BSC Test 3 & 4 study guide
BSC Test 3 & 4 study guide BSC 114
Popular in Principles Of Biology I
Popular in Department
This 36 page Bundle was uploaded by madys70ss on Thursday October 6, 2016. The Bundle belongs to BSC 114 at University of Alabama - Tuscaloosa taught by in Fall 2016. Since its upload, it has received 5 views.
Reviews for BSC Test 3 & 4 study guide
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 10/06/16
Biology Test 3 Chapter 14a: Gregor Mendel: o “Father of genetics” o Austrian monk o ~1860: Breeding experiments in monastery garden Mendel started with strains of peas w/ variable characters o Characters: Features that differ between individuals Ex: Flower color o Trait: Differences in a character Ex: Purple flowers or white flowers Starting strains were obtained from seed suppliers & were true- breeding o True-breeding: All individuals are identical & self- fertilization gives rise to offspring like parents generation after generation Peas will self-fertilize, but can be made to hybridize o Stamens (male organ) removed to prevent self-fertilization o Pollen (male gametes) transferred from white to purple Hybridize: Produce offspring between genetically different strains o Hybrid: Offspring of genetically different parents Monohybrid cross: A mating in which 1 character is followed o P: (parental) generation o F 1first filial) offspring of the P mating o F 2 Offspring of an F 1ating o X indicates mating, or cross Mating for monohybrid cross: o P: Purple x white F =1100% purple o F 1lants allowed to self-fertilize o F : Purple x purple F : 75% purple, 25% white 1 2 o 6 other characters gave the same result: One trait disappears in F 1 reappears in F 2 Mendel concluded that these phenomena are universal (exceptions discovered later) Mendel’s explanation: o Every individual has 2 copies of each gene o There are different variants (alleles) of the gene Ex: A purple allele & a while allele o In an individual w/ 2 different alleles, only 1 contributes to the character The expressed trait is dominant The now-expressed trait is recessive o Each gamete has only 1 of the 2 alleles The genome contains the instructions (genetic code) to make proteins (& other molecules) o There are 2 genomes in every cell o 2 alleles of a different gene- even though they are different, each will produce a functional protein The human genome contains 20,000-25,000 genes, & 2 copies of each. There may be variation between genes (each variant allele), most of it harmless & part of normal genetic variation Phenotype: Physical attributes; Ex- purple & white flowers Genotype: Genetic makeup; Ex- which alleles are present o Let P represent the purple flower color allele (dominant) o Let p represent the white flower color allele (recessive) o Since each individual has 2 alleles, there are 3 possible genotypes: PP (purple phenotype, homozygous) Pp (purple phenotype, heterozygous) pp (white phenotype, homozygous) o Homozygous: Both alleles are the same o Heterozygous: Alleles are different A Punnett square diagrams the outcomes of fertilization o Vertical: The 2 egg genotypes, P & p o Horizontal: The 2 sperm genotypes, P & p Once meiosis happens, half of the gametes have a P allele & half of them have a p allele Probability: Branch of math that deals w/ the likelihood of some event o Probability that a certain event occurs: Total ¿outcomeswitha particularresuof possibleoutcomes¿ ¿ Mendel’s law of segregation: o There are different variants (alleles) of some heritable factor that causes a trait (gene) o In an individual w/ 2 different alleles, only 1 contributes to the character (dominance/recessiveness) o During gamete formation, alleles segregate from each other, so each gamete has 1 allele o Each individual receives 1 allele from each parent Scientific theory: An explanation of a phenomenon that cannot be observed directly, accounting for the “inner workings” of the system o You can’t prove a theory is true, you can just make it more likely to be true through experimentation Dihybrid cross: 2 characters YyRr (Y is yellow, y is green; R is round, r is wrinkled) o F 1 100% yellow & round o F 2 9/16 yellow & round 3/16 yellow & wrinkled 3/16 green & round 1/16 green & wrinkled Law of independent assortment (AKA Mendel’s second law): Alleles for 2 genes segregate independently during gamete formation o Ex: YyRr parents: Gamete w/ Y can have R or r with equal probability o Ratios are consistent w/ complete independence For independent genes, probability of any dihybrid phenotype/genotype can be calculated from each monohybrid probability Chapter 14b: Some phenotypes do not conform to simple dominance/recessiveness o Incomplete dominance: Heterozygote has an intermediate phenotype Ex: Red & white snapdragons will yield a pink snapdragon Segregation of alleles follows Mendelian rules Different nomenclature: C = red allele & C = white allele Ex: White spotting in cats SS cats are mostly white Ss cats have some white ss cats have no white at all o Co-dominance: The heterozygote has properties of both homozygotes Ex: Human MN blood groups Gene encodes glycoproteins expressed on surface of red blood cells. Two alleles, M & N, encode 2 protein variants MM individuals have only M protein, NN individuals have only N, & MN have both o Multiple alleles: Gene has more than 2 alleles A B Ex: There are 3 alleles of the I gene; I , I , & i (i is recessive to the other two) A A A IB B& IBi have type A blood I I & I i have type B blood ii have type O blood A B I I have type AB blood The I gene encodes an enzyme that synthesizes an extracellular carbohydrate A o I enzyme produces “A” type carbohydrate o I enzyme produces “B” type carbohydrate o i enzyme produces no carbohydrate ABO blood group is important in transfusion. Immune system produces antibodies against foreign molecules, but not against self o A phenotype individuals have anti-B antibodies o B phenotype individuals have anti-A antibodies o O individuals have both anti-A & anti-B antibodies o AB individuals have neither antibody o Epistasis: Genotype at one gene affects phenotypic expression of a second gene Shows up as a deviation from 9:3:3:1 ratio in dihybrid cross Ex: B & C genes affect mouse hair color. 