Genetics- key basis of modern bio Evolution- key basis of modern bio Physiology- how many functions Sociology-

how the organisms exist in population communities and ecosystems 1. 2. 3. 4. 5. 6. 7. Organism ( Three domains of life) Order Reproduction Growth and development Energy processing Response and environment Regulation Evolutionary adaption Bacteria Archaea Eukarya

-Protist -Kingdom Plantae -Kingdom Fungi -Kingdom Animilia

Prokaryote (bacteria)- a type of cell containing no membrane enclosed nucleus nor other membrane enclosed organelles. Eukaryote- a type of cell with a nucleus and membrane- enclosed organelles Ch.1 Evolution Fossils are common 1.

2.
3. Basic evolution -genetic variation for traits -based on the form of the traits they carry -change in the pop. Of genetic based traits EVOLUTION is the core theme of bio. All organisms have RNA Only viruses use R(resistance)

Population with varied inherited traits

Elimination of individuals with certain traits Reproduction of survivors

Ch.2 Compounds-organisms are compsed . Isotopes have the same number of protons but not the same number of neutrons The distribution of electron s determines an atoms chemical properties Oxygen Nitrogen Carbon Form the main components of molecules Hydrogen Outer electronic shell = valence shell. Determines the chemical properties of an atom Atoms share electron to fill the outer shell (2 in the first shell, 8 in each additional shell) CH4 CO2 Methane is non-polar Water is polar Question- What is chemically wrong? Answer- The compound does not meet the valence requirements of carbon Ionic Bonds H-C=C-H

-The transfer of electron can bond atoms together Ionic Bonds- attractions between ions of opposite charge Hydrogen Bonds are weak bonds -Hold two strands of DNA molecule together -Help create a proteins shape Chemical reactions do not create or destroy matter, they only rearrange it in carious ways C6H12O6 = Sugar 6CO2+6H20-> C6H12+02 = The breakdown of sugar by oxygen C6H12O6+ 6O2= 6CO2+ 6H20= Photosynthesis Water sticks Together Water heats up slowly and absorbs a lot of heat (energy) Hydrogen Bonds are stable in ice. In liquid, it constantly breaks and re-forms Solution- a liquid consisting of a uniform mixture of two or more substance Water is a Solvent The dissolving agent is the solvent ; the substance dissolved is the solute. pH is normally 7.4. I person cannot survive for a few minutes if the pH is 7.0 or 7.8 CO2 is the main product of fossil fuel combustion

Ch. 3 Big Ideas (Introduction to Organic Compounds) Organic Compounds= Carbon-based compounds Shape of molecules determine its biological activity -Isomers

Same molecular formula, but different shape and properties

Methamphetamine and a medicine for sinus decongestion

Testosterone Estradiol

Hydroxyl group Carbonyl group Amino group Phosphate group Methyl group

Chemical Groups (Functioning of Biological Molecules)

Enzymes- specialized macromolecules (PROTEINS) that speed up chemical reactions in cells Monosaccharaides- are the simplest carbohydrates (organic compound) -Simple sugars

Polysaccharides -Starch -Glycogen -Cellulose -Chitin Lipids-Fats made from glycerol (alcohol) and fatty acids Steroids- Lipids with 4 carbon rings 3.11 Proteins made from Amino acids Shape of a protein determines its function -Primary structure -Secondary structure -Tertiary structure DNA and RNA are types of Nucleic Acids DNA makes genes DNA make RNA makes proteins (on the RIBOSOMES) 3 class biological molecule -carbohydrates -enzymes

Cholesterol Steroids

Glucose (aldose), fructose (ketose)

-Unsaturated-fewer double bonds -Saturated- no double bonds

The sequence of amino acids Folding back on itself Overall form

Ch.4 Microscopes Cell theory- all living organisms are composed of cells and all cells come from other cells Electron microscope (EM) focuses a beam of electrons through a specimen r into its surface -cannot use to study living organisms Light microscopes can be used to study living organisms Large cells have more surface area than small cells, but have much less surface area Prokaryotes are bacteria. Have a nucleoid but no membranes surround the DNA Eukaryote cells have a membrane-enclosed nucleus Eukaryote cells are 10x larger than prokaryote cells Animal cells and plant cells are similar Primary function of RIBOSOMES?

