Exam 4 (quizlet with all) Flashcards
1
Q
Silent Mutation
A
- change at the DNA level
- point mutation alters a codon but doesn’t result in a change of amino acid
- wobble codon helps bc more than one codon can code for an amino acid
2
Q
Poly-A tail
A
- Located at 3’ end of euk mRNA
- Plays a role in translation by enhancing binding of small ribosomal subunit to mRNA
- If absent: mRNA is degraded in cytoplasm
3
Q
Neutral mutation
A
- Changes the coded amino acid but does not alter function of protein
- effect is negligible
- Can occur in protein-coding region or any part of genome
4
Q
IF-2
A
- plays direct role in initiation
- interacts with mRNA and charged tRNA
- stabilizes them in the P site
5
Q
Amino acids join by _____
A
- peptide bonds
6
Q
miRNA
A
- Controls gene expression (RNA-induced gene silencing)
- a reduction in expression of tumor cells is seen
- Probably involved in later stage of tumor progression
7
Q
Base/Base Pair substitution
A
- point mutation
- The alteration of a single nucleotide of a triplet by substitution which changes the codon
- may or may not have an impact, still kinda readable
- When one nucleotide is changed, its corresponding base on other strand is also impacted
2 types:
1. transition
2. transversion
8
Q
Visible mutation
A
- Alters a normal or wild-type visible phenotype
- Most easily observable mutation bc affects morphological trait
9
Q
Induced mutation
A
Mutations that occur as result of outside/extraneous factors (natural or artificial agents)
Ex:
- UV radiation from sun (natural)
- chemicals (artificial)
10
Q
Insulators
A
- A boundary element (DNA sequence) that limits the range of enhancers/silencers
11
Q
Cloverleaf model of tRNA
A
- Proposed by Robert Holley
- tRNA displays secondary structure
12
Q
Clonal evolution of cancer
A
- Multiple rounds of clonal evolution (replication) allow tumor cells to become aggressive (malignant)
- Tumors are clonal: these cells originated from a common ancestral cell that accumulated specific mutations
13
Q
DNA repair in general:
A
- Requires two nucleotide strands
2. Many types of DNA damage can be corrected by more than one path
14
Q
Epigenetics in tumourogenesis
A
- study of factors that affect gene expression, but do not alter nucleotide sequence of DNA
- Changes in methylation/acetylation of DNA/histones
- changes in chromatin structure
15
Q
Environment correlation with cancer
A
- what you are exposed to environmentally has an affect on you
16
Q
Reactive Oxidants (oxidative damage/radicals)
A
- By-products of processes of metabolism and self-defense
- DNA is damaged by the byproducts of normal cellular processes called reactive oxygen species
- can produce more than 100 types of chemical modifications in DNA, including modifications to bases, loss of bases, and single stranded breaks
Ex: superoxide (O2-), hydroxl radicals, hydrogen peroxide (H2O2)
17
Q
Initiation factors (IFs)
A
- proteinaceous
- enhance binding affinity of various translational components
- At least 3 used in initiation
18
Q
Mismatch repair
A
- DNA repair mechanism distinguishes strand with error from strand without
- found by DNA methylation
- newly synthesized DNA strand temporarily unmethylated in bacteria
- repair enzyme recognizes the mismatch and binds to the unmethylated strand
- creates a nick in the backbone of the unmethylated strand
- mismatch repaired by DNA polymerase & ligase
- not in eukaryotes
19
Q
Philadelphia Chromosome
A
- formed by the c-ABL gene on chromosome 9 and is translocated into the BCR gene on chromosome 22
- chronic myelogenous leukemia
- The proto-oncogene on 9 fuses w/ BCR gene on 22
- allows cells to escape control of cell cycle
20
Q
Negative inducible operon
A
- Active repressor is present/binded to operator, so no transcription occurs
- transcription OFF, active repressor
- inducer makes repressor inactive
- transcription occurs
21
Q
Base Excision Repair (BER)
A
- Corrects DNA that contains damaged DNA base, clipped out
- Incorrect base pair
- DNA glycosylase excises wrong base
- leaves behind apurinic/apyrimidinic site
- endonuclease nicks strand
- DNA polymerase fills gap with correct base, ligase seals
- fixes pyrimidine dimers
22
Q
trp Operon (tryptophan)
A
- Negative repressible operon
- transcription normally ON bc of inactive repressor
- must be turned OFF
- Lots of tryptophan (corepressor) present
- goes back to operon to activate the repressor
- stop tryptophan production
23
Q
What is the attachment site for amino acids on ALL tRNA’s?
A
- CCA site on the 3’ end of amino acids
- BUT tRNAs are specific for a particular amino acid.
