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Questions and Answers

What is the main function of cohesins during chromosome replication?

  • To help chromosomes align along the middle of the cell (correct)
  • To attach chromosomes to the mitotic spindle
  • To condense DNA into nucleosomes
  • To separate sister chromatids

    • Which type of chromatin is tightly packed and not expressed?

  • Nucleosome
  • Solenoid
  • Heterochromatin (correct)
  • Euchromatin

    • What occurs during the 'G1' phase of the eukaryotic cell cycle?

  • Cytoplasmic division
  • Primary growth and preparation for S phase (correct)
  • Nuclear division
  • DNA replication

    • What is the purpose of cell cycle checkpoints?

    <p>To detect and respond to errors before cell cycle progression (C)</p> Signup and view all the answers

    How many chromosomes does a haploid human cell contain?

    <p>23 (B)</p> Signup and view all the answers

    During which phase of the M phase do sister chromatids separate?

    <p>Anaphase (B)</p> Signup and view all the answers

    What is the role of the mitotic spindle made of microtubules?

    <p>To arrange chromosomes during mitosis (B)</p> Signup and view all the answers

    Which type of cell division do prokaryotic cells primarily use?

    <p>Binary fission (C)</p> Signup and view all the answers

    What defines a diploid cell?

    <p>Two complete sets of chromosomes (A)</p> Signup and view all the answers

    What happens during cytokinesis in animal cells?

    <p>Use of a contractile ring to cleave the cell (B)</p> Signup and view all the answers

    What is the primary role of Rubisco in the process of carbon fixation?

    <p>To catalyze the addition of CO2 to RuBP (B)</p> Signup and view all the answers

    What is the significance of the difference between the C4 and CAM pathways in plants?

    <p>C4 plants minimize photorespiration spatially while CAM plants do so temporally (C)</p> Signup and view all the answers

    What distinguishes RNA from DNA?

    <p>RNA uses uracil instead of thymine (A)</p> Signup and view all the answers

    Which statement about the phosphodiester bonds in nucleic acids is correct?

    <p>They are formed between the phosphate group of one nucleotide and the 3' OH group of another (A)</p> Signup and view all the answers

    What does Chargaff's rule state about the relationships between purines and pyrimidines in DNA?

    <p>The proportion of A and G equals the proportion of C and T (C)</p> Signup and view all the answers

    In DNA replication, what does the term 'semi-conservative' imply?

    <p>Each new DNA molecule consists of one old and one new strand (A)</p> Signup and view all the answers

    What is the role of DNA polymerase during DNA replication?

    <p>It matches template bases with complementary nucleotides and links them (C)</p> Signup and view all the answers

    How do G and C base pairs differ from A and T base pairs in DNA structure?

    <p>G forms 3 hydrogen bonds with C, while A forms 2 with T (B)</p> Signup and view all the answers

    What characterizes the opposite orientations of the strands in the double helix structure of DNA?

    <p>The strands are anti-parallel, allowing complementary base pairing (A)</p> Signup and view all the answers

    What enzyme is primarily responsible for initiating DNA replication?

    <p>DNA polymerase (A)</p> Signup and view all the answers

    What is the purpose of the G2/M checkpoint in the cell cycle?

    <p>To ensure chromosomes are fully replicated (D)</p> Signup and view all the answers

    Which statement describes a gain-of-function mutation in proto-oncogenes?

    <p>Only one copy needs to be mutated for oncogenic activity (A)</p> Signup and view all the answers

    In meiosis, what significant event occurs during prophase I?

    <p>Homologous chromosomes undergo synapsis (B)</p> Signup and view all the answers

    What is the main genetic outcome of crossing over in meiosis?

    <p>Increased genetic variation among offspring (C)</p> Signup and view all the answers

    What is true about recessive pedigrees?

    <p>Can skip generations if parents are unaffected (D)</p> Signup and view all the answers

    What does the ABO blood typing system demonstrate?

    <p>Codominance of IA and IB alleles (B)</p> Signup and view all the answers

    What is epistasis in genetic inheritance?

    <p>One gene modifying the expression of another gene (C)</p> Signup and view all the answers

    Which statement about sex determination in humans is correct?

    <p>The presence of the SRY gene determines maleness (D)</p> Signup and view all the answers

    What is the primary consequence of nondisjunction during meiosis?

