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Exam #2 Content Flashcards

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1
Q

Proteins

A

Gene products, early evidence from mutations in metabolic pathways

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2
Q

Archibald Garrod

A

Inborn errors of metabolism
-Alkaptonuria: showed the first case of recessive inheritance in humans
-Phenylketonuria
aka: blocks in metabolic pathways

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3
Q

Phenylketonuria Block

A

Pathway to Phe to Tyrosine
-Newborn PKU test
-Phenylalanine hydroxylase

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4
Q

Alkaptonuria Block

A

Homogenetic acid oxidase
-Homogenetic acid to maleylacetoacetic acid pathway

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5
Q

Beadle and Tutum (1941)

A

Worked with mutants of fungus neurospora crassa ( a bread mould)
-Discovered that genes provide instructions for making protein

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6
Q

One Gene: One Enzyme Hypothesis
AKA: One Gene: One Polypeptide Hypothesis

A

B&T proved garrods hypothesis that genes have a biochemical role
-There must be 1 gene responsible for synthesizing 1 enzyme
-Neurospora can synthesize nearly every biomolecule it needs
-Used radiation to induce mutations in neurospora
-Determined which biomolecule the mutant could no longer synthesize

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7
Q

Adrian Srb and Norman Horowitz’s

A

Experiment with neurospora crassa mutants deficient in argenine production led to the biosynthetic pathways for argenine

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8
Q

Folded Structure

A

Following translation polypeptides fold up and assume higher order structure and may interact with other polypeptides
-Cannot predict what folded structure is going to look like from amino acid sequence

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9
Q

Primary Structure

A

Amino acid sequence or protein
-Polypeptide formation
-Peptide bonds hold amino acid sequence together

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10
Q

Secondary Structure

A

Primary folds to form repeating shapes
-2 types: alpha helix and beta sheets
-Certain amino acids are better at making each bond
-Secondary structures are stabalized by the formation of H bonds btwn atoms located in the polypeptide back bone

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11
Q

Tertiary Structure

A

Can be seen during translation
-Short regions of secondary structure fold into a 3D structure
-Structure determined by hydrophobic and ionic interactions and H bonds and Van Der Waals
-Final form of proteins that are composed of a single polypeptide

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12
Q

Quaternary Structure

A

Most proteins do not have quaternary form
-Usually formed by proteins that are made up of more than 1 polypeptide
-Various polypeptides associate with one another to make a functional protein

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13
Q

Mutations

A

Heritable change in genetic material
-Provide allelic variation
-Pro: foundation for evolutionary change
-Con: cause of many diseases
-b/c mutations can be harmful organisms have developed ways to repair damaged DNA

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14
Q

Types of Mutations (3 Main types)

A

1.) Chromosome Mutations
2.) Genome Mutations
3.) Single Gene Mutations

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15
Q

1.) Chromosome Mutations

A

Changes in chromosome structure

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16
Q

2.) Genome Mutations

A

Changes in chromosome #

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17
Q

3.) Single Gene Mutations

A

Relatively small changes in DNA structure that occur within a particular gene

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18
Q

Human Hemoglobin

A

One gene encodes one polypeptide
-Sickle cell anemia

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19
Q

Post-Translational Processing

A

Can modify polypeptide structure
-Cleavage may remove an amino acid
-Cleavage may split polyprotein
-Chemical constituent addition may modify a protein

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20
Q

Single-Gene Mutations

A

Point Mutations
-Change of a single base pair
-base substitutions
-Transition and Transversion

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21
Q

Point Mutations

A

Transition:
-change pyrimidine (C,T) to another pyrimidine
-change purine (A,G) to another purine
Transversion:
-change of pyrimidine (C,T) to purine (A,G) or purine to pyrimidine
Transitions are more common than Transversions

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22
Q

Transition (Point Mutations)

A

Change pyrimidine (C,T) to another pyrimidine or purine (A,G) to another purine
-more common than Transversion

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23
Q

Transversion (Mutations)

A

Change pyrimidine (C,T) to purine (A,G) or purine to pyrimidine
-less common than Transition

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24
Q

Gene Mutations

A

Can alter the coding sequence within a gene

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25
Q

Silent Mutations

A

Base Substitution
-does not alter amino acids sequence of polypeptide
-does not alter sequence b/c genetic code is degenerate (more than 1 codon can code from a single amino acid)