24
Q
Translation
A
- of mRNA is the biological polymerization of amino acids into polypeptide chains (how triplet ribonucleotides of mRNA direct specific amino acids into their correct position in the polypeptide)
- occurs in association with ribosomes; 5’ to 3’ direction
- FOR BOTH EUK AND PROK
- occurs in the cytoplasm
- ribosomes are necessary
25
Q
Termination steps of translation
A
- Stops codons (UAG, UAA or UGA) enter A-site
- GTP-dependent release factors cleave polypeptide chain from terminal tRNA
- tRNA released from ribosome, ribosome dissociates into subunits
26
Q
Transversion
- draw
A
- Type of base substitution/point mutation
- A purine replaces a pyrimidine, or vice versa
27
Q
Euk gene regulation with chromatin structure:
A
- Acetylation of histones
- opens chromatin allowing transcription - Methylation of histones
- can change chromatin packing, usually causing tightening (heterochromatin) - Methylation of DNA
- transcriptionally inactive parts of chromosome
RITS!!
28
Q
Depurination
A
- The loss of one nitrogenous base in a double-helix DNA molecule
- The lost base is purine (adenine or guanine)
- leaves an apurinic site(empty spot) on one DNA strand
- DNA replication generates a random base there (often A)
- mutation bc can not go back and fix it once placed
29
Q
Inherited forms of prion diseases
A
- Fatal Familial Insomnia
- Sickle Cell Anemia
- Alzheimer’s, huntingtons, parkisons
30
Q
In proks: how does transcription and translation occur?
A
- simultaneously
31
Q
Benign tumor
A
- Cancerous cells remain localized in the body
- when a cell
32
Q
Cell cycle checkpoints
A
- G1/S
- cell monitors its size, determines whether DNA is damaged - G2/M
- processes are monitored prior to mitosis (like DNA replication and repair) - M
- checkpoint occurs during mitosis, spindle fiber formation/attachment to kinetochores monitored.
- Mitosis can be arrested, trigger apoptosis
33
Q
Attenuation
A
- Premature termination of transcription
- Yields unstable protein
- Occurs w/ high levels of tryptophan (secondary structure)
34
Q
RNA Interference
A
- The process in which the introduction of dsRNA into a cell causes degradation of mRNAs containing the same sequence
35
Q
Conditional mutation
A
- only expressed under certain environmental conditions
- present in genome
ex: Temperature sensitive - variable function at different temperatures
36
Q
Transition
- draw
A
- Type of base substitution/point mutation
- Like replaces like, purine for a purine, or pyrimidine for pyrimidine
37
Q
Loss of heterozygosity
A
- loss of allele
- Occurs when the second wild-type allele is mutated in a tumor
- The cell is no longer heterozygous
- now homo for cancer
- predisposition of inherited cancer expression increases
38
Q
lac operon: For maximum transcription of the structural genes
A
- no glucose present
- only lactose
- the repressor must be bound by lactose (to inactivate the repressor)
- CAP must be bound to the CAP-binding site
39
Q
Start codon of mRNA (AUG) in prokaryotes codes for…
A
- Modified amino acid
- formylmethionine (fmet)
40
Q
Differences between prok and euk gene regulation:
A
- Euk genes are NOT organized into operons
- Chromatin affects gene expression in euks
- Activators are more common in euks than repressors
- Regulation of gene expression has transcriptional activator proteins which bind to DNA in regulatory promoter, interact with other molecules
41
Q
Euk gene regulation with transcription:
A
Transcriptional activator proteins:
- Bind to regulatory promoter in DNA
- Interact w/ other components (initiation complex)
- Enhancers/silencers, insulators, MULTIPLE REGULATORY ELEMENTS
42
Q
P-site
A
- Peptidyl site on ribosome
- Holds tRNA bound to the growing polypeptide chain
43
Q
Shine-Dalgarno sequence
A
- The ribosomal binding site on mRNA for prokaryotic translation
- located upstream of start codon
- A consensus sequence
- The small subunit binds and is positioned here
44
Q
Kozak sequence
A
- In eukaryotic translation
- NOT essential in every eukaryote sequence
- When present, is ESSENTIAL for translation initiation on mRNA
- Analogous to Shine-Dalgarno found in prokaryotes mRNA
45
Q
Biochemical mutation
A
- Do not always affect morphological characters
- mutation in a biochemical pathway
Ex: sickle-cell anemia, hemophilia
46
Q
If termination codon appears in middle of mRNA molecule from mutation…?