    <p>Aneuploidy in gametes (A)</p> Signup and view all the answers

    Which type of genetic mapping involves recombinant frequency?

    <p>Linkage analysis (A)</p> Signup and view all the answers

    What defines the principle of independent assortment during a dihybrid cross?

    <p>The independent alignment of different chromosome pairs (D)</p> Signup and view all the answers

    How does genomic imprinting affect gene expression?

    <p>Inactivates genes based on parental origin (D)</p> Signup and view all the answers

    Which abnormality is commonly associated with the aneuploidy of sex chromosomes?

    <p>Turner syndrome characterized by a single X chromosome (D)</p> Signup and view all the answers

    What is a key difference between prokaryotic and eukaryotic mRNA?

    <p>Prokaryotic mRNA often has multiple coding sequences. (D)</p> Signup and view all the answers

    What are the stop codons that terminate elongation in translation?

    <p>UAA, UAG, UGA (D)</p> Signup and view all the answers

    What role do transcription factors play in gene expression regulation?

    <p>They recruit RNA polymerase to the promoter region. (C)</p> Signup and view all the answers

    Which type of mutation causes a change in the encoded amino acid?

    <p>Missense mutation (B)</p> Signup and view all the answers

    What is the primary function of the large subunit of the ribosome?

    <p>It catalyzes peptide bond formation. (A)</p> Signup and view all the answers

    Which of the following statements is true about the lac operon?

    <p>It operates under negative control when lactose is absent. (A)</p> Signup and view all the answers

    What is a characteristic of post-transcriptional gene regulation?

    <p>It includes processes like mRNA splicing and export. (D)</p> Signup and view all the answers

    What does the term 'wobble' refer to in tRNA base pairing?

    <p>The ability of tRNA to bind more than one codon. (B)</p> Signup and view all the answers

    What is the effect of RNA interference (RNAi) on gene expression?

    <p>It selectively knocks down gene expression. (B)</p> Signup and view all the answers

    Which mechanism of gene expression regulation directly involves chemical modifications of histones?

    <p>Chromatin structure changes (B)</p> Signup and view all the answers

    What is the core function of a promoter in gene transcription?

    <p>It is where the regulatory proteins bind. (B)</p> Signup and view all the answers

    What initiates the elongation cycle during translation?

    <p>The recognition of the start codon by the small subunit. (D)</p> Signup and view all the answers

    Which class of RNA is specifically involved in carrying amino acids to the ribosome?

    <p>tRNA (A)</p> Signup and view all the answers

    What determines an organism's phenotype?

    <p>Interaction between genotype and environment (D)</p> Signup and view all the answers

    Which of the following is NOT a property of water?

    <p>High density in solid form (B)</p> Signup and view all the answers

    What is the role of ribosomes in the cell?

    <p>Protein synthesis (A)</p> Signup and view all the answers

    Which structure in the cell is responsible for detoxification and calcium storage?

    <p>Smooth ER (B)</p> Signup and view all the answers

    How does competitive inhibition affect enzyme activity?

    <p>It competes with the substrate for binding at the active site (A)</p> Signup and view all the answers

    Which of the following correctly describes the function of chloroplasts?

    <p>Synthesize ATP using light energy (C)</p> Signup and view all the answers

    In the context of cellular compartments, what is the function of lysosomes?

    <p>Digest and recycle cellular components (B)</p> Signup and view all the answers

    Which of the following is true about the first law of thermodynamics?

    <p>Energy can only change from one form to another (D)</p> Signup and view all the answers

    What is the role of helicase during DNA replication?

    <p>To unwind the DNA double helix (B)</p> Signup and view all the answers

    What characterizes an endergonic reaction?

    <p>Requires input of energy (A)</p> Signup and view all the answers

    Which of the following accurately describes the fluid mosaic model of cell membranes?

    <p>Membranes consist of diverse proteins embedded in a fluid bilayer (C)</p> Signup and view all the answers

    What type of DNA repair targets a specific kind of damage?

    <p>Photorepair (C)</p> Signup and view all the answers

    How does DNA polymerase synthesize new DNA strands?

    <p>In a 5’ to 3’ direction (B)</p> Signup and view all the answers

    Which property of enzymes is essential for their function?

    <p>Enzymes can only work in a narrow temperature range (C)</p> Signup and view all the answers

    What is the main function of telomerase in eukaryotic cells?

