genetics final review talar tfnakjian oh: t, th 8-9 am natural sci i room 2108 [email protected]...
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Genetics Final Review
Talar TfnakjianOH: T, TH 8-9 am Natural Sci I room [email protected]
Emily LingOH: Mon 9-10 AM SH 149Wed 3-4 PM SH [email protected]
Online Evaluationhttps://eee.uci.edu/programs/biotutor/bio97b.php
Talar [email protected]
Emily [email protected]
I will hold 1 extra office hour Monday at 3-3:50PM in SH149
This power point will be uploaded after the review…or at least by the weekend.
Disclaimer Topics discussed in this review are by
no means everything you are expected to know.
We are not in direct contact with the professor. Do not rely solely on this review and expect to get a 100%.
Outline What are bacteria What are viruses/phages Antibiotic resistance in bacteria Modes of DNA movement between cells
Steps required for cloning
1- remove the nucleus form an egg.
2- inject a nucleus from the organism being cloned into the enucleated egg.
3- inject the egg into a surrogate mother who will birth the organism.
The result is an organism that is genetically identical to the donor of the nucleus.
Cloning a gene1. Cut the desired gene with restriction enzyme.2. Cut the vector with the same restriction
enzyme.3. Insert the desired gene into the vector4. Seal the gap with DNA ligase5. This result is a recombinant DNA molecule6. Insert the recombinant DNA into a host for
replication.
Characteristics of a vector A vector should have:a) a replication origin.b)A selectable marker like an antibiotic
resistancy gene.c) Restriction site to insert desired genes.
Terms to know… Restriction site: A short DNA sequence that
can be cleaved by a restriction enzyme. Restriction Enzyme: A restriction enzyme,
or restriction endonuclease, cleaves DNA at a specific sequence
Tip: review Factor VIII cloning in your notes.
Outline Review the structure of the human gene:
regions to know that are related to replication and transciption-translation
Recombinant DNA Genetic Engineering (Transgenic or GM
organism) Uses in therapies for disease and agriculture
Gene therapy
What does it mean to be linked? The idea is that we have many
chromosomes containing lots of genes , and not all genes can segregate independently.
Genes located close together on the same gene must be inherited together.
The usual Independent Assortment
A a
B
Stem cellafter chrmreplication
Half of the time
©2000 Lee BardwellA a
B b b
aa
B B
A
b
A
b
aa
b b
A
B
A
B
Half of the time MEIOSIS I
Yellow green
Round wrinkled
A
a
B
b
A
a
B
bA
a
B
b
gametes
Stem cell
Meiosis I + II
Gametes produced with two unlinked genes
©2000 Lee Bardwell
25%
25%
25%
25%
Equal probabilities!
AB/ab
haplotype
haplotype
©2003 Lee Bardwell
Ab/aB
haplotype
haplotype
Recessive alleles are cis
Recessive alleles are in trans
A
a
B
b
A
a
b
B
Yellow,Rounddiploid cell
Yellow,Rounddiploid cell
Non-parental chrms
A Bab A b a B a b
©2000 Lee Bardwell
ab/ab x AB/ab
A B a bA b a B
35% : 18% : 16% : 31%
226 : 114 : 102 : 202644 progeny were scored
To figure out the recombination frequencies simply add the recombinant type frequencies.
In this case 18% + 16%
©2001 Lee Bardwell
ab/ab x AB/ab: 39% AB 11% Ab 11% aB 39% ab
ad/ad x AD/ad: 42% AD 8% Ad 8% aD 42% ad
bd/bd x BD/bd: 46% BD 4% Bd 4% bD 46% bd
Ar Be
Ar Du
Be Du
22 cM
16 cM
8 cM What’s the order of the genes?
Fine-Scale Mutations -
Involve less than 1000 base pairs
Often, just a single base pair is changed
Include substitutions, deletions, insertions, duplications
©1999 Lee Bardwell
5’----------GAATTC---------3’3’----------CTTAAG---------5’Insertion:5’----------GAACTTC---------3’3’----------CTTGAAG---------5’Duplication:5’----------GAATATTC--------3’3’----------CTTATAAG--------5’
5’----------GAATTC---------3’3’----------CTTAAG---------5’Substitutions:5’----------GATTTC---------3’3’----------CTAAAG---------5’5’----------GAGTTC---------3’3’----------CTCAAG---------5’Deletion:5’----------GAATC----------3’3’----------CTTAG----------5’
Substitutions• Silent- TGT (Cys)--> TGC (Cys)
GCA (Ala)--> GCN (Aladoes no result in a different amino acid (N = any)
• Missense-TGT (Cys)--> TGG (Trp)
• Nonsense- TGT (Cys)--> TGA (STOP)
Spontaneous MutationsI. Mistakes
Replication errors Polymerase sometimes incorporates the wrong
base.It has a proofreadingactivity that takes care of the misincorporations. Howeever some mistakes may not be corrected
Recombination errors Unequal crossing over, etc.