A
- Termination occurs, and polypeptide chain is prematurely terminated
47
Q
Haploinsufficiency
A
- One copy of a product on a gene is not enough for wild-type phenotype
- Result of loss-of-function mutation
48
Q
Regulator protein
A
- Is either a repressor or activator, interacts with the operator to either stop/start transcription
49
Q
30S initiation complex
A
- everything in the initiating step (+mRNA, small ribosome)
- attaches to mRNA
- small ribosomal subunit
50
Q
T/F: some tumor suppressor genes are involved in DNA repair
A
- true
51
Q
Catabolite repression
A
- The inhibition of the lac operon when glucose is present
- glucose causes decline of cAMP
- Positive control
52
Q
Mutation rate
A
- How often a mutation will occur in a single generation or in forming a single gamete
- Varies between different organisms & gene to gene
- HOT SPOTS are a sequence in the DNA that appear to be highly susceptibility to mutation
53
Q
unequal crossing over
A
- crossing over takes place and ends up adding to one chromosome while deleting from the other
- any areas that are repetitive seem to attract this type of change
54
Q
Trypotophan levels affect on transcription
A
- tryptophan levels are high
- attenuation occurs to terminate transcription (i.e. folded secondary structure of 5’ UTR on operon inhibits it) - tryptophan levels are low
- antitermination occurs, production of tryptophan occurs
55
Q
Different protein structures:
A
- Primary
- sequence of AA’s - Secondary
- interaction between aa in certain areas of the polypeptide chain
- folds and twists of polypeptides (beta sheets or alpha helix)
- R groups extend outward from the helix - Tertiary
- interaction of secondary structure
- 3D conformation of the entire chain
- level gives the protein its specific function by the way its folded - Quaternary
- 2 or more polypeptides interact
56
Q
R groups on amino acids
A
- Yield different characteristics
can cause aa to be:
1. Nonpolar: hydrophobic
2. Polar: Hydrophilic
3. Polar: Positively Charged (Basic, proton acceptor)
4. Polar: Negatively Charged (Acidic, proton donor)
57
Q
BAX homodimer
A
- promotes apoptosis
- we make more of this if cell is in trouble
58
Q
Malignant tumor
A
- Tumor cell invades other tissues in the body
59
Q
core promotor
A
- determines the accurate initiation of transcription by RNA pol II
60
Q
Barbara McClintock
A
- discovered transposable elements
- maize
61
Q
Photoreactivation Repair
A
- depends on photoreactivation enzyme (PER)
- Enzyme that breaks covalent bonds that link pyrimidine dimers so that normal pairing is restored
- cleaves the bonds between thymine dimers, directly reversing the effect of UV radiation on DNA
- Requires blue light from UV used to excise/ (photon of light) to cleave the dimer
- in E. coli only, humans lack this
62
Q
SOS repair
A
- Last resort of DNA repair
- Allows DNA replication to continue WITH errors and lesions (gaps)
- DNA synthesis becomes error-prone (inserting random and possible incorrect nucleotides)
- CAN BE MUTAGENIC
63
Q
Elongation steps of translation
A
- Second charged tRNA enters A-site facilitated by EF-Tu; AUG codon passed down to P-site
- Peptide bond formation between AA in P and A, releases AA in P, goes to charged tRNA on A-site, which then moves down; uncharged tRNA moves to E-site then exits
- Translocation: Continued movement of ribosome down mRNA
64
Q
N terminus vs C Terminus
A
- N Terminus contains amino group
- 5’ end - C terminus contains carboxyl group
- 3’ end
65
Q
Where on the tRNA does the amino acid bind to?
A
- acceptor stem is where tRNA is going to grab aa
- at its 3’ end
66
Q
Purines vs Pyrimidines
- pairing
A
- Purines: A and G
- Pyrimidines: C, T, U
- Pairs: A=T and G=C
67
Q
RISC
RNA-induced silencing complex
A
- Combines w/ miRNA or siRNA, then binds to mRNA
- if mRNA is complementary, mRNA degradation
- If mRNA isn’t exactly complementary, translation inhibition
68
Q
Ionizing radiation
A
- More energetic than UV radiation
- more dangerous bc penetrate deeper causing free radicals can break DNA
Ex: X-rays, gamma rays, cosmic rays
69
Q
IF-1
A
- enhances dissociation between small and large ribosomal subunit
- blocks the A site from binding to tRNA
70
Q
Tautomer/Tautomeric shifts
A
- different forms of a compound (bases can take on several different forms)
- shifts allow H bonding with non-complementary base pairs which can lead to permanent base pair changes and mutations
- keto enol forms of T and A, amino imino forms of C and G
Ex: multiple forms of a nitrogenous base - diff forms can pair with its wrong complementary base
- unstable form, can jump back to stable form
- if not, results in transition mutation
71
Q
Directionality of amino acids
A
- the amino acid group (5’ end of transcript) and the carboxyl group (3’ end) give directionality
- cause hydrogen bonds to form within a polypeptide chain
72
Q
Vascularization
A
- The process of angiogenesis (growth of new blood vessels)
- the genes to control it are over expressed in tumor cells
- tumor cells need nutrients, so increase in this gives it to them
- Genes that inhibit vascularization become inactivated
73
Q
What happens with the transposition of Ds element (when accompanied by Ac element, which provides transposase)
A
- Ds can be inserted in a gene, preventing gene expression.
- Can also jump out of gene during development causing mosiacism (corn ex, spots of color(purple) in a colorless corn!)
