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BIOL 2030 > Section 2 - Module 8 > Flashcards

Section 2 - Module 8 Flashcards

1
Q

What does nucleotide sequences specify?

A

Amino acid sequence

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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

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3
Q

Ala

A

Alanine

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4
Q

A

A

Alanine

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5
Q

Cys

A

Cysteine

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6
Q

C

A

cysteine

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7
Q

Asp

A

aspartic acids or aspartate

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8
Q

D

A

aspartic acids or aspartate

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9
Q

Glu

A

glutamic acid or glutamate

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10
Q

E

A

glutamic acid or glutamate

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11
Q

Phe

A

phenylaniline

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12
Q

F

A

phenylaniline

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13
Q

Gly

A

glycine

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14
Q

G

A

glycine

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15
Q

His

A

Histadine

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16
Q

H

A

Histidine

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17
Q

Ile

A

isoleucine

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18
Q

I

A

isoleucine

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19
Q

Lys

A

Lysine

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20
Q

K

A

lysine

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21
Q

Leu

A

Leucine

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22
Q

L

A

Leucine

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23
Q

Met

A

Methionine

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24
Q

M

A

Methionine

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25
Q

Asn

A

asparagine

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26
Q

N

A

asparagine

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27
Q

Pro

A

proline

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28
Q

P

A

proline

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29
Q

Gln

A

Glutamine

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30
Q

Q

A

glutamine

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31
Q

Arg

A

arginine

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32
Q

R

A

Arginine

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33
Q

Ser

A

serine

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34
Q

S

A

serine

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35
Q

Thr

A

Threonine

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36
Q

T

A

Threonine

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37
Q

Val

A

valine

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38
Q

V

A

valine

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39
Q

Trp

A

tryptophan

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40
Q

W

A

tryptophan

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41
Q

Tyr

A

Tyrosine

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42
Q

Y

A

Tyrosine

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43
Q

What is the amino acid structure?

A

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)

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44
Q

What is unique in each amino acid?

A

The R-group

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45
Q

What type of bond joins amino acids?

A

peptide bond

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46
Q

What forms peptide bonds?

A

dehydration reaction

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47
Q

Primary structure

A

sequence of amino acids

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48
Q

Secondary structure

A

interaction between amino acids causes the primary structure to fold, resulting in structure such as the alpha helix and beta strands.

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49
Q

Tertiary structure

A

secondary structure further folds, and creates a single 3D protein

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50
Q

Quaternary Structure

A

two or more polypeptide chains associate to create a larger complex

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51
Q

What is the 3 nucleotides in DNA called?

A

Triple code

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52
Q

What is the 3 nucleotides in mRNA called?

A

Codon

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53
Q

Equation for possible codons

A

4^n (n = # nucleotides per codon)

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54
Q

With 3 bases how many possible codons are there?

A

64 possible codons (MORE THAN ENOUGH)

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55
Q

How do codons effect translation?

A

mRNA codons instruct the ribosome to incorporate specific amino acids into a polypeptide (the process of translation)

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56
Q

What is the same for ALL tRNA molecules

A

amino acid attachment site

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57
Q

What is the amino acid sequence site sequence?

A

5’-CCA-3’

58
Q

What does the anticodon do?

A

reads the information in a mRNA sequence by base pairing with a codon

59
Q

How many sense codons are there?

A

61

60
Q

What are sense codons?

A

they code for amino acids

60
Q

Is the start codon a sense codon?

A

Yes

61
Q

AUG

A

the start codon, initiates translation, codes for the amino acid methionine (MET)

61
Q

What are the 3 nonsense codons?

A

The stop codons, they terminate translation, and do NOT code for amino acids. They are UAA, UAG, and UGA

62
Q

T/F. multiple codons per amino acid except methionine (Met) and Tryptophane (Trp).

A

True

63
Q

What strand is mRNA sequence the same as?