9:4:3 ratio. The white genotype cc prevents expression of the black/brown phenotype. o Polygenic inheritance: Multiple genes affect the same character & have additive affects on phenotype Ex: Skin color, height Traits are followed through families using pedigrees o Circle= female, square=male o Affected= filled, unaffected= unfilled Dominant traits are always expressed in one (or more) parents, recessive traits are often not expressed by either parent Most human genetic diseases are recessive, caused by genes that produce defective proteins: o Cystic fibrosis: Chloride channel protein o Tay-Sachs disease: Enzyme that degrades lipids o Sickle cell disease: Hemoglobin protein Some conditions & diseases are dominant: o Achondroplasia (dwarfism) o Huntington’s disease (nervous system deterioration) Carrier: One recessive gene is had but not exhibited in the phenotype Prenatal diagnosis: o Sample of fetal tissue is obtained: amniotic fluid (contains fetal cells), or from chorionic villus (fetal portion of placenta) o Karyotype analysis detects wrong # or other chromosomal defects o DNA analysis to detect specific mutations Chapter 15a: Segregation: o Organisms have 2 copies of each gene, but gametes have only one o Somatic cells have 2 copies of each chromosome, but gametes only one Assortment: o Genes segregate independently of one another o Non-homologous chromosomes segregate independently th Chromosome Theory of Inheritance (early 20 century): Genes reside on chromosomes Thomas Hunt Morgan chose prosophila to examine genetic mechanisms: o Short generation time (~10 days) o 100s of offspring from one pair o Survive well in the lab o 1 genetic variant: White eyes (vs. normal red eyes) o White eye allele w +recessive) o Wildtype allele w (dominant, red eyes) Experimentation: o P: Red-eyed female x white-eyed male o F :1All red Red is dominant to white o F :2F 1rother x F s1ster Females were 100% red & males were 50% red & 50% white o Explanation: Females & males are genetically different, XX & XY respectively. The Y chromosome is not a functional homolog of the X Males are haploid for genes on the X o Although the X & Y are not homologs (do not contain the same genes), they segregate during meiosis o White eye gene is on the X chromosome st Provided the 1 conclusive evidence in support of the chromosomal theory of inheritance, that genes reside on chromosomes Chromosomal sex determination: o XY (in humans, fruit flies) o XO: Females have 2 X’s, males have one X (no Y) o ZW: Females are ZW, males are ZZ (birds, butterflies) o Haplo-diploidy: Females are diploid, males are haploid (bees, wasps, ants) Key feature of sex-linked traits: Fathers transmit X chromosome to daughters, but never to sons o An affected father produces heterozygous daughters o A heterozygous mother produces 50% affected sons, but 100% normal daughters (although ½ of daughters will be carriers) Sex-linked traits are more often observed in males because they have only one X chromosome o Duchenne muscular dystrophy o Hemophilia o Red-green color blindness Female mammals inactivate one X, so each cell has only one active X o Inactive X= Barr body o Inactivation occurs early in development, is random, & pattern of inactivation is inherited through subsequent mitoses o Tortioseshell & calico cat: Alleles for black & orange fur on X. Each patch of black fur represents a “clone” of cells in which the orange allele X has been deactivated. White fur is due to a separate gene (epistasis). Chapter 15b: Test cross: Cross to an individual homozygous for recessive alleles o When crossed w/ a heterozygous individual, there is a 1:1:1:1 ratio Some genes behave as if intermediate, neither independent nor dependent o Ratios vary across the body o P: Gray body, normal wings x black body, vestigial wings o F : All gray body, normal wings 1 o F x1black body, vestigial wings o F :2All different ratios & combos (Gray body, normal wings & black body, vestigial wings were overwhelmingly prevalent) + is also used to denote dominance In the previous fly experiment, it seems like the gray body & normal wing alleles stayed together & the black body & vestigial wing alleles stayed together o Explanation: These genes are on the same chromosome- tend to be inherited together instead of sorting independently o These genes are linked- on the same chromosome Mendel’s Law of Independent Assortment is true if genes are on different chromosomes For genes on the same chromosome: o Usually deviate from independence (no classes are 25%) due to linkage o Usually deviate from dependence (no classes are 0% or 50%) Crossing over: Breakage & rejoining between non-sister homologous chromatids in meiotic prophase 1 The 2 most frequent F c2asses represent the phenotypes of the P generation, & are called the parental classes The 2 least frequent F 2lasses are called the recombinant classes Morgan: The extent of crossing over is proportional to distance along the chromosome between the genes o Can be used to map gene positions o The recombinant (non-parental) classes are 17% of the total in this situation o 1% recombination= 1 map unit= 1 centimorgan o Distance: Black & vestigial genes are 17 map units apart o Map distances are additive Experiments like the previous are used to construct a linkage map o Further evidence for the chromosome theory (existence of chromosomes) Genes that are very far from each other on the same chromosome act as if they are on different chromosomes (follow the Law of Independent Assortment) Mendel didn’t discover linkage because all of the traits he studied were too far apart from each other Aneuploidy: Too few or too many copies of a chromosome o Monosomy (1 chromosome) o Trisomy (3 chromosomes) o Caused by error in chromosome distribution during meiosis (non-disjunction). Affected gamete will produce an aneuploid zygote. o Most common autosomal aneuploidy: trisomy 21= Down syndrome o Aneuploidy for other autosomes are very rare- cause fetal death o Sex chromosome aneuploidy is tolerates better b/c of inherent mechanisms to adjust gene dose XXY: Klinefelter syndrome Male sex organs, some female development. Testes underdeveloped & sterile & some mental retardation XYY: Tall but otherwise normal XO: Turner syndrome Sterile female XXX: Normal female Deletion: Portion of chromosome is missing. Many/most have dominant mutant effects o Cri du chat syndrome: Missing end of chromosome 5. Individuals have cat-like cries