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
2
Q
Avery, McCarty, MacLeod (1944)
A
Tested DNA, RNA, & proteins in heat-killed pathogenic bacteria
Discovered that the transforming agent was DNA
3
Q
Bacteriophages
A
virus that infects bacteria; composed of DNA & protein
4
Q
Hershey and Chase (1952)
A
DNA entered infected bacteria -> DNA must be the genetic material!
5
Q
Chargaff’s Rules:
A
DNA composition varies between species
Ratios: %A = %T and %G = %C
C & T Pyrimidine , A & G = Purines
6
Q
Rosalind Franklin (1950’s)
A
X-ray crystallography = images of DNA
Provided measurements on chemistry of DNA
7
Q
James Watson & Francis Crick (1953)
A
Discovered the double helix
8
Q
DNA = Double Helix: Backbone & Rungs
A
“Backbone” = sugar + phosphate
“Rungs” = nitrogenous bases
9
Q
Nitrogenous Bases
A
Adenine (A), Guanine (G)
Thymine (T), Cytosine (C)
A-T, C-G pure as gold,
10
Q
What bonds are between base pairs of the 2 strands holding together molecule like zipper?
A
HYDROGEN BONDS
11
Q
DNA strands = Antiparallel
A
Antiparallel, One strand (5’ -> 3’), other strand runs in opposite,
upside-down direction (3’ -> 5’)
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)
13
Q
Prokaryotic DNA
A
Double-stranded
Circular
One chromosome
In cytoplasm
Supercoiled DNA
(nucleoid)
No histones
14
Q
Eukaryotic DNA
A
Double-stranded
Linear
Usually 1+ chromosomes
In nucleus
Chromatin = DNA wrapped
around histones (proteins)
15
Q
DNA Replication:
A
Making DNA from existing DNA
16
Q
Meselson & Stahl (DNA Replication)
A
Replication = semiconservative & occurs 5’ -> 3’
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
18
Q
Helicase
A
unwinds DNA at origins of replication & creates replication forks
19
Q
Primase
A
Adds RNA primer to start replication
20
Q
DNA polymerase III
A
adds complimentary nucleotide bases covalently to leading strand (new DNA is made 5’ → 3’)
21
Q
Okazaki Fragments:
A
Short segments of DNA that grow 5’->3’ that are added onto the Lagging Strand
22
Q
DNA pol I
A
replace RNA primer w/ DNA
23
Q
DNA Ligase
A
joins 3’ end of DNA that replaces primer to rest of leading strand seals together fragments of lagging strand
24
Q
Topoisomerase
A
relieves overwinding strain ahead of replication forks by breaking, swiveling, rejoining DNA strands
25
Lagging strand grows?
in 3’→5’ direction by the addition of
Okazaki fragments
26
Gene Expression
process by which DNA directs the synthesis of proteins (or RNAs)
one gene-> one RNA molecule (which can
be translated into a polypeptide)
27
Central Dogma
DNA -> RNA -> Proteins
28
TranSCRIPTion
DNA -> RNA
29
TranSLATion
RNA -> Proteins
30
Ribosome =
Site of translation
31
Difference between flow of genetic information between eukaryotes & prokaryotes
Prokaryotes = no nucleus so DNA can legit touch RNA & Ribosome
Eukaryotes = have nucleus containing RNA and DNA but ribosome = in cytoplasm
32
One gene = how many RNA molecules?
1
33
DNA
Nucleic acid composed of
nucleotides
Double stranded
Deoxygenated (Deoxyribose=sugar)
Thymine
Template for individual
34
RNA
Nucleic acid composed of
nucleotides
Single-stranded
Ribose=sugar
Uracil
Many different roles!