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26
Q

Missense Mutations

A

Base Substitution
-does alter amino acid sequence

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27
Q

Nonsense Mutations

A

Base Substitution
-changes a normal codon to a termination/STOP codon

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28
Q

Frameshift Mutations

A

Addition/Deletion
-addition or deletion of nucleotides in multiples of one or two
-shifts the reading frame so that a completely different amino acid sequence occurs down downstream from the mutation

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29
Q

Mutation effect on Genotype and Phenotype

A

In natural populations the wild-type is the most common genotype
-Forward Mutations, Reverse Mutations, and Variants

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30
Q

Forward Mutations

A

Changes wild-type genotype into a new variation

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31
Q

Reverse Mutations
AKA: Reversion

A

Reverts the mutant allele back into the wild-type
-opposite of forward mutations

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32
Q

Variants

A

When a mutation alters an organisms phenotypic characteristics
-characterized by their differential ability to survive
-Deleterious Mutations, and Beneficial Mutations

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33
Q

Deleterious Mutations (Variant)

A

Decreases chances of survival
-most extreme: lethal mutations (interrupt an essential process and results in death)

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34
Q

Beneficial Mutations (Variant)

A

Enhanced survival and reproductive success or an organism

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35
Q

Conditional Mutants

A

Affect phenotype only under a defined set of conditions
-expression of conditional mutations depends on environment around organisms
e.g. temperature-sensitive mutation

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36
Q

Gene Mutations to Promoter

A

Mutations can alter promoter sequences
- Up promoter mutations, Down promoter mutations

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37
Q

Up Promoter Mutations

A

Make promoter more like the consensus sequence
-may increase rate of transcription

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38
Q

Down Promoter Mutations

A

Make promoter less like the consensus sequence
-may decrease rate of transcription

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39
Q

Mutations and Splicing

A

Mutations may affect a splice recognition sequence
-may alter ability of pre-mRNA to be properly spliced

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40
Q

Neutral Mutations

A

No positive or negative effects
-in humans a vast majority of mutations occur in the large portion of the genome that do not contain genes and therefore have no effect on gene products
-silent mutations are also neutral mutations

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41
Q

Phenotype and Mutations

A

Depends on how protein function is changed by a mutation

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42
Q

Null Mutation

A

No gene function
-no gene product or non-functional product
-usually recessive but can be dominant

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43
Q

Hypomorphic Mutations

A

Reduced gene function
-protein retains part of it’s activity
-usually recessive but can be dominant

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44
Q

Hypermorphic Mutations

A

Enhances gene function
-protein functions more efficient
-usually dominant
-extremely rare

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45
Q

Neomorphic Mutations

A

Novel gene function
-protein has novel properties or is expressed ectopically
-at the wrong place or at the wrong time
-dominant

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46
Q

Mutations

A

Can occur spontaneously or be induced

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47
Q

Spontaneous Mutations

A

Result from abnormalities in cellular/ biological processes
-underlying cause originates in with in the cell
-e.g. errors in DNA replication

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48
Q

Induced Mutations

A

Caused by environmental agents
-agents that are known to alter DNA structure are termed: Mutagens

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49
Q

Mutagens

A

Can be chemical or physical agents
-agents known to alter DNA structure
-alter DNA structure in different ways
-e.g. radiation

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50
Q

Frequency of Gene Mutations
(How often mutations happen)

A

Very rare: b/c of mechanisms that protect against or repair mutations
-frequencies show great variation depending on type of gene and organisms
-range: 1 mutation in a gene in 10^4 to 10^8 gametes
-mutations rates differ b/c of gene size in nucleotide sequence and others

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51
Q

Luria-Delbruck Fluctuation

A

Demonstrated that mutations are not adaptive but occur spontaneously

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52
Q

Luria and Delbruck Experiment and Hypothesis

A

Studied resistance of E.Coli to bacteriophage
-ton^r (T one resistance)
-Hypothesis: is ton^r due to spontaneous mutations or to a physiological adaptation that occurs at a low rate
-became known as the “fluctuation test”