as infants, mental retardation, facial abnormalities, etc. Translocation: Ends of 2 chromosomes are exchanged. Break in chromosome may disrupt an important gene o Philadelphia chromosome causes leukemia Chapter 16 DNA-bacteria relationship: o Exposure to extract from lethal S bacteria transforms the harmless R strain into a pathogenic strain (transformation) o Theory: Strain S has the pathogenicity allele; strain R has the non-pathogenicity allele o DNA was identified as the genetic material Each nucleotide has 3 components: o Base (T, A, G, or C) o Deoxyribose sugar o Phosphate Adjacent nucleotides are joined into polynucleotides through sugar-phosphate bonds Each DNA strand has a polarity based on sugar orientation, 5’ or 3’ Sugar-phosphate backbone w/ base rungs 2 polynucleotide strands pair side-by-side to make a double helix Parallel strands are held together by hydrogen bonds between complementary bases: o A-T o C-G Pairing is always 1 purine (2 rings) & 1 pyrimidine (1 ring) The 2 strands have opposite 5’ to 3’ polarity (are anti-parallel) 2 strands wind around each other in a 3D helical structure, the double helix o A-T & G-C pairing & double helix were discovered by Watson & Crick in 1953, based on 2 types of data: Chargoff’s Rules: Analytical chemistry shows that amount of A=T & amount of G=C X-ray diffraction experiments of Rosalind Franklin showed helical structure, spacing of bases, & position of sugar & phosphates on the outside DNA molecules are measured in base pairs o One base pair= A pair of complementary nucleotides DNA molecules are huge DNA synthesis: 2 strands separate & each strand acts as the template for synthesis of the complementary strand o Nucleotide to be added is a triphosphate (ex. dTTP) o dTTP dTMP (added to DNA) + PP i o Addition occurs only at the 3’ end of the growing strand o Catalyzed by enzyme DNA polymerase The 2 old strands separate in local regions, producing a replication bubble Each bubble has 2 replication forks where new nucleotides are added Each new strand is synthesized 5’ to 3’ At each replication fork one strand is synthesized toward the fork (top), & one away from the fork (bottom) As synthesis continues, more “old” DNA becomes single- stranded, & the fork moves Because DNA is synthesized only 5’ to 3’, one strand is synthesized discontinuously, that is, in short fragments o Leading strand (top): Continuous synthesis o Lagging strand (bottom): Discontinuous synthesis. Short fragments are called Okazaki fragments. Replication forks move apart until the entire molecule is replicated o Circular chromosomes (bacteria): Single origin of replication o Linear chromosomes (eukaryotes): Many origins of replication DNA polymerase: Enzyme that adds nucleotides Each chromatid contains 1 dsDNA molecule (1 old strand, 1 new strand) DNA replication occurs during S phase: 2 DNA molecules= 2 chromatids After mitosis each chromosome= 1 chromatid= 1 DNA molecule Mispaired or damaged nucleotides result from: o Chemical or light damage, especially UV light o Mistakes in DNA synthesis Excision: A nuclease recognizes & removes the mispaired region Repair: DNA polymerase fills in the gap by the synthesis mechanism Chromatin: Combination of DNA & proteins o Histones: Small basic proteins (associate via opposite charge to acidic DNA molecule) o Nucleosome: Complex of 8 histone proteins DNA is wound around nucleosomes: “beads on a string” o Nucleosome fibers are further wound into 10 nm & 30 nm fibers & arranged in loops in the chromosome Chapter 17a: Protein function is determined by its sequence of amino acids (Translation) o The primary structure of the protein is determined by the sequence of a messenger RNA. (Transcription & RNA processing) o The sequence of a messenger RNA is determined by the sequence of a gene Concluded in 1930s: Genes are the instructions to create proteins “One gene: one protein” experiment: o Beadle & Tatum o Wildtype fungus Neurospora grows on minimal medium (medium lacks arginine) Cells can make their own essential compounds (including arginine) o Several mutant strains (defect in genes) are identified that cannot grow on minimal medium Mutants are defective in making some essential compound o The 3 mutant strains survive on minimal medium supplemented w/ arginine The mutation is the inability to make arginine o Some of the mutant strains survive on media supplemented w/ ornithine & citrulline (molecules similar to arginine) Differences between the strains define a biochemical pathway o Interpretation: Arginine is synthesized from precursor molecules: Unnamed precursor ornithine citrulline arginine Each step is catalyzed by an enzyme, which is represented by a class of mutants o Since the mutants differ in growth on ornithine & citrulline, it is possible to determine the order in which the genes act o Each gene encodes one enzyme Encode: Contains the instructions for One gene: one enzyme (Later expanded to one gene: one protein) Flow of genetic info: DNA RNA Protein o Transcription: Synthesis of RNA using DNA template RNA processing: RNA molecules are modified o Translation: Synthesis of protein using RNA template Transcription & translation are similar in prokaryotes & eukaryotes, except: o In eukaryotes, the original RNA copy is often modified before becoming a messenger RNA (RNA processing) o In eukaryotes the mRNA must exit through the nucleus (nuclear pores) Transcription: o Copies a limited region of one DNA strand Gene: A segment of DNA that is transcribed Each gene has a start signal & a stop signal Some DNA segments are not part of any gene & are not transcribed 6 9 o Chromosome= Long piece of DNA, 10 -10 base pairs in length o Transcription units (=genes): Shorter segments that are transcribed o Spacer DNA is not transcribed o RNA polymerase carries out transcription RNA: o Usually single-stranded o Contains ribose instead of deoxyribose sugar o Contains uracil (U) base instead of thymine (T) Process of transcription: o Initiation: Each transcription unit is defined by a start signal (promoter) & stop signal (terminator) Each signal is a particular DNA sequence Other proteins are required for transcription initiation: bind to promoter & nearby sequences Very complex in eukaryotes: Cluster of many accessory proteins forms at promoter Simpler in prokaryotes: One or a few proteins o