35
pre-mRNA
precursor to mRNA, newly transcribed and not edited
36
mRNA
edited version; carries the code from DNA that specifies amino acids
37
tRNA
carries a specific amino acid to ribosome based on its anticodon to mRNA codon
38
miRNA/siRNA
micro/small interfering RNA; binds to mRNA or
DNA to block it, regulate gene expression, or cut it up
39
mRNA (5’ → 3’)
complementary to
DNA template bc template (3' -> 5')
40
mRNA triplets (codons)
code for amino acids in
polypeptide chain
41
Redundancy Genetic Code
1+ codons
code for each of 20 AAs
42
Reading frame (genetic code)
groups of 3 must be read in correct groupings
43
Transcription unit
stretch of DNA that codes for a polypeptide or RNA (ex: tRNA, rRNA)
44
RNA polymerase
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)
45
Initiation (Transcription) in Bacteria
RNA polymerase binds directly to promoter in DNA
46
Initiation (Transcription) in Eukaryotes
TATA Box
Promoter Region
Transcription Factors
47
TATA box + Promoter region (initiation, transcription) Euk
DNA sequence (TATAAAA) in promoter region upstream from
transcription start site
48
Upstream DNA
toward the 5' end of the coding strand for the gene
49
Downstream DNA
toward the 3' end
50
Coding Strand
determines the correct nucleotide sequence of mRNA
not in transcription
3' -> 5'
complimentary nucleotide sequence
51
Template strand
base for mRNA transcription
antisense strand, non coding, take part in transcription & Help formation of mRNA.
5’ to 3’ no complimentary sequence
52
Antiparallel nature of DNA
2 strands, each with a backbone of alternating phosphate & sugar groups
Strands run in opposite directions (5' -> 3' & 3' -> 5')
53
Transcription factors (initiation, transcription) eukaryotes
must recognize TATA box before RNA polymerase can bind to DNA promoter
54
Transcription Initiation complex
Transcription Factors + RNA Polymerase =
55
Elongation (Transcription )
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
Termination (Transcription) Prok
RNA polymerase transcribes a terminator sequence then mRNA and polymerase detach NOW mRNA ready to use
57
Termination (Transcription) Euk
polyadenylation signal sequence then mRNA and polymerase detach NOW called pre-mRNA
58
Eukaryotic cells modify RNA after transcription
5’ cap
3’ poly-A tail
59
5’ cap
(modified guanine)
60
3’ poly-A tail
(50-250 A’s) are added
61
Functions for 5' cap & 3' poly-A tail
1. Export from nucleus
2. Protect mRNA from enzyme degradation
3. Attach mRNA to ribosomes in cytoplasm
62
RNA Splicing
Pre-mRNA has introns (noncoding sequences) &
exons (codes for amino acids)
Splicing = introns cut out, exons joined together
63
RNA splicing (cont.) snRNPs
snRNPs join with other
proteins to form a spliceosome
64
RNA Splicing (cont. Spliceosome)
catalyze (makes faster) the process of removing introns &
joining exons
Ribozyme = RNA acts as enzyme (catalytic role)
65
Why do we have introns?
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
Components of Translation
mRNA = message
tRNA = interpreter
Ribosome = site of translation
67
tRNA
Transcribed in nucleus. Specific to each amino acid. Transfer AA to ribosomes
68
Anticodon
pairs w/ complementary mRNA codon
69
Wobble (translation)
Base-pairing rules between 3rd base of codon & anticodon are
not as strict.
70
Aminoacyl-tRNA-synthetase:
enzyme that binds tRNA to specific amino acid
71
Ribosomes
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
Ribosome active sites
A site: holds AA to be added
P site: holds growing polypeptidechain
E site: exit site for tRNA
73
Initiation (tranSLATion)
Small subunit binds to start codon (AUG) on mRNA
tRNA carrying Met attaches to P site
Large subunit attaches
74
Elongation (tranSLATion) Codon Recognition
tRNA anticodon matches codon in A site
75
Elongation (tranSLATion)Peptide bond formation:
AA in A site forms bond w/ peptide in P site
76
Elongation (tranSLATion): Translocation
tRNA in A site moves to P site; tRNA in P site moves to E site (then exits)
77
Termination (tranSLATion):
Stop codon reached & translation stops
Release factor binds to stop codon; polypeptide = released
Ribosomal subunits dissociate
78
Protein Folding
During synthesis, polypeptide chain coils & folds spontaneously
Chaperonin: protein that helps polypeptide fold correctly
79
Post-Translational Modifications
Attach sugars, lipids, phosphate groups, etc.
