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Genetics > 9.3, 9.4, 11, 12 > Flashcards

9.3, 9.4, 11, 12 Flashcards

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Biology 101 flashcards
1
Q

_____ consist of one small ribosomal subunit and one large ribosomal subunit

A

Ribosomes

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2
Q

The sequence _____ is found at the very 3′ end of all tRNAs, the amino acid attachment site.

A

5′-CCA-3′

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3
Q

Single-stranded, 75 nucleotides, cloverleaf shape with four double-helical stems and three single-stranded loops.

A

tRNA

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4
Q

A nucleotide triplet in a tRNA molecule that aligns with a particular codon in mRNA under the influence of the ribosome; the amino acid carried by the tRNA is inserted into a growing protein chain.

A

anticodon

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5
Q

anticodon is complementary to:

A

the mRNA codon for the amino acid carried by the tRNA

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6
Q

tRNAs are transcribed with:

A

the standard four nucleotides

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7
Q

;All tRNAs fold into virtually the same inverted L-shaped three-dimensional ____ conformation.

A

cloverleaf

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8
Q

The anticodon in tRNA and the codon in the mRNA interact by:

A

specific RNA:RNA base pairing

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9
Q

anticodons are oriented and written in the _____ direction

A

3′-to-5′

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10
Q

tRNAs have four important structural features:

A

(1) the sequence CCA at the 3′ end; (2) modified nucleotides such as dihydrouridine, pseudouridine, and inosine; (3) an overall inverted L shape; and (4) an anticodon.

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11
Q

Amino acids are attached to tRNAs by enzymes called:

A

aminoacyl-tRNA synthetases

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12
Q

The tRNA with an attached amino acid is said to be

A

charged tRNA

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13
Q

First step of charging tRNA

A

carboxyl group of the amino acid reacts with the α-phosphate of ATP to form 5′-aminoacyl-AMP and release pyrophosphate

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14
Q

Second step of charging tRNA

A

the amino acid is transferred to the adenosine (A) of the invariant CCA sequence at the 3′ end of the tRNA, and AMP is released as a by-product.

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15
Q

If the wrong amino acid is attached…

A

there is no way to prevent it from being incorporated into a growing polypeptide chain - amino acids are “illiterate”

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16
Q

to prevent mistakes, aminoacyl-tRNA synthetases have a ______ that discriminates between chemically similar amino acids such as valine (Val) and isoleucine (Ile), which differ by only a single CH2 group

A

two-step mechanism

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17
Q

The first discrimination step

A

rejects amino acids that do not fit into the activation site because they are too large

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18
Q

The second discrimination step

A

Val-tRNAIle, but not Ile-tRNAIle, fits into a separate active site of the synthetase and is hydrolyzed to valine and tRNAIle

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19
Q

______________ allows tRNAs to recognize more than one codon

A

Wobble base pairing

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20
Q

the third codon

A

the wobble position

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21
Q

inosine (I), a rare modified base in tRNA, can base pair to

A

C, U, A

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22
Q

Therefore, because of wobble base pairing, cells require ______ tRNAs to read all of the codons.

A

fewer than 61

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23
Q

Sedimentation coefficients in ______ measure the size of the molecule.

A

Svedberg (S) units

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24
Q

In bacteria, the small and large subunits are _________ and form a ____ particle.

A

30S and 50S; 70S

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25
Q

The eukaryotic subunits are _________, and they form an ______ particle.

A

40S and 60S, 80S

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26
Q

rRNAs fold up by _________ into stable secondary structures.

A

intramolecular base pairing

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27
Q

_____, assisted by the ribosomal proteins, catalyze protein synthesis.

A

rRNAs

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28
Q

Key sites of interaction in the ribosome:

A

A, P, E sites in the small subunit and the peptidyl transferase center in the large subunit.

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29
Q

The ___________ is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG

A

Shine–Dalgarno sequence

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30
Q

a nucleic acid motif that functions as the protein translation initiation site in most eukaryotic mRNA transcripts. (surrounding the first AUG in eukaryote mRNAs)

A

Kozak sequence

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31
Q

_______ bring the initiator tRNA to the ribosomal small subunit and prevent premature binding of the large subunit.

A

Initiation factors

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32
Q

In eukaryotes, additional initiation factors facilitate:

A

mRNA scanning and circularization.