-Protein synthesis Ribosomes make proteins for use in the cells and exports -Free ribosomes are found in the cytoplasm Chromatin=DNA+proteins Organelles Endoplasmic Reticulum Smooth ER does not have ribosomes Rough ER has ribosomes S.ER makes many kinds of compounds (lipids and steroids) R.ER makes membranes (Phospholipids) Makes proteins (ribosomes are attaches) Endocytosis is a machinery for cellular receiving and shipping Peroxisomes- metabolic compartments that do not arise from the endomembrane -Can break down fatty acids used for fuel and can detoxify Mitochondria harvest chemical energy from food Cilia are smaller than flagella Cell Junctions There are 3 types of junctions found in animal tissues

Adhere, interact, communicate Ch. 5 Osmosis- the diffusion of water across a membrane Solute molecules dissolved in water Tonicity- the ability of a surrounding solution to cause a cell gain or lose water Isotonic- when there is no net gain or loss of water Hypertonic- when there is a net loss of water Hypotonic- when too much water comes in and the cell can burst Osmoregulation- is the control of water balance Plant cell is better off under Hypotonic conditions Wilting is caused by Hypertonic condition Aquaporin- a protein channel that facilitates the entry of water into plant cells, kidney cells, red blood cells -a single Aquaporin allows the entry of 3 billion water molecule per second Cells Transform Energy As The Perform Work Forms of Energy Kinetic energy is the energy of motion -Moving objects can perform work by transferring motion to other objects Potential energy is energy that matter possesses Chemical energy - potential energy available for release in a chemical reaction Exergonic reaction releas e energy Endergonic reaction yields energy Every working cell produces thousands exergonic and endergonic reactions The total of the cellular reaction is called metabolism Metabolic pathway is a series of chemical reactions that builds or breaks down complex molecules Cellular Respirations slowly releas es the metabolic potential of energy stored in sugar DNA is a macromolecule most similar to ATP

Tight Junctions-plasma membranes seal and prevent leakage of molecules Anchoring junction- acts like rivets holding cells together Gap Functions- are channel that allow small molecules to flow through protein-lined pores

Enzyme Inhibitors -A chemical that interferes with an enzymes activity is called an inhibitor -Competitive Inhibitor -Blocks the Active site (substrate fits) -Non-competitive inhibitor -Allosteric site is where the inhibitor acts (shape changer) Inhibitors as Regulators Feedback inhibition- if a cell produces more of a product than it needs, the product may act as an inhibiter of an enzyme early in the pathway -A pathway is a series of enzyme-mediated steps that products for cells Ch.6 (How cells harvest chemical energy) Photosynthesis- and cellular respiration provide energy for life Cellular Respiration uses glucose and it produces non-energy molecules CO2 and water and the energy molecule ATP Cellular respiration: Glucose + O2 produces CO2 + H2O ATP + heat 37% vs. 25% -Cell vs. automobile energy capture efficiency The human brain consumes a high proportion of activity -A very metabolically active tissue Oxygen strongly attracts electrons Redox reaction-the gain of electrons is reduction and the loss of electrons is oxidation NADH and electron transport chains NAD+ -A coenzyme (a cofactor) When reduced NAD+ becomes NADH Electronic transport chain The transfer of electrons is organic The final electronic acceptor is oxygen and water is produced Stages of cellular respiration There are three main pathways -Glycolysis -Pyruvate oxidation and the citric acid cycle -Oxidative phosphorylation - Breaks glucose up into two molecules with 3 carbons each -Pyruvate Process captures energy as ATP molecules Takes place in the cytoplasm (cell fluid outside of the nucleus) - Completes the breakdown of glucose to carbon dioxide Takes place in the MITOCHONDRIA Generates energy - The main function of the GYCOLYSIS and ACID OXIDATION Produces a lot of ATP -Reduction and oxidation always go together therefore redox

Ch. 8 Cellular Basis of reproduction and inheritance Cell division-where a cell divides to reproduce. Genetically identical daughter cells Binary fission steps The DNA is duplicating and moving toward the ends of the cell The cell elongates DNA duplication is complete and the cell has grown about 2x Divion and separation Chromosomes Humans have 46 (2N) Dogs have 78 Interphase is when cell metabolic activity is high and the cell performs its various functions -makes more cytoplasm, organelles, proteins and grows -Chromosomes duplicate

Proteins incorrectly folded can cause serious health problems Alzheimers and Parkinsons are caused by an accumulation of incorrectly folded proteins -No test problem from Ch.8 -Bring Pencil Wednesday.