Elongation: Short segments of DNA (10-20 nts) become transiently single-stranded & act as a template for RNA synthesis RNA molecule is extended one nucleotide at a time, using nucleoside triphosphates, analogous to DNA synthesis Direction of RNA synthesis: Always 5’ to 3’ o Termination: Transcription ends when (or just after) the RNA polymerase transcribes the terminator sequence In prokaryotes, the product of transcription is the mRNA, often used without further modification More complex in eukaryotes: o Product of transcription in a pre-mRNA or primary transcript which undergoes RNA processing o mRNA is exported from nucleus RNA processing: 1) Capping: A modified nucleotide is added to the 5’ end of the RNA o Purpose: Necessary for ribosome attachment. May also affect mRNA stability 2) Polyadenylation: 50-200 adenosine nucleotides are added to the 3’ end o Purpose: Increases mRNA stability 3) RNA splicing: Internal segments of RNA molecules are removed, & adjacent parts are joined back together o Removed segment: Intron o Retained segment: Exon o Organelle where splicing takes place: Spliceosome o Purpose: Introns encode meaningless sequences & must be removed before translation Only 1.5% of the human genome consists of protein-coding sequences o Non-coding portion consists of: 26% intron sequences 72% spacer DNA & genes that encode RNA products Chapter 17b: Translation: Protein synthesis by ribosomes, based on sequence of bases in messenger RNA o Participants: Messenger RNA: Produced by transcription (plus RNA processing in eukaryotes) RNA that is “read” by ribosome to make a protein Each set of 3 nucleotides specifies 1 amino acid- called a codon o 61 codons, each specifies one of 20 amino acids o Methionine (Met) is usually the 1 amino acid, AUG is usually the start codon o 3 codons (UAA, UAG, & UGA) have no amino acid; act as stop codons Ribosome: Molecular “machine” that carries out translation; Ex- Synthesizes proteins Complex of several dozen proteins & 3 RNA molecules 2 ribosomal subunits, large & small Transfer RNA: “Adapter” molecule in translation RNA molecules of ~80 nucleotides Folded due to intramolecular base pairing Amino acid attached to 3’ end by enzyme aminoacyl tRNA synthase One or more tRNAs for each amino acid Anticodon: A 3-nucleotide region that base pairs with the codon on mRNA during translation Transcribe: Some language converted from one medium to another; Ex: Converted from oral to written o Transcription: DNA to RNA (different forms of same nucleic acid language) Translate: One language to another o Translation: Nucleic acid “language” to protein language Translation: o Initiation: Ribosome begins translation at 3-nucleotide sequence AUG, which codes the amino acid methionine Prokaryotes: Recognizes & binds to a sequence close to the AUG codon Eukaryotes: Binds to the 5’ end of mRNA & scans to st find the 1 AUG codon o Elongation: Ribosome moves 3 nucleotides down, reading the next 3-nucleotide sequence & attaching the 2 nd amino acid to Met. Continues over and over again until termination occurs Ex: Ribosome moves 3 nucleotides down to the next codon CCU, pro-tRNA recognizes CCU codon, & ribosome attaches Pro to Met o Termination: Occurs at a 3-nucleotide sequence that does not specify any amino acid Ex: Ribosome moves 3 nucleotides down to UGA, terminates translation, & releases protein Met-Pro- Glu-Phe 3 functional sites in the ribosome: E, P, & A 1) P site: tRNA w/ growing polypeptide attached. tRNA w/ its amino acid enters the A site 2) & 3) Peptide bond between the polypeptide & the amino acid tRNA in the A site. GTP hydrolysis provides energy. Polypeptide is now attached to A-site tRNA. 4) Ribosome moves 3 nucleotides down the mRNA (GTP GDP). Polypeptide tRNA now in the P site. tRNA exits from the E site. Protein folding: Protein folds into its 3D shape during synthesis & afterward Polyribosomes: A single mRNA may be translated by more than 1 ribosome at the same time Intracellular targeting: Proteins destined for rER, nucleus, mitochondria, chloroplast, etc. have targeting signals (i.e. “address labels”) as part of the amino acid sequence Messenger RNA: “Template” for translation, nucleotide sequence specifies amino acid sequence Transfer RNA: Accessory molecule in translation All RNAs are synthesized by transcription Mutation: Abnormal genetic information o Types of mutations: Large-scale: Aneuploidy, deletions, & translocations Small-scale: Point mutations Substitution: One nucleotide is substituted for another. Types of substitutions: o Missence mutation: Change in 1 amino acid (Ex.- Sickle cell disease) o Nonsense mutation: Codon changed to a stop codon (UAA, UGA, or UAG), causing premature termination of the protein o Silent mutation: Nucleotide change has no affect on amino acid sequence o Frameshift mutation: 1 or 2 base insertions or deletions. Protein reading “frame” is based on translation start site. Disruption in reading frame causes wrong amino acid at all points “downstream” Most severe if at 5’ (beginning) end of gene/mRNA Lower: Premature termination o Mutagen: A chemical or condition that produces mutations. Does so by breaking DNA, or damaging bases Ex: Chemicals in cigarette smoke, UV light, X-rays, etc. Mendel: A gene is a discrete heritable unit that produces a phenotype Beadle & Tatum: One gene contains the instructions to produce one enzyme (or protein) Modern view: A gene is the DNA sequence that encodes a protein or RNA product Biology Test 4 Chapter 18a: Gene expression: Gene to final product, all steps o Gene mRNA Protein Differential gene expression: Each cell expresses only a subset of its genes. Typical human cell expresses only around ~20% of its genes. o Cell types are different because they express different subsets of their genes. o Some genes are expressed by many/all cell types (Ex.- ATP synthase) o Some genes are expressed by a single cell type (Ex.