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53
Q

Luria and Delbruck theories

A

*Physiological adaptation theory
-predicts that the # of ton^r bacteria is essentially constant in different bacterial populations
*Spontaneous Mutation theory (proven right)
-the # of ton^r bacteria will fluctuate in different bacteria populations

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54
Q

Causes of Spontaneous Mutations

A

Spontaneous mutations can arise by chmeical changes (spontaneous lesions on DNA molecule)
1.) Depurination (most common)
2.) Deamination
3.) Oxidation
4.) Tautomeric Shift

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55
Q
  1. Depurination (Cause of Spontaneous Mutations)
A

Involves removal of purine (A or G) from DNA
-covalent bond btwn deoxyribose and a purine base is somewhat unstable, and occasionally undergoes a spontaneous rxn w/ water that releases base from sugar
-site where that happens is called a apurinic site

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56
Q

Apurinic site

A

Site in depurination where base is released from sugar
-site can be repaired
- if repair system fails, a mutation may result during subsequent rounds of DNA replication
Apurinic site-> transversions
-usually replaced by T
-Apyrimidinic site also occur but less frequently

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57
Q
  1. Deamination (Cause of Spontaneous Mutations)
A

Spontaneous lesions
C->T :Transition

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58
Q
  1. Oxidation (Cause of Spontaneous Mutations)
A

DNA may suffer oxidation damage by the by-products of normal cellular processes
H2O2: hydrogen peroxide
OH: hydroxyl radicals
O2: Superoxide radicals
G->T :Transversion

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59
Q

Tautomer and Tautomeric Shifts

A

Isomers that differ in a single proton shift in the molecule creating a change in the bonding structure of the molecule
-purine and pyrimidines can exits in one of several forms

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60
Q
  1. Tautomeric Shifts (Cause of Spontaneous Mutations)
A

In nucleotides can result in mutations due to anomalous base pairings

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61
Q

Important Tautomer’s

A

-Keto (standard): -enol (anomalous) former thymine and guanine
-Amino (standard): -imino (anomalous) forms of cytosine and adenine
-these shifts allow hydrogen bonding with noncomplementary bases

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62
Q

Induced Mutations

A

Caused by environmental agents
-arise from DNA damage caused by chemicals or radiation

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63
Q

Chemical Mutagens

A

3 types:
-Base modifiers (alter base)
-intercalating agents (destroy double helix)
-Base analogues (disguised as bases)

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64
Q

Base Modifiers (Chemical Mutagen)

A

Covalently modify structure of a nucleotide
-Nitrous acid: replaces amino groups with Keto groups (NH2 to double bonded O)
-causes deamination
-modified bases do not pair with appropriate nucleotides in daughter strand (can change C to U, A to hypoxanthire)

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65
Q

Intercalating Agents (Chemical Mutagen)

A

Flat planar structures that intercalate or insert themselves into double helix
-distort helical structure
-DNA with these mutagen is replicated daughter strand may contain single-nucleotide additions and/or deletions resulting in frame shift
-acridine dyes: cause frameshift by intercalating btwn purines and pyrimidine
-proflavin

66
Q

Base Analogs (Chemical Mutagen)

A

Substitute for purines and pyrimidines during nucleic acid replication
-become incorporated into daughter during DNA replication
-5-bromouracil-thymine analogue can be incorporated into DNA instead of thymine
-promote change of AT pair to GC pair in DNA replication

67
Q

The Ames Test

A

Used to assess the mutagenicity of compounds
-uses strains of salmonella typhimuriam selected for increased sensivity to mutagens and their ability to reveal mutations
-many known carcinogens have been shown by the Ames test to be strong mutagens

68
Q

Physical Mutagens (Induced Mutations)

A

-Ionizing Radiation
-Non-Ionizing Radiation

69
Q

Ionizing Radiation (Physical Mutagens: Induced Mutations)

A

X-Rays and Gamma rays
-short wavelength and high energy
-can penetrate deeply into biological molecules
-can cause: double-strand break, deletions, and inversions

70
Q

Mutations Frequency

A

Mutation Frequency increases linearly increased does of radiation

71
Q

Electromagnetic Spectrum and Radiation

A

Short wavelength, high energy
-gamma (ionizing)
-x-rays (ionizing)
-infrared (ionizing)
-Visible light (non-ionizing)
-ultra violet (non-ionizing)
-microwaves (non-ionizing)
-radio waves (non-ionizing)