Locus the position of a specific gene on a chromosome Stages of Mitosis Interphase DNA has duplicated Mitosis

Mitosis the duplicated _chromosomes _ divide and separate Cytokinesis the cytoplasm divides and two cells are formed

Prophase chromosomes condense

Prometaphase spindle fibers (microtubules) attach to chromosome kinetochores and push chromosomes to a central plane Metaphase chromosomes lined up on metaphase plate Anaphase centromeres split and duplicated chromosomes move apart ___metaphase___ plate Stage finished when chromosomes reach cell poles

Cytokinesis differs for plant and animal cells. Myosin is an ATP-dependent motor protein (muscle movement) Growth Factors signal the cell cycle control system Cancer Tumor-mass of cancer cells -Benign tumor -Malignant tumor Carcinomas Sarcomas Leukemias Cancer treatment -Surgery -Radiation -Chemotherapy Mitosis, Meiosis -prophase -metaphase -anaphase -telophase and cytokinesis Animal -Metastasis-spread of cancer beyond the original site Drugs that block specific steps in the cell cycle

Telophase nuclear envelopes surround sets of chromosomes Cytokinesis (animal) cleavage furrow is formed and cell divides

Meiosis-related vocab Homologous chromosomes two chromosomes, one of paternal origin, the other of maternal origin, that are identical in appearance and pair during meiosis Somatic -Diploid- an organism or cell having double the basic haploid number of chromosomes Germ line -Gametes - a mature sexual reproductive cell, as a sperm or egg that unites with another cell to form a new organism. (Have a single set of chromosomes) Fertilization produces a zygote -Haploid- pertaining to a single set of chromosomes How plant cells can grow Two type of cell wall

-Primary- Changes easily -Secondary -like concrete (rebar in concret e)

Meiosis reduces the chromosome number from diploid to haploid. Interphase-chromosomes duplicate Prophase I- chromosomes coil an pair -Synapsis- homologs pair -Crossing over- symmetric pairing and cross wise exchange -Metaphase I- tetrads aligned on the metaphase plate -Annaphase I- homologs separate Meiosos II- same as mitosis except that every cell starts out as a haploid Mitosis and meiosis have important similarities and differences Independent orientation of chromosomes in meiosis and random fertilization lead to varied offspring Allele- an alternate form of the gene Homologous chromosomes may carry different versions of genes Ex. Differing genetic info (coat color and eye color) on homologous chromosomes Crossing over further increases genetic variation (recombination) Chiasma- the site of crossing over -The visible manifestation of crossing over Symmetrical pairing and crosswise exchange -Breakage at the same place of homologous chromosomes Genetic recombination Recombinant chromosomes have gene (allele) combination different than the parental chromosomes

-Reduction division

Karyotype- (a photographic inventory of an individuals chromosomes) an ordered display of the magnified image of an individuals chromosomes arranged in pairs Chromosome 21 is one of the smallest chromosomes An extra copy of Chromosome 21 causes Down syndrome (Trisomy 21) Down Syndrome increases rapidly with maternal age Human females are born with all the eggs they will have in their life The eggs are frozen in prophase I -The old egg hypothesis Nondisjunction- the failure of chromosomes to separate properly

