Exam 4 Study Guide
Exam 4 Study Guide Bio 1510
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This 35 page Study Guide was uploaded by Nausheen Zaman on Saturday December 5, 2015. The Study Guide belongs to Bio 1510 at Wayne State University taught by Dr. Nataliya Turchyn in Summer 2015. Since its upload, it has received 140 views. For similar materials see (LS) Bas Life Mch in Biology at Wayne State University.
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Date Created: 12/05/15
Exam 4 Study Guide (Chapters 13, 14, 15) Fall 2015 BIO 1510 ● What determines sex of an organism ● Male traits on X and Y chromosomes ● Sex-linked Disorders ● Problems with X and Y Chapter 13 chromosomes Chromosomes, Mapping and ● Problems with autosomal Meiosis - Inheritance chromosomes ● Linked genes and Connection recombination ● Recombination formula What Determines Sex of an Organism ● Sex determination in Drosophila (fruit flies) - based on # of X chromosomes ○ Two X chromosomes = female ○ One X and one Y chromosome = male ● Sex determination in humans - based on presence of the Y chromosome ○ Two X chromosomes = female ○ Having a Y chromosome = male ● Fun fact! Some insects genders are based on number of chromosomes or the number of X chromsomes ○ Male grasshoppers = XO (O = zero, meaning they only have one X chromosome) Male Traits on the X and Y Chromosomes ● What is ‘Male’ on the Y Chromosome? ○ In humans, the Y chromosome has the sex-determining region Y (SRY) gene ■ encodes testis determining factor (TDF) protein ■ Swyer syndrome - non-functional SRY gene ● Y chromosome affected, X chromosome is normal ● Male genotype (XY), female phenotype (no testes, female external genitalia, uterus but no ovaries) ■ People with this syndrome usually sterile ● What is ‘Male’ on the X Chromosome? ○ Males must also produce androgens (e.g. testosterone) and respond to them ■ Androgens - male sex hormones ○ X chromosome of males has a gene that encodes androgen receptor ■ Androgen insensitivity syndrome - androgen receptor is mutated ● X chromosome is affected, Y chromosome is normal ● Male genotype (XY), female phenotype (no testes) ■ Androgen sensitivity makes men sterile Sex-linked Disorders ● Associated with sex chromosomes (X or Y) ○ X-linked disorders show up in both genders ○ More often in males (only have one X chromosome) ● Hemophilia (blood-clotting disorder) caused by an X-linked recessive allele ● Humans have 25K protein encoded gene (2000 on X, 78 on Y ← these genes involved in sex determination) – non- homologous ● Sex-linked disorders associated with these genes ● Divided into Y-linked and X-linked ○ Y-linked only found in males (they have the Y chromosome), X-linked found in both males and females ○ X-linked disorders more common in males than females (they only have one X chromosome) ● Human males have only one allele for each gene located on the X chromosome → they cannot be homo- dominant/recessive or heterozygous for X-linked disorders, but they can be phenotypically normal or affected ● Human females CAN be homo-dominant/recessive or heterozygous because they have two X chromosomes ● In order for a female to be infected, she should inherit two alleles from her parents ● Males only inherit one allele from mom to be infected Nondisjunctions ● Problems with the X and Y Chromosomes ○ Nondisjunction - failure of homologous chromosomes/sister chromatids to seperate properly during Meiosis I or Meiosis II ■ Example used in the book shows a mistake occurring during Anaphase I or II ○ Aneuploid - gametes that have one more/less chromosome ■ Monosomy - one chromosome is absent ● Monosomic individual generated when aneuploid gametes have 22 chromosomes fuses with a normal gamete having 23 chromosomes ● has 45 chromosomes in each of their somatic cells ■ Trisomy - extra chromosome is present ● Trisomic individual generated when aneuploid gametes having 24 chromosomes fuse with gamete that has 23 chromosomes ● has 47 chromosomes in their somatic cells Nondisjunctions and Autosomal Disorders ● Nondisjunction of Sex Chromosomes ○ XX + Y = XXY male ■ Klinefelter syndrome - enlarged breasts, underdeveloped testes ○ O + X = XO female ■ Turner syndrome - no breast growth, infertile ○ YY + X = XYY male ○ XX + X = XXX female ■ The above two nondisjunctions have normal phenotypes ○ Y + O = YO zygote ■ Doesn’t survive as there are only 78 chromosomes present in gene ■ All of them determine sex in the zygote and nothing else ● Problems with Autosomal Chromosomes ○ Edwards syndrome - trisomy 18 ■ Babies born with this die within a few months ○ Down syndrome - trisomy 21 ■ Can survive to adulthood ■ Mother’s age influences risk Testing for Genetic Problems ● Amniocentesis ○ Collecting fetal cells from amniotic fluid through a syringe and needle for examination ○ Performed between 14-20 weeks of pregnancy ■ Amniotic fluid - fluid that surrounds the fetus ■ water breaking = amniotic fluid ○ Biochem tests reveal whether the baby has sickle cell anemia or not and tests enzymes and other proteins (results found in several weeks) ○ Fetal cells after 2-3 weeks are used for karyotyping: ■ All the cells are dyed ■ Each chromosome has a certain pattern that shows when dyed (allows scientists to study chromosomes) ■ We can tell the number, gender and length of chromosomes ○ With amniocentesis – risk of miscarriage ● Chorionic villus sampling ○ Obtains fetal cells from chorionic villi (finger-shaped growths found in placenta) for karyotyping ○ Performed between 8-12 weeks of pregnancy ○ More popular than amniocentesis ■ Earlier in pregnancy ■ Less invasive (uses suction of tissue sample instead of needle) ■ Gives faster results than amniocentesis Linked Genes ● If Two Alleles are on the Same Chromosomes, They can be Inherited Together ○ In paternal and maternal chromosome #10… ○ Gene X - hair color ■ A = dominant allele ■ a = recessive allele ○ Gene Y - eye color ■ B = dominant allele ■ b = recessive allele ○ Linked genes - genes located on the same chromosome ■ Can be inherited together (like red hair and freckles) IF there is no crossing over ■ Causes parental gametes ● 4 gametes will be produced with unaffected chromosomes ● … But not Always ○ If crossing over occurs ■ Parental and recombinant gametes will be produced ■ Recombinant gametes - gametes with new combo of alleles ○ Recombinant gametes for because of crossing over between genes X and Y Recombination/Crossing Over ● Using Recombination to Measure Distance Between Genes ○ Gene X and Y located on same chromosome in Drosophila ■ + - normal ■ vestigial wings = short wings ● 415 mat phenotype ● 405 pat phenotype ● 92 mat-pat phenotype (gray vestigial) ● 88○patBecause of crossing over between wing size and body color genes (this gave rise to recombinant offspring) ● Recombination frequency = recombination (translated into the distance between linked genes) ○ Wing size + body color are located 18 cMs aparts from each other on the same chromosome using formula ● Crossing over most likely to happen when two genes are far apart from each other than when they are next to each other ● Which Genes are Closer to Each Other? ○ If only crossing over event 1 (#1 in picture) occurs: aBC, Abc (2 crossing over events occur) ○ If only crossing over event 2 (#2 in picture) occurs: ABc, abC (2 crossing over events occur) ○ If both crossing over events 1 and 2 (cross over at #1 and then cross back over at #2) occur: AbC, aBc (2 events occur) Supplemental Pictures + Recombo Formula ● Actions of DNA polymerase 3 ● DNA Replication enzymes and functions ● DNA replication and synthesis Chapter 14 ● Types of DNA repair DNA: The Genetic Material ● Meselson-Stahl Experiment ● Avery and Hershey-Chase Experiment DNA Polymerase 3 and Functions ● DNA Replication Process ○ Replication of DNA begins at several specific site along DNA molecule (origins of replication/replication origins) ○ DNA polymerase 3 - works with other enzymes to generate DNA strands ○ Eukaryotes have many origins of replication ○ Prokaryotes only have ONE origin of replication ● Actions of DNA Polymerase 3 ○ DNA polymerase 3 moves along template strand in 3’ → 5’ direction ■ Adds free nucleotides only to a free 3’ OH of daughter strand ○ Daughter strand formed/synthesized in 5’ → 3’ direction ○ Summary: ■ Always moves along daughter strand in a 3’ à 5’ direction (top to bottom end) ■ Creates phosphodiester bond ■ When template strand sees unpaired T, pairs a free-floating A to complete strand (2H bond created) ● 3H bond created between C and G ■ Makes daughter strand from 5’ – 3’ direction DNA Replication Enzymes and Functions ● DNA Replication Continues ○ DNA gyrase - stops DNA from twisting ○ DNA helicase - opens up helix (unzips your genes) ○ DNA polymerase 3 - requires a primer (DNA primase, an RNA polymerase, constructs this primer) to which it adds first nucleotide ■ Adds nucleotides to 3’ end ■ Leading strand - replicates towards replication fork ● Synthesized continuously (gets preferential treatment because of its leading status) ■ Lagging strand - elongates from replication fork ● Synthesized discontinuously (doesn’t get preferential treatment because it lags all the time :() ● Production of Okazaki fragments occurs here ○ DNA polymerase 1 - removes RNA and fills in gaps ○ DNA ligase - attaches Okazaki fragments to lagging strand DNA Replication ● DNA Replication Fork ○ Leading and lagging strands → make daughter (leading and lagging) strands ○ Without SSB (single-strand binding proteins), parents strands come back together ■ SSBs keep them apart ○ RNA Primer Facts ■ Complementary to DNA (means that nitro bases of RNA primer can form hydro bonds with nitro bases of DNA) ● A (RNA primer) = T (DNA) ● G (RNA primer) = C (DNA) ● U (RNA primer) = A (DNA) ■ RNA primer and DNA run antiparallel to each other (opposite directions ● DNA – 3’ → 5’ ends ● RNA Primer – 5’ → 3’ ends st ■ Last ribonucleotide has a free 3’ OH to which DNA polymerase 3 can attach to 1 deoxyribonucleotide DNA Synthesis ● DNA Synthesis ○ Only one primer required to initiate and propagate leading daughter strand synthesis (Domino effect for leading strand) leading daughter strand synthesized CONTINUOUSLY in 5’ → 3’ direction ○ Unlike the leading daughter strand… ■ The lagging daughter strand is synthesized DISCONTINUOUSLY in small segments ● These segments are called Okazaki fragments (only lagging daughter strands have them because they are problematic) ● Think of lagging daughter strand = rusty car, Okazaki fragments = pieces that keep falling out the car ■ Multiple RNA primers needed to synthesize lagging daughter strand ○ DNA polymerase 3 (true for all other polymerases) ALWAYS moves along leading and lagging parent strands in the 3’ → 5’ direction, makes leading and lagging daughter strands in the 5’ → 3’ direction ○ When DNA polymerase 3 encounters preceding primer, lifts lower arm ○ DNA polymerase 1 - removes RNA primer, fills gaps between Okazaki fragments with deoxynucleotides ■ DNA polymerase 1 (prokaryotes) – very similar to DNA polymerase 3, can only add deoxynucleotides to a free 3’ OH of another nucleotide ■ DNA repair enzyme (eukaryotes) used instead of DNA polymerase 1 ○ DNA ligase - joins Okazaki fragments together with phosphodiester bonds (Handyman of DNA synthesis) ○ DNA polymerase 3 puts lower arm into a new location + synthesizes a new Okazaki fragment until it reaches previous RNA primer Telomerases ● Why Do Chromosomes become Shorter? ○ 3’ end of lagging strand CANNOT be replicated ■ Overtime telomeres become shorter when cells are being divided ○ Telomeres become shorter because of DNA repair polymerase – similar to DNA polymerase 1 ○ Cannot replace last RNA primer of lagging daughter strand due to lack of nucleotides with a 3’ hydroxyl group (3’ OH) ○ Telomeres found in eukaryotes ● How Does Telomerase Work? ○ Reverse transcriptase – enzyme that uses RNA to make DNA (has its own RNA molecules) ○ Telomerase RNA is used to rebuild the telomere (a repetitive DNA sequence ie. TTGGGG) ○ Attaches unpaired nitro bases to telomerase RNA with H-bonds ○ Telomerase uses its RNA molecule as a template