Bio exam 3 study guide PDF

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Summary of material covered for test 3 for Dr. Whitehead's BIOL 1030; study guide for test 3; Fall 2015...

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Bio Study Guide Exam 3 Chapter 8: The Cellular Basis of Reproduction and Inheritance Cell Division Purposes of cell division:  Growth  Asexual reproduction  Replacement  Repair Daughter cells are genetically identical to parent cells Sexual reproduction: two parents contribute genetic information to produce unique offspring Asexual reproduction: offspring are genetically identical to single parent Prokaryotic cell division = binary fission  Chromosome duplicates; copies move  Cell elongates  Plasma membrane pinches in the center; more cell wall forms. Parent cell becomes two daughter cells Chromatin: DNA in a loose state, contains DNA and proteins Chromosomes: chromatin coiled up with cells get ready to divide Chromatid: each side of a chromosome divided longitudinally, 2 chromatids per chromosome Cell Cycle Interphase = duplication of contents  G1 – first gap  S – DNA synthesis  G2 – second gap Mitosis (cell division)  Prophase o Genetic information forms chromosomes so that each daughter cell has equal amount of DNA o Mitotic spindle forms  Prometaphase o Nuclear envelop breaks apart and disappears o Mitotic spindle grows, some attach to sister chromatids at kinetochores  Metaphase o Everything lines up along the center (metaphase plate) for organization  Anaphase o Mitotic spindle changes in 2 ways  Portions attached to chromosomes shorten  Others get longer to help push ends of cell o Chromosomes move away from each other  Telophase o Each copy of genetic info is on the far ends of the cell o Nuclear envelope reforms o Mitotic spindle breaks and disappears o Cytokinesis

 Division of cytoplasm  Usually beings during telophase  In animal cells: cleavage furrow, ring made of microfilaments  In plant cells: cell plate forms, grows outward to divide cell Mitotic spindle = microtubules, used to position the chromosomes at a specific position inside of the cell and move the chromatids to opposite sides of the cell to ensure that each daughter cell gets a full set of chromosomes Animal Cytokinesis Ring made of microfilaments form a cleavage furrow

Plant Cytokinesis Vesicles with material line up in middle, cell plate forms

Deepening of the cleavage furrow pinches cell into two

Cell plate grows outward to divide cell into two

Factors that influence cell division  Essential nutrients – energy, carbon, electrons  Growth factors – compounds produced by other cells that tell a cell to reproduce or not  Density-dependent inhibition – cells don’t like to be too crowded  Anchorage dependence – animal and plant cells will typically only divide if in contact with a surface Cell cycle control is important because if they are not controlled, they can mutate or multiply too much and become cancerous. Cell cycle checkpoints are stop or go signals; the cell will not continue division is not given the “go” signal 3 major checkpoints: G1 (in middle of G1), G2 (end of G2), M(middle of mitosis) Meiosis Objective = to create four haploid cells for reproductive purposes Diploid cells have two of each kind of chromosome because one is inherited from the mother and the other is inherited from the father (variety). These are homologous chromosomes, which are similar (but not identical) chromosomes that carry the same genes in the same order, but the alleles for each trait may not be the same. A life cycle is a series of changes in form that an organism undergoes, returning to the starting state. Transitions of form involve growth and asexual or sexual reproduction. Humans have a diplontic life cycle. Somatic cells = 23 homologous pairs of chromosomes Gametes = no pairs of chromosomes, only 23 single chromosomes

Interphase: chromosomes duplicates Meiosis I  Prophase I o Homologous pairs match up  synapsis, creates tetrad