Sex chromosomes play a key role in sex determination -In humans males are XY females are XX -The X and Y homologous even though there is a lot of difference between them ( 9-23-11) Ch.9 patterns of inheritance Historical Background-(Mendels Laws)-Punnett square (same as lab) Heritable factors are discrete Heredity; transmission of traits from one generation to the next Genetics ; the scientific study of heredity Character; an inheritable feature that varies among individuals Inbreeding; mating between close relatives Complete dominance: progeny display parental phenotypes Mendels Laws Alleles- alternative versions of genes (genetic embodiment of traits) and allow variation of sa character. An organism inherits two alleles, 1 from each parent for every character If alleles differ, one is dominant and one is recessive Genotype- genetic component of a trait Phenotype; appearance of a trait Sperm and egg each carry 1 allele per character= Law of segregation Heterozygotes : different alleles Homozygous: identical alleles Independent Assortment = 2 monohybrid crosses Dependent (inheritance) assortment data did not support; hypothesis refuted. (Dont observe) RrYy = RY,Ry,rY,ry Wild-type traits- traits most prevalent in natural populations Pedigree- Display inheritance of a trait, show dominant or recessive, can determine genotype of family members First generation (grandparents) Second generation (parents, aunts, and uncles) third generation (two sisters) Many inherited diseases controlled by single gene Recessive- needs 2 alleles for disease Heterozygot es- carries Amniocentesis and Chorionic villus sampling -karyotyping and biochemical tests Ultrasound imaging -visual examination for anatomical defects Variations on Mendels Laws Mendels peas displayed Complete Dominance -One allele always dominant Neither allele is dominant? -Incomplete dominance -Co-dominance

- Neither allele is dominant nor does expression of both alleles occur Hypercholesterolemia: very high blood cholesterol levels Expression of both occurs - Expression of both alleles produced a heterozygote distinct from either homozygote Still supports Mendels conclusion Sickle-cell alleles are co-dominant, confer malaria resistance Pleiotrophy- one gene influence multiple a Polygenic inheritance- one phenotype character results from combination of several genes. -Skin color is influenced by multiple genes Chromosomal basis of inheritance Linked genes: gene located close together on same chromosome- typically inherited together Crossing over produces new allele combinations Recombination Frequency measures relative distance between linked genes greater distance between genes- higher likelihood of recombination Ch. 10 Virus life cycle -Viruses -Herpesviruses -Life Cycle

-Cold sores, genital herpes, chicken pox amd other human viruses -virus enters cell -Virus DNA goes to the nucleus -Once activated , virus takes over the cells molecules -Cell lysis?

Bacteriophage -bacteria eaters (Lytic life cycle) 1940s What is hereditary material? Edwin Schroedinger- German physicist

Hershey- Chase Experiment They labeled one sample of T2 phage with radioactive sulfur and a different sample with radioactive phosphorus Phosphorus is found in DNA, but not protein Sulfur is found in protein, but not DNA Structure of DNA? Made up of nucleotides Nucleic acids (DNA, RNA) -Nucleotides

-Phosphate -Sugar (deoxyribose) -Bases (-nitrogenous) A=,T, G=, C (in DNA) (hydrogen bond in chemical structure) DNA Polymer (Repeating Units) A phosphodiester bridge attaches adjoining nucleotides. -DNA has a covalent sugar-phosphate backbone Double Polymer (Double Helix) Watson and Crick- model of DNA Rosalind Franklin- x-ray image of DNA crystal um Hydrogen bonds hold the DNA polymers together to form a duplex About 3% the strength of a covalent bond -There are many hydrogen bonds in a DNA duplex The different polymers of DNA have a reverse polarity -5 phosphate end -3 hydroxyl end DNA replication -DNA reproduces itself -semi-conservative replication AT CG GC AT TA

-Attaches a sugar to the adjoining phosphate group

parental molecule

Replication Components -Parental DNA molecules -Daughter DNA molecules -DNA Polymerase (enzyme) -DNA ligase

-makes DNA

-Links pieces of DNA Process -DNA unwinds -DNA daughter molecules are made sometimes in short stretches -DNA is only synthesized 5 to 3 DNA to RNA to Protein -Central Dogma -Transcription -Making RNA -Nucleus -Translation -Making protein -Cytoplasm -Protein is the basis of many functions and structures in the cell Codon- three RNA bases in a row -mRNA conveys info for translation

-mRNA is a messenger RNA -One codon, for methionine, is responsible for an amino acid and a start signal Template- the strand of DNA that codes for RNA -Only one strand of DNA serves as a template RNA polymerase synthesizes the RNA from DNA Initiation -Unwinding of DNA and attachment of RNA polymerase to the DNA -start of transcription Elongation Termination What does following mRNA code AUG Met or start ser-arg -asp-stop-phe-leu???? (memorize start and stop codons) UCU AGA GAU UAA UUU UUG

