Intro to Biology Exam 2 study guide PDF

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Professor Rami Alsaber's Intro to Biology core class...

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Core: Intro to Biology

Prof. Rami Alsaber

_____ Exam #2: Study Guide

Lecture 6: Human Evolution How did humans evolve? 

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Some early primate adaptations for life in trees were inherited by humans o Binocular vision provided early primates with accurate depth perception o Early primates had grasping hands o A large brain facilitated hand-eye coordination and complex social interactions The oldest hominid fossils are from Africa The earliest Australopithecines could stand and walk upright Several species of Australopithecus emerged in Africa The genus homo diverged from the Australopithecines 2.5 million years ago The evolution of homo was accompanied by advances in tool technology o Next figure: representative hominid tools Neanderthals had large brains and excellent tools Modern humans (Cro-Magnons) emerged only 150,000 years ago o Paleolithic burial o The art of Cro-Magnon people Cro-Magnons and Neanderthals lived side by side Several waves of hominids emigrated from Africa o There are several competing hypotheses for the evolution of Homo sapiens  The :African replacement” hypothesis suggests that H. sapiens evolved in Africa, then migrated throughout the Near East, Europe, and Asia, displacing the other hominid species that were present in those regions  The “multiregional” hypothesis suggests that populations of H. sapiens evolved in many regions simultaneously from the already widespread populations of H. erectus The evolutionary origin of large brains may be related to mutation in genes that affect the size of jaw muscles The evolutionary origin of human behavior is highly speculative The cultural evolution (Memetic Evolution) of humans now far outpaces biological evolution

Lecture 7: Classical Genetics Patterns of Inheritance 

Theories before Mendel o Blending inheritance: offspring are simple mixing of the parents’ traits forming an intermediate appearance

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o Many problems! Some important concepts that Mendel did not know o Genes are carried at specific locations on chromosomes called loci o A given gene can come in several alternative forms: alleles  e.g., A, B, O blood groups  Eye color alleles o Adults have two copies of each gene carried in homologous chromosomes  Homozygous: both copies identical  Heterozygous (hybrid): two copies are different How did Gregor Mendel lay the foundation for modern genetics? o Mendel’s experimental design was well planned. o Pea plants were a good choice.  Reproductive structures enclosed within petals  This normally prevents cross-pollination Mendel artificially caused cross pollination  Self-pollination is normal, simplifying self-crosses  True-breeding varieties were already available o Mendel chose to examine single traits individually. o Mendel followed traits through several generations. o Mendel applied numerical analysis to his data.  He made ratios and took averages. Monohybrid Crosses o Experiments with flower color: purple and white true-breeding plants  Parental generation (P):  One parent true-breeding purple; other true-breeding white  Offspring: first filial generation (F1)  All were purple  Somewhat consistent with blending inheritance; but Mendel continued  Self-fertilized F1 generation to produce F2 generation  White flowers reappeared among the F2 blending refuted  About ¾ purple and ¼ white o White trait had “receded” into background; recessive o Purple trait had “dominated” white: dominant Mendel explains his results o Pairs of physical units in each individual determine the trait (on homologous chromosomes) o Pairs separate during gamete formation  Each gamete receives only one of the physical units (one allele for each gene) = Mendel’s Law of Segregation of alleles

