bio comp. multiple choice
Biology 101
The Chemistry of Life
• Elements, Atomic Number, Atomic Weight, Atomic Structure (Protons [ +] Neutrons [0] Electrons [−]), Isotopes (standard, heavy, radioactive), Charged Molecules (anions [−] cations [+]
• Organic vs. Inorganic molecules, small molecules vs. macromolecules, monomeric molecules vs. polymeric molecules.
• The chemistry of water: The definition of pH (pH = -log [H+]), the pH scale, the polar nature of water. (You should know what the electronegative atoms that occur in organic compounds are: oxygen and nitrogen).
• Types of chemical bonds: Strong bonds: covalent bonds. Weak bonds: hydrogen bonds, hydrophobic bonds (or interactions), ionic bonds, and Van der Waals interactions.
• The biological polymeric macromolecules: Nucleic acids (DNA, RNA), proteins, carbohydrates, and lipids. Monomer subunits and bonds that hold the biological polymeric macromolecules together: Nucleic Acids (DNA, RNA) are made of nucleotide monomers held together by phosphodiester bonds. Proteins are made of amino acid monomers held together by peptide bonds. Carbohydrates or polysaccharides are made of monosaccharides held together by glycosidic bonds. And lipids are frequently triglycerides consisting of glycerol molecules esterified to fatty acid molecules. (There are also other types of lipids).
• Structure and function of nucleic acids and proteins: Structure of double helical DNA (double stranded DNA = dsDNA). The chemical nature of base pairs (base pairs are hydrogen bonded purine-pyrimidine complexes, GC, AT, or AU). The mechanism of DNA replication (in vivo DNA synthesis involves both leading strand continuous and lagging strand discontinuous DNA synthesis) including the various proteins involved (DNA polymerases, DNA ligase, DNA helicases, primase, and single stranded binding
proteins). You should be familiar with and know the function of the origin of replication, primase, the direction of synthesis of nucleic acids, the difference between leading and lagging strand synthesis, and Okazaki fragments.
• The Central Dogma also known as the Information Flow Theory (DNA -> RNA -> Protein).
Steps: 1) DNA Replication (DNA synthesis catalyzed by DNA polymerases and involves many other enzymes and proteins), 2) Transcription (RNA synthesis catalyzed out by RNA polymerase), and 3) Translation (Protein synthesis catalyzed by ribosomes, which have 2 subunits each one of which contains at least one major rRNA and many ribosomal proteins. Translation also involves the base pairing of the codons of the mRNA to the anticodons of aminoacylated tRNAs, i.e. tRNA esterified to their specific amino acids).
• The function of reverse transcriptase (a RNA dependent DNA polymerase which synthesizes a complementary DNA, cDNA, from a RNA template) and why it is an exception to the central dogma.
• The proof that DNA is the genetic material (the Griffith Experiment, the Avery, McLeod, McCarty Experiment; The Hersey-Chase Experiment).
• The mechanism of transcription, the subunit structure of RNA polymerase, particularly the function of the sigma factor/subunit in prokaryotes and the general transcription factors among which are TFIID and other TFIIs in eukaryotes and the function of the promoter site (the TATA consensus sequence to which RNA polymerase initially binds). The difference between prokaryotic and eukaryotic genes: the presence of introns in eukaryotic genes. The three steps involved in the processing of eukaryotic primary RNA transcripts (i.e., pre mRNAs) into mature mRNAs: 1) 5’ capping with m7G, 2) 3’ polyA tailing, and 3) splicing (excision of introns and religation of exons by spliceosomes made of RNPs [snRNA complexes]).
• The mechanism of translation. The structure (ribosomes are complexes of rRNAs and proteins) and function of ribosomes, the genetic code, the synthesis of aminoacyl tRNAs, the peptidyl transferase reaction, the translocation of ribosomes, the termination of protein synthesis. (You must know how codons via base pairing to the anticodons of aminoacyl tRNAs specify the next amino acid added by the peptidyl transferase reaction which is catalyzed by the large ribosomal subunit to the growing polypeptide during the elongation step of translation). The involvement of the protein “rho” in the termination of prokaryotic translation.
