EXAM 3 Flashcards
1
Q
OPERONS
A
Two or more genes that may be arranged together under a single promoter
2
Q
PARTS OF AN OPERON
A
Promoter (controls the ability of RNA Polymarase to transcribe)
Two or more genes
Terminator ar end
3
Q
lac OPERON
A
Promoter, Operator Site, CAP Site, lacZ, lacY, lacA
4
Q
PROMOTER
A
Binds to RNA Polymerase
5
Q
OPERATOR STE
A
Binds to the lac repressor protein
6
Q
CAP SITE
A
Binds to Catabolite Activator Protein (CAP)
7
Q
lacZ
A
Encodes for beta-galactosidase enzyme
This cleaves lactose into galactose and glucose
Also converts small amounts of lactose into allolactose
8
Q
lacY
A
Encodes for lactose permease
This transports lactose and analogues into the cytoplsm
9
Q
lacA
A
Encodes for galactose transacetylase
This covalently modifies lactose and its analogues
10
Q
lacI
A
Not part of lac operon
Has its own promoter
Encodes for lac repressor protein
Small amount of this protein is needed
11
Q
cAMP-CAP
A
Complex that binds to the CAP DNA site near the lac opereon promoter
12
Q
REGULATORY GENE
A
i-promoter
lacI
CAP Site
13
Q
cAMP
A
cyclic adenosine monophosphate
cyclic AMP
14
Q
SCENERIO 1
A
NO Glucose: High levels of cAMP Lactose Present: allolactose is present The presence of cAMP-CAP and absence of lac repressor allow RNA Polymerase to transcribe Lactose is metabolized
15
Q
SCENERIO 2
A
NO Glucose: High levels of cAMP NO Lactose: allolactose is not present lac I repressor is bound to operator lac I protein represses lac Z,Y,A transcription (CAP is bound) Neither sugra is metabolized
16
Q
SCENERIO 3
A
Glucose Present: Low levels of cAMP Lactose Present: allolactose present cAMP levels low, so no cAMP-CAP compound lac I repressor is inactive (allolactose) Glucose is metabolized only
17
Q
SCENERIO 4
A
Glucose Pesent: Low levels of cAMP NO Lactose: allolactose is not present cAMP levels low, so no cAMP-CAP compound lac I is active (no allolactose) lac I repressor binds to operator site Glucose is metabolized only
18
Q
TRP OPERON
A
Involved in the biosynthesis of the amino acid tryptophan.
Contains trpE,D,C,B,A
trpL gene encodes a short peptide called the leader peptide that functions in attenuation
trpR gene is not part of the operon, it encodes the trp repressor
19
Q
TRP OPERON PARTS
A
trpR, Promoter, Operator, Attenuator Sequence, trpE, trpD, trp,C, trpB, trpA
20
Q
ATTENUATOR SEQUENCE
A
This facilitates the termination of transcription
21
Q
FEATURES OF TRP OPERON AND ATTENUATION REGION
A
Contains 4 regions for coupling.
1-2 OR 2-3 OR 3-4
So 3 stem-loop secondary structures
If there is GC-rich, 3-4 hybridize to form a stem-loop, the U-rich region causes transcription attenuation.
22
Q
SCENARIO
A
When tryptophan is abundant, it acts as a corepressor.
It binds to the trp repressor and activates
trp repressor binds to operator, inhibits transcription
23
Q
ATTENUATION
A
Occurs because of coupling of translation and transcription
Occurs under high levels of tryptophan
24
Q
trpL
A
Plays a critical role in attenuation
Encodes short peptide of 14 amino acids
This peptide contains 2 tryptophan amino acids
25
REGION 1
Codes for trpL peptide with 2 tryptophan amino acids
26
REGION 2
Complementary to region 1 and 3
27
REGION 3
Complementary to region 2 and 4
28
REGION 4
Is GC-rich followed by many Uricil, and followed by the beginning of trpE coding sequence
29
SCENARIO NO COUPLING
The ribosome cannot bind
1-2 hybridization
3-4 hybridization
Transcription terminates intrinsically just past trpL gene
30
SCENARIO HIGH TRP
Attenuation will happen
Sufficient amounts of tRNA, translation of trpL progress until STOP codon.
