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Class:BIO 2450 - GENETICS
Subject:Biology
University:Texas State University - San Marcos
Term:Spring 2010
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Genetic Drift Is infinite pop. size possible? 1)-Changes in allele freq. due to random fluctuations -occurs in ALL populations 2) Yes, it is impossible, but the pop. size can be large enough where chance/drift is minimal
What is the effective population size? What is the formula? The effective number of adults contributing gametes to the next generation Ne = (4xNfxNm) / (Nf + Nm) Ne = effective pop. size Nf = # breeding females Nm = # breeding males
When does genetic drift occur? ALWAYS! But...more important in small populations
1) Bottleneck 2) Founder events 1) Situations when a pop. is significantly reduced by catastrophe 2) Dispersal & colonization by a smaller group from a larger pop.
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Give 2 defs. of natural selection with HW Equilibrium 1) Process by which traits evolve to make organisms, "adapted" to environment 2) Differential reproduction of genotypes, resulting in changed allele frequencies - individuals w/ certain alleles reproduce more often than those w/ alternate alleles
Fitness of genotypes Defs - 1) Absolute fitness 2) Relative fitness 1) Mean number of offspring an individual of a particular genotype has 2) degree tp which individuals of a particular genotype reproduce relative to inds. w/ other genotype
How do you calculate relative fitness? Problem: i.e. AA - 6, Aa - 9, aa - 12 --> AA has low fitness relative fitness: compare with highest fitness for each aa - 12/12 = 1, Aa - 9/12 = .75, AA - 6/12 = .5
1) Frequency after selection 2) Relative genotype freq. selection 3) Allelic frequency after selection 4) Change in allelic freq. caused by sel. 1) p ^2 x w11(finess), 2pq x w12, q^2 x w22 2) p' = p^2xw11 / average w, H' = 2pq x w12 / average w, Q' = q^2 x w22 / average w 3) p' = p' + 1/2(H') q' = 1 - p' 4) Change of p = p' = p
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How do you calculate mean fitness? p^2 x W1 + 2pq x W12 + q^2 x W22
How do species arise? Via the evolution of reproductive isolation
1) Prezygotic barriers 2) Post zygotic barriers 1) - habitat - behavioral - temporal - morphological 2) - hybrid inviability (weakness) - hybrid sterility
Dobzhansky - Mueller Speciation model 1) The Dobzhansky-Muller model proposes that hybrid incompatibilities are caused by the interaction between genes that have functionally diverged in the respective hybridizing species. 2) Two genes have not seen each other before, and are incompatible
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Identify these: Vp = Vg + Ve 1) Vp = Phenotypic variance 2) Vg = Genetic Variance 3) Ve = Environmental variance
What does variance mean? And what is its formula? How would you calculate std. deviation from this? 1)How much individuals vary from the mean --> results in different shapes of distribution, even with same mean 2) Var = s^2 = Sum of (Xi - average x)^2 / (n-1) 3) Std. deviation = s = square root of Var = sq. root of s^2
Remember the rules of std. deviation 1) 66% w/in 1 sd 2) 95% w/in 2 sd 3) 99% w/in 3 sd
Remember the Mimulus guttatus graphs? Explain them 1) The first graph was P, which the genetic variation was based on ENVIRONMENTAL factors alone, they were inbred lines 2) The 2nd graph was F1 and they were ALL heterozygotes, and their genetic variation was based on ENVIRONMENTAL factors alone 3) 3rd graph was F2, had increased variance due to GENETIC and ENVIRONMENTAL factors
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Describe the 3 types of DNA replication, which process does DNA actually replicatate? 1) Semiconservative, which is where one strand in each daughter strand is from the parent strand 2) Conservative, a completely new strand forms from parents strand 3) Dispersive, strands are broken up into pieces and mixed in with daughter strand 4) SEMI-CONSERVATIVE
Meselson–Stahl experiment 1) The Meselson-Stahl experiment was an experiment by Matthew Meselson and Franklin Stahl in 1958 which supported the hypothesis that DNA replication was semiconservative. 2) Used 15N, which was a heavy nitrogen
DNA Polymerase which direction does it synthesize? how is it read? 1) A DNA polymerase is an enzyme that catalyzes the polymerization of deoxyribonucleotides into a DNA strand. 2) SYNTHESIZES - 5' --> 3' 3) READS - 3' --> 5'
Describe first 3 steps of DNA replication (Prokaryotes) 1) Supercoiling relaxed by topoisomerases (DNA gyrase) 2) Initiator proteins (DNAa) bind to origin of replication (denaturation and untwisting), 9bp sequence repeats - binding site 3) DNA Helicase binds and untwists DNA
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Describe last 3 steps in DNA replication (prokaryotes) 4) DNA Primase binds to DNA Helicase & builds RNA primer (5-12 nucleotides) 5) DNA Polymerase III binds, begins SYNTHESIS of new strand 5'-->3' direction 6) ssDNA binding proteins stabilize replication bubbble (prevents DNA from coming back together)
Leading strand Describe its main characteristics 1) DNA replication is CONTINUOUS 2) as a WHOLE, DNA replication is SEMI-DISCONTINUOUS
Lagging strand, describe how are the fragments joined? 1) - DNA replication is DISCONTINUOUS - Okazaki Fragments are built on lagging strand 2) DNA Polymerase I removes primer, fills DNA - DNA Ligase seals gaps w/ phosphodiester bonds
Describe DNA gyrase fully It is a toposiomerase, which introduces negative supercoiling in ahead of replication fork to compensate