Review of Ch.10 Material Process of Replication- needs to split to replicate -Leading strand, lagging strand and ligase -Polarities Process of transcription -3 steps -Initiation, elongation, termination Translation -Genetic code Transfer RNA molecules serve as interpreter during translation RNA is like DNA. 2 chemical differences -2 hydroxyl on the sugar Base Thymine has 1 ring. 2 hydrogen bonds between A and T 3 hydrogen bonds between G and C Uracil- 1 ring like thymine Base, sugar, phosphate= DNA and RNA Deoxy ribose (sugar) 3 types of RNA are needed for translation -mRNA (messenger) -tRNA (transfer RNA) -rRNA( ribosomal) - Uracil which similar to thymine DNA

-Uracil

-DNA has only a 3 prime hydroxyl sugar

Rings T=1 A=2 C=1 G=2 RNA can form secondary structures (can fold back on itself) -folds back on itself in regions of complementary bases RNA is present as only one short strand -NO double helix Has Uracil in it instead of Thymine No duplex in RNA just single short strand Key features of tRNA -Shape -Anticodon loop -Amino acid attachment site Carrier specific amino acids and are detectors of information on codons Transfer RNA molecules serve as interpreters during translation -Anticodon- Three bases in the anticodon are complimentary to one of the codons -Specific amino acid attachment site 20 enzymes for each amino acid Family of Enzymes that contributes to tRNA function -family of enzymes that has 20 different varities of an enzyme -There are a total of about 20 amino acids on earth -Each enzyme attaches a specific enzyme to a tRNA based on its anticodon ATP supplies energy Cellular respiration is where ATP comes from Ribosomes build polypeptides 3 essential components for translation Ribosomes tRNA mRNA Initiation steps -a mRNA binds to the small ribosomal subunit The signal the two subunits to come together Elongation -Codon recognition-knows what amino acid to add next -Peptide bond formation -Translocation - transfer _________________________________________________________ The Central Dogma Transcription is making of RNA from a DNA template Translation is making of protein from info in the mRNA Mutations can change the meaning of genes Mutation- any change of the nucleotide sequence of DNA -Nucleotide substitution -Indels- insertions or deletions Types of Mutation -Missense mutation- a change results (sub.) in a different amino acid -Nonsense mutation- changes an amino acid codon into a stop action -Mutation in DNA causing a change in the AGA (arg) codon and changing it into a UGA (stop) codon Insertions or deletions -Consequences of indels can be serious because they can change the reading frame Reading frame- the normal order of codons Spontaneous mutations arise through errors in replication or crossing over Mutations are agents that cause mutations -UV light -Radiation -Chemicals Emerging viruses are health threats that appear suddenly -HIV, Ebola, SARS Three processes contribute to the emergence of human disease viruses -Mutation -Viruses from other species -Spread from isolated populations AIDS virus makes DNA on an RNA template AIDS is caused by the HIV virus -Hereditary nucleic acid in HIV is RNA Reverse transcriptase -Makes DNA from RNA HIV life cycle The DNA made by HIV goes into the nucleus and inserts itself in the host chromosome becoming a provirus HIV infects and kills white blood cells Bacteria can transfer DNA in 3 ways -Transformation -Transduction -Conjugation

-RNA viruses lack DNA replication proofreading mechanisms -SARS -H1N1 -AIDS was unnoticed for decades

-Flow of genetic info is backward

-Fragments of DNA from other bacteria are taken up -A virus transfers DNA from one bacteria to another

-Transfer of DNA from one cell to another by an F factor DNA has to be incorporated into the host chromosome A plasmid is a small circular double strand DNA molecule -in the bacteria, but not integrated into the chromosome -integrated into the bacterial chromosome R(resistant) plasmids- are a serious human health hazard Ch.11 Operon -Cluster of genes -The lac operon produce beta-galactosidase and related enzymes Promoter -The DNA site to which the RNA polymerase attaches for transcription Operator DNA control sequence Regulatory gene -Produces the repressor protein Other types of operon -Trp operon