74
Q
Importance of Cap and poly A tail in eukaryotes
A
- the cap at the 5’ end is critical in the initiation of translation
- small subunit scans for AUG
- cap helps the ribosome get situated
- poly A tail can loop back around and help get ribosome set up on RNA and get it in the right place
75
Q
RITS
RNA-induced transcription silencing complex
A
- Targets specific promoters or chromatin regions of DNA
- recruits chromatin remodeling enzymes
- methylation occurs, heterochromatin forms
- transcription inhibited
- TEMPORARILY HALTS GENE EXPRESSION
76
Q
Jacob and Monod (1961)
A
- First described the operon model
- Operon is the basic unit of transcription control in bacteria
- Found the lac operon is inducible
77
Q
Deamination
A
- An amino group in cytosine or adenine is converted to a keto group (tautomeric shift)
- changes base pairing
- Can occur spontaneously or from chemical mutagens
- alteration in the base pairing specificities of two bases during DNA replication
Ex: HNO2 is a chemical mutagen
78
Q
lac Operon
A
- A negative inducible enzyme system, transcription is normally off and must be turned on (induced)
- Lactose (inducer) inactivates the repressor (when binds to it) to activate transcription
- RNA polymerase can now transcribe
- Lactose breaks down to glucose
- positive inducible when glucose is absent/low (off turns on)
- CAP/cAMP binds to promoter
79
Q
Elongation requires these components:
A
- 70S complex
- Charged tRNAs
- Elongation factors(EF-G and EF-Tu)
- GTP hydrolysis
80
Q
IF-3
A
- Initiation factor
- Binds to small subunit to block large subunit from binding to small one
- Helps small subunit to attach to mRNA
81
Q
Translation occurs where in eukaryotes AND prokaryotes?
A
The cytoplasm
82
Q
Interstrand crosslinking
A
- mutagenic and toxic
- Covalently bonding 2 strands together across DNA strands
- Blocks replication by inhibiting DNA separation
- cell death (apoptosis)
- Chemotherapy drugs do this to treat cancer
83
Q
LINES
A
- long interspersed nuclear elements
- encode own reverse transcriptase
- has retrotransposons (can function on own)
84
Q
Charging
A
- The activation process of tRNA’s chemically linking to respective amino acids
- Charged tRNA has its amino acid attached to it
- Cell has 30-50 diff tRNAs for 20 amino acids (Wobble hypothesis)
85
Q
Positive Inducible
A
- transcription off
- inactive activator
- stimulates transcription
- inducer makes activator active, turns on
ex: Catabolite repression - when glucose is highly present, genes required to metabolize
- other sugars are repressed
86
Q
Riboswitches
A
- Alternative secondary structures of mRNA sequence in the 5’ UTR that impact gene expression (upstream from coding sequences)
- Default/antiterminator conformation: no ligand binded, RNA polymerase transcribes
- Terminator conformation: ligand binds to ligand-binding site, changes riboswitch conformation, RNA poly. can’t transcribe
87
Q
Age correlation with cancer
A
- as an individual ages their likely hood of developing cancer increases
- the older a cell is, the more likely it has the chance to undergo mutations
88
Q
Ac (activator) element
A
- A mutation that is autonomous (can transpose alone)
- functional
89
Q
Gain-of-function mutation
A
- Results in a gene product with enhanced/new functions
- produces new trait (or appearance of new trait in tissue)
- Due to change in amino acid sequence of protein that confers new activity
- tends to be dominant
90
Q
Euk gene regulation with post-transcription:
A
- Alternative splicing/exon shuffling occurs
- certain exons are expressed, choosing from isoforms of exons (while all introns are cut out)
- generate diff forms of mRNA with pre mRNA
- 5’ and 3’ alternative splice sites
- pre-mRNA -> mature mRNA - RNAi: short sequence (sequence-specific) causes degradation of mRNAs w/ same sequence
91
Q
Nutritional mutation
A
- Results in loss of ability to synthesize an amino acid or vitamin
ex: auxotrophs
92
Q
tRNA
A
- adapts specific triplet codons in mRNA to their correct amino acids before translation can proceed
- deliver amino acids to ribosomes
- have 20 tRNAs that are specific for a particular AA, but all tRNAs have the same attachment site (CCA)
93
Q
Collinearity
A
- The correspondence between the sequence of triplets and sequence of amino acids
94
Q
Repressible enzyme
A
- Production/transcription is OFF when a product is present
- ON unless repressor is present
- when there is enough of it need to be able to turn it OFF use a repressor
- Able to be repressed but is usually induced
95
Q
protein structure
A
- polypeptides can fold up to form proteins
96
Q
P element
A
- A Drosophila transposable element that causes mutations in the flies
97
Q
Adaptive/facultative enzymes
A
- Produced when needed
98
Q
if an __________________ is bound, transcription should be on
A
- activator/inducer
99
Q
Roles of small subunit and large subunit during elongation:
A
- Small
- decodes mRNA triplets (yields codons) - Large
- peptide bond synthesis
100
Q
Somatic mutation
A
- Mutation occurring in any cell in body except germ cells (just somatic cells)
- nonsex cells
- passed to daughter cells by mitosis