- Globin, insulin) o Gene regulation: Mechanism of differential gene expression Steps at which gene expression is regulated: o Transcription (most important) o Splicing (euks only) o Translation o mRNA stability o Protein stability Regulation of bacterial transcription: o All living organisms need the amino acid tryptophan o The bacterium E. Coli can make tryptophan from a precursor molecule in 3 steps However, if tryptophan is in the environment, the enzyme is not expressed Humans cannot produce tryptophan, must consume it in food o The three trp enzymes are the products of 5 genes (2 enzymes are dimer proteins) o The 5 genes are adjacent & transcribed as a single long mRNA o Operon: Cluster of bacterial genes w/ similar functions. Operon is transcribed as one long mRNA, so all genes turn on/off at the same time & equal amounts of protein are made Trp operon: Cluster of 5 genes for tryptophan synthesis o Trp operon is transcribed when tryptophan is absent, but not when it is present When tryptophan is available the trp operon is repressed but turned on when tryptophan is absent Mechanism of repression: A protein repressor produced by the trpR gene binds to the operator, a DNA sequence at the beginning of the operon, blocking transcription Tryptophan is a co-repressor: Binds to the protein repressor Tryptophan bound to repressor Repressor is active Repressor binds to operator No transcription No tryptophan Repressor is inactive Operon is transcribed General mechanism of transcriptional regulation: A regulatory protein (or more than one) binds to a sequence in the DNA molecule near the promoter. 2 types: o Negative regulation: Binding of the regulatory protein prevents transcription Ex.- Trp repressor regulation of trp operon o Positive regulation: Binding of the regulatory protein(s) is necessary for transcription Ex: Lac operon encodes enzymes that break down lactose, & is active only when glucose is absent & lactose is present (both negative & positive regulation) Regulation of eukaryotic transcription: o Eukaryotic genes are more complex & gene regulation occurs at multiple levels o Transcriptional regulation: DNA binding proteins (transcription factors) bind to control elements (DNA sequences) & activate transcription (positive) or repress (negative) o Control elements may be close to or far away from the gene being regulated Close: Proximal control elements & promoter Distant: Distal control elements= enhancers. May be 1000s of base pairs from the gene. o Transcription factor proteins bind to control elements to promote transcription. General transcription factors & mediators bind to proximal control elements & the promoter Activators bind to enhancers o Proteins bound to enhancers make contact w/ & stimulate RNA polymerase via looping of the intervening DNA o Differential gene expression is due to specific combinations of activator proteins o Cell-specific transcription results from different combinations of transcription factors Ex: Liver cells express albumin & not crystallin & lens cells express crystallin & not albumin Differential presence of trxn (transcription) factors is due to earlier differential gene expression Different cell types come about through a sequence of differential expression of transcription factors Last “generation” of trxn factors turns on genes that encode specialized proteins Chromatin: Combo of DNA & proteins o Histones: Small basic proteins o DNA wraps around histone complexes & coils into compact structures o Chromatin structure is regulated by chemically modifying histones & DNA o Histone acetylation: Addition of acetyl groups (acid) promotes a “looser” chromatin structure & promotes gene expression o DNA methylation: Methyl groups are added to base C. Represses transcription. Modifications & patterns of gene expression are passed down at cell division to descendant cells= epigenetic inheritance. Alternative splicing: Primary transcript may be sliced in different ways o Ex: 2 alternative troponin mRNAs w/ different exons. Different proteins will be translated from these mRNAs Small RNAs may regulate mRNA stability & translation Non-coding RNAs do not code for protein sequences o miRNAs (micro RNAs) & siRNAs (short interfering RNAs). Both are 20-23 nt RNA molecules o Complementary to some RNAs. Binding of miRNA to target mRNA induces mRNA degradation or translation inhibition Chapter 18b: The development of a multicellular organism w/ hundreds or thousands of cell types requires regulation of the gene expression o At the correct time: Ex: The crystalline genes are expressed only when eyes are developing o In the correct location: Ex: Only the developing lens expresses crystalline Cells have specialized functions b/c they express unique genes. Ex: o Liver cells- albumin o Lens cells- crystalline o Some pancreatic cells- insulin o Red blood cells- globins Differentiation: Cellular specialization. Cell acquires its final specialized form. Determination: Cells acquire information & become committed to a particular fate in the organism Determination precedes differentiation A cell commits to a particular fate (determination) & then acts on it (differentiation) Determination is under genetic control o Ex: Determination of muscle cell identity requires the expression of MyoD, a master regulatory gene o MyoD encodes a transcription factor protein that promotes expression of other muscle-specific genes Pattern formation: Spatial control of gene expression, determination, & differentiation o Different patterns arise b/c regulatory molecules are distributed asymmetrically Asymmetric regulatory molecules: Unequal cytokinesis & different cytoplasmic contents (molecules= cytoplasmic determinants) o Ex: Bicoid protein= Transcription factor Early gene expression in the embryo results from concentrations of bicoid protein Subsequent differential gene expression leads to the larval body pattern in drosophilia Different extracellular signals (process is called induction) Homeotic genes: “Master genes” that control cellular identity o Homeotic proteins are transcription factors o Mutations in homeotic genes in drosophilia cause mistakes in segment identity (antenna leg) o Genetic hierarchies in early fruit fly development result in the proper expression of homeotic genes o Homeotic genes regulate the anterior-posterior development of all bilateral animals Animals have a common evolutionary origin & genetic blueprint Cancer: Disease of unregulated cell proliferation Mutations cause changes in cell behavior o Loss of inhibition of proliferation o Loss of cell adhesion- ability to leave tumor & move elsewhere o Ability to stimulate vascularization Cell proliferation is genetically controlled through signaling processes & regulation of transcription