryptophan
41
Tyr
Tyrosine
42
Y
Tyrosine
43
What is the amino acid structure?
Consists of a central carbon (alpha C) attached to (1) amino group (NH3+), (2) a carboxyl group (COO-), (3) a hydrogen atom (H), and (4) a radical group (R-group)
44
What is unique in each amino acid?
The R-group
45
What type of bond joins amino acids?
peptide bond
46
What forms peptide bonds?
dehydration reaction
47
Primary structure
sequence of amino acids
48
Secondary structure
interaction between amino acids causes the primary structure to fold, resulting in structure such as the alpha helix and beta strands.
49
Tertiary structure
secondary structure further folds, and creates a single 3D protein
50
Quaternary Structure
two or more polypeptide chains associate to create a larger complex
51
What is the 3 nucleotides in DNA called?
Triple code
52
What is the 3 nucleotides in mRNA called?
Codon
53
Equation for possible codons
4^n (n = # nucleotides per codon)
54
With 3 bases how many possible codons are there?
64 possible codons (MORE THAN ENOUGH)
55
How do codons effect translation?
mRNA codons instruct the ribosome to incorporate specific amino acids into a polypeptide (the process of translation)
56
What is the same for ALL tRNA molecules
amino acid attachment site
57
What is the amino acid sequence site sequence?
5'-CCA-3'
58
What does the anticodon do?
reads the information in a mRNA sequence by base pairing with a codon
59
How many sense codons are there?
61
60
What are sense codons?
they code for amino acids
60
Is the start codon a sense codon?
Yes
61
AUG
the start codon, initiates translation, codes for the amino acid methionine (MET)
61
What are the 3 nonsense codons?
The stop codons, they terminate translation, and do NOT code for amino acids. They are UAA, UAG, and UGA
62
T/F. multiple codons per amino acid except methionine (Met) and Tryptophane (Trp).
True
63
What strand is mRNA sequence the same as?
the non-template strand
64
Degeneracy
some amino acids are specified by more than one codon
65
Synonymous codons
codons that specify the same amino acids
66
How can the codon be generate but NOT AMBIGUOUS?
a codon never specifies more than one amino acid
67
Which base is most commonly changed for synonymous codons?
the 3rd (3') base
68
T/F. Mutations in the third position have major effects in the amino acid specification?
False. This is rarely the case since it may code synonymously
69
What are the two types of degeneracy?
Partial and complete
70
Partial Degeneracy
changing the third base in a Condon from a purine to a purine (A-G), or from a pyrimidine to a pyrimidine (C-U)
71
Complete degeneracy
changing the third base in a codon to any of the four bases (glycine is an example GGU, GGC, GGA, GGG)
72
What accommodates degeneracy?
Isoaccepting tRNA and wobble effect
73
Isoaccepting tRNA
tRNAs bind ('accept') same amino acid, but recognize different codons (by using different anticodons)
74
Wobble effect
allows same aa-tRNA to pair with more than one codon (allows the same anticodon to base pair with more than one codon)
75
How many different tRNAs are there?
30
76
How many amino acids are there?
20
77
Where does wibble occur?
between the 1st (5') base of an anticodon of t-RNA (wobble position) and the 3rd (3') base of a codon of mRNA
78
What is formed with the codon from the 1st (5') base of an anticodon being allowed to move slightly 'wobble" from its normal position?
non-Watson & Crick base pair
79
Where is the wobble position?
1st base of anticodon - 5'
80
What is inosine (I)
an intermediate in the metabolism of purine. It is essential for proper translation of the genetic code in wobble base pairs
81
RFs
reading frames
82
What does RF refer to?
To protein coding regions of the mRNA
83
What does RF do?
specifies a single protein starting and ending at internal sites within the mRNA.
84
What do all RFs begin with?
AUG
85
RF rules?
1) codons made up of three nucleotides read 5'-3'
2) no overlapping, each base is part of only one codon
3) no gaps
4) message is translated in a reading frame set by the initiator codon, AUG
86
What is an open reading frame?
a portion of RNA molecule that, when translated into amino acids, contains no stop codons.
87
What is the correct reading frame?
the reading frame which goes from start to stop
88
Say a DNA sequence has six possible reading frames, where are they from?