72
Q

Non-Ionizing Radiation (Physical Mutagens: Induced Mutations)

A

Includes UV light
-less energy
-cannot penetrate deeply into biological molecules
-causes the formation of cross-linked pyrimidine dimers
-thymine dimers may cause mutations when that DNA strand is replicated

73
Q

Ultra-Violet Radiation

A

Effective mutagen
-creates pyrimidine dimers that distort DNA conformation in such a way that errors tend to e introduced during DNA replication

74
Q

Defective Excision Repair: Xeroderma Pigmentosum

A

Inherited disease (autosomal recessive)
-associated with mutations in at least 7 genes encoding proteins involved in the nucleotide excision repair systems
-extreme sunlight sensitivity (UV radiation) development of skin cancers and other severe conditions

75
Q

How to repair damaged DNA

A

4 types
-Base excision repair (BER)
-Nucleotide excision repair (NER)
-Mismatch excision repair (post dna rep)
-Proofreading by DNA polymerase (during dna rep)

76
Q

Base Excision Repair (BER)

A

Prior to DNA replication
-corrects damage caused by
*Oxidation
*Deamination
*Alkylation
-these base legions can be spontaneous or induced

77
Q

Nucleotide Excisions Repair (NER)

A

Prior to DNA replication
-corrects DNA damage caused by UV induced pyrimidine dimers

78
Q

BER steps

A

Recognition of erroneous base by DNA glycosylase
-Cutting of DNA backbone by AP endonuclease
Example: Uracil is noncomplementary
1. uracil DNA glycosylase recognizes and excises incorrect base
2. AP endonuclease recognizes lesion and nicks DNA strand
3. DNA polymerase and DNA ligase fills gap
4. Mismatch repair

79
Q

NER

A

Mechanism to correct DNA damage caused by UV induced pyrimidine dimers
1. region with dimer is cut out
2. gap filled by dna polymerase fragments are joined by ligase

80
Q

Mismatch Excision Repair in Human Cells

A

Errors after proofreading
1. Removal of mutations by nuclease
2. Gap filled by DNA polymerase
3. Sealing nick by DNA ligase

81
Q

Differential Gene Expression

A

Basis for development, cellular differential and physiological cellular responses
-expression of gene can be controlled on different levels

82
Q

Transcription Control

A

The most common regulatory mechanism of gene expression

83
Q

Transcription & Translation in Prokaryotic Cells

A

Coupled both spatially and temporally (space and time)
-b/c Prokaryotes have no defined nucleus transcription and translation happen in the cytoplasm and both happen at the same time
-a newly synthesized mRNA is immediately complexed to ribosomes and protein synthesis begins

84
Q

Gene Expression in Prokaryotes

A

Genes are clustered into regulatory units
-structural genes for enzymes that carry out a sequence of related reactions and are found together in the same regulatory region
-regulatory units are transcribed into a single polycistronic mRNA

85
Q

Cistron

A

Another name for a gene

86
Q

Prokaryotic Regulation on gene expression due to environmental changes

A

Gene expression studies a lot on E. Coli
-Enzymes could be:
*Inducible (adaptive): lac operon
*Constitutive
*repressible: trp operon
-Regulation maybe under positive or negative control

87
Q

Preferred Carbon source for bacteria

A

Glucose

88
Q

Lac Operon

A

Transcribes only if…
- no glucose is available
- lactose is present

89
Q

Regulatory Elements

A

Almost always located upstream of the gene cluster they control and are cis-acting
-lac operon

90
Q

Molecules that bind to cis-acting site

A

Are trans-acting elements
-lac repressor protein
-trans binds to cis

91
Q

Lac Operon Control

A

-Negative control
-Enzyme Induction
-I^- Mutation
-O^c Mutation
-I^s Mutation

92
Q

Negative Control of lac operon

A

Wild type
-no lactose present: repressed
-repressor binds to operator, block transcription
-no transcription = no enzyme

93
Q

Enzyme Induction

A

Lactose present: Induced
- No binding occurs: transcription proceeds
-operator-binding region is altered when bound to lactose
-transcription = translation = enzymes produced
-lac repressor undergoes allosteric change-> allosteric protein
-in this example enzyme induction results from a relief of repression