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Summarize DNA replication 1) It is SEMI-CONSERVATIVE - each parent strand pairs w/ newly made strand 2) It is SEMI-DISCONTINUOUS - continuous in one direction, discontinuous in the other
Differences between prokaryotic and eukaryotic replication 1) Eukary have a lot more JUNK DNA 2) Eukary have multiple origins of replication 3) Eukary have multiple ARS's (autonomously replicating sequences) 4) In Drosophilia, the diploid set of chromosomes us replicated in about 3 mins = 6x faster than E.Coli (which has 100x less DNA than Drosophilia) 5) Problems at the Telomeres
Who were Garrod and Bateson? 1) Studied Alpkaptonuria, disease that makes you pee "black" 2) First evidence of gene-enzyme relationship 3) They determined that it was a genetically controlled trait
Genetic Diseases, Describe 1) Result from nonfunctional enzymes 2) Most diseases are recessive
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Who were Beadle and Tatum? Beadle and Tatum's key experiments involved exposing the bread mold Neurospora crassa to x-rays, causing mutations. In a series of experiments, they showed that these mutations caused changes in specific enzymes involved in metabolic pathways. These experiments led them to propose a direct link between genes and enzymatic reactions, known as the "one gene, one enzyme" hypothesis.
Describe a metabolic pathway, what can go wrong? Draw picture
What is the central Dogma? 1) DNA(transcription) --> 2) mRNA/Ribosomes(translation) --> 3) Protein
Describe Transcription, 4 steps 1) DNA READ by RNA Polymerase (3' -> 5') 2) Complimentary mRNA MADE/SYNTHESIZED from (5'->3') 3) Chemistry similar to DNA synthesis BUT (5' -> 3') 4) NO PRIMER needed to initiate transcription
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Describe the end process of Transcription, what is RNA similar to? 1) At end of transcription, polymerase releases RNA and detaches 2) RNA is identical to NONTEMPLATE strand, (EXCEPT... Uracil replaces Thymine)
Describe the four kinds of RNA 1) Messenger RNA, mRNA, translated to produce a polypeptide 2) Transfer RNA, tRNA, brings amino acid to ribosome 3) Ribosomal RNA, rRNA, components of ribosome 4) Small nuclear RNA, snRNA, involved in processing mRNA
Watson and Crick Watson and Crick were James D. Watson and Francis Crick who, using x-ray diffusion data collected by Rosalind Franklin, proposed the double helix or spiral staircase structure of the DNA molecule in 1953
Describe DNA Polymerase I, II, III 1) 3'->5' exonuclease (Proofreading) and 5'->3' exonuclease activity (RNA Primer removal). 2) involved in reparation of damaged DNA; has 3'->5' exonuclease activity. 3) the main polymerase in bacteria (elongates in DNA replication); has 3'->5' exonuclease proofreading ability.
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1) Structural genes 2) RNA genes 1) genes that code for a polypeptide/protein 2) NOT TRANSLATED, genes that code for tRNA, rRNA, transcripts are FINAL PRODUCT
Describe RNA polymerase in 1) Prokaryotes 2) Eukaryotes 1) denatures DNA & synthesizes RNA 2) II - transcribes structural genes I, III - transcribes others RNA genes
Names the three genes in transcription in Prokaryotes Promotor, RNA coding sequence, terminator
Name the 2 specific sequences that are important for transcription initiation in prokaryotes 1) 5' TTGACA 3', position 35 (35 bp upstream) 2) 5' TATAAT 3', position 10 (10 bp upstream) promotors initiate interaction w/ RNA polymerase
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Describe initiation of transcription in prokaryotes 1) sigma factor binds to RNA polymerase, this is a HOLOENZYME 2) holoenzyme binds to promotor regions 3) RNA polymerase deanatures 17 bp "transcription bubble" 4) transcription begins 5) sigma factor falls off
Describe termination of transcription in prokaryotes 1) rho dependent 2) rho independent 1) rho protein has two domains, one binds to RNA, one to ATP, binds to recognition site at terminator region, then ATP is hydrolyzed and RNA unwound from DNA template, released 2) Sequence upstream from terminator has INVERTED REPEAT, causes RNA transcript to form STEM-LOOP structure followed by series of U's, HAIRPIN formation, destabilizes RNA-DNA complex
Describe the regulatory elements in EUKARYOTES for transcription Pieces of DNA that regulate transcription 1) Positive elements - activate transcription rate 2) negative elements - repress transcription rate
What do the regulatory elements in transcription for eukaryotes? 1) Transcription factors, regulatory factors 2) Promoters, 3) enhancer elements - requires for maximal transcription; silencer elements - repress gene transcription
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Describe differences between prokaryotic and eukaryotic transcription 1) In prokaryotes, the RNA transcript functions directly as the mRNA molecule, the protein and gene are COLLINEAR, also bacteria lack a nucleus, so an mRNA begins to translated on ribosome before being completely transcribed, they are COUPLED 2) In eukaryotes, the gene and the translated protein are NOT COLINEAR, you remove the introns, the genes are in pieces, also transcription and translation are NOT COUPLED, mRNA must migrate from nucleus to cytoplasm
Introns An intron is a DNA region within a gene that is not translated into protein, but it is transcribed.. They are excised to produce the MATURE mRNA in EUKARYOTES
What are the: 1) 5' cap 2) 3' poly (A) tail 1) methalation at 5' end, a capping enzyme adds a guanine nucleotide, essential for ribosomal binding to 5' end of mRNA 2) Determines longevity & stability of mRNA
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 Genetic Drift Is infinite pop. size possible?1)-Changes in allele freq. due to random fluctuations