3 possible RF in top strand, and 3 possible RF in bottom strand. EACH will give a different protein
89
Point mutations or base substitution
Alter a single nucleotide
90
What can base substation cause?
missense, nonsense, or silent mutations
91
Missense mutation
change amino acid
92
Nonsense mutation
prematurely code for stop codon
92
Silent mutation
change nucleotide, but the codon still codes for the same amino acid
93
What causes frameshift mutations?
insertion and deletion of nucleotides
94
When does adding/deleting nucleotides not results in a frame shift
when 3 nucleotides is added/deleted (any other number as long of not a multiple of 3 works)
95
What is the goal of translation?
protein synthesis
96
In translation what is the process converting?
converting genetic information stored in nucleic acid sequences into proteins
97
Where does translation of an mRNA taka place?
on a ribosome
98
What direction if mRNA read?
5' to 3' direction
99
Where are amino acids attached on the growing polypeptide chain?
carboxyl (C) terminus
100
What direction (Structures) are polypeptides made?
amino (N) to carboxyl (C) direction
101
In bacteria what process allows for polyribosome (or polysome)?
Multiple ribosomes can simultaneously translate the same mRNA molecule
102
What are prokaryotic requirements for translation?
mRNA template, tRNAs (transfer RNAs), amino acids, ribosomes, many accessory proteins, energy provided by GTP hydrolysis
103
Prokaryotic mRNA is _
polycistronic (multiple ORFs)
104
What is the Shine-Dalgarno sequence?
is a ribosomal binding site in bacterial and archaeal messenger RNA. Before the start sequence
105
Name for RNA-protein complex
ribonucleoprotein
106
What does prokaryotic ribonucleoprotein look like?
3 RNA molecules (23S + 5S, and 16S) and 2 sub-units (30S + 50S = 70S)
107
What are the three tRNA binding sites?
Aminoacyl binding site(A), peptidyl binding site(P), and exit site (E)
108
What is causing only one codon to be read at a time by tRNA?
small subunits holding mRNA
109
What does contact between amino acids at the end of tRNA with catalytic region of the large subunit cause?
Joins the amino acids together to form peptide bonds
110
What is a common antibiotic target?
translational apparatus (e.g. biding to tRNA sites, blocking exit tunnel...)
111
Four translation steps:
1) tRNA charging
2) initation
3) elongation
4) termination and peptide release
112
What is tRNA charging?
The attachment of an amino acid to the tRNA. All amino acids are attached to the adenine (A) nucleotide in the 3' end acceptor stem
113
What is the energy source for binding of aa to tRNA?
ATP
114
tRNA + aa = ?
aminoacyl-tRNA
115
What correctly attached an amino acid to the appropriate tRNA?
aminoacyl-tRNA synthetase
116
How many different aminoacyl-tRNA synthase are there?
20
117
How many amino acids do aminoacyl-tRNA synthase recognize for attachment to the correct set of tRNA's?
One
118
Initiation requirements
1) mRNA
2) small and large ribosome subunit
3) initiator-tRNA
4) initiation factors (IFs)
5) Guanosine triphosphate (GTP)
119
IF-3 binding to the small subunit results in what? (in prokaryotes)
Prevents the large subunit from binding, thus allowing the small subunit to attach to mRNA.
120
What is initiator tRNA charged with?
fMET amino acid (N-formylmethionine)
121
IF-3 protein function
keep the small and large ribosomes seperated
122
IF-1 and 2 functions
facilitates initiator-tRNA binding to the correct site
123
What forms the 70S initiation complex?
initiation factor proteins dissociate and the large ribosome subunits binds
124
Key steps in elongation?
1) entry of aa-tRNA into the A site of the ribosome
2) peptide bond formation
3) ribosome translocation
4) exit of tRNA from E-site of the ribosome
125
Elongation requirements
1) aa-tRNAs (or charged tRNAs)
2) 70S initiation complex
3) Elongation factors (EFs)
4) GTP
126
A-site (aminoacyl) function
accepts the incoming aa-tRNA carrying the next amino acid to be added to the chain
127
P-site (peptidyl) function
holds the tRNA carrying the growing polypeptide
128
E-site (exit) function
discharged tRNA's leave the ribosome from this site
129
What catalyses peptide bond formation?
peptidyl transferase
130
Ribosome movement (translocation) is facilitated by what?
elongation factors
131
What direction does ribosome translocate on the mRNA?
5' to 3' direction
132
When does protein synthesis terminate?
When the ribosome translocates to a stop codon
133
What does release factor (RF) protein binding to the A site trigger?
Release of the polypeptide from the P-site tRNA
134
Eukaryotic mRNA is _
monocystronic (single ORF)
135
What does eukaryotic ribosome complex look like?
3 RNA molecules (28S + 5S, and 18S) and 2 sub-units (60S + 40S = 80S)
136
Do eukaryotes have consensus sequences for ribosome binding?
no
137
What facilitates ribosome binding for eukaryotes?
5- CAP and 3' poly(A) tail