    <p>To replicate telomere ends (B)</p> Signup and view all the answers

    During active transport, what role do carrier proteins play?

    <p>Utilize energy to move molecules against a concentration gradient (D)</p> Signup and view all the answers

    Which statement about prokaryotes is FALSE?

    <p>They possess membrane-enclosed organelles (B)</p> Signup and view all the answers

    What structural feature is crucial for the termination of transcription in prokaryotes?

    <p>A hairpin loop in the RNA (A)</p> Signup and view all the answers

    What differentiates eukaryotic mRNA from prokaryotic mRNA?

    <p>Eukaryotic mRNA undergoes splicing (A)</p> Signup and view all the answers

    Which metabolic pathway involves the breakdown of glucose to extract energy?

    <p>Cellular respiration (C)</p> Signup and view all the answers

    What is the primary function of the Golgi apparatus?

    <p>Modification, sorting, and packaging of proteins (A)</p> Signup and view all the answers

    What statement is true about Okazaki fragments during DNA replication?

    <p>They are created on the lagging strand (C)</p> Signup and view all the answers

    Which RNA type is responsible for carrying amino acids during translation?

    <p>Transfer RNA (tRNA) (B)</p> Signup and view all the answers

    What function do SSBs (Single-Strand Binding proteins) serve during DNA replication?

    <p>Maintain single-stranded DNA stability (A)</p> Signup and view all the answers

    In eukaryotes, where does transcription occur?

    <p>In the nucleus (A)</p> Signup and view all the answers

    During which stage of translation is the polypeptide chain elongated?

    <p>Elongation (D)</p> Signup and view all the answers

    What is the main purpose of alternative splicing of mRNA?

    <p>To produce multiple different proteins from a single gene (D)</p> Signup and view all the answers

    Which enzyme catalyzes the synthesis of RNA during transcription?

    <p>RNA polymerase (D)</p> Signup and view all the answers

    Flashcards

    Binary fission

    A type of cell division in prokaryotic cells, where a single cell splits into two.

    Mitosis

    The process of nuclear division in eukaryotic cells, ensuring the genome is passed to daughter cells.

    Cytokinesis

    The cytoplasmic division of a eukaryotic cell, splitting it into two separate cells.

    Karyotype

    The complete set of chromosomes in a species or individual, organized by size and features.

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    Haploid (1n)

    A single set of chromosomes necessary to define a species(e.g., humans have 23 chromosomes).

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    Diploid (2n)

    Two complete sets of chromosomes (e.g., humans have 46 chromosomes).

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    Chromosome replication

    The process of duplicating chromosomes before cell division.

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    Cell cycle checkpoints

    Control points in the cell cycle that ensure accurate duplication and division, stopping the process if errors are detected.

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    Heterochromatin

    Tightly packed chromatin that is not expressed(not active).

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    Euchromatin

    Loosely packed chromatin that is active and available for expression.

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    Carbon Fixation

    The initial step in the Calvin cycle where CO2 is incorporated into an organic molecule (RuBP), forming PGA.

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    Rubisco

    Enzyme that catalyzes carbon fixation in the Calvin cycle, has two activities (carboxylation and oxidation).

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    Photorespiration

    A process where Rubisco adds O2 instead of CO2 to RuBP, leading to CO2 release and reduced photosynthetic efficiency.

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    C4 Pathway

    A photosynthetic pathway that minimizes photorespiration by spatially separating the initial carbon fixation.

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    CAM Pathway

    A photosynthetic pathway that minimizes photorespiration by temporally separating the initial carbon fixation, typically found in plants in arid environments.

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    Nucleotide

    The fundamental building block of nucleic acids (DNA and RNA), composed of a sugar, a nitrogenous base, and a phosphate group.

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    DNA

    A double-stranded nucleic acid molecule that carries the genetic instructions for an organism.

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    Complementary Base Pairs

    Specific pairs of nitrogenous bases that form hydrogen bonds with each other in DNA (A-T, G-C).

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    DNA Replication

    The biological process of copying a cell's DNA.

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    DNA Polymerase

    Enzyme responsible for synthesizing new DNA strands during replication, adding nucleotides to the 3' end.

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    Eukaryotic mRNA

    Carries a single coding sequence for a single protein, unlike prokaryotic mRNA.

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    Codon

    A three-nucleotide sequence that specifies an amino acid.