Between similar seqs on non-homologous chrms --> translocation
Between similar seqs within a chrm --> inversion or deletion
Between tandemly repeated seqs on homologous chrms --> duplication or deletion
Refer to lecture slides for more details
II. endogenous DNA Damage
Spontaneous base damage Deaminations, depurinations
-Byproducts of metabolism Oxygen radicals that damage DNA
Deamination of CytosineNH
H
H
H
O N
N
2
H*
H
H
O N
N
O
*Thymine has CH3 here
deNHn
Cytosine Uracil
©2000 Lee Bardwell
H
Endogenous DNA damage
Induced MutationsCause by outside
sources
Cause by: -Chemicals
Natural In foods, e.g. aflatoxin
Man-made/man-increasedNitrogen Mustard - WWI nerve gas
Benzopyrene - smoke from coal, autos, cigs -Ultraviolet (UV) Radiation (from sun)>> Pyrimidine dimerIonizing radiation
Natural: radon gas, cosmic raysMan-made: x-rays, nuclear tests
what happens to the Damage DNA? =(
-Tolerated (ignored)-Repaired-Can kill the cell or cause the cell to kill itself -Can become fixed, resulting in a mutation
Note fixed≠ repaired
Uracil DNA glycosylase
An enzyme that removes Uracil from DNA
Resulting abasic site is filled in by polymerase
Uracil in DNA comes mainly from deamination of cytosine
That may be why DNA uses thymine instead of uracil
If the uracil isn’t removed, it will pair with A, causing C/G --> T/A transition.
©2007 Lee Bardwell
5’-GAATTU-3’3’-CTTAAG-5’
5’-GAATT_-3’3’-CTTAAG-5’
5’-GAATTC-3’3’-CTTAAG-5’
Nucleotide Excision Repair
Carried out by a multi-protein complexRemoves bulky adducts from DNA, e.g.
Pyrimidine dimers caused by UV Benzopyrene-DNA adducts
Nearby nucleotides are also excisedResulting single-strand gap is filled in
by polymerase
©2000 Lee Bardwell
Outline Cancer: a loss of growth regulation
Disease of somatic cells Oncogenes and Tumor Suppressor
Genes Spontaneous and Induced Mutations Malignant and Benign 6 Factors of a Successful Cancer Cell Hereditary Cancers
Key words to knowGenotype frequency = proportion
of individuals in a population with a specific genotype
Allele frequency = proportion of alleles in a population
Population = group of organisms of the same species living in the same geographical area
Gene pool = all alleles in population
The big picture…
Relationship between allele frequencies and genotype frequencies
How to predict what AF’s and GF’s will be in future generations
Hardy & Weinberg
Developed a simple mathematical model of the transmission of alleles from generation to generation
Based on this equation, if we know the allele frequencies in a population then we can calculate the allele frequency in the next
generation
(p+q)2 = p2 + 2pq + q2 = 1 This gives you the genotype frequencies.
To count alleles in the next generation either actually count the alleles in the gene pool Or use the shortcut.
freq(A) = freq(AA) + 1/2 freq(Aa)
freq(a) = freq(aa) + 1/2 freq(Aa)
Hardy –weinberg condition Allele frequencies will remain unchanged under
assumptions of hardy-Weinberg
Mating is random Allelic frequencies are the same in males and
females All genotypes have equivalent viability and fertility Mutation does not occur Migration into the population is absent Population is large so that allelic variations do not
occur by chance
Things to watch out for
If we know GF’s in a generation of a pop, then we can always calculate AF’s, whether or not HW equil.
If we know AF’s, we can only calculate GF’s (in this or the next generation) if the populations is in HW equilibrium
Let’s walk through an Example… An autosomal recessive disease affects
1/100 people In a population. Calculate the frequency of carriers.
So the info we are given is:genotype frequency = q2
we need to get the allele frequency first q= 1/10=.1P=.9To calculate carrier frequency simply do 2pq= 2(.1)(.9)= .18
X-linked With X- linked things are a little different
only with males. The genotype frequencies for males is
the same as the allele frequency.
Let’s work on another problem - One out of five females are
affected by a certain X- linked disease which causes them to have a shy personality. Calculate the heterozygote frequency in males and females:
Solution in this case q2 is given > q= (1/5)
~0.45 p= 0.55 Males don’t have a carrier because they
only have one copy of X Female carriers: 2pq= 2x .45x .55= .50
Forces that can cause deviation from HW ratios1. Gene flow (e.g., migration)2. Genetic drift3. Mutation4. Natural Selection5. Non-random mating (e.g.,
inbreeding)
©2005 Lee Bardwell
Outline What keeps unfavorable genes in gene
pool: When Bad alleles can be good as well Slow selection against recessive alleles
in diploids Mutation-selection equilibrium Heterozygote superiority
Outline What are bacteria What are viruses/phages Antibiotic resistance in bacteria Modes of DNA movement between
cells
A straight forward lecture(s).