94
Q

I- Mutaion

A

Mutant Repressor gene
-no lactose present: Constitutive
-operator binding region of repressor is altered
-no binding occurs: transcription proceeds = enzyme produced

95
Q

O^c Mutations

A

Mutant Operator Gene
-no lactose present: Constitutive
-nucleotide sequence of operator gene is altered: no binding occurs
-transcription proceeds = enzyme produced

96
Q

I^s Mutation

A

Mutant Repressor gene
- lactose present: repressed
- lactose binding region is altered, no binding to lactose
-repressor always bound to operator, blocking transcription = no enzyme produced

97
Q

Catabolite-activation protein (CAPs)

A

Involved in repressing expression of lac operon when glucose is present
-Inhibition: Catbolite repression

98
Q

In Absence of Glucose

A

cAMP levels increase
-results in formation of a CAP-cAMP complex
-this binds to CAP site of promoter
-stimulates transcription
-positive control

99
Q

In Presence of Glucose

A

cAMP levels decrease
-CAP-cAMP complexes are not formed
-transcription is not stimulated

100
Q

Gene Expression in an Operon

A

May be..
-Inducible (adaptive)
-Constitutive
-Repressor (trp operon)
-positive or negative control

101
Q

A Repressible Gene System

A

The enzyme for Tryptophan production form an operon
-in presence of tryptophan: operon is repressed
-tryptophan acts as a co-repressor

102
Q

Summary of Repressible Gene System

A

-The tryptophan (trp) operon in E. Coli is a repressible gene system
-trp operon is activated in the absence of trp
-trp operon is repressed in the presence of trp

103
Q

Summary of Absence and Presence of Glucose

A

Absense: stimulates transcription
Presence: does not stimulate transcription

104
Q

Inducible Gene Expression

A

Turned on when signal molecule is present
-lac operon

105
Q

Constitutive Gene Expression

A

Always “on”

106
Q

Repressible Gene Expression

A

Turned off when signal molecule is present
-trp operon

107
Q

Negative Control of Regulation

A

Expression is normally blocked by teh repressor
-the inducer: repressed control of the lac operon
-the repressor: compression control of the trp
operon

108
Q

Positive Control of Regulation

A

Expression requires the positive signal of the activator CAP_cAMP bound to the CAP site
-the CAP-cAMP system of the lac operon

109
Q

Transcription in Eukaryotes

A

Occurs in nucleus
-not coupled to translation
-requires chromatin remoldeling

110
Q

Gene Regulation in Eukaryotes

A

More complex than in prok bc of:
- larger amount of DNA
- large # of chromosomes
-DNA is associated w/ proteins in the form of chromatin
- spatial seperation of transcription and translation (in nucleus-cytoplasm, respectively)
- mRNA processing
- RNA stability
- cellular differentiation in eukaryotes

111
Q

Differential Gene Expression

A

Basis for:
- development
- cellular differentiation
- physiological cellular responses

112
Q

Expression of a Gene

A

Can be controlled on 6 different levels
1. Transcriptional control
2. RNA processing control (alternative splicing)
3. RNA transport and localization control
4. Translation control
5. mRNA degradation control
6. protein activity control

113
Q

Eukaryotic Benefits of Gene Regulation

A

Can respond to
-changes in nutrient availability
-environmental changes

114
Q

Plant and Animal Multicellularity

A

Are multicellular
-more complex cell structure
- much greater level of gene expression

115
Q

Gene regulation is necessary to ensure

A

Temporal and Spatial expression
1. Gene expressed in pattern during various developmental life stages
- some only expressed in embryonic and some only expressed in adulthood
2. differences among distinct cell types
- nerve and muscle cells look different b/c of gene expression not DNA content

116
Q

Chromatin Structure

A

3D packing of chromatin affects gene expression
- 2 conformations: Closed Conformation, Open Conformation

117
Q

Closed Conformation (Chromatin Structure)

A

Tightly packed
- transcription may be difficult or impossible

118
Q

Open Conformation (Chromatin Structure)