for rebuilding the telomere by adding deoxynucleotides to it ○ Remember C has 3 H-Bonds to G, A has 2 H-bonds to T ○ Telomere consists of deoxynucleotides and telomerases add deoxynucleotides to the telomere using RNA molecule inside as a template until it is long enough → DNA primase creates RNA primer → RNA primer’s last ribonucleotide has 3’ OH group where DNA polymerase can attach the first deoxynucleotide → DNA polymerase synthesizes lagging daughter strand in 3’ – 5’ direction, grow from 5’ – 3’ end DNA Damage and Repair ● How can DNA be Damaged? ○ In presence of UV light, adjacent T can create covalent bond with each other rather than H-bonds with A ○ T-dimer/Pyrimidine dimer causes DNA to be kinked ○ Kinked copy of DNA can cause mutations that lead to diseases like cancer if left unrepaired ○ Kinked uncorrected T-dimers can cause melanoma (skin cancer) in humans ● Photorepair (uses one enzyme) ○ Also called photoreactivation repair – mechanism that uses a photolyase (an enzyme that repairs T-dimers, binds to T- dimers and breaks covalent bond in order for the A-T Hydro-bond to occur) to repair thymine dimers ○ Photolyase activated in visible blue light ○ Used by bacteria, fungi and plants to fix T-dimers, but not by humans ● Excision Repair (uses three enzymes) ○ Used by humans to repair thymine dimers and incorrect/damaged nucleotides ○ Excision repair enzymes divided into 2 groups: ■ Exonucleases – cleave nucleotides from the ends of DNA/RNA ■ Endonucleases – cleave nucleotides in the middle of DNA/RNA ○ Single-stranded gap/break is created with endonucleases/ionizing radiation (X-rays and gamma rays) → DNA polymerase fills in the gap with missing deoxynucleotides using undamaged DNA strand as a template → DNA ligase seals nick left in sugar-phosphate backbone of repaired DNA strand by creating a phosphodiester bonds Meselson-Stahl Experiment ● E. Coli were grown in a heavy isotope of nitrogen, N15 ● All DNA incorporated N15 ● Cells were then switched to media containing lighter isotope of nitrogen N14 ● DNA was extracted from the cells at various time intervals ● DNA replication is semiconservative (every daughter DNA molecule always consists of one parent strand and one new strand) ● E. Coli are prokaryotes ○ Gen 0 – E.coli whose DNA was labelled and immersed in 15N ○ Gen 1 – E.coli whose DNA was immersed in N15 and replicated in N14 ○ Gen 2 – E.coli whose DNA replicated in the N14 ● Results… ○ Gen 0 – Heavy density molecules that produced a band at the bottom of the tube ○ Gen 1 – Labelled with both N14 and N15, of intermediate density and had a band in the middle of the tube ○ Gen 2 – Two band were formed; DNA labeled with N14 and N15 were of intermediate density, DNA labelled with N14 were of lighter density (the band at the top of the tube) ● Concluded that during DNA replication, parent strands come apart and are used as a template for a daughter strand, making two new daughter DNA, and in Gen1 they have both characteristics of parent and new strand, and in Gen 2 there were characteristics of affected parent strand (N15) and unaffected parent strand (N14) Avery Experiment ● Worked with bacteria that transferred genetic material between each other (transformation) ● Removed almost all proteins from bacteria and found no reduction in transforming activity ● Concluded that protein was not genetic material ○ However, since he didn’t remove ALL genetic material some scientists doubted his results ● Hershey-Chase Experiment ○ Used different radioactive isotopes to label DNA and proteins in bacteriophages (viruses that affect DNA) ○ New bacteriophage passed genetic information into host cell, which was then used to produce new viruses ○ Found material used to specify new generations of viruses were made of DNA ● Avery Experiment – worked with Hershey-Chase and assisted them with bacterial studies of DNA (some bacteria mate – transformation) ● Hershey-Chase Experiment – wanted to know whether gen info is stored in proteins or DNA Hershey-Chase Experiment ● Wanted to know what