Other Topics to Understand Characteristics of Bacteria Characteristics of Viruses & Phages How Antibiotics Work
Targets components that are different from infected host (like humans) Best ones target structures ONLY
associated with the micro-organism (like a cell wall of a bacteria)
Modes of DNA Transfer Conjugation – F-plasmid Transformation – DNA from environment Transduction – via Virus/Phage
A Question… 13. Antibiotic resistance genes are
typically found in: A. plasmids B. transposable elements C. viruses D. A and B E. A, B and C
D. A and B
A Question… 12. The process in which recipient
cells acquire genes from free DNA molecules in the surrounding medium is called A. transduction B. ligation C. transformation D. conjugation E. transposition
C. Transformation
A Question… 14. If you wanted to reproductively clone
your cat Trixie, you would need to take take a haploid/diploid/polyploid nucleus from a somatic cell/gamete of Trixie, and put it into an enucleated egg. A. haploid, somatic cell B. haploid, gamete C. diploid, somatic cell D. diploid, gamete E. polyploid, gamete
C. Diploid, Soma
An 8kb plasmid is digested with EcoRI (E) and/or BamHI (B), and the digests are run on an agarose gel and stained. The results are shown below; molecular size standards are shown on the left.
Answer: B
Based on the results of the gel, which plasmid map looks the most correct? Fill in answer E if you think none of them are correct. The light grey lines are to help you gauge distance.
A B C D E
A Question… 5. Which of the following statements are
TRUE?: A. All eggs produced by the same woman are
genetically identical to each other. B. All sperm produced by the same man are
genetically identical to each other. C. Both A and B are true. D. All the gametes produced by a person are
genetically identical to a somatic cell of that individual.
E. None of the statements (A-D) are true.
E. None True
Outline Brief: review the structure of the human
gene: regions to know that are related to replication and transcription-translation
Recombinant DNA Genetic Engineering (Transgenic or GM
organism) Uses in therapies for disease and agriculture
Gene therapy
A Question… 16. If you wanted to express a cloned human
gene in the bacterium E. coli, so that you could grow up the bacteria in large batches and make the corresponding human protein, you would need to: A. Remove the human introns B. Swap the human promoter/enhancer for a
bacterial promoter C. Change the codons because otherwise the wrong
amino acids would be specified D. A and B E. B and C
D. A and B
A Question…29. Your uncle had a heart attack at an early age. Since early onset heart disease is a multifactorial trait, one important piece of information you need to know to assess your risk is to know the fraction of alleles you share with your uncle. The fraction of your alleles that you share with your uncle is...
Answer: ¼ or 25%
Outline Cancer: a loss of growth regulation
Disease of somatic cells Oncogenes and Tumor Suppressor
Genes Spontaneous and Induced Mutations Malignant and Benign 6 Factors of a Successful Cancer Cell Hereditary Cancers
What are some of these genes that lead to cancer when mutated?
Oncogenes Gas pedal for cell proliferation Mutation --> Gas pedal stuck down
Tumor suppressor genes Brakes for cell division Mutation --> Brakes don’t work
©2001 Lee Bardwell
The Difference
A Question… 7. Fill in the blanks. A gene that encodes a
protein required for the repair of certain types of DNA damage is likely to be a _______. A gene that encodes a protein required to relay a signal telling a non-dividing cell to divide is likely to be a _______. A. oncogene; tumor-suppressor gene B. tumor-suppressor gene; oncogene C. oncogene; oncogene D. tumor-suppressor gene; tumor-suppressor gene E. malignant, hemizygous
B. TSG; Oncogene
Outline What keeps unfavorable genes in gene
pool: When Bad alleles can be good as well Slow selection against recessive alleles
in diploids Mutation-selection equilibrium Heterozygote superiority
A Question…29. Your uncle had a heart attack at an early age. Since early onset heart disease is a multifactorial trait, one important piece of information you need to know to assess your risk is to know the fraction of alleles you share with your uncle. The fraction of your alleles that you share with your uncle is...
An uncle shares 50% of the same DNA as his brother (the father). 50% of the genes from the father is transferred to you. Multiplication rule: the event: “What is the chance that the 50% similarity between your Uncle and your father is passed to you?