-An activator Eukaryote gene expression DNA packing -DNA must be packaged. Its a thousand times longer than the diameter. Packaged during condensation during meiosis and mitosis Nucleosome- DNA wound twice around an octamer of 8 histone proteins High gene expression=high levels of mRNA and protein produced Low gene expression= low protein and RNA Eukaryotes can chemically modify chromosomes to change level of gene expression 8 proteins in the nucleosome=Histone EP INHERITANCE (10/3/11) class 17 Eukaryote Gene Gene expression control determines the amount of mRNA and protein Levels of control (Control of Eukaryote gene expression) -DNA packing -Epigenetic modifications -Transcription factors and DNA elements (TATA binding protein) TATA box is the TBP binding site near the gene transcription TBP is the protein that serves as an anchor for many transcription factors that control gene expression -Small RNAs (MicroRNAs (miRNA) ) Play multiple roles -Post-transcriptional regulation Antennapedia , legs instead of antennae, in Drosophila melanogaster -Mutations in hox genes Signal transduction pathway -A series of molecular changes on a cells surface to a specific response in the cell Cloning Differentiated means cells that have mutated from the zygote to the adult stage -Differentiated cells express only a small % of genes Nuclear transplantation can be used to clone animal cells Cloning experiments first performed in the 1950s Post-blastocyst cloning strategies -reproductive cloning -Therapeutic cloning Therapeutic stem cell cloning- supply cells for repair of damaged or diseased organs Cancer is caused by multiple mutations in genes that control cell division Oncogene- a gene that is predisposed to cause cancer Proto-oncogene - have normal cell function inclu. Coding for growth factors, stimulation of cell division, affect growth factor function Tumor suppressor genes produce proteins whose normal function is to inhibit cell division p53 Carcinogens are cancer- causing agents that alter and make cells cancerous

-Multiple aspects -Fund. Development pathway genes that play a similar role in animals

Ch.12 DNA Technology and Genomics Genes can be cloned in recombinant plasmids Recombinant genes : combination of DNA from 2 different sources Plasmids: small circular DNA molecules that can replicate separately from the host bacterial chromosome -Plasmids can be used for gene cloning Gene cloning: the production of multiple identical copies of a piece of DNA Restriction enzymes: enzymes that cut at a specific DNA sequence DNA ligase: joins two adjoining nucleotides by covalent bonds (UNDERSTAND CELL-BASE CLONING ) (FIGURE 12.1B) 1. Plasmid is isolated

2. 5.
3. 4. Recombinant DNA utility

The cells DNA is isolated The plasmid is cut with an enzyme The cells DNA is cut with the same enzyme

Combination of the 2. Ligation (The targeted fragment. (disneycollegeprogram )

Gene use -A gene for pest resistance is inserted into plants -altered bacteria for cleaning up toxic waste

Protein use

-A protein is used to make stone washed genes -used to dissolve blot clots in heart attack therapy Enzymes ate used to cut and paste DNA In nature, restriction enzymes protect bacterial cells from other organsims such as viruses Each restriction enzyme is specific for a different short DNA sequence -4 to 8 bases

-Each sequence (/DNA location) which will be cut is called a restriction site -Double strand cut cDNA is complementary DNA -Complementary to mRNA Eukaryotic genes are split -Alternating coding and non- coding DNA regions -Coding=exons -Non-coding=introns Pilobolus-group of amebae Libraries and Probes -cDNA library - a represent ative collection of all of the cDNAs in the genome -Probe- a labeled nucleic acid used to identify specific sequences in the genome and find specific sequences in a library ( used to sent out to investigate something in space,) -Single stranded DNA (Radioactive nucleic acid probe) Recombinant cells and organisms can mass-produce gene products Laboratory culture: bacterium, yeast, mammalian cells Whole organisms: Insect viruses in insects, mammals Genetically modified organisms are transforming agriculture GMO: Genetically Modified Organisms The most common plant vector(agent for carrying recombinant gene) Is the Ti plasmid from a soil bacteria species GMOs raise concerns about human health and environmental health -The Biosafety Protocol requires identification of GMOs -Growing GMOs near wild relatives could result in spread of recombinant genes -Pollination -Resistance (super weed with herbicide resistance or insect resistance) Gene therapy may someday help treat a variety of diseases Somatic gene therapy: in somatic cells Bone marrow cells multiply throughout life Germ line gene therapy: change in the heritable DNA SCID Severe combined immunodeficiency disease 2000, a gene trial

10 young children treated

9 showed improvement 3 developed leukemia

DNA profiling: the analysis of genetic markers can produce a DNA profile

The vector caused mutations

Forensics : the scientific analysis of criminal evidence

DNA profiling: the analysis of DNA samples to determine whether they came from the same person

PCR is used to amplify DNA sequences

Polymerase chain reaction (PCR) : target s a specific section of DNA and amplify it in the laboratory (A polymerase is an enzyme whose central function is associated with polymers of nucleic acids such as RNA and DNA. The primary function of a ..)