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    Genetic Code Redundancy

    Multiple codons can code for the same amino acid.

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    Ribosome

    Cellular structure that synthesizes proteins by translating mRNA.

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    Anticodon

    Three-nucleotide sequence on tRNA that complements a codon.

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    Wobble Pairing

    Less stringent base pairing between the 3' base of the codon and the 5' base of the anticodon.

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    Translation Initiation

    The beginning of protein synthesis.

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    Translation Elongation

    Adding amino acids to the growing polypeptide chain.

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    Translation Termination

    End of protein synthesis. Stop codon.

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    Point Mutation

    A change in a single base pair of a gene.

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    Operon

    Group of genes that are co-transcribed and co-regulated.

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    Transcriptional Regulation

    Control of gene expression at the level of transcription.

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    Promoter

    DNA region that RNA polymerase binds to initiate transcription.

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    Transcription Factors

    Proteins that can influence transcription via DNA binding.

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    DNA Replication (prokaryotes)

    The process of copying a circular DNA molecule, starting at one point and proceeding in both directions.

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    Replisome

    A complex of proteins involved in DNA replication, including DNA polymerase.

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    Semi-discontinuous Replication

    DNA replication where one strand is copied continuously (leading strand) and the other is copied in fragments (lagging strand).

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    Okazaki Fragments

    Short DNA fragments synthesized on the lagging strand during replication.

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    Eukaryotic Replication

    DNA replication in organisms with multiple chromosomes which have linear DNA.

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    Telomeres

    Protective caps at the ends of linear chromosomes.

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    Telomerase

    Enzyme that replicates the ends of linear DNA.

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    DNA Repair Mechanisms (Specific)

    Repair systems that target specific types of DNA damage.

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    Photorepair

    A specific repair mechanism for thymine dimers caused by UV light.

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    Excision Repair

    A general DNA repair mechanism that removes damaged DNA regions.

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    Central Dogma

    DNA to RNA to protein: the flow of genetic information.

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    Transcription

    The synthesis of RNA from a DNA template.

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    Promoter Sequence

    Specific DNA sequence where RNA polymerase binds to initiate transcription.

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    Alternative Splicing

    A process where a single gene can produce multiple different proteins by different combinations of exons.

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    G1/S checkpoint

    A critical point in the cell cycle where the cell checks for proper size and components before DNA replication.

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    Cancer

    Uncontrolled cell proliferation and metastasis (movement of cells).

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    Proto-oncogene

    A normal gene that can become an oncogene (cancer-causing) when mutated.

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    Tumor suppressor gene

    A gene whose protein detects problems and stops the cell cycle.

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    Diploid

    Having two sets of chromosomes (one from each parent).

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    Haploid

    Having one set of chromosomes.

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    Synapsis

    Association between homologous chromosome pairs during meiosis I.

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    Crossing over

    Genetic recombination between non-sister chromatids during meiosis I.

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    Independent assortment

    Random orientation of homologous chromosomes during meiosis I, leading to different combinations of alleles in gametes.

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    Monohybrid cross

    A genetic cross between parents that differ in only one trait.

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    Principle of Segregation

    Each individual receives one copy of a gene from each parent which separate during meiosis.

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    Dihybrid cross

    A genetic cross between parents that differ in two traits.

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    Principle of Independent Assortment

    Alleles assort independently during a dihybrid cross.

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    Genetic mapping

    Determining the relative positions of genes on chromosomes.

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    Cell Theory

    All living things are made of cells, cells are the smallest units of life, and new cells arise from pre-existing cells.

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    Atoms

    The smallest stable units of matter.

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    Element

    A substance made up of only one kind of atom.

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    Covalent Bond

    A chemical bond formed by the sharing of electrons between atoms.

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    Ionic Bond

    A chemical bond formed by the attraction between oppositely charged ions.

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    Hydrogen Bond

    A weak chemical bond formed by the attraction between a slightly positive hydrogen atom and a slightly negative atom.

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    Water Cohesion

    Water molecules' attraction to each other.

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    Water Adhesion

    Water molecules' attraction to other charged surfaces.

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    pH Scale

    A scale used to measure the concentration of hydrogen ions in a solution.

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    Hydrocarbons

    Organic molecules composed solely of carbon and hydrogen atoms.