0.50 x 0.50 = .25 = 25%
Reasoning
17 &18.THIS PROBLEM IS WORTH 2 POINTS – FILL IN BOTH NUMBERS ON YOUR SCANTRON(Note – this is a tough problem meant to challenge the best-prepared students)
A polymorphic region in the human genome can be detected by a marker called 9Q17. As such, the polymorphic region is named the "9Q17 polymorphism", or 9Q17P for short. There are 4 common alleles of 9Q17P, named after the size of the bands seen on a Southern blot when EcoRI-digested genomic DNA is probed with radioactively-labeled 9Q17 marker DNA. 9Q17P is very tightly linked to the Huntington gene, the gene associated with the autosomal dominant, delayed-age of onset disease Huntington's disease. Three generations of a family, some members of which have Huntington's disease, are typed for 9Q17P. Alice has the 2 kb and 4 kb alleles, and her husband Ben has the 3 kb and 5 kb alleles. Alice and Ben have a son named Chuck, who has the 2 kb and 3 kb alleles. Chuck is married to Doris, who has the 4 kb and 5 kb alleles, and they have a 10-year-old son named Ed. Ben and Chuck have the symptoms of Huntington's disease.
(i). If Ed has the 3 kb and 4 kb alleles, is it likely that Ed will get HD?(ii). If Ed has the 2 kb and 5 kb alleles, is it likely Ed will get HD?
A. (i) = yes; (ii) = NOB. (i) = yes; (ii) = yesC. (i) = NO; (ii) = yesD. (i) = NO; (ii) = NO
E. (i) = NO; (ii) = maybe
A. Yes, No
17 &18.THIS PROBLEM IS WORTH 2 POINTS – FILL IN BOTH NUMBERS ON YOUR SCANTRON(Note – this is a tough problem meant to challenge the best-prepared students)
A polymorphic region in the human genome can be detected by a marker called 9Q17. As such, the polymorphic region is named the "9Q17 polymorphism", or 9Q17P for short. There are 4 common alleles of 9Q17P, named after the size of the bands seen on a Southern blot when EcoRI-digested genomic DNA is probed with radioactively-labeled 9Q17 marker DNA. 9Q17P is very tightly linked to the Huntington gene, the gene associated with the autosomal dominant, delayed-age of onset disease Huntington's disease. Three generations of a family, some members of which have Huntington's disease, are typed for 9Q17P. Alice has the 2 kb and 4 kb alleles, and her husband Ben has the 3 kb and 5 kb alleles. Alice and Ben have a son named Chuck, who has the 2 kb and 3 kb alleles. Chuck is married to Doris, who has the 4 kb and 5 kb alleles, and they have a 10-year-old son named Ed. Ben and Chuck have the symptoms of Huntington's disease.
(i). If Ed has the 3 kb and 4 kb alleles, is it likely that Ed will get HD?(ii). If Ed has the 2 kb and 5 kb alleles, is it likely Ed will get HD?
A. (i) = yes; (ii) = NOB. (i) = yes; (ii) = yesC. (i) = NO; (ii) = yesD. (i) = NO; (ii) = NO
E. (i) = NO; (ii) = maybe
Reasoning
21-24. In a certain population of students at Hardy-Weinberg equilibrium, one of every twenty-five individuals is affected by an autosomal recessive condition called ʻsleepyheadnessʼ, which causes them to fall asleep during important lectures.
21. What is the frequency of heterozygous carriers of ʻsleepyheadnessʼ in this population?
22. What is the allele frequency p of the dominant SH allele? What is the allele frequency q of the recessive SH allele? Your answer should take the form “p = __, q = __”.
23. Assume the population consists of 100 students. One day, the Professor kicks all four sleeping students out of the class, so now the population consists of 96 students. What are the allele frequencies of the dominant SH allele (p) and the recessive sh allele (q) in the new population? Your answer should take the form “p = __, q = __”.
24. Is the new population is Hardy-Weinberg equilibrium (yes or no)?
The Question
21-24. In a certain population of students at Hardy-Weinberg equilibrium, one of every twenty-five individuals is affected by an autosomal recessive condition called ʻsleepyheadnessʼ, which causes them to fall asleep during important lectures.
21. What is the frequency of heterozygous carriers of ʻsleepyheadnessʼ in this population? 0.32 (or 8/25)
22. What is the allele frequency p of the dominant SH allele? What is the allele frequency q of the recessive sh allele? Your answer should take the form “p = __, q = __”. p = 0.8 (or 4/5), q = 0.2 (or 1/5)
23. Assume the population consists of 100 students. One day, the Professor kicks all four sleeping students out of the class, so now the population consists of 96 students. What are the allele frequencies of the dominant SH allele (p) and the recessive sh allele (q) in the new population? Your answer should take the form “p = __, q = __”. p = 0.833 (or 5/6), q = 0.167 (or 1/6).
24. Is the new population is Hardy-Weinberg equilibrium (yes or no)? No
Answers