- not transmitted to next generation
101
Q
Negative repressible operon
A
- transcription ON
- inactive repressor
- activator (corepressor) introduced to bind to repressor, makes repressor active
- transcription off
102
Q
Evolution of transposons to be useful
A
- not all are mutagenic, but MOST are
- Many elements have evolved to increase copy number without killing the host (insert into untranscribed region of genome)
Ex: HeT-A and TART elements function as telomeres in Drosophila chromosomes - keep proper chromosome length
103
Q
Beadle and Tatum (1940s)
- experiment and conclusions
A
- Used bread mold to study mutations
- exposed UV to spores and grew on complete media, switched to minimal media
- if they died they had a nutritional mutant
- used ones that failed on minimal, on selective to find the type of mutant
- quaternary structure of proteins led to the one gene, one polypeptide hypothesis
RESULTS:
1. One-Gene:One-Enzyme Hypothesis - each gene encodes production of a specific enzyme
2. becomes One-Gene:One-Polypeptide Chain Hypothesis - each gene encodes for a POLYPEPTIDE, not enzyme
104
Q
Retrotransposons vs DNA transposons
A
- Retrotransposons
- jump and transpose by reverse transcriptase (the RNA intermediate, copies RNA to DNA)
- active in genome - DNA transposons
- do not jump
- inactive in genome
105
Q
Tumor-suppressing genes
A
- Genes whose products normally regulate cell-cycle checkpoints/initiate apoptosis, to suppress tumor formation
- When inactivated, experiences loss-of-function mutation
- Recessive-acting mutation: if both alleles of this gene are inactivated
- cell can become tumorigenic
106
Q
Post-translational modifications for proteins include:
A
- Molecular chaperones
- they are proteins
- function by mediating the folding process to prevent misfolding and prevent the formation of alternative incorrect patterns
- assist in protein unfolding and folding
- Signal sequence
- do not become part of the final product
107
Q
Enhancers
A
- A transcription regulatory element (sequence) that enhances transcription at a distance from the promoter
- Opposite of silencer
108
Q
Provirus (cancers associated with virus)
A
- Its viral genome is inserted in host chromosome near proto-oncogene, or tumor suppressing cells
- mutations arise in proto-oncogene to yield oncogenes in the host chromosome
- Errors in viral system more common
- errors can be introduced to new cells via HOMOLOGOUS RECOMBINATION
- HPV vaccination!
109
Q
Pseudodominance
A
- Wildtype allele is somehow inactivated (mutated)
- if cell is heterozygous
- recessive trait is expressed
110
Q
UV radiation
A
- MAJOR ISSUE: Pyrimidine dimers
- Two identical pyrimidines on same DNA strand covalently bond, ignoring base pair
- Distorts DNA conformation, inhibits normal replication(causes death)
- A result of UV radiation
- Repaired by Nucleotide Excision Repair or Photoreactivation Enzyme Repair
111
Q
Signal transduction and cancer
A
- The process of transmitting growth signals from external environment to cell nucleus.
- In cancerous cells
- transduction is defected, continuous growth signals sent to cell, malignant cells don’t respond to external signals from surrounding cells
112
Q
Prions
A
- Aggregates of misfolded protein
- Is infectious(acquired by eating/transfusion/growth hormone) and heritable
- Leads to disease like mad cow and scrapie
- An EXCEPTION to Central Dogma bc protein changes from an abnormal protein
- secondary protein structure disease
113
Q
Bcl2/BAX heterodimer
A
- inactive complex
- bc do the opposite jobs of eachother
114
Q
promotor elements
A
- short nucleotide sequences that bind to specific regulatory factors
- regulate transcription
- decide where it begins and which direction it occurs
115
Q
Activator Proteins
A
- bind to DNA in regulatory promoter and interact with other components
- core promoter with TATA box is necessary
- focus on pol II because it transcribes mRNA
116
Q
Apoptosis
A
- Programmed cell death
- A repair mechanism to prevent cancer
117
Q
Germ line mutations
A
- Mutation occurring in gametes
- they are passed to future generations
- heritable and are the basis for the transmission of genetic diversity and evolution, as well as genetic diseases
118
Q
Transposons (transposable elements)
A
- Repetitive and mobile DNA segments (“jumping genes”)
- jump from one part of the genome to another, using cut and paste to move
- Present in ALL organisms
- Make up 50% of human genome
- Can cause mutations (by inserting into genes, causing rearrangements)
- Parts of transposable element:
1. flanking direct repeats - 3-12 bp, does NOT hop w/ element (not apart of element)
2. terminal inverted repeats - at ends of element, inverted complement of 1 another
119
Q
Open reading frame
A
- Section of DNA between start and stop codon
120
Q
Ribosome
A
- The protein synthesis machine, made up of protein and RNA (50 diff types)
- Contains two subunits, one large & one small
- Most abundant organelle
- Contain 80% of RNA (rRNA)
121
Q
Spontaneous mutation
A
- Changes in nucleotide sequence of genes that appear to have no known cause
- no specific agents involved and assumed to be accidental
- occur during DNA replication