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    Macromolecules

    Large organic molecules, including carbohydrates, proteins, and nucleic acids.

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    Amino Acids

    The building blocks of proteins.

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    Enzyme

    A biological catalyst that speeds up chemical reactions.

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    Active Transport

    The movement of molecules against their concentration gradient, requiring energy.

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    Passive Transport

    The movement of molecules down their concentration gradient, requiring no energy.

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    Endocytosis

    The process of taking material into a cell via vesicles.

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    Study Notes

    What is Science?

    • Science aims to understand the natural world through observation and reasoning
    • Science is both descriptive and hypothesis-driven
    • Science is in a constant state of change as new data, methods, and ideas arise

    Science Uses Deductive and Inductive Reasoning

    • Deductive reasoning uses general principles to make specific predictions (big to small)
      • Example: natural selection used to explain changes in population
    • Inductive reasoning uses specific observations to make general conclusions (small to big)
      • Example: fossils show life on earth has changed over time

    Descriptive Science vs. Hypothesis-Driven Science

    • Science begins with observations
    • Much of science is purely descriptive
      • Example: classifying and describing life in a given habitat
      • Example: genomic sequencing
    • A systematic approach to understanding the natural world
      • The scientific method: observation → question → hypothesis → prediction → conclusion

    Experiments and Variables

    • Control experiment- independent variable is unaltered (purpose: minimize effects of factors other than the one being tested)
    • Independent variable- what is being changed (x-axis)
    • Dependent variable- what is being measured (y-axis)

    Pseudoscience

    • Describes claims, beliefs, or practices that purport to be science
    • Does not use accepted scientific methods to draw conclusions
    • The claims or beliefs often cannot be tested
      • Example: astrology and intelligent design

    Key Concepts in the Practice of Science

    • Science vs. pseudoscience: can be tested to see if true vs. cannot be tested
    • Basic vs. applied: expand general knowledge vs. solve real-world problems
    • Objective vs. self-correcting: science is directly stated vs. peer review and reproducibility
    • Scientific theories: supported by substantial direct observation, experimental evidence, and scientific reasoning
      • Expresses idea of which we are most certain
      • Is not guess or conjecture

    Key Concepts of Practice in Science (Reductionism and Systems Biology)

    • Reductionism: breaks a complex process down to its component parts (advanced understanding in many areas of biology)
    • Systems biology: focuses on how components work together (relies on modeling biological processes; may allow prediction of emergent properties)

    Living Systems Share Several Characteristics

    • All living systems consist of cells (might just be one cell)
    • Connection between structure and function is a major theme in biology.
    • Living systems store and process information (in the form of DNA)
    • Living systems transform energy (plants- sun to chemical energy; humans- eat their energy)
    • Living systems grow and reproduce.
    • Living systems adapt and evolve.

    What Determines an Organism's Phenotype?

    • Determined by genotype (genetic material) and environmental influences
    • Produces phenotype (observable traits)

    Classifying Organisms

    • Need to make, label, and organize all of the diversity
    • Each organism is named using a binomial system (genus species)
    • All organisms descend from one common ancestor

    Cell Theory

    • All organisms are composed of cells
    • Cells are the smallest living things
    • Cells arise only from existing cells.
      • All cells today represent a continuous line of descent from the first living cell.

    Atoms are the Smallest, Stable Unit of Cells

    • Element- substance with one type of atom with the same number of protons, cannot be broken down
    • Atomic number- number of protons in an atom
    • Valence electron- electrons in the outermost energy level
    • Isotope- atoms of the same element that have different numbers of neutrons
    • Atomic mass- sum of mass of protons and neutrons in atom
    • Carbon is the basis for most biological molecules

    Atoms Contain Discrete Energy Levels

    • Greater potential energy moving away from the nucleus
    • The number and arrangement of electrons mediates reactions
    • Octet rule- atoms tend to completely fill outer energy levels

    Electrical Charges and Atoms

    • Electronegativity- electrons are not shared equally, distribution of charge is unequal
    • Cation- positively charged ion (formed when an atom loses an electron)
    • Anion- negatively charged ion (formed when an atom gains an electron)

    Atoms Form Molecules from Chemical Bonds

    • In order from strongest to weakest: covalent- sharing of electron pairs, ionic- attraction of opposite charges, hydrogen- sharing of a H atom