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 Laws of chance determine which gametes get which allele o Paired condition is restored at fertilization o Dominance: one allele can mask expression of the other (capital case representation)  Explains why all F1 flowers were purple  Other allele is recessive (lower case representation) o True-breeding plants: homozygous o Hybrids: heterozygous o Chromosome behavior in cell division actually reflects Mendel’s explanation. o Genotype is the combination of alleles carried by an individual. o Phenotype is the appearance. o Punnett square: method for following alleles during cross  Genotypes of gametes are row and column headings  Cells represent the possible individuals  Can use to calculate probabilities o Can use Mendel’s hypothesis to predict results for other crosses  Test cross: cross dominant phenotype to recessive  Can determine genotype of dominant individual  Mendel’s hypothesis can be used to predict the outcome of new types of single-trait crosses Mendelian Genetics o How are multiple traits inherited?  Mendel hypothesized that genes on different chromosomes are inherited independently How are multiple traits on different chromosomes inherited? o Mendel’s Law of Independent Assortment  Crossed plants differing in two traits: seed color and seed shape  F1 individuals all showed dominant trait for each gene  F2: 9:3:3:1 ratio among offspring  Consistent with each trait being inherited independently o Events of meiosis explain independent assortment How are multiple traits on the same chromosomes inherited? o Genes on the same chromosome tend to be inherited together  Such genes are said to be linked  Do not assort independently  F2 ratio deviates from 9:3:3:1 o Example: flower color and pollen shape in sweet peas o Recombinant genotypes are explained by events during meiosis

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If linkage were always complete, no recombinants types would appear in F2  Crossing over during prophase I explains recombinants  The closer two loci are, the more rare recombinants are: chromosome mapping How is sex determined? o Sex chromosomes  Differ significantly from autosomes  Females have two X chromosomes, males one X and one Y  True of mammals and some insects; other patterns occur  Y is much smaller than the X  These pair up during prophase; act as homologues  Sex chromosome carried by sperm determines sex How are sex-linked genes inherited? o Sex-linked genes  Genes carried on X- or Y- chromosomes (we consider X only)  Few genes on Y- mostly for sex determination  Males carry only one copy of genes on X chromosome  They will always express a recessive sex-linked trait  Inherit traits from their mothers  Patterns of sex-linked inheritance  Differ between males and females  Fruit fly eye color example

Lecture 8: Human Genetics 

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What are some variations on the Mendelian rules of inheritance? o What if Mendel chose different genes?  Review assumptions of Mendel:  Traits are controlled by a single gene  There are two alleles for each trait  One allele is completely dominant over the other  There are other possibilities Incomplete dominance o Incomplete dominance: intermediate phenotypes in heterozygotes  Snapdragon example  Biochemical explanation: activity of enzyme in pathway Multiple alleles o A single gene may have multiple alleles  Many examples: eye color in fruit flies, Marfan syndrome  Example: human ABO blood groups

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 Six possible genotypes  Both A and B are dominant to O (codominance)  Biochemical explanation: antibodies to cell-surface antigens Polygenic inheritance and pleiotropy o Many traits are influenced by several genes polygenic inheritance  Many genes contribute to a single trait  Example: grain color in wheat, eye color in humans o Single genes affect more than one phenotypic trait Pleiotropy  Example: SRY gene (sex determination), Melanin gene (albinism) Influence of the environment o Example: Himalayan rabbit fur color o Many traits probably influenced by environment (IQ, skin color, etc.) How are human genetic disorders investigated? o It is unethical to perform experimental crosses on humans o Analyze inheritance patterns in families: pedigrees  Family pedigrees: family history of disease o Molecular Testing: DNA analysis of parents can identify disease genes How are human disorders caused by single genes inherited? o Some disorders are recessive  Must be homozygous to have condition  Heterozygotes are called carriers  Examples: cystic fibrosis, albinism  Sometimes heterozygotes have mild form of disease  Example: sickle-cell trait o Sickle-Cell Anemia is caused by a defective allele for hemoglobin synthesis o Some are caused by dominant allele (e.g. Huntington’s Disease) o Some disorders are sex-linked  Will be expressed in males more often than in females  Frequently skip generations  Examples: red-green color blindness, hemophilia How do errors in chromosome number affect humans? o Some genetic disorders are caused by abnormal numbers of sex chromosomes  Effects of nondisjunction of the sex chromosomes during meiosis o Can result in an aneuploid: individual whose chromosome number is greater or less than normal o Polyploid: organism or cell containing three or more sets of chromosomes  Occurs due to a cell division error  Frequently seen in plants, rare in animals  Can have advantageous results

o Genetic conditions caused by abnormal numbers of sex chromosomes  Turner Syndrome (XO)  Trisomy X (XXX)  Klinefelter Syndrome (XXY)  XYY Males o Some genetic disorders are caused by abnormal numbers of autosomes  Trisomy 21 (Down Syndrome)  Down Syndrome frequency increased with maternal age Lecture 9: DNA DNA: The Molecule of Heredity 