- low rate of this occuring
Ex: replication errors
122
Q
_________________ are the second most leading cancer causing agent. A number of inherited cancers are caused by defects in genes that control ________
A
- viruses
- DNA repair
123
Q
SINES
A
- short interspersed nuclear elements
- lack retrotransposons (need LINE to do reverse transcriptase)
- most common transposable element in the human - Alu element (SINE)
124
Q
genome instability
A
- duplications, deletions, rearrangements, chromosome breaks, fusions (translocations)
- genome instability is a characteristic of cancer cells
125
Q
Telomerase
A
- The enzyme activated in my tumors cells
- repairs telomeres at chromosome ends
- allows unlimited cell division
126
Q
A-site
A
- Aminoacyl-tRNA site on ribosome
- Holds incoming, new activated amino acid
127
Q
Constitutive enzymes
A
- Enzymes that are produced continuously
- regardless of chemical makeup of environment
128
Q
Similarities in gene expression regulation between euks and proks:
A
- Both have DNA-binding proteins that influence RNA polymerase initiation
- Both have repressors and activators
129
Q
Bcl2 homodimer
A
- blocks apoptosis
- continue onto cell cycle
130
Q
Ames test
A
- Tests if chemical cpds are mutagens by seeing if chemical can mutate the mutation back to normal (mutant his- bacteria used)
1. His- mutant bacteria mixed w/ liver enzyme mixed w/ chemical of interest (potential mutagen)
2. Plated on minimal media w/out histidine
3. Colonies present: revertant mutation allows bacteria to grow, from his- to his+
4. No colonies: the chemical cpd is NOT a mutagen/carcinogen
131
Q
Alkylation
A
- add an alkyl groups to keto/amino groups of nucleotides
- base pairing affinities are altered and will pair incorrectly
132
Q
Regulatory mutation
A
- Affect the regulation of gene expression
- can disrupt an entire pathway
- not making the correct amount of a protein
133
Q
Proteins made up of __ common amino acids and all contain”
A
- 20
1. Amino group
2. Hydrogen
3. R group (variable)
4. Carboxyl group
134
Q
Cyclins
A
- the cell controls progress through the cell cycle by cyclins
- dimers are apart of cyclins
1. BAX homodimer
2. Bcl2 homodimer
3. Bcl2/BAX heterodimer
135
Q
Why was bread mold useful for use:
A
- Easy to grow in lab
- Vegetative form is haploid
- can see recessive mutations easily!
136
Q
Ds (dissociation) element
A
- dissociation
- A mutation that is nonautonomous (can’t transpose without Ac)
- Is smaller than Ac element
- Can transpose in(mutant)/out(wildtype) of a gene
- Can jump out of a gene, restoring that gene’s expression
- If transposes, chromosome breaks & is lost
- broken fragment yields no gene expression (mutant)
137
Q
Aminoacyl tRNA synthetases
A
- The enzyme used in process of charging to link tRNA’s w/ their respective amino acid
- A cell has 20 of these, one for each amino acid (unique one for each)
- Requires ATP
138
Q
Comparison of Prok and Euk translation
A
- Genetic code is conserved, both have initiating AUG
- Transcription/translation occur simultaneously in proks
- mRNA is short-lived in bacteria, highly variable in euks
- Ribosomal subunits are diff, creates differences in initiation
139
Q
Base analogs
A
- Compounds that can substitute for purines and pyrimidines during nucleic acid biosythesis
- mimics a base, but is not a base
- Can lead to tautomeric shifts which creates mutations
- UV light sensitivity
ex:
5-Bromouracil is a thymine analog
140
Q
Proteins can be:
A
- Enzymes hexokinase)
- Structural: actin/myosin
- Signal transducers: G proteins
- Combinations: hexokinase
141
Q
Homologous Recombination Repair
A
- Type of double-strand break repair
- Both strands break and sister chromatid (identical) is present
- dips down to sister for template
- 3’ invades homologous sister chromatid
- synthesis across damaged region
142
Q
Antibiotics
A
- can target differences between eukaryotic and prokaryotic protein synthesis mechanisms
Ex: fMet and Met start codon between the two, respectively
143
Q
Direct DNA repair
A
- A specific protein (enzyme) directly removes a specific incorrect group
- Repairs pyrimidine dimers
144
Q
Kuru in humans
A
- Arises in people who eat scrapie-ridden sheep brain
145
Q
What is NOT evidence of genomic instability?
A
- Rapid cell division bc external factors like signal transduction affect it
146
Q
p53 tumor suppressor gene
A
- “Guardian of the genome”
- Protein that binds to DNA to repair mutated DNA/activate genes that stop cell division in cell w/ mutated DNA
- Defects in p53 gene implicated in 50% of cancers
- tumor suppressing genes are recessive acting mutation
147
Q
Nonsense mutation
A
- change in a triplet that will code for a stop codon
- causing premature termination of translation
148
Q
Post replication repair
A
- type of homologous recombination repair
- separated into single strand, but know that template strand is being replicated with DNA damage still present
- NOT ERROR PRONE
- responds after the damaged DNA has escaped repair and has failed to be completely replicated
149
Q
T/F: translocations are drivers of chromosomal rearrangements
A
- true
150
Q
Why are Transposable Elements common?
