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
Termination steps of translation
1. Stops codons (UAG, UAA or UGA) enter A-site
2. GTP-dependent release factors cleave polypeptide chain from terminal tRNA
3. tRNA released from ribosome, ribosome dissociates into subunits
26
Transversion
| - draw
- Type of base substitution/point mutation
| - A purine replaces a pyrimidine, or vice versa
27
Euk gene regulation with chromatin structure:
1. Acetylation of histones
- opens chromatin allowing transcription
2. Methylation of histones
- can change chromatin packing, usually causing tightening (heterochromatin)
3. Methylation of DNA
- transcriptionally inactive parts of chromosome
RITS!!
28
Depurination
- 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
Inherited forms of prion diseases
1. Fatal Familial Insomnia
2. Sickle Cell Anemia
3. Alzheimer's, huntingtons, parkisons
30
In proks: how does transcription and translation occur?
- simultaneously
31
Benign tumor
- Cancerous cells remain localized in the body
| - when a cell
32
Cell cycle checkpoints
1. G1/S
- cell monitors its size, determines whether DNA is damaged
2. G2/M
- processes are monitored prior to mitosis (like DNA replication and repair)
3. M
- checkpoint occurs during mitosis, spindle fiber formation/attachment to kinetochores monitored.
- Mitosis can be arrested, trigger apoptosis
33
Attenuation
- Premature termination of transcription
- Yields unstable protein
- Occurs w/ high levels of tryptophan (secondary structure)
34
RNA Interference
- The process in which the introduction of dsRNA into a cell causes degradation of mRNAs containing the same sequence
35
Conditional mutation
- only expressed under certain environmental conditions
- present in genome
ex: Temperature sensitive
- variable function at different temperatures
36
Transition
| - draw
- Type of base substitution/point mutation
| - Like replaces like, purine for a purine, or pyrimidine for pyrimidine
37
Loss of heterozygosity
- 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
lac operon: For maximum transcription of the structural genes
- 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
Start codon of mRNA (AUG) in prokaryotes codes for...
- Modified amino acid
| - formylmethionine (fmet)
40
Differences between prok and euk gene regulation:
1. Euk genes are NOT organized into operons
2. Chromatin affects gene expression in euks
3. Activators are more common in euks than repressors
4. Regulation of gene expression has transcriptional activator proteins which bind to DNA in regulatory promoter, interact with other molecules
41
Euk gene regulation with transcription:
Transcriptional activator proteins:
1. Bind to regulatory promoter in DNA
2. Interact w/ other components (initiation complex)
- Enhancers/silencers, insulators, MULTIPLE REGULATORY ELEMENTS
42
P-site
- Peptidyl site on ribosome
| - Holds tRNA bound to the growing polypeptide chain
43
Shine-Dalgarno sequence
- 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
Kozak sequence
- 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
Biochemical mutation
- Do not always affect morphological characters
- mutation in a biochemical pathway
Ex: sickle-cell anemia, hemophilia
46
If termination codon appears in middle of mRNA molecule from mutation...?
- Termination occurs, and polypeptide chain is prematurely terminated
47
Haploinsufficiency
- One copy of a product on a gene is not enough for wild-type phenotype
- Result of loss-of-function mutation
48
Regulator protein
- Is either a repressor or activator, interacts with the operator to either stop/start transcription
49
30S initiation complex
- everything in the initiating step (+mRNA, small ribosome)
- attaches to mRNA
- small ribosomal subunit
50
T/F: some tumor suppressor genes are involved in DNA repair
- true
51
Catabolite repression
- The inhibition of the lac operon when glucose is present
- glucose causes decline of cAMP
- Positive control
52
Mutation rate
- 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
unequal crossing over
- 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
Trypotophan levels affect on transcription
1. tryptophan levels are high
- attenuation occurs to terminate transcription (i.e. folded secondary structure of 5' UTR on operon inhibits it)
2. tryptophan levels are low
- antitermination occurs, production of tryptophan occurs
55
Different protein structures:
1. Primary
- sequence of AA's
2. 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
3. Tertiary
- interaction of secondary structure
- 3D conformation of the entire chain
- level gives the protein its specific function by the way its folded
4. Quaternary
- 2 or more polypeptides interact
56
R groups on amino acids
- 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
BAX homodimer
- promotes apoptosis
| - we make more of this if cell is in trouble
58
Malignant tumor
- Tumor cell invades other tissues in the body
59
core promotor
- determines the accurate initiation of transcription by RNA pol II
60
Barbara McClintock
- discovered transposable elements
| - maize
61
Photoreactivation Repair
- 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
SOS repair
- 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
Elongation steps of translation
1. Second charged tRNA enters A-site facilitated by EF-Tu; AUG codon passed down to P-site
2. 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
3. Translocation: Continued movement of ribosome down mRNA
64
N terminus vs C Terminus
1. N Terminus contains amino group
- 5' end
2. C terminus contains carboxyl group
- 3' end
65
Where on the tRNA does the amino acid bind to?