-occurs in ALL populations

2) Yes, it is impossible, but the pop. size can be large enough where chance/drift is minimal
 What is the effective population size? What is the formula?The effective number of adults contributing gametes to the next generation

Ne = (4xNfxNm) / (Nf + Nm)



Ne = effective pop. size
Nf = # breeding females
Nm = # breeding males
 When does genetic drift occur?ALWAYS!

But...more important in small populations
 1) Bottleneck 2) Founder events1) Situations when a pop. is significantly reduced by catastrophe

2) Dispersal & colonization by a smaller group from a larger pop.
 Give 2 defs. of natural selection with HW Equilibrium 1) Process by which traits evolve to make organisms, "adapted" to environment

2) Differential reproduction of genotypes, resulting in changed allele frequencies
- individuals w/ certain alleles reproduce more often than those w/ alternate alleles
 Fitness of genotypes Defs - 1) Absolute fitness 2) Relative fitness1) Mean number of offspring an individual of a particular genotype has
2) degree tp which individuals of a particular genotype reproduce relative to inds. w/ other genotype
 How do you calculate relative fitness?Problem:

i.e. AA - 6, Aa - 9, aa - 12 --> AA has low fitness

relative fitness: compare with highest fitness for each

aa - 12/12 = 1, Aa - 9/12 = .75, AA - 6/12 = .5
 1) Frequency after selection 2) Relative genotype freq. selection 3) Allelic frequency after selection 4) Change in allelic freq. caused by sel.1) p ^2 x w11(finess), 2pq x w12, q^2 x w22

2) p' = p^2xw11 / average w, H' = 2pq x w12 / average w, Q' = q^2 x w22 / average w

3) p' = p' + 1/2(H')
q' = 1 - p'

4) Change of p = p' = p
 How do you calculate mean fitness?p^2 x W1 + 2pq x W12 + q^2 x W22
 How do species arise?Via the evolution of reproductive isolation
 1) Prezygotic barriers 2) Post zygotic barriers 1) - habitat
- behavioral
- temporal
- morphological

2) - hybrid inviability (weakness)
- hybrid sterility
 Dobzhansky - Mueller Speciation model 1) The Dobzhansky-Muller model proposes that hybrid incompatibilities are caused by the interaction between genes that have functionally diverged in the respective hybridizing species.