A
- Cellular Function Hypothesis
- TE serve a function in the cell - Genetic Variation Hypothesis
- provides variation and is regulated by the cell
- good thing - Selfish DNA Hypothesis
- TE serves no purpose, they EXIST JUST to spread
151
Q
Regulation control can be positive or negative
A
- Negative (REPRESSOR PRESENT)
- gene expression occurs unless shut off by regulatory molecule, aka the repressor
- stop transcription when bound - Positive (INDUCER PRESENT)
- transcription occurs only if regulatory molecule directly stimulates RNA production, aka the inducer
152
Q
Silencers
A
- A transcription regulatory element (sequence) that prevents transcription at a distance from the promoter
- Opposite of enhancer
153
Q
What mutation on the lac operon results in constitutive expression of the structural genes?
A
- transcription occurs in presence/absence of lactose
- A mutation on operator
ex: Operator changes shape, repressor can’t bind to repress transcription
154
Q
When tryptophan levels are high, attenuation occurs to terminate transcription (i.e. folded secondary structure of 5’ UTR on operon inhibits it)
A
When tryptophan levels are low, antitermination occurs, production of tryptophan occurs
155
Q
Glucose levels and cAMP
A
- High glucose levels, low cAMP levels
- no lactose
- transcription repressed, no lac mRNA - Low glucose levels, low cAMP levels
- lactose present
- repressor is inactivated
- very little lac mRNA transcribed - Low glucose levels, high cAMP levels
- lactose present
- abundanct lac mRNA transcribed
156
Q
Translocation of c-MYC
A
- chromosome 8 can involve proto-oncogene on chromosome 8
- translocates next to immunoglobulisn gene on chromosome 14 which changes the background and can cause problems
157
Q
Lethal Mutation
A
- Disrupts a process essential to survival of an organism
- kills of a cell or organism
- some diseased phenotypes
158
Q
Euk gene regulation with RNA stability:
A
Amount of mRNA is regulated by:
- Transcription
- Perisistence of mRNA (turnover)
- Different mRNAs have diff stabilities
- some destroyed quickly by host RNases.
- Remember, Proteins come from mature mRNA
159
Q
Loss-of-function mutation
A
- Mutation that reduces or eliminates the function of the gene product
- alters protein so much it does not work or is improperly regulated
- tends to be recessive
160
Q
Archibald Gerrod (1908)
A
- Suggested genes encoded enzymes
- that there is a relationship between genotype and proteins
161
Q
Stanley Prusiner and his laboratory (1982)
A
- Discovered that Scrapie in sheep was due to infectious protein (prions)
- When abnormal protein molecule contacts normal one, the normal becomes abnormally conformed
- is a chain rxn
162
Q
Dicer
A
- Cleaves dsRNA precursors into siRNA or miRNA
163
Q
E-site
A
- Exit site where empty tRNA’s exit ribosome
164
Q
RNA-induced gene silencing steps
A
- dsRNA (precursor) in nucleus
- Dicer enzyme complex cuts dsRNA to siRNA or miRNA
- siRNA/miRNA joins RISC or RITS as part of gene expression
165
Q
Nucleotide Excision Repair (NER)
A
- if damage extends beyond one base, we use this
- usually bulkier distorts/alters the double helix
- Damaged DNA is recognized
- Double-strand is unwound, held apart by SSB proteins
- Excision on either side of damaged DNA, cut around
- polymerase adds correct sequence
- fixes pyrimidine dimers
166
Q
Genetic mutation
A
- An inherited change in genetic information (either in daughter cells or individuals)
- The source of all genetic variation
167
Q
Frameshift mutation
A
- Insertion/Deletion
- most frequent form of mutation
- Mutation that alters the triplet reading frame during translation
- Occurs from the insertion/deletion of one or more nucleotides in a gene
- can be severe if it occurs early in the coding sequence because will mess up every triplet set of codons, which will mess up the entire amino acid
168
Q
Initiation steps of translation
A
- AUG Codon uses fMet in prokaryotic translation
1. mRNA and IF1 bind to small subunit
2. Initiator tRNA binds to mRNA - More IFs (IF2 and IF3) bind to initiation complex to enhance charged fMet-tRNA binding to small subunit
3. Large subunit binds to initiation complex - GTP is hydrolyzed so IFs can be released. Elongation factors on tRNA to begin elongation
169
Q
What are the two types of retrotransposons?