bacteriophages pass onto bacteria when they infect them (DNA/protein) ● Used radioactive materials (S35) to label bacteriophage DNA and bacteriophage protein (P32) ● Why sulfur? Proteins are made of amino acids, some amino acids have cystine/methionine in their structure and sulfur binds to the sulfur in cystine/methionine structures ● Why phosphorous? DNA is constructed out of a sugar-phosphate backbone, and deoxynucleotide contain phosphorous in their P-groups so P binds to DNA ● Bacterstl pellet checked for radioactivity ○ 1 experiment – S35 was found in the liquid above the solid pellet ○ 2ndexperiment – P32 was found in the bacterial pellet ● This suggested that DNA was the material that was passed into bacteria, concluding that DNA was genetic material transferred from bacteriophages to bacteria ● Different Types of RNA and Functions ● Transcription Processes ● RNA Splicing Chapter 15 ● Genetic Code ● Translation and Elongation Genes and How They Work Processes ● Point Mutations ● Chromosomal Mutations Types of RNA and their Functions ● Ribosomal RNA (rRNA) ○ RNA found in ribosomes ● Transfer RNA (tRNA) ○ Temporary link between amino acids and mRNA that is being translated ● Messenger RNA (mRNA) ○ Actual template for amino acid assembly in polypeptide synthesis ● Small nuclear RNA (snRNA) ○ Involved in mRNA processing ● Signal Recognition Particle RNA (SRP RNA) ○ Needed for proteins produced in rough endoplasmic reticulum Transcription Processes Transcription begins with… ● RNA Polymerase moves in the 3’ → 5’ direction along DNA ○ Transcribes only ONE of two DNA strands ○ Template/antisense strand = transcribed strand ○ Non-transcribed strand = coding/sense strand ■ Same sequence as RNA except for T in place of U ● RNA polymerase adds ribonucleotides to the 3’ end of growing RNA chain ○ Promoter is a region of DNA template strand where RNA polymerase binds and initiates transcription ○ Promoter not transcribed into RNA ○ TATA box (region of DNA consisting of A and T bases) in prokaryotes/eukaryotes Transcription in Eukaryotes ● Transcription factors - proteins that help RNA polymerase to locate promoter and initiate transcription ○ Each gene controlled by several transcription factors Transcription in Prokaryotes ● RNA polymerase doesn’t need transcription factors to bind to the promoter ● RNA polymerase uncoils the DNA and uses only one strand (template) to synthesize RNA ● As RNA synthesis continues, RNA strand peels away from DNA template RNA Splicing Steps: 1. snRNPs containing a snRNA and protein come together at the ends of an intron 2. Intron must contain a GU at 5’ end, AG at the 3’ end, and an A (Adenine) within the branch site 3. U1 snRNP → 5’ end of intron 4. U2 snRNP → branch site 5. U4, U5, U6 snRNPs → 3’ and branch site 6. All snRNPs come together, splicing intron at 5’ and 3’ ends 7. 5’ end connects at ‘A site’, forms a lariat 8. U1, U4 snRNPs are released 9. U5, U6 snRNPs shift positions 10. Exons connected and lariat, U2, U5, U6 are released together 11. Rest of the snRNPs dissociated from lariat, which eventually degrades Genetic Code ● mRNA is a blueprint for polypeptides ● How do ribosomes ‘read’ the mRNA and know what amino acids to link together to form polypeptide? ○ When ribosomes move along mRNA → they ‘read’ three ribonucleotides at a time in the 5’ → 3’ direction ○ This is called a reading frame ■ A set of three ribonucleotides → codon ■ One codon = one amino acid ○ Genetic code tells which codons code for each of the twenty amino acids ■ Some amino acids are encoded by more than one codon ● UUA/UUG = Leucine ● 61 codons specify for 20 amino acids (some amino acids have only one codon to code them) Translation ● The appropriate amino acid must be attached to its tRNA molecule ○ Performed by aminoacyl-tRNA synthetase ● tRNA has two important sites: ○ Accepting site ○ Anticodon ■ Contains three ribonucleotides complementary to the mRNA codon ■ Anticodon-codon pairing is antiparallel ● tRNA anticodon ● It is mRNA codon (not tRNA anticodon) that determines what