• Events that occur during posttranslational modification of proteins.
• Factors that contribute to the 2 and 3 dimensional structure of proteins (You should know which amino acids are hydrophobic and hydrophilic). Knowledge of the nature of alpha-helices, beta-structure, and disulfide bridges.
Cell Structure
• Structure of prokaryotic and eukaryotic cells. The differences between pro- and eukaryotic cells. Differences between plant and animal cells. Structure of cell membranes.
Energetics and Metabolism
• Function of ATP. Synthesis of ATP. Glycolysis, Krebs cycle (a.k.a., TCA cycle or Citric Acid cycle), Photosynthesis, Respiration, and electron transport. Definition of a catalyst. How enzymes function as catalysts.
• Photosynthesis is the use of the energy from the sun to synthesize carbon compounds (by the Calvin Benson Cycle). The reactants for photosynthesis are CO2 and H2O. The products are carbon compounds and oxygen.
• Photosynthesis in eukaryotes is carried out in chloroplasts.
• Respiration in eukaryotes results in the synthesis of ATP in the mitochondria by harvesting energy derived from passing electrons down the electron transport (respiratory) chain.
• Chloroplasts and mitochondria were free living prokaryotes prior to becoming endosymbiots within eukaryotic cells.
Chromosomal Structure, Cell Division (Mitosis and Meiosis)
• Chromosomes are complexes of DNA and proteins (histones-H1, H2A, H2B, H3, and H4). * The “beads on a string model”, nucleosomes, histones, histone core octomers. The nature of non-coding chromosomal DNA: tandemly repetitive DNA (satellite, mini- and microsatellite DNA), interspersed repetitive DNA (transposon-like, retroposon-like repetitive DNA such as AluI repeated sequences). Gene families (such as the hemoglobin gene family which arose via gene duplication and reduplication followed by the acquisition of different mutations in the different copies of the gene).
• Haploid (n) and diploid (2n). An organism with a chromosome number of 2n=16 has a diploid chromosome number of 16 and a haploid chromosome number of 8. • During gametogenesis, the reduction of chromosome number from diploid to haploid occurs during Meiosis I.
Mendelian Genetics (genetics of diploid organisms)
• DNA and heredity. Mono- and dihybrid crosses.
Phage and Bacterial Genetics (genetics of haploid organisms)
• Bacterophages (phages) and bacteria are haploid.
• Gene can be transferred horizontally from cell to another cell (as versus vertically from parent to progeny or daughter cells during binary fission) by the processes of 1) transformation, 2) conjugation, and 3) transduction
• Transformation is the uptake of DNA from the medium by a bacterial cell.
• Conjugation is the transfer of genetic material from one bacterium to another via a pillus (a conjugation tube). This transfer is usually mediated by a F-plasmid (a fertility plasmid).
• Transduction is the transfer of DNA from one cell to another mediated by a phage by catalysis.
• Gene Mutations: Types and consequences of mutations (point or substitution mutations and rearrangement mutations, insertions and deletions which may cause frameshifts). The origin (generation) of mutations (spontaneous or caused by mutagens).
Regulation of Gene Expression
• Prokaryotic gene expression: the lac and trp operons.
• Eukaryotic gene expression: Transcriptional regulation, transcription factors (you should be familiar with both general transcription factors, GTFs, which in eukaryotes function similarly to prokaryotic sigma factor, and regulatory transcription factors/proteins which are either activators or repressors), stability of RNAs and proteins.
• Transcription factors (DNA binding regulatory proteins which activate or repress transcription by binding to the regulatory region of genes).
Recombination DNA and Biotechnology
• Restriction enzymes, DNA sequencing, synthesis of recombinant molecules. Plasmids and phage cloning vectors
• Polymerase chain reaction (PCR): in vitro DNA synthesis.