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How did scientists discover that genes are made of DNA? o Transformed bacteria revealed the link between genes and DNA  1920s: Griffith worked with bacteria that caused pneumonia  Two strains: R and S  R—did not cause pneumonia in mice  S—did cause pneumonia  Mixed heat-killed S-strain and living R-strain  Could cause pneumonia  Isolated living S-strain bacteria from infected mice  Some substance from dead S-strain transformed R-strain  Avery, MacLeod, and McCarty showed DNA was the transforming material The Hershey-Chase Experiment o Side by side experiments are performed with separate bacteriophage (virus) cultures in which either the protein capsule is labeled with radioactive sulfur or the DNA core is labeled with radioactive phosphorus  The radioactively labeled phages are allowed to infect bacteria  Agitation in a blender dislodges phage particles from bacterial cells  Centrifugation concentrates cells, separating them from the phage particles left in the supernatant o Results:  Radioactive sulfur is found predominantly in the supernatant.  Radioactive phosphorus is found predominantly in the cell fraction, from which a new generation of infective phage can be isolated  Conclusion: The active component of the bacteriophage that transmits the infective characteristic is the DNA. There is a clear correlation between DNA and genetic information Molecular Genetics

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o DNA is the molecule that carries hereditary information  Information is in discrete units called genes  Genes are segments of DNA located on chromosomes  Chromosomes are composed of DNA and proteins DNA Monomers: Nucleotides o There are 4 kinds of nucleotide, depending on nitrogen-containing base  Bases: adenine (A), guanine (G), cytosine (C), and thymine (T)  Each nucleotide is composed of 3 parts:  Phosphate  Deoxyribose sugar  Nitrogen base  Chargaff’s rules: A=T,;C=G What is the structure of DNA? o Helical structure revealed by x-ray diffraction  1952—Maurice Wilkin and Rosalind Franklin  Showed that DNA had the shape of a helix; dimensions of helix were measured  Diameter of helix was 2nm  Distance between nucleotides was 0.34nm  Distance per turn was 3.4nm (how many nucleotides per turn?) o Double helix/complementary base pairing  1953—James Watson and Francis Crick  Used Franklin’s data and Chargaff’s information to deduce structure  Sugar-phosphate backbone from helix  Nitrogen-containing bases from rungs  Pairs form: one form each sugar-phosphate backbone  Pairing rles: A with R, G with C  Explains Chargaff’s rules  Backbones are antiparallel  Each strand is directional: free sugar (3’) on one end, phosphate (5’) on other  The directions of the two strands are opposite  Car headlight-taillight analogy; traffic on two-lane road o Hydrogen bonds between complementary bases hold the 2 DNA strands together o Information is encoded in the order of nucleotides  The small number of nucleotides (4) made many scientists skeptical that DNA was the hereditary molecule  Information depends on the sequences of nucleotides, not their number How does DNA replication ensure genetic constancy during cell division? o The replication of DNA is a critical event in a cell’s life

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o DNA replication produces two DNA double helices, each with one old strand and one new strand  DNA replication is necessary for cell division  DNA replication requires several enzymes  DNA helicase  DNA polymerase  DNA ligase  Replication is semiconservative (part old/part new) o Proofreading produces almost error-free replication of DNA o Yet, mistakes do happen Error in DNA synthesis o DNA errors, proofreading, and repair  DNA polymerase: 1 mistake per 10,000 base pairs  Error rate reduced to 1 mistake per billion base pairs by proofreading enzymes  Enzymes use complementary DNA strand to repair damage  Excise mismatch, replace with correct base o Other sources of errors in DNA  Spontaneous chemical degradation  Ultraviolet radiation  Aging o Mutations as a result of replication errors can have serious health consequences