2) Two genes have not seen each other before, and are incompatible
 Identify these: Vp = Vg + Ve1) Vp = Phenotypic variance

2) Vg = Genetic Variance

3) Ve = Environmental variance
 What does variance mean? And what is its formula? How would you calculate std. deviation from this?1)How much individuals vary from the mean --> results in different shapes of distribution, even with same mean

2) Var = s^2 = Sum of (Xi - average x)^2 / (n-1)

3) Std. deviation = s = square root of Var = sq. root of s^2
 Remember the rules of std. deviation 1) 66% w/in 1 sd

2) 95% w/in 2 sd

3) 99% w/in 3 sd
 Remember the Mimulus guttatus graphs? Explain them1) The first graph was P, which the genetic variation was based on ENVIRONMENTAL factors alone, they were inbred lines
2) The 2nd graph was F1 and they were ALL heterozygotes, and their genetic variation was based on ENVIRONMENTAL factors alone
3) 3rd graph was F2, had increased variance due to GENETIC and ENVIRONMENTAL factors
 Describe the 3 types of DNA replication, which process does DNA actually replicatate?1) Semiconservative, which is where one strand in each daughter strand is from the parent strand
2) Conservative, a completely new strand forms from parents strand
3) Dispersive, strands are broken up into pieces and mixed in with daughter strand

4) SEMI-CONSERVATIVE
 Meselson–Stahl experiment 1) The Meselson-Stahl experiment was an experiment by Matthew Meselson and Franklin Stahl in 1958 which supported the hypothesis that DNA replication was semiconservative.

2) Used 15N, which was a heavy nitrogen
 DNA Polymerase which direction does it synthesize? how is it read?1) A DNA polymerase is an enzyme that catalyzes the polymerization of deoxyribonucleotides into a DNA strand.

2) SYNTHESIZES - 5' --> 3'

3) READS - 3' --> 5'
 Describe first 3 steps of DNA replication (Prokaryotes)1) Supercoiling relaxed by topoisomerases (DNA gyrase)

2) Initiator proteins (DNAa) bind to origin of replication (denaturation and untwisting), 9bp sequence repeats - binding site

3) DNA Helicase binds and untwists DNA
 Describe last 3 steps in DNA replication (prokaryotes)4) DNA Primase binds to DNA Helicase & builds RNA primer (5-12 nucleotides)

5) DNA Polymerase III binds, begins SYNTHESIS of new strand 5'-->3' direction

6) ssDNA binding proteins stabilize replication bubbble (prevents DNA from coming back together)
 Leading strand Describe its main characteristics 1) DNA replication is CONTINUOUS

2) as a WHOLE, DNA replication is SEMI-DISCONTINUOUS
 Lagging strand, describe how are the fragments joined?1) - DNA replication is DISCONTINUOUS
- Okazaki Fragments are built on lagging strand

2) DNA Polymerase I removes primer, fills DNA
- DNA Ligase seals gaps w/ phosphodiester bonds
 Describe DNA gyrase fullyIt is a toposiomerase, which introduces negative supercoiling in ahead of replication fork to compensate
 Summarize DNA replication 1) It is SEMI-CONSERVATIVE - each parent strand pairs w/ newly made strand

2) It is SEMI-DISCONTINUOUS - continuous in one direction, discontinuous in the other
 Differences between prokaryotic and eukaryotic replication 1) Eukary have a lot more JUNK DNA
2) Eukary have multiple origins of replication
3) Eukary have multiple ARS's (autonomously replicating sequences)
4) In Drosophilia, the diploid set of chromosomes us replicated in about 3 mins = 6x faster than E.Coli (which has 100x less DNA than Drosophilia)
5) Problems at the Telomeres
 Who were Garrod and Bateson?1) Studied Alpkaptonuria, disease that makes you pee "black"
2) First evidence of gene-enzyme relationship
3) They determined that it was a genetically controlled trait

