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AP Bio > Unit 6: Gene Expression & Regulation > Flashcards

Unit 6: Gene Expression & Regulation Flashcards

1
Q

Frederick Griffith (1928) Finding

A

living R bacteria transformed into
deadly S bacteria by unknown, heritable substance

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2
Q

Avery, McCarty, MacLeod (1944)

A

Tested DNA, RNA, & proteins in heat-killed pathogenic bacteria
Discovered that the transforming agent was DNA

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3
Q

Bacteriophages

A

virus that infects bacteria; composed of DNA & protein

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4
Q

Hershey and Chase (1952)

A

DNA entered infected bacteria -> DNA must be the genetic material!

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5
Q

Chargaff’s Rules:

A

DNA composition varies between species
Ratios: %A = %T and %G = %C
C & T Pyrimidine , A & G = Purines

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6
Q

Rosalind Franklin (1950’s)

A

X-ray crystallography = images of DNA
Provided measurements on chemistry of DNA

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7
Q

James Watson & Francis Crick (1953)

A

Discovered the double helix

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8
Q

DNA = Double Helix: Backbone & Rungs

A

“Backbone” = sugar + phosphate
“Rungs” = nitrogenous bases

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9
Q

Nitrogenous Bases

A

Adenine (A), Guanine (G)
Thymine (T), Cytosine (C)
A-T, C-G pure as gold,

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10
Q

What bonds are between base pairs of the 2 strands holding together molecule like zipper?

A

HYDROGEN BONDS

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11
Q

DNA strands = Antiparallel

A

Antiparallel, One strand (5’ -> 3’), other strand runs in opposite,
upside-down direction (3’ -> 5’)

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12
Q

How is DNA packaged? - Histones

A

the wrapping of DNA affects how genes are turned on or off ex: when chromosomes are tightly packed, it makes it more difficult for the transcription process to occur effectively. DNA is usually bound around the histones (supercoiled = does not express)

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13
Q

Prokaryotic DNA

A

Double-stranded
Circular
One chromosome
In cytoplasm
Supercoiled DNA
(nucleoid)
No histones

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14
Q

Eukaryotic DNA

A

Double-stranded
Linear
Usually 1+ chromosomes
In nucleus
Chromatin = DNA wrapped
around histones (proteins)

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15
Q

DNA Replication:

A

Making DNA from existing DNA

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16
Q

Meselson & Stahl (DNA Replication)

A

Replication = semiconservative & occurs 5’ -> 3’

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17
Q

DNA Replication = Semiconservative meaning

A

2 strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand. This results in two DNA molecules with one original strand and one new strand

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18
Q

Helicase

A

unwinds DNA at origins of replication & creates replication forks

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19
Q

Primase

A

Adds RNA primer to start replication

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20
Q

DNA polymerase III

A

adds complimentary nucleotide bases covalently to leading strand (new DNA is made 5’ → 3’)

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21
Q

Okazaki Fragments:

A

Short segments of DNA that grow 5’->3’ that are added onto the Lagging Strand

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22
Q

DNA pol I

A

replace RNA primer w/ DNA

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23
Q

DNA Ligase

A

joins 3’ end of DNA that replaces primer to rest of leading strand seals together fragments of lagging strand

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24
Q

Topoisomerase

A

relieves overwinding strain ahead of replication forks by breaking, swiveling, rejoining DNA strands

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25
Q

Lagging strand grows?

A

in 3’→5’ direction by the addition of
Okazaki fragments

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26
Q

Gene Expression

A

process by which DNA directs the synthesis of proteins (or RNAs)
one gene-> one RNA molecule (which can
be translated into a polypeptide)

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27
Q

Central Dogma

A

DNA -> RNA -> Proteins

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28
Q

TranSCRIPTion

A

DNA -> RNA

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29
Q

TranSLATion

A

RNA -> Proteins

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30
Q

Ribosome =

A

Site of translation

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31
Q

Difference between flow of genetic information between eukaryotes & prokaryotes

A

Prokaryotes = no nucleus so DNA can legit touch RNA & Ribosome

Eukaryotes = have nucleus containing RNA and DNA but ribosome = in cytoplasm

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32
Q

One gene = how many RNA molecules?