A
- SINES and LINES
- which can be mutagens causing diseases, such as:
1. Hemophilia (LINEs disrupt a gene)
2. Breast cancer (Alu insertion into a gene from SINEs)
170
Q
Peptidyl transferase & ribozyme
A
- Peptide formation is catalyzed by this enzyme, or so it’s believed…WRONG
- Actually, it’s the use of a catalytic ribosome, a ribozyme
171
Q
Mutagens
A
- Chemicals or substances that induce mutations in genes, have potential to change DNA
Ex: carcinogen
172
Q
Operon
A
- A single transcriptional unit of DNA that contains a promotor, operator, and structural genes in that order
Ex: lac operon
173
Q
Oncogene
A
- proto-oncogenes that have received a gain of function mutation
- dominant cancer phenotype
- cancer causing genes
174
Q
Inducible enzyme
A
- Present only when specific chemical substrates are present (the inducer: ex is lactose)
- OFF but gets turned on when inducer present
- role of substrate is to act as an INDUCER and turn it ON
- Production/transcription is ON when inducer is present
175
Q
What is the attenuation sequence on the trp operon?
A
- It is the 3-4 complementary base pairing on the transcribed mRNA from the trp operon (high trp levels).
When tryptophan levels are low: Transcription continues if the transcribed mRNA complementary base pairs at 2 and 3 sequence
176
Q
Missense mutation
A
- change of one nucleotide of a triplet
- can result in the creating of a new triplet that codes for a different amino acid
177
Q
What happens when tryptophan levels are low?
A
- Transcription continues (is not attenuated)
- when the transcribed mRNA sequence has secondary folded structure at 2 and 3 sequence from complementary base pairing
- Ribosome is translating, goes to region 1
178
Q
Null mutation
A
- Mutations that result in complete loss of function
Ex: haploinsufficiency - protein doesn’t work as well as it should
179
Q
Fatal Familial Insomnia
A
- Disease usually begins between 40-60
- inherited form of prion, most often in runs in families
- Minor difficulty falling asleep, occasional muscle movement problems
- lose ability to sleep
- muscle twitching, rapid heart rate, dementia
- death 7-36 mos. of illness
180
Q
Strand Slippage
A
- A mutation that leads to either a trinucleotide/dinucleotide expansion/contraction during DNA replication
- spontaneous reactions which form a loop of mispaired bases
- can insert or delete in the looped area
- see it in repetitive areas (ex: TTTTTT)
- The larger number of tri/dinucleotide repeats, the more severe disease symptoms
181
Q
Proto-oncogene
A
- Regulates cell division and growth
- tumor suppressor gene
- When mutated, becomes an oncogene (DOMINANT): a cancer-causing gene, a proto-oncogene that experienced a gain-of-function mutation
182
Q
Nonhomologous end-joining Repair
A
- Type of double-strand break repair
- when chromosome broken
- Occurs prior to replication, during G1
- Protein kinase & complex binds to free ends of broken
- DNA, trims ends, and ligates pieces together
- take broken chromosomes and stick back together and hope nothing important was deleted
- SOME NUCLEOTIDE SEQUENCES ARE LOST DURING END JOINING
- error prone
183
Q
CAP
A
- Catabolite activator protein
- enhances RNA polymerase binding to promoter with help of cAMP
- Helps activate the expression of the lac operon
184
Q
Metastasis
A
- Tumors that move to other sites
185
Q
What role does glucose play in inhibiting CAP binding?
A
- Presence of glucose yields decline in cAMP
- CAP needs cAMP to bind to promoter of lac operon
- RNA polymerase seldom binds/transcribes
186
Q
70S initiation complex
A
- Large subunit
- associates after IF-3 dissociates
- functional ribosome with A, P and E sites where protein synthesis takes place
187
Q
Cancer
A
- A genetic disorder at the cellular level
- when cells lose the ability to know when to stop dividing which causes a mass of cells
- proliferation=abnormal cell growth and division
- defects in normal restraints that keep cells from spreading to and colonizing other parts of the body (metastasis)
188
Q
Anticodon
A
- three consecutive ribonucleotides complementary to the codon(on mRNA)
- found on tRNA
189
Q
Hydroxylation
A
- adds OH group
- when you modify it leads to mispairing
190
Q
Multi-hit hypothesis
A
- discovered by Alfred Knudson (1971)
- several mutations must occur on a cell before it becomes cancer
- Genetic predisposition: more likely to have multiple hits & acquire cancer
191
Q
There are ____ more DNA in humans derived from transposable elements, than DNA encoding all human proteins ( ___of human genome sequence derived from TE)
A
- 20x
- 50%
192
Q
Intercalating Agents
A
- they are mutagenic bc they distort DNA structure
- Chemicals that that wedge between base pairs of DNA
- cause base pairs to distort and DNA strands to unwind
- Affect replication/repair
- cause deletions/insertion during these processes
- frameshift mutation
Ex: Ethidium bromide used in labs to stick to DNA
193
Q
Behavioral mutation
A
Mutation that affects the behavior patterns of an organism
Ex: mating behavior of fly is impaired if it can’t beat wings
- defect may be in flight muscles
- difficult to analyze