    Water Structure and Properties

    • Cohesion- attraction of water molecules to each other (maintains liquid state, surface tension)
    • Adhesion- attraction of water molecules to charged (polar) surfaces (capillary action)
    • High specific heat- amount of heat required to change 1 g of substance by 1 C (maintains internal temps, absorbs heat from chemical reactions)

    Water Properties

    • High heat of vaporization- amount of energy required to change 1 gram of substance from liquid to gas
    • Water as a solvent- Water clusters around charged and polar molecules
    • Solid water is less dense than liquid water (organization of nonpolar- cluster in water and do not dissolve)
    • Cannot form hydrogen bonds
    • Ionization- Water rarely and spontaneously form ions

    pH Scale

    • Measured hydrogen ion concentration
    • Higher pH value means lower hydrogen ion concentration (more OH-)
    • Logarithmic scale- difference of 1 is ten-fold change in hydrogen ion concentration
    • Acidity- as pH decreases (More protons (H+), lower pH (1,2,3), more acidic)
    • Basic- as pH increases

    Carbon is the Framework

    • Carbon atoms may bind to other carbon atoms, or to atoms of hydrogen, oxygen, nitrogen, phosphorus, or sulfur
    • Hydrocarbons- hydrogens bonded to chain of carbons
    • Different atoms bond to form amino acids
      • Have electronegativities associated with each, forming polar regions

    Functions of Macromolecules

    • Carbs- energy storage and structural support
    • Proteins- enzyme and structural support
    • Nucleic acids- storage of genetic information (in form of RNA)
    • Lipids- energy storage, membrane structure, cell communication

    Nucleotide Strands and Bonds

    • DNA 5' group look for phosphate group
    • DNA 3' group look for hydroxyl group
    • Phosphodiester bonds- linkage between 3' carbon atom of one sugar and the 5' carbon atom of another molecule

    Types of Bases

    • Purines- adenine and guanine (double ringed)
    • Pyrimidines- cytosine, thymine, uracil (single ringed)
    • Linked together to form a nucleic acid
      • C and G and A and T (U in RNA)
      • Hydrogen bonds between the nitrogenous bases

    Amino Acids

    • Each amino acid has a different R group
    • 20 total amino acids
    • 4 main types (non polar and neutral, polar and neutral, acidic and polar, basic and polar)
    • Linked together via a peptide bond (covalent bond through dehydration reaction)

    Protein Structure

    • N terminus- 5'
    • C terminus- 3'
    Level Examples Contributing Bonds
    Primary Amino acid sequence Covalent (peptide)
    Secondary Alpha-helix, beta-sheet H bonds
    Tertiary 3D structure H bonds, ionic, covalent, hydrophobic
    Quaternary Subunit interactions H bonds, ionic, covalent, hydrophobic

    Denaturation

    • Changes in chemical and physical conditions in the environment
    • Protein unfolds and deactivates
    • Can restore if conditions are right (renaturation)
    • Extreme conditions cause to adapt

    Common Features and Differences Between Prokaryotic and Eukaryotic Cells

    • Plasma membrane separates the cell interior from the extracellular environment
    • DNA is genetic material
    • Control of gene expression
    • Metabolic pathways (glycolysis, respiration, photosynthesis)
    • Eukaryotic cells have internal, membrane-enclosed compartments
    • Prokaryotic cells tend to be smaller
    • Prokaryotic cells are unicellular
    • Prokaryotic and eukaryotic cells have different propulsion systems

    Cellular Compartments and Functions

    • Nucleus: Protects DNA and separates RNA synthesis from protein synthesis, nuclear envelope (separates inside from outside), nuclear pores (openings for protein and RNA movement), nucleolus (synthesis of RNA components in ribosomes)
    • Lysosomes: Digestive enzymes help recycle building blocks for cellular reactions

    Cellular Compartments and Function (Golgi Apparatus, Peroxisomes, ER)

    • Golgi apparatus: Protein and lipid modification from ER, protein sorting and packaging
    • Peroxisomes: Oxidation of fatty acids, biosynthetic reactions, detoxification
    • ER: Calcium storage and detoxification, Rough ER: protein synthesis, Smooth ER: lipid synthesis

    Cytoplasm vs. Cytosol

    • Cytoplasm- everything inside cell membrane
    • Cytosol- just the liquid portion of the cytoplasm