Regions 1-2 are blocked by ribosome
3-4 hybridization
Transcription terminates intrinsically at U-rich sequence
31
SCENARIO LOW TRP
No attenuation
Happens due to coupling
Ribosome stalls in trpL region 1
Region 1 is Blocked, thus region 2 hybridizes with 3
Region 4 is left alone, intrinsic termination does not occur
32
SCENARIO NO RNA POLYMERASE
```
Attenuation will happen
Translation is not happening
1-2 Hybridization
3-4 Hybridization
Dormant state
```
33
CATABOLISM
Breakdown of a substance
Typically inducible
EX. Lactose/allolactose metabolism
34
ANABLISM
Biosynthesis of a substance
Typically repressible
EX. Tryptophan synthesis
35
POSTTRANSLATIONAL REGULATION - FEEDBACK INHIBITION
Feedback inhibition is a common mechanism to regulate enzyme activity
1. Change the allosteric enzyme configuration
2. Ability to bind is impacted
3. Enzyme function is inhibited
36
POSTTRANSLATIONAL REGULATION - MODIFICATION
Covalently modify the structure of the enzyme
Might be irreversible e.g.:
Proteolytic Processing means trimming of aa off a protein
Attachment of sugar or lipids
May be reversible e.g.:
Phosphorylation, Acetylation, Methylation
37
ALLOSTERIC ENZYME SITES
1. Catalytic site - Binds to substrate
| 2. Regulatory site - Binds to final product
38
TRANSLATIONAL REGULATION-REPRESSORS
Repressors inhibit translation
Translational regulatory proteins are known as translational repressors
EX. Binding of repressors near the Shine-Dalgarno sequence and/or start codon sterically hinders ribosome from initiating translation
39
TRANSLATION REGULATION-ANTISENSE RNA
Synthesis of antisense RNA means it is complementary to the mRNA
If these hybridize, it prevents the ribosome from initiating translation
40
TRANSCRIPTION FACTORS (TFs)
Proteins that influence the ability of RNA polymerase to transcribe a given gene
Generated by specific proteins
41
GENERAL/BASAL TFs
TF2D, TF2B, TF2F, TF2E, TF2H
These bind to the core promoter and its progression to elongation
Required for all transcription
42
REGULATORY TFs
Influence the transcription rate
Influence the ability of RNA to begin transcription
Most do NOT bind directly to RNA polymerase
Interact with TF2D via TAF subunits
43
REGULATORY ELEMENTS
TFs that recognize cis-regulatory elements near the core promoter
44
ACTIVATOR
Increases the rate of transcription
45
ENHANCER
The DNA sequence the ACTIVATOR binds to
46
REPRESSOR
A regulatory protein that decreases the rate of transcription
47
SILENCER
The DNA sequence the REPRESSOR binds to
48
DOMAINS
Regions of transcription factor proteins that have specific functions
49
MOTIF
A domain that has a similar structure in many different proteins
EX. Two alpha-helices helix-turn-helix (medium-medium)
EX. Two aplha-helices helix-loop-helix (short-long)
50
HOMODIMERS
Formed by two identical transcription factors
51
HETERODIMERS
Two different transcription factors
52
PROTEIN DIMERIZATION
When proteins associate with each other
| Leucine Zippers, a motif of two alpha-helices
53
ORIENTATION INDEPENDENT
```
Orientation independent (can function forward or reverse with respect to the gene)
Located with 200 nucleotides upstream of the promoter (exceptions)
```
54
TF2D & MEDIATOR
Interacts with REGULATORY TFs via TAF subunits
These interactions influence TF2D's ability to interact with the core promoter or RNA Pol2, subsequently basal transcription apparatus
55
TFs MODULATION
Ensure proper gene regulation, TFs must also be controlled
| EX: Binding of a hormone, protein-protein interaction, covalent modification
56
CREB PROTEIN
Cyclic AMP Response-Element Binding PROTEIN
57
ACTIVATION OF CREB PROTEIN
1. Extracellular signaling molecule
2. Receptor activates G protein
3. G protein activates adenylyl cyclase enzyme, which synthesizes cAMP
4. cAMP acts as second messenger and binds to activate protein Kinase A
5. Kinase A travels to the nucleus
6. Kinase A Phosphorylates of an already bound CREB Protein
7. Both un and phosphorylated CREB proteins bind to CREs
8. The CREB-CBP complex can initiate process
58
NUCLEOSOME REPOSITIONING
ATP hydrolysis repositions nucleosomes creating nucleosome-free regions.
SWI/SNF is one of the used
59
HISTONE VARIANTS
H1, H2A, H2B, H3, H4
| Several of these genes function as histone variants
60
HISTONE CODE
Over 50 mammalian enzymes
| Acetylation (facilitates transcription factors to bind and transcribe), Phospohrilation, Methylation (Silencing)
61
EXPRESSION OF GENE
Always will require a free region (NFR) where the regulatory sequence can be exposed, this will always create a potential to be transcribed.