o Neighboring cells may stimulate or inhibit cell division o Entry into mitosis involves adoption of an internal genetic program Cancer results when cells accumulate mutations that inactivate or override normal proliferative controls 2 types of genes regulate normal cell division: o Proto-oncogenes encode proteins that promote cell division o Tumor-suppressor genes encode proteins that repress cell division Both sets of regulatory controls are subject to mutation: o Oncogenes (mutant versions of proto-oncogenes): Mutant proteins promote cell division, but lack the ability to be regulated o Mutant tumor-suppressor genes encode defective proteins that do not repress cell division Proto-oncogenes become oncogenes by: o Overexpression due to gene rearrangement, or gene amplification (too many copies) o Point mutations resulting in overexpression o Point mutations that cause too much activity or inactivate regulatory sites Growth factor signaling pathway stimulates cell division o Step 3: G-protein Ras turns on & off in response to ligand bonding to receptor o Mutant Ras is always active, even in the absence of the signal Unregulated cell division Cancer Chapter 19: Virus: Non-living obligate intracellular parasites o Only reproduce within living cells All living organisms have viruses Viruses may have restricted host range or infect many related organisms Viral structure: o Capsid: Protein shell that surrounds the genome Many copies of one or a few different types of proteins Many configurations & shapes Some also have a membrane that surrounds the capsid, the viral envelope o Viral genetic material is diverse: double-stranded DNA, ssDNA, dsRNA, or ssRNA Bacteriophage (or simply phage): Viruses that infect bacteria Lytic cycle (kills the host cell): 1) Virus attaches to outside of host cell 2) Genetic material is injected into cell 3) Virus hijack’s the bacterium’s transcription/translation machinery to make its proteins & replicate its genome 4) Bacterium is lysed (it explodes) & newly made phage particles are released to infect new cells Lysogenic infection: Phage exists within the host cell w/o reproducing or killing the host o Viral DNA is integrated within the bacterial chromosome & passed to progeny o Lysogenic phages can become lytic Animal viruses: o Diverse genome types & modes of infection o Many animal viruses infect only certain cell types: Influenza virus: Cells of the respiratory tract Papovavirus: Skin cells (warts) HIV: Particular types of T lymphocytes (white blood cells) o Animal viruses use a wide variety of DNA/RNA molecules as genetic material Reproductive cycle: 1) Envelope fuses w/ host plasma membrane, releasing genetic material into cell 2) ssRNA genome is used as a template to make mRNA (by an RNA-dependent RNA polymerase) 3) mRNA is the template for new RNA genomes 4) mRNAs are translated into capsid & envelope proteins, into rER/Golgi system, ending up at cell surface 5) Capsid assembles around new RNA 6) Assembled viral molecules are budded off with host plasma membrane surrounding them Ebola: o Genome is an ssRNA molecule, 19 kbases o Contains 7 genes: 1 gene for RNA-dependent RNA polymerase 5 genes for capsid proteins 1 gene for a regulatory protein HIV, a retrovirus: ssRNA genome is copied into dsDNA by enzyme reverse transcriptase. DNA acts as a template for synthesis of mRNA/genome Antibiotics are effective against bacterial infection but not viruses. Antibiotics are selective poisons that inhibit bacterial metabolism. Do not affect eukaryotic metabolism. o Ex: Penicillin inhibits bacterial wall synthesis; tetracycline inhibits bacterial protein synthesis o Because viruses lack their own metabolism & have few of their own enzymes, they borrow host enzymes for replication, transcription, etc. Much smaller number of viral-specific functions to poison HIV: Reverse transcriptase & envelope protein processing Herpes virus: DNA replication Ebola: No targets yet identified Vaccine: A weakened/inactivated virus is injected & body makes antibodies (provides immunity to future infection) Viroids: Circular RNA molecules (no capsids) that replicate in plants. Disrupt cell replication. Prions: Misfolded proteins that can induce the misfolding of other copies of the same protein o The causative agent of mad cow & related diseases Viruses are related in structure & sequence to other intracellular genetic “parasites” o Transposable elements (euks) & transposons (bacteria): Segments of DNA that excise themselves from the chromosome & reinsert at another location o Plasmids: DNA circles that replicate independently of the host genome (bacteria & fungi) Chapter 20: Biotechnology: Methods used in medicine, pharmaceutical industry, forensics, etc. 2 largely unrelated methods: o DNA manipulation & gene analysis. Recombinant DNA, PCR, DNA sequencing, DNA hybridization. o Stem cell & organismal cloning methods based on nuclear transportation & cell manipulation Recombinant DNA: Replication of foreign DNA in a host organism, AKA DNA cloning o Host: Usually a bacterium Foreign DNA will be replicated if joined to bacterial DNA that: o Has its own origin of replication o Is beneficial to host (Ex: Antibiotic resistance) Vector: Bacterial DNA that is fused to foreign DNA molecule & causes it to be replicated o Most vectors are modified plasmids or bacteriophage Many bacterial species contain small circular accessory chromosomes, plasmids In recombinant DNA excerpts, DNA from a foreign source is joined to a plasmid; foreign DNA is replicated as cells divide, making many copies from 1 starting molecule o AKA gene cloning or DNA cloning o Plasmid here is a cloning vector Method of joining foreign & vector DNA: o Cut w/ restriction enzyme (cuts DNA at a specific sequence) o Mix molecules, which transiently join via sticky ends (complementary single stranded DNA) o Make new covalent bonds w/ DNA ligase Cloned euk genes may be expressed in bacteria o Problem: Bacterial & eukaryotic transcription & translation regulatory signals are different Solution: Use only the euk protein-coding region. Use bacterial regulatory sequences. o Problem: Euk genes have introns, bacteria lack the ability to splice Solution: Clone cDNAs (copies of mRNAs), which lack introns Synthesis: Start with a population of mRNA. o RNA is copied to DNA by enzyme reverse transcriptase, which