 Genetic Diseases, Describe1) Result from nonfunctional enzymes
2) Most diseases are recessive
 Who were Beadle and Tatum?Beadle and Tatum's key experiments involved exposing the bread mold Neurospora crassa to x-rays, causing mutations. In a series of experiments, they showed that these mutations caused changes in specific enzymes involved in metabolic pathways. These experiments led them to propose a direct link between genes and enzymatic reactions, known as the "one gene, one enzyme" hypothesis.
 Describe a metabolic pathway, what can go wrong?Draw picture
 What is the central Dogma?1) DNA(transcription) -->
2) mRNA/Ribosomes(translation) -->
3) Protein
 Describe Transcription, 4 steps1) DNA READ by RNA Polymerase (3' -> 5')
2) Complimentary mRNA MADE/SYNTHESIZED from (5'->3')
3) Chemistry similar to DNA synthesis BUT (5' -> 3')
4) NO PRIMER needed to initiate transcription
 Describe the end process of Transcription, what is RNA similar to?1) At end of transcription, polymerase releases RNA and detaches

2) RNA is identical to NONTEMPLATE strand, (EXCEPT... Uracil replaces Thymine)
 Describe the four kinds of RNA1) Messenger RNA, mRNA, translated to produce a polypeptide
2) Transfer RNA, tRNA, brings amino acid to ribosome
3) Ribosomal RNA, rRNA, components of ribosome
4) Small nuclear RNA, snRNA, involved in processing mRNA
 Watson and CrickWatson and Crick were James D. Watson and Francis Crick who, using x-ray diffusion data collected by Rosalind Franklin, proposed the double helix or spiral staircase structure of the DNA molecule in 1953
 Describe DNA Polymerase I, II, III1) 3'->5' exonuclease (Proofreading) and 5'->3' exonuclease activity (RNA Primer removal).
2) involved in reparation of damaged DNA; has 3'->5' exonuclease activity.
3) the main polymerase in bacteria (elongates in DNA replication); has 3'->5' exonuclease proofreading ability.
 1) Structural genes 2) RNA genes1) genes that code for a polypeptide/protein

2) NOT TRANSLATED, genes that code for tRNA, rRNA, transcripts are FINAL PRODUCT
 Describe RNA polymerase in 1) Prokaryotes 2) Eukaryotes1) denatures DNA & synthesizes RNA

2) II - transcribes structural genes
I, III - transcribes others RNA genes
 Names the three genes in transcription in ProkaryotesPromotor, RNA coding sequence, terminator
 Name the 2 specific sequences that are important for transcription initiation in prokaryotes1) 5' TTGACA 3', position 35 (35 bp upstream)

2) 5' TATAAT 3', position 10 (10 bp upstream)

promotors initiate interaction w/ RNA polymerase
 Describe initiation of transcription in prokaryotes 1) sigma factor binds to RNA polymerase, this is a HOLOENZYME
2) holoenzyme binds to promotor regions
3) RNA polymerase deanatures 17 bp "transcription bubble"
4) transcription begins
5) sigma factor falls off
 Describe termination of transcription in prokaryotes 1) rho dependent 2) rho independent 1) rho protein has two domains, one binds to RNA, one to ATP, binds to recognition site at terminator region, then ATP is hydrolyzed and RNA unwound from DNA template, released

2) Sequence upstream from terminator has INVERTED REPEAT, causes RNA transcript to form STEM-LOOP structure followed by series of U's, HAIRPIN formation, destabilizes RNA-DNA complex
 Describe the regulatory elements in EUKARYOTES for transcription Pieces of DNA that regulate transcription 1) Positive elements - activate transcription rate 2) negative elements - repress transcription rate
 What do the regulatory elements in transcription for eukaryotes?1) Transcription factors, regulatory factors

2) Promoters,

3) enhancer elements - requires for maximal transcription; silencer elements - repress gene transcription
 Describe differences between prokaryotic and eukaryotic transcription 1) In prokaryotes, the RNA transcript functions directly as the mRNA molecule, the protein and gene are COLLINEAR, also bacteria lack a nucleus, so an mRNA begins to translated on ribosome before being completely transcribed, they are COUPLED
2) In eukaryotes, the gene and the translated protein are NOT COLINEAR, you remove the introns, the genes are in pieces, also transcription and translation are NOT COUPLED, mRNA must migrate from nucleus to cytoplasm
 IntronsAn intron is a DNA region within a gene that is not translated into protein, but it is transcribed.. They are excised to produce the MATURE mRNA in EUKARYOTES
 What are the: 1) 5' cap 2) 3' poly (A) tail 1) methalation at 5' end, a capping enzyme adds a guanine nucleotide, essential for ribosomal binding to 5' end of mRNA
2) Determines longevity & stability of mRNA
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