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33
Q

What are the two protein elongation factors function repeatedly to grow the polypeptide chain?

A
  1. EF-Tu brings charged tRNAs to the ribosome A site to be joined to the polypeptide chain in the P site.
  2. EF-G binds in the A site and promotes the translocation of tRNAs from the P and A sites to the E and P sites.
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34
Q

In eukaryotes, the analogous elongation factors are:

A

eEF1α and eEF2.

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35
Q

What are the translation release factors?

A

Proteins

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36
Q

How is translation terminated?

A

Release factors bind stop codons and release the polypeptide chain from the tRNA in the P site.

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37
Q

Other factors ____ the ribosome to begin another round of translation.

A

recycle

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38
Q

A ______ counteracts the effects of a nonsense mutation

A

tRNA suppressor

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39
Q

The two criteria for gene regulation mechanisms

A

1) Response to environmental cues
2) Toggle on and off

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40
Q

Regulatory proteins and their binding sites that control transcription

A

Genetic switches

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41
Q

DNA components (cis-acting):

A

promoter & operator

42
Q

Protein components (trans-acting):

A

Activator & Repressor

43
Q

Activator or repressor proteins bind to ___________ to control its accessibility to RNA polymerase.

A

operator sequences in the vicinity of the promoter

44
Q

Allosteric effectors bind to ____________

A

regulatory proteins

45
Q

Repressor protein controls the lac operon

A

Negative control

46
Q

The lac operon is transcribed only in the presence of _______

A

lactose

47
Q

an operon required for the transport and metabolism of lactose in E. coli and many other enteric bacteria

A

lac operon

48
Q

a region of DNA where RNA polymerase begins to transcribe a gene

A

promoter

49
Q

A segment of DNA where the repressor binds to, thereby preventing the transcription of certain genes

A

operator

50
Q

DNA-binding transcription metabolite that positively modulates an allosteric Enzyme or regulates one or more genes by increasing the rate of transcription

A

activator

51
Q

blocks the attachment of RNA polymerase to the promoter

A

repressor

52
Q

An agent capable of activating specific genes. A molecule that inhibits the action of the repressor of an operon, preventing it from freely binding with the operator gene and disabling its function.

A

Inducer

53
Q

A group of genes or a segment of DNA that functions as a single transcription unit. It is comprised of an operator, a promoter, and one or more structural genes that are transcribed into one polycistronic mRNA.

A

operon

54
Q

How are operons regulated?

A

They contain regulatory DNA sequences (binding sites) that control transcription of the operon

55
Q

chaperons that help repair other proteins which may become partially denatured through excessive heating

A

Heat shock proteins (HSPs)

56
Q

mechanisms that affect gene expression only on the same chromosomal allele

A

Cis-acting factors

57
Q

The gene that encodes the soluble ______ protein can reside on any chromosome, often located far away from the gene whose expression it regulates

A

trans-acting

58
Q

Operators are ____-acting

A

cis

59
Q

Catabolite repression of the lac operon

A

positive control

60
Q

_______ levels control the lac operon

A

Glucose

61
Q

By bending the DNA template, the DNA-bound CAP and cAMP can interact physically with RNA polymerase and increases that enzyme’s affinity for:

A

the lac promoter.

62
Q

Two regulators turn the operon “on” and “off” in response to lactose and glucose levels:

A

the lac repressor (negative) and catabolite activator protein (CAP) (positive)

63
Q

The _____ ensures the sequential utilization of different carbon sources depending on the bacterial cells’ nutritional environment.

A

lac operon

64
Q

Metabolic pathways and additional levels of regulation

A

attenuation

65
Q

Gene order in the trp operon corresponds to reaction order in:

A

the biosynthetic pathway

66
Q

Two mechanisms regulate trp operon:

A

1) trp repressor: trpR switch off trp operon in the presence of tryptophan
2) Attenuation

67
Q

The trp mRNA leader sequence contains

A

an attenuator region and two tryptophan codons

68
Q

The attenuation of transcription is mediated by

A

the abundance of tryptophan and translation of a leader peptide

69
Q

Can attenuation be used as a mechanism for regulating gene expression in eukaryotes?