- acceptor stem is where tRNA is going to grab aa
| - at its 3' end
66
Purines vs Pyrimidines
| - pairing
1. Purines: A and G
2. Pyrimidines: C, T, U
3. Pairs: A=T and G=C
67
RISC
| RNA-induced silencing complex
- Combines w/ miRNA or siRNA, then binds to mRNA
- if mRNA is complementary, mRNA degradation
- If mRNA isn't exactly complementary, translation inhibition
68
Ionizing radiation
- More energetic than UV radiation
- more dangerous bc penetrate deeper causing free radicals can break DNA
Ex: X-rays, gamma rays, cosmic rays
69
IF-1
- enhances dissociation between small and large ribosomal subunit
- blocks the A site from binding to tRNA
70
Tautomer/Tautomeric shifts
- 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
Directionality of amino acids
- 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
Vascularization
- 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
What happens with the transposition of Ds element (when accompanied by Ac element, which provides transposase)
- 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
Importance of Cap and poly A tail in eukaryotes
- 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
RITS
| RNA-induced transcription silencing complex
- Targets specific promoters or chromatin regions of DNA
- recruits chromatin remodeling enzymes
- methylation occurs, heterochromatin forms
- transcription inhibited
- TEMPORARILY HALTS GENE EXPRESSION
76
Jacob and Monod (1961)
- First described the operon model
- Operon is the basic unit of transcription control in bacteria
- Found the lac operon is inducible
77
Deamination
- 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
lac Operon
- 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
Elongation requires these components:
1. 70S complex
2. Charged tRNAs
3. Elongation factors(EF-G and EF-Tu)
4. GTP hydrolysis
80
IF-3
- Initiation factor
- Binds to small subunit to block large subunit from binding to small one
- Helps small subunit to attach to mRNA
81
Translation occurs where in eukaryotes AND prokaryotes?
The cytoplasm
82
Interstrand crosslinking
- 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
LINES
- long interspersed nuclear elements
- encode own reverse transcriptase
- has retrotransposons (can function on own)
84
Charging
- 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
Positive Inducible
- 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
Riboswitches
- 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
Age correlation with cancer
- 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
Ac (activator) element
- A mutation that is autonomous (can transpose alone)
| - functional
89
Gain-of-function mutation
- 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
Euk gene regulation with post-transcription:
1. 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
2. RNAi: short sequence (sequence-specific) causes degradation of mRNAs w/ same sequence
91
Nutritional mutation
- Results in loss of ability to synthesize an amino acid or vitamin
ex: auxotrophs
92
tRNA
- 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
Collinearity
- The correspondence between the sequence of triplets and sequence of amino acids
94
Repressible enzyme
- 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
protein structure
- polypeptides can fold up to form proteins
96
P element
- A Drosophila transposable element that causes mutations in the flies
97
Adaptive/facultative enzymes
- Produced when needed
98
if an __________________ is bound, transcription should be on
- activator/inducer
99
Roles of small subunit and large subunit during elongation:
1. Small
- decodes mRNA triplets (yields codons)
2. Large
- peptide bond synthesis
100
Somatic mutation
- 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
Negative repressible operon
- transcription ON
- inactive repressor
- activator (corepressor) introduced to bind to repressor, makes repressor active
- transcription off
102
Evolution of transposons to be useful
- 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
Beadle and Tatum (1940s)
| - experiment and conclusions
- 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
Retrotransposons vs DNA transposons
1. Retrotransposons
- jump and transpose by reverse transcriptase (the RNA intermediate, copies RNA to DNA)
- active in genome
2. DNA transposons
- do not jump
- inactive in genome
105
Tumor-suppressing genes
- 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
Post-translational modifications for proteins include:
1. 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
Enhancers
- A transcription regulatory element (sequence) that enhances transcription at a distance from the promoter
- Opposite of silencer
108
Provirus (cancers associated with virus)
- 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
Pseudodominance
- Wildtype allele is somehow inactivated (mutated)
