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GENE 315 > EXAM 3 > Flashcards

EXAM 3 Flashcards

1
Q

OPERONS

A

Two or more genes that may be arranged together under a single promoter

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2
Q

PARTS OF AN OPERON

A

Promoter (controls the ability of RNA Polymarase to transcribe)
Two or more genes
Terminator ar end

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3
Q

lac OPERON

A

Promoter, Operator Site, CAP Site, lacZ, lacY, lacA

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4
Q

PROMOTER

A

Binds to RNA Polymerase

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5
Q

OPERATOR STE

A

Binds to the lac repressor protein

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6
Q

CAP SITE

A

Binds to Catabolite Activator Protein (CAP)

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7
Q

lacZ

A

Encodes for beta-galactosidase enzyme
This cleaves lactose into galactose and glucose
Also converts small amounts of lactose into allolactose

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8
Q

lacY

A

Encodes for lactose permease

This transports lactose and analogues into the cytoplsm

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9
Q

lacA

A

Encodes for galactose transacetylase

This covalently modifies lactose and its analogues

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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

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11
Q

cAMP-CAP

A

Complex that binds to the CAP DNA site near the lac opereon promoter

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12
Q

REGULATORY GENE

A

i-promoter
lacI
CAP Site

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13
Q

cAMP

A

cyclic adenosine monophosphate

cyclic AMP

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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
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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
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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
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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
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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

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19
Q

TRP OPERON PARTS

A

trpR, Promoter, Operator, Attenuator Sequence, trpE, trpD, trp,C, trpB, trpA

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20
Q

ATTENUATOR SEQUENCE

A

This facilitates the termination of transcription

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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.

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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

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23
Q

ATTENUATION

A

Occurs because of coupling of translation and transcription

Occurs under high levels of tryptophan

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24
Q

trpL

A

Plays a critical role in attenuation
Encodes short peptide of 14 amino acids
This peptide contains 2 tryptophan amino acids

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25
Q

REGION 1

A

Codes for trpL peptide with 2 tryptophan amino acids

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26
Q

REGION 2

A

Complementary to region 1 and 3

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27
Q

REGION 3

A

Complementary to region 2 and 4

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28
Q

REGION 4

A

Is GC-rich followed by many Uricil, and followed by the beginning of trpE coding sequence

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29
Q

SCENARIO NO COUPLING

A

The ribosome cannot bind
1-2 hybridization
3-4 hybridization
Transcription terminates intrinsically just past trpL gene

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30
Q

SCENARIO HIGH TRP

A

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

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31
Q

SCENARIO LOW TRP

A

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

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32
Q

SCENARIO NO RNA POLYMERASE

A 
Attenuation will happen
Translation is not happening
1-2 Hybridization
3-4 Hybridization
Dormant state
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33
Q

CATABOLISM

A

Breakdown of a substance
Typically inducible
EX. Lactose/allolactose metabolism

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34
Q

ANABLISM

A

Biosynthesis of a substance
Typically repressible
EX. Tryptophan synthesis

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35
Q

POSTTRANSLATIONAL REGULATION - FEEDBACK INHIBITION

A

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
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36
Q

POSTTRANSLATIONAL REGULATION - MODIFICATION

A

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

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37
Q

ALLOSTERIC ENZYME SITES

A
  1. Catalytic site - Binds to substrate

2. Regulatory site - Binds to final product

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38
Q

TRANSLATIONAL REGULATION-REPRESSORS

A

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

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39
Q

TRANSLATION REGULATION-ANTISENSE RNA

A

Synthesis of antisense RNA means it is complementary to the mRNA
If these hybridize, it prevents the ribosome from initiating translation

40
Q

TRANSCRIPTION FACTORS (TFs)

A

Proteins that influence the ability of RNA polymerase to transcribe a given gene
Generated by specific proteins

41
Q

GENERAL/BASAL TFs

A

TF2D, TF2B, TF2F, TF2E, TF2H
These bind to the core promoter and its progression to elongation
Required for all transcription

42
Q

REGULATORY TFs

A

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
Q

REGULATORY ELEMENTS

A

TFs that recognize cis-regulatory elements near the core promoter

44
Q

ACTIVATOR

A

Increases the rate of transcription

45
Q

ENHANCER

A

The DNA sequence the ACTIVATOR binds to

46
Q

REPRESSOR

A

A regulatory protein that decreases the rate of transcription

47
Q

SILENCER

A

The DNA sequence the REPRESSOR binds to

48
Q

DOMAINS

A

Regions of transcription factor proteins that have specific functions

49
Q

MOTIF

A

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
Q

HOMODIMERS

A

Formed by two identical transcription factors

51
Q

HETERODIMERS

A

Two different transcription factors

52
Q

PROTEIN DIMERIZATION

A

When proteins associate with each other

Leucine Zippers, a motif of two alpha-helices

53
Q

ORIENTATION INDEPENDENT

A 
Orientation independent (can function forward or reverse with respect to the gene)
Located with 200 nucleotides upstream of the promoter (exceptions)
54
Q