A

1

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33
Q

DNA

A

Nucleic acid composed of
nucleotides
Double stranded
Deoxygenated (Deoxyribose=sugar)
Thymine
Template for individual

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34
Q

RNA

A

Nucleic acid composed of
nucleotides
Single-stranded
Ribose=sugar
Uracil
Many different roles!

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35
Q

pre-mRNA

A

precursor to mRNA, newly transcribed and not edited

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36
Q

mRNA

A

edited version; carries the code from DNA that specifies amino acids

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37
Q

tRNA

A

carries a specific amino acid to ribosome based on its anticodon to mRNA codon

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38
Q

miRNA/siRNA

A

micro/small interfering RNA; binds to mRNA or
DNA to block it, regulate gene expression, or cut it up

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39
Q

mRNA (5’ → 3’)

A

complementary to
DNA template bc template (3’ -> 5’)

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40
Q

mRNA triplets (codons)

A

code for amino acids in
polypeptide chain

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41
Q

Redundancy Genetic Code

A

1+ codons
code for each of 20 AAs

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42
Q

Reading frame (genetic code)

A

groups of 3 must be read in correct groupings

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43
Q

Transcription unit

A

stretch of DNA that codes for a polypeptide or RNA (ex: tRNA, rRNA)

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44
Q

RNA polymerase

A

Separates DNA strands and transcribes mRNA
mRNA elongates in 5’ → 3’ direction
Uracil (U) replaces thymine (T) when pairing toadenine (A)
Attaches to promoter (start of gene) and stops at terminator (end of gene)

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45
Q

Initiation (Transcription) in Bacteria

A

RNA polymerase binds directly to promoter in DNA

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46
Q

Initiation (Transcription) in Eukaryotes

A

TATA Box
Promoter Region
Transcription Factors

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47
Q

TATA box + Promoter region (initiation, transcription) Euk

A

DNA sequence (TATAAAA) in promoter region upstream from
transcription start site

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48
Q

Upstream DNA

A

toward the 5’ end of the coding strand for the gene

49
Q

Downstream DNA

A

toward the 3’ end

50
Q

Coding Strand

A

determines the correct nucleotide sequence of mRNA
not in transcription
3’ -> 5’
complimentary nucleotide sequence

51
Q

Template strand

A

base for mRNA transcription
antisense strand, non coding, take part in transcription & Help formation of mRNA.
5’ to 3’ no complimentary sequence

52
Q

Antiparallel nature of DNA

A

2 strands, each with a backbone of alternating phosphate & sugar groups
Strands run in opposite directions (5’ -> 3’ & 3’ -> 5’)

53
Q

Transcription factors (initiation, transcription) eukaryotes

A

must recognize TATA box before RNA polymerase can bind to DNA promoter

54
Q

Transcription Initiation complex

A

Transcription Factors + RNA Polymerase =

55
Q

Elongation (Transcription )

A

RNA polymerase adds RNA nucleotides to the 3’ end of the growing chain (A-U, G-C) As RNA polymerase moves, it untwists
DNA, then rewinds it after mRNA is made

56
Q

Termination (Transcription) Prok

A

RNA polymerase transcribes a terminator sequence then mRNA and polymerase detach NOW mRNA ready to use

57
Q

Termination (Transcription) Euk

A

polyadenylation signal sequence then mRNA and polymerase detach NOW called pre-mRNA

58
Q

Eukaryotic cells modify RNA after transcription

A

5’ cap
3’ poly-A tail

59
Q

5’ cap

A

(modified guanine)

60
Q

3’ poly-A tail

A

(50-250 A’s) are added

61
Q

Functions for 5’ cap & 3’ poly-A tail

A
  1. Export from nucleus
  2. Protect mRNA from enzyme degradation
  3. Attach mRNA to ribosomes in cytoplasm
62
Q

RNA Splicing

A

Pre-mRNA has introns (noncoding sequences) &
exons (codes for amino acids)
Splicing = introns cut out, exons joined together

63
Q

RNA splicing (cont.) snRNPs

A

snRNPs join with other
proteins to form a spliceosome

64
Q

RNA Splicing (cont. Spliceosome)

A

catalyze (makes faster) the process of removing introns &
joining exons
Ribozyme = RNA acts as enzyme (catalytic role)

65
Q

Why do we have introns?