- if cell is heterozygous
- recessive trait is expressed
110
UV radiation
- 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
Signal transduction and cancer
1. The process of transmitting growth signals from external environment to cell nucleus.
2. In cancerous cells
- transduction is defected, continuous growth signals sent to cell, malignant cells don't respond to external signals from surrounding cells
112
Prions
- 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
Bcl2/BAX heterodimer
- inactive complex
| - bc do the opposite jobs of eachother
114
promotor elements
- short nucleotide sequences that bind to specific regulatory factors
- regulate transcription
- decide where it begins and which direction it occurs
115
Activator Proteins
- 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
Apoptosis
- Programmed cell death
| - A repair mechanism to prevent cancer
117
Germ line mutations
- 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
Transposons (transposable elements)
- 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
Open reading frame
- Section of DNA between start and stop codon
120
Ribosome
- 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
Spontaneous mutation
- 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
_________________ are the second most leading cancer causing agent. A number of inherited cancers are caused by defects in genes that control ________
- viruses
| - DNA repair
123
SINES
- short interspersed nuclear elements
- lack retrotransposons (need LINE to do reverse transcriptase)
- most common transposable element in the human - Alu element (SINE)
124
genome instability
- duplications, deletions, rearrangements, chromosome breaks, fusions (translocations)
- genome instability is a characteristic of cancer cells
125
Telomerase
- The enzyme activated in my tumors cells
- repairs telomeres at chromosome ends
- allows unlimited cell division
126
A-site
- Aminoacyl-tRNA site on ribosome
| - Holds incoming, new activated amino acid
127
Constitutive enzymes
- Enzymes that are produced continuously
| - regardless of chemical makeup of environment
128
Similarities in gene expression regulation between euks and proks:
1. Both have DNA-binding proteins that influence RNA polymerase initiation
2. Both have repressors and activators
129
Bcl2 homodimer
- blocks apoptosis
| - continue onto cell cycle
130
Ames test
- 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
Alkylation
- add an alkyl groups to keto/amino groups of nucleotides
| - base pairing affinities are altered and will pair incorrectly
132
Regulatory mutation
- Affect the regulation of gene expression
- can disrupt an entire pathway
- not making the correct amount of a protein
133
Proteins made up of __ common amino acids and all contain"
- 20
1. Amino group
2. Hydrogen
3. R group (variable)
4. Carboxyl group
134
Cyclins
- 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
Why was bread mold useful for use:
1. Easy to grow in lab
2. Vegetative form is haploid
- can see recessive mutations easily!
136
Ds (dissociation) element
- 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
Aminoacyl tRNA synthetases
- 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
Comparison of Prok and Euk translation
1. Genetic code is conserved, both have initiating AUG
2. Transcription/translation occur simultaneously in proks
3. mRNA is short-lived in bacteria, highly variable in euks
4. Ribosomal subunits are diff, creates differences in initiation
139
Base analogs
- 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
Proteins can be:
1. Enzymes hexokinase)
2. Structural: actin/myosin
3. Signal transducers: G proteins
4. Combinations: hexokinase
141
Homologous Recombination Repair
- 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
Antibiotics
- can target differences between eukaryotic and prokaryotic protein synthesis mechanisms
Ex: fMet and Met start codon between the two, respectively
143
Direct DNA repair
- A specific protein (enzyme) directly removes a specific incorrect group
- Repairs pyrimidine dimers
144
Kuru in humans
- Arises in people who eat scrapie-ridden sheep brain
145
What is NOT evidence of genomic instability?
- Rapid cell division bc external factors like signal transduction affect it
146
p53 tumor suppressor gene
- "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
Nonsense mutation
- change in a triplet that will code for a stop codon
| - causing premature termination of translation
148
Post replication repair
- 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
T/F: translocations are drivers of chromosomal rearrangements
- true
150
Why are Transposable Elements common?