A

Highly extended
- transcription can take place

119
Q

Chromatin Remodeling

A

2 common ways chromatin structure is altered
- Covalent Modification of histones
- ATP-Dependent Chromatin Remodeling

120
Q

Covalent Modification of Histones (Chromatin Remodeling)

A

Histones (that form nucleosomes) and post-transcriptional modifications
- creates opening and closing of chromatin structure
*amino terminals of histones are modified in various ways
- acetylation, phosphorylation, methylation
- histone acetyltransferase (HAT)
- histone deacetylase (HDAC)

121
Q

Histone Acetyltransferase (Chromatin Remodeling: Covalent Modification of Histones)
- aka HAT

A

Adds acetyl groups
- lossens interactions between histones and DNA
- mediates effects of activators

122
Q

Histone Deacetylase (Chromatin Remodeling: Covalent Modification of Histones)
- aka HDAC

A

Removes acetyl groups
- tightens interaction between histones and DNA
- mediates effects of repressors

123
Q

ATP- dependent Chromatin Remodeling

A

SWI/ SNF is one of the best studied chromatin remodeling complexes
- repositioning of nucleosomes
- allows for different chromosomal regions to be accessible to transcription proteins

124
Q

DNA Methylation

A

Associated w/ decreased gene expression
- acts as a mechanism for gene silencing: prevents binding of regulatory factors, and by affecting chromatin status
- adds methyl group to cytosine w/in C-G dinucleotides (often located in regulatory regions of genes)

125
Q

Core promoters

A

Minimum part of promoter needed for accurate initiation of transcription (by RNA P II)
- 80 bp long
2 types
- Focused Core Promoters
- Dispersed Core Promoters

126
Q

Focused Core Promoter

A

Specify transcription initiation at a single specific start site
- short nucleotide sequences bound by a specific regulatory factors
-serves as a platform for assembly of RNA P II
Important components
- Inr (initiator element)
- TATA box (TA rich sequence)
- BRE (TFIIB recognition element)
- MTE (motif ten element)
- DPE (downstream promoter elements)

127
Q

Dispersed Core Promoters

A

Direct initiation from several weak transcription start sites

128
Q

More About Focused Promoters

A
  • Regulatory/ control elements
  • affect binding of RNA polymerase to the promoter
  • DNA sequences bound by transcription factors
  • Can be proximal to the promoter
  • vary location
  • but often found in100 to 200 region
  • Can be distal to the promoter
  • enhancers: stimulate transcription (can do from long distance)
  • silencers: inhibit transcription (can also do from long distance)
129
Q

Regulatory Transcription Factors

A

Proteins that influence ability of RNA polymerase to transcribe a given gene
2 Main Types
- General Transcription Factors
- Regulatory Transcription Factors

130
Q

General Transcription Factors

A

Required for
- binding RNA polymerase to core promoter
-progression to elongation stage
- are necessary for basal transcription

131
Q

Regulatory Transcription Factors (Specific)

A

Regulate rate of transcription of nearby genes
- influence ability of RNA polymerase to begin transcription of a particular gene

132
Q

Elements Found in Focused Promoters

A

-Distance Enhancer
- Proximal Promoter
- Core Promoter
- Termination Sequence
- Coding Region

133
Q

Regulatory Transcription Factors recognize…

A

Cis regulatory elements located near core promoter
- sequences known as: response elements, control elements or regulatory elements

134
Q

Binding of these proteins…

A

Affects transcription of an associated gene
- Activator: regulatory protein that increases the rate of transcription is termed an activator
*enhancer: sequence it binds to
- Repressor: regulatory protein that decreases the rate of transcription
*silencer: sequence it binds to

135
Q

Promoters

A

Nucleotide Sequences
- serves as recognition sites for transcription machinery
includes
- TATA box
- proximal sequences (GC, CAAT and more)
- enhancers and silencers

136
Q

TATA Box (TATA A/T AAR)

A

Region RNA Polymerase binds to
TATA A/T AAR (R is any purine)

137
Q

Transcription Factors

A

Transcription Regulatory Proteins
- target cis-acting sites of gene regulation expression
- may be modulated by : phosphorylation or coactivator binding

138
Q

Human Metallothionein IIA gene (hMTIIA)

A

Example of how genes can be transcriptionally regulated through promoters, enhancers and transcription factors