A

Some regulate gene activity
Alternative RNA Splicing: produce different combinations of exons
One gene can make more than one polypeptide!
20,000 genes → 100,000 polypeptides

66
Q

Components of Translation

A

mRNA = message
tRNA = interpreter
Ribosome = site of translation

67
Q

tRNA

A

Transcribed in nucleus. Specific to each amino acid. Transfer AA to ribosomes

68
Q

Anticodon

A

pairs w/ complementary mRNA codon

69
Q

Wobble (translation)

A

Base-pairing rules between 3rd base of codon & anticodon are
not as strict.

70
Q

Aminoacyl-tRNA-synthetase:

A

enzyme that binds tRNA to specific amino acid

71
Q

Ribosomes

A

rRNA + proteins,made in nucleolus
2 subunits: Active sites: A site: holds AA to be added & P site: holds growing polypeptide chain
E site: exit site for tRNA

72
Q

Ribosome active sites

A

A site: holds AA to be added
P site: holds growing polypeptidechain
E site: exit site for tRNA

73
Q

Initiation (tranSLATion)

A

Small subunit binds to start codon (AUG) on mRNA
tRNA carrying Met attaches to P site
Large subunit attaches

74
Q

Elongation (tranSLATion) Codon Recognition

A

tRNA anticodon matches codon in A site

75
Q

Elongation (tranSLATion)Peptide bond formation:

A

AA in A site forms bond w/ peptide in P site

76
Q

Elongation (tranSLATion): Translocation

A

tRNA in A site moves to P site; tRNA in P site moves to E site (then exits)

77
Q

Termination (tranSLATion):

A

Stop codon reached & translation stops
Release factor binds to stop codon; polypeptide = released
Ribosomal subunits dissociate

78
Q

Protein Folding

A

During synthesis, polypeptide chain coils & folds spontaneously
Chaperonin: protein that helps polypeptide fold correctly

79
Q

Post-Translational Modifications

A

Attach sugars, lipids, phosphate groups, etc.
Remove amino acids from ends
Cut into several pieces
Subunits come together

80
Q

Free ribosomes:

A

synthesize proteins that stay in cytosol & function there

81
Q

Bound ribosomes (to ER):

A

make proteins of
endomembrane system (nuclear envelope, ER, Golgi, lysosomes, vacuoles, plasma membrane) & proteins
for secretion, Uses signal peptide to target location

82
Q

Signal peptide:

A

20 AA at leading end of polypeptide Signal-recognition particle (SRP):determines destination

83
Q

Signal-recognition particle (SRP):

A

brings ribosome to ER

84
Q

Polyribosomes

A

A single mRNA can be
translated by several
ribosomes at the same
time

85
Q

Mutations occur in DNA & affect RNA + Proteins

A

changes in the genetic material of a cell

86
Q

Chromosomal Mutation

A

large-scale; always causes disorders or
death (eg. nondisjunction, translocation, inversions, duplications,
large deletions)

87
Q

Point Mutations

A

change single nucleotide pair of a gene: Substitution & Frameshift (insertion/deletion)

88
Q

Substitution Mutation

A

– replace 1 with another
Silent: same amino acid (no effect)
Missense: different amino acid (change shape & function)
Nonsense: stop codon, not amino acid

89
Q

Frameshift (insertion/deletion) Mutation

A

mRNA read incorrectly;
nonfunctional proteins (will kill itself) (whole line - fucked)