1. Cellular Function Hypothesis
- TE serve a function in the cell
2. Genetic Variation Hypothesis
- provides variation and is regulated by the cell
- good thing
3. Selfish DNA Hypothesis
- TE serves no purpose, they EXIST JUST to spread
151
Regulation control can be positive or negative
1. Negative (REPRESSOR PRESENT)
- gene expression occurs unless shut off by regulatory molecule, aka the repressor
- stop transcription when bound
2. Positive (INDUCER PRESENT)
- transcription occurs only if regulatory molecule directly stimulates RNA production, aka the inducer
152
Silencers
- A transcription regulatory element (sequence) that prevents transcription at a distance from the promoter
- Opposite of enhancer
153
What mutation on the lac operon results in constitutive expression of the structural genes?
- transcription occurs in presence/absence of lactose
- A mutation on operator
ex: Operator changes shape, repressor can't bind to repress transcription
154
When tryptophan levels are high, attenuation occurs to terminate transcription (i.e. folded secondary structure of 5' UTR on operon inhibits it)
When tryptophan levels are low, antitermination occurs, production of tryptophan occurs
155
Glucose levels and cAMP
1. High glucose levels, low cAMP levels
- no lactose
- transcription repressed, no lac mRNA
2. Low glucose levels, low cAMP levels
- lactose present
- repressor is inactivated
- very little lac mRNA transcribed
3. Low glucose levels, high cAMP levels
- lactose present
- abundanct lac mRNA transcribed
156
Translocation of c-MYC
- 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
Lethal Mutation
- Disrupts a process essential to survival of an organism
- kills of a cell or organism
- some diseased phenotypes
158
Euk gene regulation with RNA stability:
Amount of mRNA is regulated by:
1. Transcription
2. Perisistence of mRNA (turnover)
- Different mRNAs have diff stabilities
- some destroyed quickly by host RNases.
- Remember, Proteins come from mature mRNA
159
Loss-of-function mutation
- 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
Archibald Gerrod (1908)
- Suggested genes encoded enzymes
| - that there is a relationship between genotype and proteins
161
Stanley Prusiner and his laboratory (1982)
- 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
Dicer
- Cleaves dsRNA precursors into siRNA or miRNA
163
E-site
- Exit site where empty tRNA's exit ribosome
164
RNA-induced gene silencing steps
1. dsRNA (precursor) in nucleus
2. Dicer enzyme complex cuts dsRNA to siRNA or miRNA
3. siRNA/miRNA joins RISC or RITS as part of gene expression
165
Nucleotide Excision Repair (NER)
- 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
Genetic mutation
- An inherited change in genetic information (either in daughter cells or individuals)
- The source of all genetic variation
167
Frameshift mutation
- 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
Initiation steps of translation
- 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
What are the two types of retrotransposons?
- 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
Peptidyl transferase & ribozyme
- 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
Mutagens
- Chemicals or substances that induce mutations in genes, have potential to change DNA
Ex: carcinogen
172
Operon
- A single transcriptional unit of DNA that contains a promotor, operator, and structural genes in that order
Ex: lac operon
173
Oncogene
- proto-oncogenes that have received a gain of function mutation
- dominant cancer phenotype
- cancer causing genes
174
Inducible enzyme
- 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
What is the attenuation sequence on the trp operon?
- 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
Missense mutation
- change of one nucleotide of a triplet
| - can result in the creating of a new triplet that codes for a different amino acid
177
What happens when tryptophan levels are low?
- 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
Null mutation
- Mutations that result in complete loss of function
Ex: haploinsufficiency
- protein doesn't work as well as it should
179
Fatal Familial Insomnia
- 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
Strand Slippage
- 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
Proto-oncogene
- 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
Nonhomologous end-joining Repair
- 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
CAP
- Catabolite activator protein
- enhances RNA polymerase binding to promoter with help of cAMP
- Helps activate the expression of the lac operon
184
Metastasis
- Tumors that move to other sites
185
What role does glucose play in inhibiting CAP binding?
- Presence of glucose yields decline in cAMP
- CAP needs cAMP to bind to promoter of lac operon
- RNA polymerase seldom binds/transcribes
186
70S initiation complex
- Large subunit
- associates after IF-3 dissociates
- functional ribosome with A, P and E sites where protein synthesis takes place
187
Cancer
- 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
Anticodon
- three consecutive ribonucleotides complementary to the codon(on mRNA)
- found on tRNA
189
Hydroxylation
- adds OH group
| - when you modify it leads to mispairing
190
Multi-hit hypothesis
- 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
There are ____ more DNA in humans derived from transposable elements, than DNA encoding all human proteins ( ___of human genome sequence derived from TE)
- 20x
| - 50%
192
Intercalating Agents
- 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
Behavioral mutation
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