A

the non-template strand

64
Q

Degeneracy

A

some amino acids are specified by more than one codon

65
Q

Synonymous codons

A

codons that specify the same amino acids

66
Q

How can the codon be generate but NOT AMBIGUOUS?

A

a codon never specifies more than one amino acid

67
Q

Which base is most commonly changed for synonymous codons?

A

the 3rd (3’) base

68
Q

T/F. Mutations in the third position have major effects in the amino acid specification?

A

False. This is rarely the case since it may code synonymously

69
Q

What are the two types of degeneracy?

A

Partial and complete

70
Q

Partial Degeneracy

A

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
Q

Complete degeneracy

A

changing the third base in a codon to any of the four bases (glycine is an example GGU, GGC, GGA, GGG)

72
Q

What accommodates degeneracy?

A

Isoaccepting tRNA and wobble effect

73
Q

Isoaccepting tRNA

A

tRNAs bind (‘accept’) same amino acid, but recognize different codons (by using different anticodons)

74
Q

Wobble effect

A

allows same aa-tRNA to pair with more than one codon (allows the same anticodon to base pair with more than one codon)

75
Q

How many different tRNAs are there?

A

30

76
Q

How many amino acids are there?

A

20

77
Q

Where does wibble occur?

A

between the 1st (5’) base of an anticodon of t-RNA (wobble position) and the 3rd (3’) base of a codon of mRNA

78
Q

What is formed with the codon from the 1st (5’) base of an anticodon being allowed to move slightly ‘wobble” from its normal position?

A

non-Watson & Crick base pair

79
Q

Where is the wobble position?

A

1st base of anticodon - 5’

80
Q

What is inosine (I)

A

an intermediate in the metabolism of purine. It is essential for proper translation of the genetic code in wobble base pairs

81
Q

RFs

A

reading frames

82
Q

What does RF refer to?

A

To protein coding regions of the mRNA

83
Q

What does RF do?

A

specifies a single protein starting and ending at internal sites within the mRNA.

84
Q

What do all RFs begin with?

A

AUG

85
Q

RF rules?

A

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
Q

What is an open reading frame?

A

a portion of RNA molecule that, when translated into amino acids, contains no stop codons.

87
Q

What is the correct reading frame?

A

the reading frame which goes from start to stop

88
Q

Say a DNA sequence has six possible reading frames, where are they from?

A

3 possible RF in top strand, and 3 possible RF in bottom strand. EACH will give a different protein

89
Q

Point mutations or base substitution

A

Alter a single nucleotide

90
Q

What can base substation cause?

A

missense, nonsense, or silent mutations

91
Q

Missense mutation

A

change amino acid

92
Q

Nonsense mutation

A

prematurely code for stop codon

92
Q

Silent mutation

A

change nucleotide, but the codon still codes for the same amino acid

93
Q

What causes frameshift mutations?

A

insertion and deletion of nucleotides

94
Q

When does adding/deleting nucleotides not results in a frame shift

A

when 3 nucleotides is added/deleted (any other number as long of not a multiple of 3 works)

95
Q

What is the goal of translation?

A

protein synthesis

96
Q

In translation what is the process converting?

A

converting genetic information stored in nucleic acid sequences into proteins

97
Q

Where does translation of an mRNA taka place?

A

on a ribosome

98
Q

What direction if mRNA read?

A

5’ to 3’ direction

99
Q

Where are amino acids attached on the growing polypeptide chain?

A

carboxyl (C) terminus

100
Q

What direction (Structures) are polypeptides made?

A

amino (N) to carboxyl (C) direction

101
Q

In bacteria what process allows for polyribosome (or polysome)?

A

Multiple ribosomes can simultaneously translate the same mRNA molecule

102
Q

What are prokaryotic requirements for translation?