amino acid will be attached to accepting site of tRNA ● tRNA without amino acid is an uncharged/empty tRNA ● Charged tRNA has amino acids attached to accepting site Translation/Elongation ● Formation of Initiation Complex ○ Initiation complex includes small ribosomal subunits, mRNA and tRNA (met) ○ mRNA binds to small ribosomal subunit along with proteins called initiation factors ○ tRNA^met binds to mRNA codon ○ Large subunit binds to small subunit+mRNA+tRNA^met, completing the initiation complex ○ Ribosome has three sites: ■ P site - holds tRNA with a growing polypeptide chain ● Also where the first tRNA^met enters ■ A site - where the rest of charged tRNAs first enter ■ E site - where uncharged tRNAs exit ● Elongation: Peptide Bond Formation ○ Elongation factors - proteins that help deliver appropriate charged tRNA → A site ○ Two amino acids (attached to tRNAs in A and P sites) form a peptide bond between each other ■ Catalyzed by peptidyl transferase of large ribosomal subunit ● Also breaks bond between polypeptide chain and tRNA in P site Elongation ● Elongation of Polypeptide ○ Amino acid attached to tRNA in P site is released from its tRNA molecule ○ Called ‘empty’/uncharged tRNA ○ Ribosome shifts down mRNA to the next codon (translocation) ■ Translocation - refers to the movement of ribosomes in the 5’ → 3’ direction ■ tRNA in P site moves to E site from which it becomes ejected and tRNA in A site moves to P site ■ new tRNA is brought into A site ● Steps: 1. Charged tRNA with anticodon matches mRNA codon @ A site with elongation factor (EF-Tu) 2. EF-Tu hydrolyzes GTP, dissociates from ribosome 3. Peptide bond formed between A site amino acid + growing chain in P site 4. Growing chain transferred to A site, tRNA in P site ‘empty’ 5. Ribosome translocation requires another EF-Tu + GTP hydrolysis 6. tRNA moves to P site → A site, next codon goes to A site, ‘empty’ tRNA to E site Prokaryotes vs. Eukaryotes ● Operon - group of genes that are transcribed into mRNA at once because they share a promoter ● Prokaryotes – bacteria and archaens (no introns in bacteria, some in archaens) ○ Bacteria have operons ● Eukaryotes – all animal cells (some eukaryotes have operons) ○ Operons more common in prokaryotes than in eukaryotes ○ Most genes have their own promoters in Eukaryotes ● Prokaryotes have polycistronic mRNA (poly – many, cistron – gene) – encodes two or more proteins ● Eukaryotes have monocistronic mRNA (mono – one) – encodes only one protein ● Prokaryotes – transcription and translation are coupled (possible because both occur in cytoplasm) ● Eukaryotes – transcription and translation are spatially and temporally decoupled ○ 5’ cap in eukaryotes have two functions ■ Protects mRNA from degradation from ribonucleases ■ Needed for translation to happen Prokaryotes vs. Eukaryotes Point Mutations ● Change of one base pair to another ○ Three types of point mutations: ■ Missense mutation - codon change alters the amino acid encoded ■ Nonsense mutation - changes a codon specifying an amino acid into a termination codon ● Both are dangerous because they alter the coding of a protein ■ Silent mutation - alters codon but doesn’t result in a change in the amino acid Chromosomal Mutations ● Deletion - part of chromosome that is deleted (makes it shorter) ● Duplication - part of chromosome that is duplicated (makes it longer) ● Inversion - segment of chromosome is broken in two places, reversed and put back together ○ Normal and inverted chromosomes are of the same length, but the order of genes are not the same ● Reciprocal translocation - nonhomologous chromosomes exchange regions with each other creating two new chromosomes ○ Crossing over usually occurs between homologous chromosomes (mat and pat chromosomes 10), however with reciprocal translocation it occurs between nonhomologous chromosomes (mat chromosome 10 and pat chromosome 5) ○ Reciprocal translocation = two types of leukemia Extra Problems and Answers :) Extra Problems and Answers :)
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