Lecture 10: Gene Expression Gene Expression and Regulation 

How are genes and proteins related? o The relationship between chromosomes, DNA, genes, and proteins  Genes provide information to make proteins  Proteins are the cell’s “molecular workers” o DNA provide instructions for protein synthesis via RNA intermediaries o The kinds of RNA and their uses  Structural differences between DNA and RNA  Ribose vs deoxyribose  U in RNA, T in DNA  RNA: single-stranded; DNA: double-stranded  The 3 kinds of RNA  mRNA (messenger RNA)  rRNA (ribosomal RNA)  tRNA (transfer RNA)

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o Overview of transcription and translation  Transcription: making RNA in the nucleus  Translation: making protein in the cytoplasm  Language analogy for remembering which is which o The genetic code uses three bases to specify an amino acid o The genetic code  Codons: why 3 is the minimum number of nucleotides that can code for 20 amino acids?  Total possible codons= 4^3 =4x4x4= 64  Stop and start codons  Redundancy of the code: more than one codon for many amino acids How is information in a gene transcribed into RNA? o Initiation  RNA polymerase binds at the promoter region (TATA)  DNA unwinds  Promoter is an important site of gene regulation o Elongation  RNA polymerase synthesizes RNA  Complementary to template strand of DNA  Base-pairing rules  DNA rewinds after polymerase passes; RNA is single-stranded o Termination  Termination signal: sequences of bases in the template strand  RNA polymerase releases completed RNA  RNA polymerase detached from DNA o Transcription is selective  Only the genes needed are expressed in a given cell  Control regions on the DNA near the promoter are important in regulation How is the base sequence of a messenger RNA molecule translated into protein? o The roles of the 3 kinds of RNA  mRNA: carries information: code for the amino acid: sequence of the protein to be synthesized  rRNA: part of the structure of ribosomes  Large ribosomal subunit  Small ribosomal subunit  tRNA: decodes the sequence of bases on mRNA  Anticodons  Carries amino acids o Recap: decoding the sequence of bases in DNA into the sequence of amino acids in protein requires transcription and translation

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 Complementary base pairing is critical to decode genetic information Protein synthesis o Initiation: tRNA and mRNA bind to a ribosome  Initiation codon, AUG: codes for methionine  Initiation complex forms  Large ribosomal subunit joins complex  Two binding sites on large subunit  Holds two tRNAs during translation o Elongation: protein synthesis  Second tRNA binds in second binding site  Peptide bond forms  Complex moves one codon along mRNA  Repeat until end of message reached o Termination: translation ends  Stop codon reached:  Special proteins bind  Ribosome releases complete protein  Ribosome and mRNA dissociate How do mutations in DNA affect the function of genes? o Mutation: change in DNA sequence of a gene o How mutations form:  Faulty base pairing during replication of DNA  Spontaneous chemical changes  Mutagens  Chemical  Radiation o Mutations provide the raw material for evolution o Three main types of mutation:  Point mutations  Insertions  Deletions o Consequences of mutations  Deletions and insertions  Frame-shift  Usually catastrophic  Nucleotide substitutions  Silent: No change to protein  Neutral: Amino acid changed, but no effect on protein  Missense Mutation: Protein function is changed  Nonsense: Result in stop codons. Protein function is destroyed

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How are genes regulated? o Proper regulation of gene expression is critical for an organism’s development and health  Gene expression: express genes needed for cell type  Expression can change over time  Environment can regulate expression  Regulation can occur at several steps during expression  Transcription  Translation  Post-translational modification of proteins  Life span of proteins o Prokaryotic (Bacterial) DNA is saturated with genes o Eukaryotic DNA contains spaces (noncoding regions) to protect the genes o Spaces can be between the genes (Satellite DNA) or within the gene itself (introns) o Eukaryotic genes contain introns (spaces) and exons (coding regions) o RNA polymerase transcribes both the exons and introns, producing a long RNA molecule. o Enzymes in the nucleus then cut out the RNA introns and splice together the exons to form the true mRNA, which moves out of the nucleus and is translated on the ribosomes....