62
TRANSCRIPTIONAL ACTIVATION MODEL
1. NFR at the 5' end where the enhancer sequence is present
2. Activator binds to the enhancer sequence
3. Protein recruits and ATP dependent remodeler (SWI)
4. Region is expanded
5. RNA Polymerase 2 attaches
6. Transcription can easily be initiated
7. RNA Pol2 knocks out some nucleosomes and rearrange them in the previous location
63
DNA METHYLATION
1. Unmethylated
2. Hemimethylated (will be observed when transcription has recently happened
3. Fully methylated
NOTE: DNA Methylation Patterns are heritable
64
CpG ISLANDS
1000-2000 nucleotides long that are C-G rich
| Don't necessarily engulf the promotor
65
METHY-CpG-BINDING
Recruit proteins such as histone acetylation, which causes the strand to compress
66
INSULATORS
DNA sequences that are are binding sites for insulator proteins that function as barriers or recruitment sites for regions in the DNA so certain regulations may occur (i.e. methylation, acetylation, etc)
67
H3K4me3
Happens when the TrxG complex and attaches 3 methyl groups to histone 4 (usually a lysine)
Very likely to be expressed
68
NON CODINGS RNA
Hybridize to other non-coding RNAs
Hybridize to
Form secondary structures
69
HOTAIR
Hox Transcript Antisense Intergenic RNA
This is a complex
Binds to two histone-modifying complexes in G-A rich regions
70
MICRO RNAs
miRNA are endogenous genes
1. Is formed
2. Folds to form a stem-loop
3. Trim down into precursor miRNA
4. Binds to esportin 5
5. Exportin 5 binds to miRNA and gets expelled from the nucleus
6. Double-strand miRNA binds to RISC (RNA Silencing Complex)
7. Searches for other complementary RNA
71
CRISPR-CAS SYSTEM
Clustered Regulatory, Interspaced, Short Palindromic Repeats
Type 2 System: Contain Crispr-Associated genes and palindromic repeats.
Locus: tract, Cas 9, Cas 1, Cas 2, Crispr (Palindromic repeats, which include phage genome and spacers)
72
ADAPTATION
1. Begins with bacterium being infected
2. Bacteriophage gets chopped and inactivate
3. Newly inserted segment from the invasive phage
4. Used in future opportunities in case a new attack happens
73
EXPRESSION
Occurs after adaptation
1. tracr gene is present and is being transcribed
2. non-coding RNA is being produced
3. complementary regions hybridize with the CRISPR sequence
4. tracrRNA base pairs
5. tracrRNA-crRNA complex bin
74
INTERFERENCE
Each spacer
75
MUTATIONS
Silent, Missense, Nonsense, Frameshift
76
TRANSITION MUTATION
A change in a single base pair of pyrimidine (C,T) to pyrimidine; or a purine (A,G) to a purine
77
TRANSVERSION MUTATION
A change in a single base pair of pyrimidine (C,T) to purine; or a purine (A,G) to a pyrimidine
78
SILENT MUTATION
Those whose substitutes don't cause changes to the amino acids afterwards
79
MISSENSE MUTATION
Those whose substitutes do cause changes to the amino acids afterward
80
NON-SENSE MUTATION
Those whose base substitutions that change a normal codon to a termination codon
81
FRAMESHIFT MUTATION
The insertion or deletion of a number of nucleotide that isn't divisible by 3
82
NON-CODING SEQUENCES MUTATION
Mutations within a promoter/regulatory gene, which can have up or down mutations (increase or decrease in transcription)
Mutation in exon/intro splice junctions
Mutations in 5'UTR/3'UTR
83
MUTATION EFFECTS ON GENOTYPE AND PHENOTYPE
Deleterious: decreases chances of survival
Beneficial: Enhances survival
Conditional: Temperature-dependent
84
SUPPRESSOR MUTATION
Seem like a reversion
Both mutations persist
Happens when Mutation 1 happens in site 1 from a gene, then Mutation 2 in site 2 happens from the gene and silences Mutation 1.
85
INTERGENIC SUPPRESSOR MUTATIONS
Occur between two different genes
86
CHROMOSOMAL REARRANGEMENT
This will silence a gene if the break occurs within the gene
| If the gene is intact its expression can be altered
87
SPONTANEOUS MUTATION
Depurination can cause a base to be lost
Termed apurinic site
These sites can be repaired
88
DEAMINATION
Removal of an amino group, primarily cytosine
| If the repair system fails it will result
89
DEAMMINATION 5 METHYL CYTOSINE
Results in the transformation of cytosine to thymine
90
INDUCED MUTATIONS
Using Nitrous Acid deamination of cytosine to uracil and adenin to hypoxinine
91
INTERPOLATION AGENTS
Flat structures that insert in between the bases, results in either insertions or deletions
92
PHYSICAL MUTIGENS
Ionizing radiation such as X-rays and UV light
X-rays can cause free radicals, reactive with O2
UV-lights causes the formation of cross-linked thymine dimers which covalently link thymine
93
DNA REPAIR
Base excision repair
Nucleotide repair
Mismatch Repair
94
BASE EXCISION REPAIR PROKARIOTIC
DNA N-glycosylase recognize abnormal bases and cleave
95
BASE EXCISION REPAIR EUKARYOTES
DNA Polymerase beta removes damaged site, DNA Polymerase epsilon can synthesis short piece oF DNA
96
NUCLEOTIDE EXCISION REPAIR
1. Two UvrA and UvrB scans for damaged DNA
2. UvrC binds to B and cuts upstream and downstream of the damaged side of the DNA
3. DNA Polymerase will fill the gap
4. DNA Ligase seals the nick
97
MISMATCH REPAIR
Intentionally focuses on the newly synthesized strand
1. Mismatch is identified, MutH and MutL is already bound to a hemimethylated DNA parental sequence
2.
3.
4. DNA Polymerase fills the cut-out daughter strand
5. DNA Ligase covalently links the strand