TF2D & MEDIATOR

A

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
Q

TFs MODULATION

A

Ensure proper gene regulation, TFs must also be controlled

EX: Binding of a hormone, protein-protein interaction, covalent modification

56
Q

CREB PROTEIN

A

Cyclic AMP Response-Element Binding PROTEIN

57
Q

ACTIVATION OF CREB PROTEIN

A
  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
Q

NUCLEOSOME REPOSITIONING

A

ATP hydrolysis repositions nucleosomes creating nucleosome-free regions.
SWI/SNF is one of the used

59
Q

HISTONE VARIANTS

A

H1, H2A, H2B, H3, H4

Several of these genes function as histone variants

60
Q

HISTONE CODE

A

Over 50 mammalian enzymes

Acetylation (facilitates transcription factors to bind and transcribe), Phospohrilation, Methylation (Silencing)

61
Q

EXPRESSION OF GENE

A

Always will require a free region (NFR) where the regulatory sequence can be exposed, this will always create a potential to be transcribed.

62
Q

TRANSCRIPTIONAL ACTIVATION MODEL

A
  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
Q

DNA METHYLATION

A
  1. Unmethylated
  2. Hemimethylated (will be observed when transcription has recently happened
  3. Fully methylated
    NOTE: DNA Methylation Patterns are heritable
64
Q

CpG ISLANDS

A

1000-2000 nucleotides long that are C-G rich

Don’t necessarily engulf the promotor

65
Q

METHY-CpG-BINDING

A

Recruit proteins such as histone acetylation, which causes the strand to compress

66
Q

INSULATORS

A

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
Q

H3K4me3

A

Happens when the TrxG complex and attaches 3 methyl groups to histone 4 (usually a lysine)
Very likely to be expressed

68
Q

NON CODINGS RNA

A

Hybridize to other non-coding RNAs
Hybridize to
Form secondary structures

69
Q

HOTAIR

A

Hox Transcript Antisense Intergenic RNA
This is a complex
Binds to two histone-modifying complexes in G-A rich regions

70
Q

MICRO RNAs

A

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
Q

CRISPR-CAS SYSTEM

A

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
Q

ADAPTATION

A
  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
Q

EXPRESSION

A

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
Q

INTERFERENCE

A

Each spacer

75
Q

MUTATIONS

A

Silent, Missense, Nonsense, Frameshift

76
Q

TRANSITION MUTATION

A

A change in a single base pair of pyrimidine (C,T) to pyrimidine; or a purine (A,G) to a purine

77
Q

TRANSVERSION MUTATION

A

A change in a single base pair of pyrimidine (C,T) to purine; or a purine (A,G) to a pyrimidine

78
Q

SILENT MUTATION

A

Those whose substitutes don’t cause changes to the amino acids afterwards

79
Q

MISSENSE MUTATION

A

Those whose substitutes do cause changes to the amino acids afterward

80
Q

NON-SENSE MUTATION

A

Those whose base substitutions that change a normal codon to a termination codon

81
Q

FRAMESHIFT MUTATION

A

The insertion or deletion of a number of nucleotide that isn’t divisible by 3

82
Q

NON-CODING SEQUENCES MUTATION

A

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
Q

MUTATION EFFECTS ON GENOTYPE AND PHENOTYPE

A

Deleterious: decreases chances of survival
Beneficial: Enhances survival
Conditional: Temperature-dependent

84
Q

SUPPRESSOR MUTATION

A

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
Q

INTERGENIC SUPPRESSOR MUTATIONS

A

Occur between two different genes

86
Q

CHROMOSOMAL REARRANGEMENT

A

This will silence a gene if the break occurs within the gene

If the gene is intact its expression can be altered

87
Q

SPONTANEOUS MUTATION

A

Depurination can cause a base to be lost
Termed apurinic site
These sites can be repaired

88
Q

DEAMINATION

A

Removal of an amino group, primarily cytosine

If the repair system fails it will result

89
Q

DEAMMINATION 5 METHYL CYTOSINE

A

Results in the transformation of cytosine to thymine

90
Q

INDUCED MUTATIONS

A

Using Nitrous Acid deamination of cytosine to uracil and adenin to hypoxinine

91
Q

INTERPOLATION AGENTS

A

Flat structures that insert in between the bases, results in either insertions or deletions

92
Q

PHYSICAL MUTIGENS

A

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
Q

DNA REPAIR

A

Base excision repair
Nucleotide repair
Mismatch Repair

94
Q

BASE EXCISION REPAIR PROKARIOTIC

A

DNA N-glycosylase recognize abnormal bases and cleave

95
Q

BASE EXCISION REPAIR EUKARYOTES

A

DNA Polymerase beta removes damaged site, DNA Polymerase epsilon can synthesis short piece oF DNA

96
Q

NUCLEOTIDE EXCISION REPAIR

A
  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
Q

MISMATCH REPAIR

A

Intentionally focuses on the newly synthesized strand

  1. Mismatch is identified, MutH and MutL is already bound to a hemimethylated DNA parental sequence
  4. DNA Polymerase fills the cut-out daughter strand
  5. DNA Ligase covalently links the strand

GENE 315 (1 decks)

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