o Nuclear envelope breaks o Crossing over o Mitotic spindle forms  Metaphase I o Spindle microtubules attach to a kinetochore o Chromosomes aligned along metaphase plate (randomly)  Anaphase I o Homologous chromosomes separate o Sister chromatids remain attached  Telophase I and Cytokinesis o Cleavage furrow forms and pinches cell into two o Nuclear envelope may or may not reform o Offspring cells are haploid, chromosomes in sister chromatid form Meiosis II  Prophase II o Nuclear envelope breaks o Mitotic spindle forms  Metaphase II o Spindle microtubules attach o Chromosomes aligned along metaphase plate  Anaphase II o Sister chromatids separate  Telophase II and Cytokinesis o Divide o Forms 4 haploid daughter cells Mitosis Both Meiosis Homologous chromosomes Interphase – chromosomes Homologous chromosomes remain separate are duplicates pair up and cross over Chromosomes  Line up at metaphase plate  pairs of homologous chromosomes Sister chromatids separate Begin with diploid parent Homologous pairs separates cells in anaphase I Happens in all cells except Sister chromatids separate in gametes anaphase II Asexual reproduction, Only occurs in reproductive growth, repair, replacement organs to produce gametes Starts with 1 parent cell to Starts with 1 diploid parent produce 2 genetically cell and undergoes 2 rounds identical diploid daughter of cell division to produce 2 cells unique haploid daughter cells Independent assortment = chromosome pairs orient independently at metaphase I, the number of combinations for chromosomes packaged into gametes = 2n

Fertilization – 2 haploid gametes combine to create 1 diploid zygote, zygote undergoes mitosis to grow and develop into a multicellular adult, allows each parent to randomly contribute a unique set of genes to a zygote, genetic variability. Synapsis = pairing of two homologous chromosomes during prophase I of meiosis Crossing over: occurs during prophase I at chiasma (location where genes cross over) Sources of genetic variation in sexually reproducing organisms  Chromosomal alignment in metaphase I  Random fertilization  Different versions of genes on homologous chromosomes  Crossing over Nondisjunction = when chromosomes or chromatids don’t separate correctly  Occurs in meiosis I o All 4 abnormal gametes  2 of n+1 gametes  2 of n-1 gametes  Occurs in meiosis II o 2 abnormal gametes  n +1  n-1 o 2 normal gametes  both n Autosomes = 22 pairs Sex chromosomes = 1 pair, XX (female) or XY(male), encode for sex characteristics and other traits, Y is smaller than X Structural mutations of chromosomes  Deletion – part of a chromosome is lost/deleted  Duplication – a section of DNA is duplicated and both copies end up in the same chromosome, can occur because of errors during duplication or meiosis  Inversion – a section of DNA is backwards  Translocation – two non-homologous chromosomes exchange sections of DNA

Chapter 9: Patterns of Inheritance Early theories  Hippocrates = Pangenes  Aristotle = particles  Blending hypothesis = traits combine into something new, blend of both Mendel – 1866: parents pass on heritable factors, which retain their own identity Pea plants are good for genetics because they have quick generation times, many varieties, selffertilization and cross-fertilization Mendel’s four hypotheses: 1) Alternate versions of genes (alleles) exist and account for variations 2) An organism inherits one allele form each parent per character 3) If the two alleles differ, one will determine the appearance of the organism; the other will not have a noticeable effect 4) A sperm and egg only carry one allele each for individual inherited characters Dominant phenotype = phenotype that will be shown by homozygous dominant and heterozygous genotypes. It is not always the most common in a population. Independent assortment:  The inheritance of one allele has no relation to the inheritance of another  How the chromosomes line up in metaphase I, nothing controls which are on each side  Random chance that a maternal chromosome is on the left (of metaphase plate), paternal is on the right, or vice-verse, or both on the same side. Each does not have a connection to the next. Testcrosses – mating between an organism with unknown genotype and a homozygous recessive, used to determine the unknown genotype through looking at the offspring Rule of multiplication – likelihood that events happen at the same time (“and”) Rule of addition – likelihood that something with more than one possible genotype will occur (“or”) Procedures that might be used to help parents obtain information about future offspring: - genetic testing - fetal testing o amniocentesis (amniotic fluid) o chorionic villus sampling (placenta) o maternal blood tests o fetal imaging Incomplete dominance: expression of both alleles, heterozygote = intermediate phenotype  pink flowers from RR x rr Codominance: both traits from the alleles are expressed individually  blood cells with both A and B proteins Multiple alleles per character: more than two alleles per gene within the population  ABO blood Multiple characters per allele: single genes that can have impact on multiple different characteristics (pleiotropy)  sick cell anemia Human skin color = polygenic inheritance (multiple genes for a single character) and… Impact of environmental factors: environment can have an impact of characters as well as genes, but only genetic influences are inherited