PCR steps repeated 25-35 times to amplify DNA 1. heat denaturation of target DNA

Separation of DNA strands Typically at 95 degrees C

2. renaturation of DNA strands allows primers to anneal to target DNA

Components of PCR in a tube->target DNA, Enzyme, (DNA pol) Gel electrophoresis separates DNA molecules by size Gel electrophoresis PO4 Positive and negative poles

Primers are short (15 20 bp) pieces of DNA complementary to target DNA 3. Amplification of new strands of DNA by a thermo- stable ________ polymerase TAQ

Gel electrophoresis: DNA is run through a polymer gel emersed in buffer to separate fragments by size Typically, the gel is made from a seaweed carbohydrate polymer The polymer acts as a molecular sieve

Mobility of large and small DNA fragments Visualization

EtBr (ethidium bromide) and UV light

STR analysis is commonly used for DNA profiling Repetitive DNA: core nucleotide sequence present in multiple copies Short tandem repeats (STRs)

Scattered throughout the genome

Different sequences in different genome locations (loci) 13 different STR sites is the standard for DNA profiling

Genomics is the study of all genes

Ch.13 Darwins Theory of Evolution

Antecedent ideas -Aristotle viewed species as permanent and perfect

Darwin (born 1809, same day as Lincoln)- naturalist at heart, but was sent to medical school (Voyage of the Beagle) Artificial Selection- process which humans have modified many species by selecting for traits are valuable -Genetic changes Natural SelectionReview Cell division-when a cell divides to reproduce -Daughter cells are genetically Asexual and sexual reproduction Chromosomes-DNA associated proteins Mitosis(metaphase, Anaphase, Telophase and Cytokinesis) Meiosis homologous chromosome, somatic cells, germ line Cancer Allele-alternate form of the gene Crossing over- Chromosomal crossover-(exchange of genetic material between homologous chromosomes) changes the relationship Karyotype- ordered display of the individual chromosome Patterns of Inheritance Monohybrid Cross-genetic cross between 2 individuals with Heterozygous-identical alleles Aa x Aa Homozygous-different alleles AA x aa Linked Genes-genes closes together on same chromosome Structure of DNA Code, (Codon) AUG-Start UAA,UAG,UGA-Stop tRNA Transcription Translation

10/19/2011(Ch.13-Evolution) creatively How populations Evolve (apple sauce, brown sugar, green tea, olive oil)

Population genetics -If there are two alleles, the frequency of one allele is p and the frequency of the other allele is q When there are two alleles (p=A, q=a), then three genotypes are possible AA (homozygote) Aa (heterozygote) aa (other homozygote)

Hardy-Weinberg equilibrium frequency of genotypes book ch.13.9 P=A=.7 q=a=.3 Mechanisms of microevolution (p.268-269) -Natural seletion genetic drift and gene flow can cause evolution -Natural selection: some genotypes survive better and produce mote off spring Natural selection is the main mechanism causing adaptive evolution. -by favoring some alleles over others, natural selection improves the match between organisms and their environment. The environment can change over time. Genetic drift: a drastic reduction in population size can cause a bottleneck which is a chance change in allele frequency. Gene flow is when individuals move from one population to another -If the populations have different allele frequencies, the frequencies can change Relative fitness Natural selection Ch.14 origin of species Defining species and mechanisms of speciation Biological species- organisms that freely interbreed Species can be isolated by habitat. That prevents some interbreeding. I.e. polar bear and grizzly (hybridization between two species of bear) -***Prezygotic barriers prevent mating -Environment *Class 23, 10/24/11 Biological species concept -Individuals that can interbreed establish a biological species -Those individuals that cannot interbreed belong to a different species Prezygotic isolation- Before formation of the zygote
Prezygotic barriers -Habitat (water, land) -Temporal (hot, cold) -Behavioral -Mechanical (genitalia) -Gametic Examples -Meadowlarks -Spotted Skunks -Blue footed -Snails -Sea Urchins