Remove amino acids from ends
Cut into several pieces
Subunits come together
80
Free ribosomes:
synthesize proteins that stay in cytosol & function there
81
Bound ribosomes (to ER):
make proteins of
endomembrane system (nuclear envelope, ER, Golgi, lysosomes, vacuoles, plasma membrane) & proteins
for secretion, Uses signal peptide to target location
82
Signal peptide:
20 AA at leading end of polypeptide Signal-recognition particle (SRP):determines destination
83
Signal-recognition particle (SRP):
brings ribosome to ER
84
Polyribosomes
A single mRNA can be
translated by several
ribosomes at the same
time
85
Mutations occur in DNA & affect RNA + Proteins
changes in the genetic material of a cell
86
Chromosomal Mutation
large-scale; always causes disorders or
death (eg. nondisjunction, translocation, inversions, duplications,
large deletions)
87
Point Mutations
change single nucleotide pair of a gene: Substitution & Frameshift (insertion/deletion)
88
Substitution Mutation
– replace 1 with another
Silent: same amino acid (no effect)
Missense: different amino acid (change shape & function)
Nonsense: stop codon, not amino acid
89
Frameshift (insertion/deletion) Mutation
mRNA read incorrectly;
nonfunctional proteins (will kill itself) (whole line - fucked)
90
Mutagens
substances of forces that cause mutations in DNA
91
Prokaryotes (everything)
Transcription & translation both in
cytoplasm
DNA/RNA in cytoplasm
RNA poly binds directly to promoter
Transcription makes mRNA (not processed)
No introns
92
Eukaryotes (everything)
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
GENE:
A region of DNA that can be expressed to produced a final
product that is either a polypeptide or an RNA molecule
94
Bacterial control of gene expression (Operon)
cluster of related genes with on/off switch
95
Operon 3 Parts
Promoter – where RNA polymerase attaches
Operator – “on/off”, controls access of RNA poly
Genes – code for related enzymes in a pathway
96
Regulatory gene
produces repressor
protein that binds to operator to block RNA
polymerase
97
Repressible Operons
Normally ON -> OFF
Anabolic (build organic molecules)
Organic molecule product acts as corepressor → binds to repressor to activate it
Ex:. trp operon
98
Inducible Operons
Normally OFF -> ON
Catabolic (break down food for energy)
Repressor is active → inducer binds to &
shuts off repressor
Ex: lac operon
99
Gene Regulation: Negative Control
operons are switched off by active form of repressor protein
Ex: trp operon, lac operon
100
Gene Regulation: Positive control:
Regulatory protein interacts directly w/ genome to increase transcription
Ex: cAMP & CRP
101
cAMP + CRP = Positive Control
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
Chromatin Structure (Gene expression)
Tightly bound DNA → less accessible for transcription
103
DNA methylation (silence)
methyl groups added to DNA; tightly packed; ↓ transcription
104
Histone acetylation (power up)
acetyl groups added to histones; ;loosened;↑ transcription
105
Transcription Initiation
Specific transcriptionfactors (activators or repressors) bind to control elements (enhancer region)
106
Activators
increase transcription
107
Repressors
decrease transcription
108
Transcription Initiation Complex (Gene expression)
Activators or Repressors bind to enhancer regions + other proteins + RNA polymerase
109
Regulation of mRNA micro RNAs
micro RNAs (miRNAs)& small interfering RNAs (siRNAs) can bind to mRNA and degrade it (complementary bases) /block translation (less complete)
110
semiconservative nature of DNA
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
Plasmids
small circular DNA molecule found in bacteria
physically separate from chromosomal DNA & replicate independently.
112
Gel Electrophoresis
used to separate DNA molecules
on basis of size and charge using an electrical current (smaller = get farther thru gel)
(DNA → + pole)
113
Gene Transformation
bacteria takes up plasmid (w/gene of
interest)
114
PCR
(Polymerase Chain Reaction): amplify (copy) piece of DNA without use of cells
115
DNA microarray assays
study many genes at the same time
116
Restriction enzymes
used to cut strands of DNA at
specific locations (restriction sites)
117
difference in DNA replication for eukaryotes vs prokaryotes
pro: 1 origin of replication, eukaryotes = many origins
118
difference in cell division of eukaryotes vs prokaryotes
pro: binary fission, euk: mitosis
119