makes DNA copies of ssRNA templates (purified from retroviruses) o cDNA is cloned like regular DNA Human protein produced in bacteria for medical uses: o Insulin o Human growth hormone o “Clot buster” drugs used to treat heart attack & stroke (TPA, streptokinase) Other organisms can be used as hosts for expressing pharmaceuticals: o Goats & sheep (drug is in the milk) o Plants (large quantities are cheap to produce) Transgenic organism: An individual that contains a foreign gene or a gene altered in the lab o Soybeans & corn resistant to herbicides o Soybeans & corn resistant to insects (poisonous protein native to bacteria) o Rice that makes its own vitamin A o Also bacterium that digests waste Gene therapy: Insert normal gene in cells to replace a mutant gene o Patient is a “transgenic organism” o Problems: How to get genes inside cells? Modified viruses How to get genes to the correct cells? o Partial success: Treatment of Severe Combined Immunodeficiency Syndrome (SCID) Problem: High incidence of leukemia Alternative to cloning for gene isolation: Polymerase Chain Reaction (PCR) o Enzymatic test tube synthesis of DNA o Components: Template DNA: Usually nuclear DNA. In forensics, this is often a trace sample (blood, hair, saliva, etc.) DNA polymerase 2 primers that bind to the template DNA o Procedure: 1) DNA template is made single-stranded by heating 2) Temperature is reduced & primers bind to complementary sequences 3) DNA polymerase copies template DNA beginning at primers 4) Cycle begins again at step 1 o Position of primers determines what fragment is synthesized. Multiple rounds of synthesis multiply the product many-fold o Typical PCR product is 100s or 1000s of base pairs in length DNA fingerprinting: Identify individuals by unique genetic characteristics o PCR using primers that flank a polymorphic region (many different alleles in the population). Template DNA from different individuals produces DNA fragments of different sizes o The Innocence Project uses DNA evidence to re-open old cases & free wrongly convicted prisoners Nucleic acid hybridization: Single stranded nucleic acids spontaneously “find” complementary strands & reform double- stranded molecules o A short molecule (or probe) with an attached fluorescent compound finds its complementary sequence In what cell types are particular genes expressed? Method: o Prepare DNA probes that detect specific mRNA sequences o Fix fly embryo (crosslink embryonic cells so that they don’t wash away) o Hybridize probes, each with a different colored label. Probes bind only to cells where the mRNA is present Under what conditions are genes expressed? Microarrays detect expression of 1000s of genes at the same time o Each spot on the array is DNA from an individual gene, bound to a solid surface o Isolate mRNA populations from 2 cell types. Label mRNA population from cell 1 with a red probe & label mRNA from 2 with a green probe o Hybridize both probe populations to the array o Results: Red: Gene is expressed in cell type 1 Green: Gene is expressed in cell type 2 Yellow: Expressed in both Black: Expressed in neither A conserved set of genes regulates similar processes in diverse animals o Ex: Pax6 gene in mice & flies is a master regulator of eye development Clone: To make one or many new individuals that are identical to an original o Easy in most plants Cuttings can be rooted & grown Even single cells o Difficult in animals- only the egg cell can develop into an embryo/whole organism o Cloning animals: Nucleus from “target” individual is transplanted into enucleated egg Embryo grows with genome of transplanted organism Dolly, cattle, mice, but no humans or primates Stem cells: Unspecialized cells that can reproduce indefinitely & differentiate into specialized cells o Typical stem cell division in an adult generates 1 precursor cell & 1 stem cell Precursor cell divides & differentiates o Ex: Hematopoetic stem cells produce all of the blood cells o Stem cells are also present in embryos: Embryonic stem cells (ESCs) ESCs are pluripotent: capable of differentiating into any cell type o Adult stem cells: Generate precursors to differentiated cells (blood, skin, intestine, etc.) Unspecialized but not pluripotent: Blood stem cells make blood cells but not muscle, skin, liver, etc. o Therapeutic applications of stem cells: replace missing/damaged cells Neuron stem cells to repair spinal cord injuries Brain stem cells to cure Parkinson’s disease Pancreatic stem cells to replace insulin-synthesizing cells (type 1 diabetes) o Problem: The right stem cells are difficult/impossible to find o What makes a stem cell a stem cell? Expression of specific regulatory genes o Can differentiated cells be turned into stem cells? Yes, by expressing regulatory genes Results in induced pluripotent stem cells (iPSs) o Future medicine: Remove small # of patient’s cells Culture under conditions to induce or return to stem cell state (iPS) Induce iPS cells to differentiate into pancreatic cells Transplant cells into patient’s pancreas Chapter 21: Genome: The entire genetic content of an organism or virus o Animals have a nuclear genome & a mitochondrial genome o Plants have nuclear, mitochondrial, & chloroplast genomes Genome sequencing: o DNA sequences are obtained ~500 base pairs at a time o A chromosome is a DNA molecule hundreds of megabases in length o Shotgun strategy: Determine sequences of randomly- generated DNA segments. “Assemble” sequences into continuous linear sequences, 1 for each chromosome. o Assembling a genome sequence from short sequenced fragments is like assembling a paragraph from sentence fragments Messenger RNAs can also be sequenced (converted 1 into DNA: cDNA (cloning) sequences of mRNAs (called “expressed sequence tags”=ESTs) are used to search genomic DNA sequences & locate them on the map Gene annotation: o Identify genes o Determine expression features (transcription unit, introns, exons, etc) o Determine function by homology to other genes Genome sizes (amount of DNA per genome) differ in predictable & unpredictable ways: o Bacteria & archaea: 1-5 megabase pairs o Eukaryotes: Single-celled eukaryote (yeast): 12 Mb Invertebrates: 100-200 Mb Plants: 120-2300 Mb Mammals: 2400-3000 Mb o There are extreme outliers: Lungfish, newts, Japanese canopy plants, etc. o General increase