A

No - in eukaryote transcription and translation do not take place in the same region of the cell

70
Q

The machinery required for regulating the distinct patterns of gene transcription in eukaryotic cells.

A

1) Trans-components
2) Cis-components
3) Coregulators

71
Q

Trans components

A

Transcription factors, general transcription factors (GTFs)

72
Q

Cis-components

A

core promoters, proximal promoters, enhancers ( proximal and distal)

73
Q

bridges transcription factors and RNA polymerase II.

A

Coactivators

74
Q

Transcriptional activator proteins - 2 functions

A

1) recruit the transcriptional machinery (including general transcription factors and RNA Polymerase II)
2) recruit proteins that modify chromatin structure (such as mediator)

75
Q

Transcription factors have modular structure: (4 things)

A

1) DNA binding
2) Activation/repression
3) Dimerization of transcription factors
4) Ligand-binding domains of transcription factors

76
Q

Multiple genes and their products import and convert _______ into glucose in a metabolic pathway.

A

galactose

77
Q

GAL4 regulates the expression of galactose/glucose through:

A

upstream activation sequences (UAS).

78
Q

GAL pathway response to environment?

A

controls the uptake and metabolism of the sugar

79
Q

Transcription factors in the yeast GAL system:

A

Cis: UAS
Trans: Gal4

80
Q

How is GAL4 activity regulated?

A

Gal4 levels are regulated by the F-box protein Grr1

81
Q

How does regulation of transcription differ between prokaryotes and eukaryotes?

A

Transcription is responsible for most gene regulation in prokaryotes but in eukaryotes gene regulation is more complicated and genes are regulated before and after transcription

82
Q

a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.

A

transcription factor

83
Q

What functional protein domains are found in transcription factors? - 3 things

A

1) a DNA binding domain, 2) one or more transcription activation and/or repressor domain, and 3) often a dimerization domain

84
Q

How can an enhancer located far away from the promoter help to activate transcription?

A

An enhancer can activate transcription from a target gene promoter through direct interaction over a large distance by creating a chromatin loop.

85
Q

________ is made up of nucleosomes that fold upon one another into a compact filament.

A

Chromatin

86
Q

Chromatin structure of genes
(3 things)

A

NFR
TADs
CTCF

87
Q

Mechanisms operate to enable dynamic access of the transcription machinery to DNA in ______ cells

A

eukaryotic

88
Q

altering the chemical structure of amino acids in histones or nucleotides in DNA to affect recruitment of transcription factors, coregulators, and general transcription factors to chromatin.

A

Chromatin modification

89
Q

remodeling nucleosomes—reposition histone octamers, remove histone octamers from DNA, or replace canonical histones in octamers with variant histones

A

Chromatin remodeling

90
Q

Histone acetylation is a type of:

A

chromatin modification

91
Q

______ leads to more open chromatin by loosening interactions between histones and DNA .

A

Acetylation

92
Q

Acetylation creates ________ with a bromodomain, which increases the affinity of the transcription factors for particular genes by binding acetylated histones.

A

binding sited for proteins

93
Q

Histone methylation

A

Lysine (K) and Arginine (R)

94
Q

Changing ________________ in nucleosomes to render DNA either more or less accessible to transcription regulators.

A

histone-DNA interactions

95
Q

Heritable changes to gene expression that are not due to changes in DNA sequences
Do not follow the Mendelian inheritance patterns

A

Epigenetic Inheritance

96
Q

the stochastic transcriptional silencing of a gene positioned adjacent to heterochromatin.

A

Position effect variegation

97
Q

the process by which only one copy of a gene in an individual (either from their mother or their father) is expressed, while the other copy is suppressed (autosomal)

A

Genomic imprinting

98
Q

Early in embryonic development in females, one of the two X chromosomes is randomly and permanently inactivated in cells other than egg cells

A

X-chromosome inactivation

99
Q

maternal imprinting

A

copy from father is turned on

100
Q

paternal imprinting

A

copy from mother is turned on

Genetics (6 decks)

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