Nature vs. nurture: argument about whether genetics or environment is more influential on an individual’s characteristics Blending hypothesis states that a new genotype is created by the combination of the parental genotypes and that alleles are lost in this process. Incomplete dominance says that the alleles are maintained, but both are expressed in a heterozygous individual. Chromosome theory of inheritance  Genes are found on specific loci on chromosomes  Chromosomes undergo segregation and independent assortment during meiosis o Segregation: during anaphase I, homologous pairs of chromosomes get segregates so that each gamete can only inherit one chromosome from each of the homologous pairs o Independent assortment: how the chromosomes line up in metaphase I, nothing controls which are on each side (mother’s on one side, father’s on other), source of genetic variation o Crossing over: occurs during prophase I at chiasma, homologous pairs swap alleles, source of genetic variation Linked genes: genes that are close to each other on the same chromosome that are typically inherited together, they do not follow Mendel’s law of independent assortment Sex-linked genes: genes located on the sex chromosomes, sex-linked = x-linked, occurs more often in males because females have two X chromosomes and can inactivate the mutated one or compensate with the normal gene on the other Sex-linked disorders = white eye color in fruit flies, color blindness in humans, hemophilia, duchenne muscular dystrophy Chapter 10: The Structure of Genetic Material Proteins were initially suspected to be the hereditary material because proteins are extremely complex and the human body is also very complex. Griffith  “transforming factor” that can be passed from one organism to another  Streptococcus pneumoniae,  Injected mouse with dangerous form of bacteria, mouse dies  Injected another mouse with the harmless form, mouse was fine  Injected third mouse with the dangerous, but boiled it first, mouse was fine  Injected fourth with a combination of killed pathogenic strep and nonpathogenic strep, mouse died Hershey and Chase  showed that DNA was the genetic material using e. coli and T2 bacteriophage, if e. coli get infected, the bacteria transforms to make viruses. Radioactive DNA, cell became radioactive after transfer of DNA DNA structure:  Double-helix structure  Nucleic acids = nucelotides, sugar-phosphate backbone o Nitrogenous base (AGCT) o Sugar (deoxyribose) o Phosphate group o Covalently bonded  Pyrimidines  single ring

o Thymine, Uracil o Cytosine  Purines  double ring o Adenine o Guanine  Hydrogen bonding between base pairs o 3 between C-G, stronger o 2 between A-T RNA uses uracil instead of thymine and has an extra hydroxyl group on the sugar, making it ribose instead of deoxyribose Watson and Crick, Chargaff o Watson and Crick’s model showed the double helix, which fit with Chargaff’s date of adenine = thymine, cytosine = guanine Semiconservative replication – new DNA is made up of one parental strand and one daughter strand, half is old/half is new 1) Hydrogen bonds are broken, DNA unwinds, replication begins 2) Whole strand opens up when the bubbles eventually merge 3) DNA polymerase attaches at 5’ end, brings nucleotides in 5’-3’ direction, 4) At replication fork, DNA polymerase turns the other direction, synthesizes in pieces because of 5’-3’ direction 5) Creates okazaki fragments 6) Ligase glues fragments together Central Dogma: DNA  RNA  Proteins transcription translation Eukaryotic cells:  Transcription occurs in the nucleus  Translation occurs in the cytoplasm Prokaryotic cells:  Both transcription and translation occur in the cytoplasm Genetic code  Redundant o More than one codon can encode for the same amino acid o 64 codons = 20 amino acids  Unambiguous o No doubt about what an amino acid encodes for o UUU only encodes for phenylalanine  Universal o In almost any organism, the codons code for the same amino acids  Without punctuation o No extra nucleotides after transcription and editing o 30 nucleotide = 10 codons Transcription 1) Initiation  RNA polymerase recognizes promoter (particular sequence in DNA that tells RNA polymerase to bind and start transcribing)