in gene # w/ complexity But mammals have fewer genes than some animals & plants o As organisms get more complex, gene density goes down (genes per Mb) This is because complex genomes (mammals) have multigene families, more spacer DNA between genes, more & larger introns Complex genomes have multiple copies of some genes= multigene families o Most genes: 1 copy/haploid genome o Ex: Genes for ribosomal RNAs (dozens to thousands of copies) Genes for globins (1 copy each of several related proteins) Genes for histones (dozens to thousands of copies for each of the 5 histone genes) Multigene families arise through duplication & evolutionary divergence Ex: Globin gene family. Multiple unique globins suited to particular O2/CO 2oncentrations (embryonic, fetal, adult, etc.) Other vertebrates have related or intermediate patterns Pseudogenes: Defective genes produced by duplication & mutation Over 50% of the genome is coding in bacteria compared to 1.5% in the human genome Human genome: o 20% introns o 5% regulatory elements (Ex: Promoters & enhancers) o 58% repetitive DNA (present in multiple copies/genome) 44% of this is transposable elements: Viral-like DNA sequences that copy themselves into new 10 cations- genomic parasites Can move into new positions in the genome by 2 mechanisms. Most repetitive DNA in complex genomes is the 2 nd“copy & paste” mechanism Transposable elements encode the enzymes that catalyze movement A lot of non-coding DNA is repetitive DNA: DNA sequences found in multiple copies per genome Simple sequence DNA: Many tandem (adjacent & repeated after one another) copies of short sequences o Ex: CAGCAGCAG o Sequence lengths from 2 to a few hundred base pairs o Common in centromeric regions Genome evolution: o Comparison of genome sequences reveals how genomes have evolved o New genes originate from gene duplication, followed by divergence through the accumulation of mutations Ex: Globin gene family, lysozyme- a-lactalbumin o New genes also originate from exon shuffling: translocation events that paste together genes in imprecise ways. Splicing can assemble new mRNAs/proteins from haphazardly-arranged gene segments Large scale rearrangements in genomes: o Human & chimp chromosome sets are very similar Humans have 23 pairs Chimps have 24 pairs o Human chromosome 2 contains same genes as chimp chromosomes 12 & 13 o During divergence from ancestor, 2 smaller chromosomes fused into human chromosome 2 o Order of genes is conserved in mammals, suggesting multiple fusion/splitting events. Ex: Human & mouse o DNA sequences can reveal evolutionary relationships, which are depicted as branching “trees”, ex: Globin gene family 3 domains of life Human-chimp-mouse relationship All animals employ a universal set of regulatory genes (homeotic/HOX genes) Chapter 22: Evolution: Descent with modification (Darwin); Change in allele frequencies in a population over time Evolutionary biologists attempt to account for the existence, characteristics, & history of current & past living organisms Scientific theory: An explanation that accounts for observations & experimental results, sometimes in disparate fields o Theories are not proven, only disproven Naturalism: Natural principles are sufficient to explain natural phenomena unless there is evidence to the contrary o No assumption about the existence of God 2 aspects to Darwin’s theory: 1) Descent with modification: Organisms change over time o Summarized by Darwin, but not really his idea since this had been shown in fossils & already recognized by scientists 2) Natural selection (the explanation for why organisms change): Differential survival & reproductive success within the population o Adaptations allow some to compete better than others Adaptation: Inherited characteristic that allows differential survival & reproduction o Analogy: Breeding of domestic plants & animals (artificial selection by humans) Current status on theory of evolution: o No doubt on descent w/ modification o Natural selection is generally accepted but there are still some questions Evidence for evolution: o It can be observed directly Insecticide resistance, apple maggots, bacterial antibiotic resistance, etc. o Homology: Features w/ common ancestry Anatomical homologies: Limb bones in tetrapods Molecular homologies: Genetic code; gene & protein similarity Vestigial structures: Non-functional homologies (pelvis in snakes & whales; fibula in birds & horses; coccyx in humans; pseudogenes, etc.) Classification of organisms: Organisms are grouped according to shared homologies Evolutionary tree: Diagrammatic representation of evolutionary relationships Homology vs. analogy: Analogy: Feature w/ similar structure/function, but independent origin (Ex: Wings of insects or birds; lens proteins in vertebrates & mollusks) o Convergent evolution: 2 or more groups develop analogous specializations. Ex: Flying squirrel & sugar glider o Fossils: Preserved remains of dead organisms Fossilization usually occurs in aquatic environments & is rare; a small subset of organisms leave fossils Fossil age determined by age of strata in which it is found Radiometric dating Older fossils are less similar to living organisms that younger fossils Homologous structures can be identified in fossils Intermediate forms between existing & ancestral forms o Biogeography: Geographic distribution of living forms Similar organisms are more likely to be found close together Similarity of organisms in Africa/South America Flora/Fauna of new islands are most similar to closest continental land mass Chapter 23: Population genetics: The behavior of genes in populations Population: A local group of the same species that mate within & mate infrequently outside of the population Species: Organisms that are capable of mating w/ each other & producing fertile offspring o A species may be composed of multiple populations Genetic variation: Degree of genetic heterogeneity in a population o Many genes have 2 or more alleles. Individuals are heterozygous for many genes. o Existing genetic variation is the raw material for evolution Evolution occurs when certain alleles or combinations of alleles change in frequency Population genetics adds genetics to Darwin’s theory Hardy-Weinberg Theorem: o Describes static distribution of
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'