Biology 102
History, Origin, and Evolution of Life on Earth
• Darwinian & molecular evolution. Population genetics, the Hardy-Weinberg theorem. • Origin of life on earth
• Differential Gene Expression in Development
• Evolution of Gene and Genomes
• Speciation
• Phylogeny, cladistics, & systematics. Characteristics (and differences) of organisms in the phyla. Differences between plants, animals, fungi and protists, between prokaryotes and eukaryotes, between single celled and multicelled organisms, vertebrates and invertebrates, etc.
• Archea vs. Bacteria: cell wall structure, nucleic acid structure, metabolic characteristics and ecological niches
• Origin and Diversification of Eukaryotes
• Fungi: Recyclers, Pathogens, and Parasites
• Plant diversity, structure, transport, nutrition, and reproduction & development. • Invertebrates Diversity
• Vertebrate Diversity
• Animal Physiology: reproduction, homeostasis, circulatory system, and nervous system
Review Topics in Genetics:
• The Nature of the Genetic Material: Chemical composition, experimental evidence that DNA is the genetic material (Experiments of 1) Griffith, 2) Avery, McLeod, and McCarty, 3) Hersey & Chase, Chargaff)
• Mendelian and the Chromosomal Theory: Mendel’s law of segregation, law of independent assortment, monohybrid and dihybrid crosses, applications of probability (Hardy-Weinberg)
• Modifications of Mendelian Principles: Gene interactions (allelic), incomplete dominance, codominance, multiple alleles
• Genotypic Interactions: Epistasis (recessive and dominant), additive gene action, polygenic inheritance.
• Sex Determination and Sex Linkage: Sex chromosomes, sex-linked genes. • Linkage and Chromosome Mapping (Diploid): Two- and three-point crosses.
• Cytogenetic: Variation in chromosome number, euploidy, aneuploidy, cytogenetics - variation in chromosome structure, duplications, deficiencies, inversions, translocations
• Quantitative and Evolutionary Genetics
• Chemistry of the Gene: Chemical and physical characteristics, the Watson and Crick model of double helical DNA, types of helical forms of DNA.
• Mechanisms of the genetic synthetic processes of the Central Dogma: The molecular mechanism of 1) DNA replication [synthesis], 2) transcription [synthesis], 3) translation [synthesis].
• DNA Replication: Semi-conservative replication [Meselson and Stahl Experiment], the origin of replication, the various proteins that constitute the replication machinery, the reason for and difference between leading and lagging strand DNA synthesis, the mechanism of lagging strand synthesis, the multiple enzymatic activities of E. coli DNA pol I [1) polymerase, 2) 5’->3 and 3) 3’->5’ exonuclease activities].
• Gene-Phenotype Relationships: Experiment of Beadle, Tatum & Ephrussi (One Gene One enzyme)
• Transcription: Promoter recognition in prokaryotes, promoter recognition in eukaryotes, RNA chain elongation and termination.
• The nature of RNA transcripts (rRNA, tRNA and mRNA) and related ribonucleoproteins: ribosomes (rRNA and protein), spliceosomes (snRNA and protein).
• The Genetic Code: Triplet nature of the genetic code, experiments that deciphered the genetic code, the Wobble Hypothesis.
• Protein Structure: The chemical characteristic of amino acid R-groups--particularly their interaction with the solvation shell of water (hydrophobic & hydrophilic R groups) and how that affects the folding of proteins into their ultimate 3 dimensional (tertiary) structure. The levels of macromolecular structure: 1) primary (sequence of monomer units), 2) secondary (structure in two dimensions--in proteins affected by disulfide bonds, alpha helices and beta-structure), tertiary (due to hydrophobic interactions), and quaternary structure (aggregates of subunits--each of which has its own tertiary structure. Example, the tetrameric protein hemoglobin which is made of 4 subunits [2 alpha and 2 beta]).
• Translation: Initiation mechanisms, elongation mechanisms, and termination mechanisms. ORFs (open reading frames of codons for translation), DNA mutations-- point mutations (silent, missense, nonsense) and insertions and deletions (possibly causing frame shifts).
• Catalysis of translation by ribosomes (the peptidyl transferase reaction which adds the next amino acid residue to the growing polypeptide and the translocase or translocation reaction which moves the ribosome down (in a 5’◊3’direction) the mRNA.