Postzygotic barriers -Reduced hybrid viability- offspring survival to the adult stage -Hybrid breakdown- enviable offspring -Reduced hybrid fertility- offspring with reproductive problems Ex. Horse + Donkey=Mule = Reduced hybrid fertility *Allopatric- Separated populations Reproductive barriers when natural populations are separated Sympatric- together fatherland (population are not isolated) Polyploidy- more than 2 sets of chromosomes Most plant species trace their origin to polyploid speciation

AB initially sterile- prepares in meiosis Sympatric speciation can be with Adaptive radiation- evolution of many diverse species from a common ancestor Genotype of the initial hybrid cell A1 A2 A3 A4 A5 B1 B2 B3 B4 B5 -Mitosis is possible -There are no homologs present -Cells can no undergo meiosis How meiosis becomes possible in hybrid cell lineages The species hybrid cells (A and B genomes) have no problem in spreading as th plant grows via mitosis. Hybrid zone provide opportunities to study reproductive isolation -Happens when separated populations of closely related species come back into contact with each other= Hybrid zones Reinforcement can occur in hybrid zones Ch.15 Tracing evolutionary History Where did life begin? The earliest fossils (stromatolites) are approximately 3.5 billion years old Stromatolites are large clumps of photosynthetic bacteria Formation of protocells When lipids are mixed with water and clay, lipid sacs can form Macroevolution-origin prokaryotes Origins of single-celled eukaryotes-oldest fossils are about 2.1 billion years old Origin of multicellular eukaryotes Radioactive isotopes with longer half lives are used to date older fossils andgeological strata in which the fossils are embedded The geological record Three era phases each with subdivisions -Paleozoic: fossils contain organisms -Mesozoic: age of reptiles (dinos) genitalia -Cenozoic: phase of evolution of mammals, birds, and insects Plate tectonics Consequences of continental drift -Altered physical features -Modern continents formed -Continents continue to drift and the Himalayas are growing (1 cm per year) Plate tectonics may imperil human life Extinctions are caused by habitat change, climate change, and changes in biological community

Two Mass extinctions -Permian Monotremes Marsupials (kangaroos, koala=) Eutherians (zebra, bear, rats) The history of life is characterized by radiations of many species that followed adaptation Evo-devo is the study of the evolutionary devel. Genetics paedomorphosis (the retention in adults of characters were juvenile features in an ancestral species) Adaption- changes in gene regulation (Pg. 307) Hyracotherium (ancestral horse) Equus (modern horse) Evolutionary trends -Species selection can result in a trend -Nat. selection can result in a trend If conditions change, a trend may revers itself Phylogeny: the evolutionary history of a species or group Fossil record *Homologies are similarities due to shared ancestry Homologous structures may look different and function differently in different species Analogies, convergent evolution -Look alike but no common ancestry (unrelated) Systematics is a discipline that focuses on classifying and naming species Cladistics: a widely used method in systematics A clade is a group of species that includes an ancestral species Shared ancestral character: the backbone originated in ancestor of all vertebrates Shared derived characters: shared by a group, but not found in ancestors Molecular systematics: using DNA sequences or other molecules to infer relatedness 3 domain system Bacteria Archaea Eukaryotes 81-90 Ch.20 Muscle

Ch.21 Food processing occurs in four stages -ingestion -digestion -absorption -elimination Chemical digestion -The breakdown of large organic molecules to their components The human digestive system Alimentary Canal oral cavity, stomach, esophagus, small and large intestines Accessory glands saliva glands, gall bladder, liver, pancreas Spincters- muscular valves that regulate the passage of food in and out of stomach 1-2 hours in the stomach 5-6 hours in the small intestine 12-24 hours in the large intestine Peristalsis- moves food through the esophagus to the stomach Mucous protects from acids prevents gastric juice from digesting the lining of the stomach The esophagus and stomach are normally separated except when food passes into the stomach. GERD= gastro esophageal reflux disease Gastric ulcers are open sores of the stomach Small intestine is the major organ of chemical digestion and nutrient absorption Break down of starch begins in the mouth and breakdown of protein begins in the stomach. The rest begins in the small intestine Sources of enzymes and bile- pancreas (E), liver(B), intinal intestinal wall Large intestine reclaims water and has other functions