90
Q

Mutagens

A

substances of forces that cause mutations in DNA

91
Q

Prokaryotes (everything)

A

Transcription & translation both in
cytoplasm
DNA/RNA in cytoplasm
RNA poly binds directly to promoter
Transcription makes mRNA (not processed)
No introns

92
Q

Eukaryotes (everything)

A

Transcription in nucleus; translation in cytoplasm
DNA in nucleus, RNA travels in/out nucleus
RNA poly binds to TATA box & transcription factors
Transcription makes pre-mRNA -> RNA processing -> final mRNA
Exons, introns (cut out)

93
Q

GENE:

A

A region of DNA that can be expressed to produced a final
product that is either a polypeptide or an RNA molecule

94
Q

Bacterial control of gene expression (Operon)

A

cluster of related genes with on/off switch

95
Q

Operon 3 Parts

A

Promoter – where RNA polymerase attaches
Operator – “on/off”, controls access of RNA poly
Genes – code for related enzymes in a pathway

96
Q

Regulatory gene

A

produces repressor
protein that binds to operator to block RNA
polymerase

97
Q

Repressible Operons

A

Normally ON -> OFF
Anabolic (build organic molecules)
Organic molecule product acts as corepressor → binds to repressor to activate it
Ex:. trp operon

98
Q

Inducible Operons

A

Normally OFF -> ON
Catabolic (break down food for energy)
Repressor is active → inducer binds to &
shuts off repressor
Ex: lac operon

99
Q

Gene Regulation: Negative Control

A

operons are switched off by active form of repressor protein
Ex: trp operon, lac operon

100
Q

Gene Regulation: Positive control:

A

Regulatory protein interacts directly w/ genome to increase transcription
Ex: cAMP & CRP

101
Q

cAMP + CRP = Positive Control

A

cAMP: accumulates when glucose = scarce
cAMP binds to CRP (cAMP receptor protein)
Active CRP → binds to DNA upstream of promoter, ↑ affinity of RNA polymerase to promoter, ↑ transcription

102
Q

Chromatin Structure (Gene expression)

A

Tightly bound DNA → less accessible for transcription

103
Q

DNA methylation (silence)

A

methyl groups added to DNA; tightly packed; ↓ transcription

104
Q

Histone acetylation (power up)

A

acetyl groups added to histones; ;loosened;↑ transcription

105
Q

Transcription Initiation

A

Specific transcriptionfactors (activators or repressors) bind to control elements (enhancer region)

106
Q

Activators

A

increase transcription

107
Q

Repressors

A

decrease transcription

108
Q

Transcription Initiation Complex (Gene expression)

A

Activators or Repressors bind to enhancer regions + other proteins + RNA polymerase

109
Q

Regulation of mRNA micro RNAs

A

micro RNAs (miRNAs)& small interfering RNAs (siRNAs) can bind to mRNA and degrade it (complementary bases) /block translation (less complete)

110
Q

semiconservative nature of DNA

A

after one round of replication, every new DNA double helix would be a hybrid that consisted of one strand of old DNA bound to one strand of newly synthesized DNA

111
Q

Plasmids

A

small circular DNA molecule found in bacteria
physically separate from chromosomal DNA & replicate independently.

112
Q

Gel Electrophoresis

A

used to separate DNA molecules
on basis of size and charge using an electrical current (smaller = get farther thru gel)
(DNA → + pole)

113
Q

Gene Transformation

A

bacteria takes up plasmid (w/gene of
interest)

114
Q

PCR

A

(Polymerase Chain Reaction): amplify (copy) piece of DNA without use of cells

115
Q

DNA microarray assays

A

study many genes at the same time

116
Q

Restriction enzymes

A

used to cut strands of DNA at
specific locations (restriction sites)

117
Q

difference in DNA replication for eukaryotes vs prokaryotes

A

pro: 1 origin of replication, eukaryotes = many origins

118
Q

difference in cell division of eukaryotes vs prokaryotes

A

pro: binary fission, euk: mitosis

119
Q
A

AP Bio (8 decks)

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