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BSC Test 3 & 4 study guide

by: madys70ss

BSC Test 3 & 4 study guide BSC 114

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Principles Of Biology I
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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


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