139
Q

Functional domains of Transcription Factors

A

Proteins that serve as transcription factors have two domains
- Trans- activating or repressing domains
- DNA Binding Domain

140
Q

Trans Activation or Repressing Domain

A

Trans- activating domain- activates
Trans- repressing domain- represses transcription through protein-protein interactions

141
Q

DNA Binding Domain

A

Directs binding of the protein to a specific sequence of DNA
*helix-turn-helix
*zinc fingers
*basic leucine zippers (bZIP)

142
Q

TFIID

A

Transcriptional activator recruits TFIID to the core promoter and/or activates its function
-thus transcription will be activated

143
Q

Enhancers

A

Enhances transcriptional activity from a distance
- acts independent of orientation

144
Q

Silencers

A

Confers stage-and tissue-specificity of expression
-acts independent of position
-properties are similar to enhancer but it silences gene expression

145
Q

Enhancesome

A

forms when activators bind to enhancers
-interacts with transcription complex

146
Q

General Transcription Factors

A

Required for the binding of RNA polymerase II to the promoter

147
Q

TFIID

A

The first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP)

148
Q

Most regulatory transcription factors…

A

do not bind directly to RNA polymerase

149
Q

TFIID and Mediator

A

Common protein complexes
-communicate the effects of regulatory transcription factors to RNA pol II

150
Q

Alternative Splicing

A

Pre-mRNA can be sliced in more than one way
- produces two alternative versions of a protein that have similar functions (b/c much of their amino acid sequences are identical
- there are still enough difference in the amino acids to give each protein its own characteristics/ function

151
Q

a-Tropomyosin (Alternative Splicing Example)

A

Protein Function: regulation of cell contraction
*Is found in
-Smooth muscle cells (uterus and small intestine)
-Striated muscle cells (cardiac and skeletal muscle)

152
Q

Alternative Spicing Process

A

Spliceosome recognizes the 5’ and 3’ splice sites and removes the intervening intron
- Alternative splicing is the primary mechanism for resulting mRNA processing
- not a random event: specific splicing pattern depends on the cell

153
Q

Splicing Factors

A

Modulate the ability of spliceosomes to recognize or choose the splice sites
- splicing repressors and activators play a key role in the choice of splice sites

154
Q

Dscam Gene mRNA

A

The combination of exons resulting from alternative splicing can result in over 38,000 versions of DSCAM protein

155
Q

Drosophila Sex Determination

A

Sex lethal (Sxl) and transformer (tra) and doublesex (dsx) genes help regulate for sex determination
- Sxl gene: acts as a switch that selects sexual development pathway by controlling splicing of Dsx transcript in a female-specific fashion

156
Q

mRNA Stability

A

Stability of Eukaryote mRNA varies greatly
- stability of mRNA can be regulated to its half-life (shortened or lengthened), influences mRNA concentration and gene expression
- factors that affect stability
1. length of poly A tail
2. destabilizing elements

157
Q

Pathways for degradation of euk mRNA

A
  • decapping pathway: attacks caps of mRNA, removal of cap
  • deadenylating: removal of poly A tail
  • endonucleolytic cleavage: attacks mRNA from middle of mRNA sequence, cuts the middle of sequence
158
Q

RNA Silencing

A

RNA induced gene silencing
- affects transtability or mRNA
- small antisense RNA on/affects specific regions of mRNA
- can also repress transcription by altering chromatin
-microRNA (miRNA)

159
Q

microRNA (miRNA)

A

Short (21-24 nt)
- double-stranded RNA
- involved in RNA silencing
- encoded in nuclear genome and transcribed by RNA pol III
- sections of miRNA gets loaded into RISC or RITS
RISC: degradation of mRNA, translation inhibitation
RITS: nuclear genome silencing
-mutants w/out normal miRNA function show developmental defeats

160
Q

Protein modification and degradation

A

Can affect ____ of proteins
- location
- structure
- function
- activity
- interactions

161
Q

Ubiquitin- mediated protein degradation

A

Recognizes substrate protein and catalyzes the addition of Ub (76 amino acid protein)
- Ub are recognized by proteasome and the protein will get cleaved into small peptides
- protein will be degraded and recycled

General Genetics (6 decks)

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