2) Elongation  RNA polymerase starts building the new RNA with RNA nucleotides on DNA 3) Termination  RNA polymerase recognizes terminator (particular sequence in DNA that tells RNA polymerase to stop), detaches, transcription ends mRNA = messenger RNA, transcribed from DNA, brings code to ribosome in the cytoplasm tRNA = transfer RNA, transfers amino acids to the ribosome rRNA = ribosomal RNA, makes up the ribosome Introns: intervening sequences, not translated, spliced out of the sequence Exons: expressed portions Cap and tail direct the mRNA for export from the nucleus, prevent degradation, and help ribosomes bind when it is time for translation RNA processing = guanine cap and poly-A tail, splicing (removing introns) tRNA as a translator:  Recognizes appropriate amino acid  Recognizes which codon the amino acid goes with  Has an amino acid attachment site at the top and anticodon at the bottom Ribosomes make proteins out of mRNA, consists of a large subunit where the tRNA is and amino acid chain forms and small subunit where the mRNA attaches Stop codons do not code for amino acids  UAA, UAG, UGA Translation 1) Initiation  mRNA binds to small ribosomal subunit, first tRNA binds at the start codon  large ribosomal subunit joins small subunit 2) Elongation  Codon recognition o Right tRNA with right amino acid come in for the next three codons  Peptide bond formation o P site has tRNA with a peptide chain o A site has new tRNA attached with amino acid, creates a peptide bond with chain in p site  Translocation o Peptide in A site moves over to the P site o A site becomes available for new tRNA to come 3) Termination  Stop codon reaches ribosome’s A site Mutagenesis = occurrence of mutations, due to spontaneous errors and/or exposure to mutagens Mutations = change in the DNA nucleotide sequence  Base substitutions  number of bases does not change, just a letter o Silent mutations - DNA sequence changes, but amino acid sequence does not; change still codes for the same thing o Missense mutations – DNA sequence changes, and the amino acid sequence changes. Similar amino acid may or may not have a big impact

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o Nonsense mutations – DNA sequence changes, but changes in a way that gives a stop codon. Translation strops, no amino acid made. Severity changes based on location of mutation on the polypeptide. Deletions or insertions  total number of nucleotide changes, changes the groups of three and what they encode for o Alter reading frame o Usually cause significant changes o Ex: sickle cell anemia

Chapter 11: How Genes Are Controlled Gene regulation = turning genes on and off Gene expression: flow of information DNA  mRNA  proteins Operon  One way that prokaryotic organisms quickly change their gene expression  Group of genes and regulatory elements that all turn off or on at the same time Lac operon  Three lactose utilization genes  Promoter = sequence where mRNA binds so that transcription can occur  Operator = “switch,” where repressor binds  When turned off: o Repressor comes from gene that is not on the codon, always on, always present in the cell o If lactose is not present, it doesn’t need to be able to use it, therefore the operon is turned off o If the repressor binds to the operator, it prevents the RNA from binding and no transcription can occur  When turned on: o Lactose binds to the repressor o Repressor can’t bind to the operator o RNA polymerase binds to the promoter, transcribes o Three genes are expressed  enzymes for lactose utilization are made Lac vs trp:  Lac: only active when repressor is not bound, use lactose, repressor off, operon turned on  Trp: only active when repressor is bound, make trp, if it is present there is no need, repressor on, operon turned off Repressors: operon is turned off when repressor binds to DNA Inactive when bound to the molecule of interest (lac operon) Active when bound to molecule of interest (trp operon) Activators: operon is turned on when activator binds to DNA Eukaryotic gene regulation is important because is allows for the multiple types of cells in the human body, despite the fact that almost all of the cells have the same genome (differentiation  neurons vs epithelial cells) Eukaryotic gene regulation  Chromosome structure

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o DNA packing  Elaborate folding and coiling  DNA wraps around 8 histones = nucleosome, connected by linkers o X inactivation  In females, one X chromosome is very compact and almost completely inactive  In tortoise shell cats:  Cat has both alleles for orange fur and black fur on X chromosome  Cell division occurs and random chromosome inactivation  In some cells the orange X is activated, in others the black X is activated, some hair is black and some hair is orange Chemical modification o Histone proteins o DNA methylation o Epigenetic inheritance: inheritance of traits that do not directly involve the nucleotide sequence  Which X chromosome is inactivated in embryonic cells is random, but that inactivation is passed to all descendants Transcriptional control o Protein assemblies  Activators and repressors impact RNA polymerase binding  Activators are more important  Default is to be off unless there is an activator present  RNA polymerase requires transcription factors to function  Silencers = repression o RNA splicing  Different mRNA molecules are made from a single gene o miRNAS  “non-coding” DNA regions actually encode for particular RNAs(miRNA)  can cause degradation of mRNA as complementary pieces  binding to mRNA to prevent binding to ribosomes and therefore prevent translation Control at later stages o Breakdown of mRNA o Translation initiation o Protein activation  Not all proteins are produced in an activated form o Protein breakdown  There are enzymes that break down proteins...