A

mRNA template, tRNAs (transfer RNAs), amino acids, ribosomes, many accessory proteins, energy provided by GTP hydrolysis

103
Q

Prokaryotic mRNA is _

A

polycistronic (multiple ORFs)

104
Q

What is the Shine-Dalgarno sequence?

A

is a ribosomal binding site in bacterial and archaeal messenger RNA. Before the start sequence

105
Q

Name for RNA-protein complex

A

ribonucleoprotein

106
Q

What does prokaryotic ribonucleoprotein look like?

A

3 RNA molecules (23S + 5S, and 16S) and 2 sub-units (30S + 50S = 70S)

107
Q

What are the three tRNA binding sites?

A

Aminoacyl binding site(A), peptidyl binding site(P), and exit site (E)

108
Q

What is causing only one codon to be read at a time by tRNA?

A

small subunits holding mRNA

109
Q

What does contact between amino acids at the end of tRNA with catalytic region of the large subunit cause?

A

Joins the amino acids together to form peptide bonds

110
Q

What is a common antibiotic target?

A

translational apparatus (e.g. biding to tRNA sites, blocking exit tunnel…)

111
Q

Four translation steps:

A

1) tRNA charging
2) initation
3) elongation
4) termination and peptide release

112
Q

What is tRNA charging?

A

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
Q

What is the energy source for binding of aa to tRNA?

A

ATP

114
Q

tRNA + aa = ?

A

aminoacyl-tRNA

115
Q

What correctly attached an amino acid to the appropriate tRNA?

A

aminoacyl-tRNA synthetase

116
Q

How many different aminoacyl-tRNA synthase are there?

A

20

117
Q

How many amino acids do aminoacyl-tRNA synthase recognize for attachment to the correct set of tRNA’s?

A

One

118
Q

Initiation requirements

A

1) mRNA
2) small and large ribosome subunit
3) initiator-tRNA
4) initiation factors (IFs)
5) Guanosine triphosphate (GTP)

119
Q

IF-3 binding to the small subunit results in what? (in prokaryotes)

A

Prevents the large subunit from binding, thus allowing the small subunit to attach to mRNA.

120
Q

What is initiator tRNA charged with?

A

fMET amino acid (N-formylmethionine)

121
Q

IF-3 protein function

A

keep the small and large ribosomes seperated

122
Q

IF-1 and 2 functions

A

facilitates initiator-tRNA binding to the correct site

123
Q

What forms the 70S initiation complex?

A

initiation factor proteins dissociate and the large ribosome subunits binds

124
Q

Key steps in elongation?

A

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
Q

Elongation requirements

A

1) aa-tRNAs (or charged tRNAs)
2) 70S initiation complex
3) Elongation factors (EFs)
4) GTP

126
Q

A-site (aminoacyl) function

A

accepts the incoming aa-tRNA carrying the next amino acid to be added to the chain

127
Q

P-site (peptidyl) function

A

holds the tRNA carrying the growing polypeptide

128
Q

E-site (exit) function

A

discharged tRNA’s leave the ribosome from this site

129
Q

What catalyses peptide bond formation?

A

peptidyl transferase

130
Q

Ribosome movement (translocation) is facilitated by what?

A

elongation factors

131
Q

What direction does ribosome translocate on the mRNA?

A

5’ to 3’ direction

132
Q

When does protein synthesis terminate?

A

When the ribosome translocates to a stop codon

133
Q

What does release factor (RF) protein binding to the A site trigger?

A

Release of the polypeptide from the P-site tRNA

134
Q

Eukaryotic mRNA is _

A

monocystronic (single ORF)

135
Q

What does eukaryotic ribosome complex look like?

A

3 RNA molecules (28S + 5S, and 18S) and 2 sub-units (60S + 40S = 80S)

136
Q

Do eukaryotes have consensus sequences for ribosome binding?

A

no

137
Q

What facilitates ribosome binding for eukaryotes?

A

5- CAP and 3’ poly(A) tail

BIOL 2030 (7 decks)

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