    Exocytosis and Endomembrane Systems

    • ER to Golgi to either: Lysosomes, Plasma membrane or environment
    • Exocytosis- outward movement

    Chloroplast and Mitochondria Comparisons

    • Similarities: Synthesize ATP, reproduce by binary fission, multiple membrane structures, circular DNA, ribosomes
    • Differences: Mitochondria metabolize sugar to synthesize ATP, chloroplasts are only found in plants, using light energy to make ATP and sugars, mitochondria has 2 membrane structures, chloroplasts have 3 membrane structures

    The Theory of Endosymbiosis

    • Mitochondria and chloroplasts originated from bacteria that were engulfed by ancestral eukaryotes
    • Mitochondria: came from bacteria that performed oxidative metabolism
    • Chloroplasts: came from bacteria that performed photosynthesis
    • Explains why both have circular DNA, ribosomes, and divide within the cell by binary fission.

    Cytoskeletal Filaments

    • Actin: Muscle contraction, cell shape, cell crawling, cytokinesis
    • Microtubules: Organization, cell swimming, mitosis
    • Intermediate filaments: Structural support

    Extracellular Matrix vs. Cell Wall

    • Extracellular matrix: Meshwork of secreted carbs and proteins, fibrous nature
    • Cell wall: Outside of plasma membrane for protection and structural support

    Molecular Composition of Cell Membranes

    • Lipids: provide structure of membrane
    • Carbs: outer surface of plasma membrane form a sugar coat (provides protection and facilitates cell-cell recognition)
    • Proteins: membrane-specific functions

    Phospholipid Structure

    • Polar hydrophilic head group
    • Two non-polar hydrophobic tails
    • Fatty acid- long chain hydrocarbons with a carboxylic acid group at one end
    • Saturated: no double bonds are present
    • Unsaturated: double bonds between one or more pairs of successive carbons

    Selective Permeability

    • Small, nonpolar molecules (O2, CO2, N2) readily diffuse through bilayer
    • Small, uncharged, polar molecules (H2O, ethanol) diffuse at slower rate
    • Large, uncharged polar molecules (glucose, amino acids) diffuse at slower rate

    Fluid Mosaic Model

    • Two-dimensional fluid in which proteins are inserted or dissolved; gives the membrane a fluid character
    • Membrane proteins: integral and peripheral
    • Cholesterol, proteins, carbs, phospholipids
    • Evidence from x-rays and neutron scattering

    Membrane Proteins

    • Integral membrane proteins: Embedded in bilayer; must destroy bilayer structure to isolate peripheral membrane proteins
    • Peripheral membrane proteins: Non-covalently bound membrane proteins or phospholipid heads, can be removed without destroying structure

    Cell Membranes are Asymmetric

    • Two faces are different in composition and function
      • Each face has different types of phospholipids, different types of proteins, different domains of TM proteins, the outer face only has carbs.

    Membrane Proteins Classified by Function

    • Receptors: detect signal molecules and initiate the cell's response
    • Identity markers: give cell identity and allow cell recognition
    • Enzymes: associate with different membranes and promote specific chemical reactions
    • Cell adhesion: one cell to attach to another or to extracellular matrix
    • Cytoskeletal attachment: transmit changes in cytoskeleton to plasma membrane; controls cell shape
    • Transport: facilitate movement of small hydrophilic molecules from one membrane side to the other

    Transport by Channel Proteins

    • Creates a pore in the membrane
    • Many involved in ion transport (function by passive transport)
    • Can be specific for certain molecules
    • Are always open or are gated

    Active Transport by Carrier Proteins

    • Use energy to create and/or maintain a concentration gradient
    • Molecules are transported or pumped up (against) the concentration gradient
    • Many active transporters are ATPases
      • Use energy from ATP hydrolysis to power movement

    Active Transport vs. Passive Transport

    • Passive: move down gradient thru channel and carrier proteins
    • Active: use energy to make or maintain gradient from low to high concentrations
      • Use ATP hydrolysis for energy

    Coupled Transport: Symporters and Antiporters

    • Symporters: ion and molecule move in same direction
    • Antiporters: use energy from ion moving down gradient to transport molecule in opposite direction

    Osmosis

    • Water will move down its concentration gradient
    • Solute concentration differs on two sides of cell membrane; influences movement of water.
    • Move towards higher solute concentration

    Types of Tonics

    • Hypertonic: higher concentration on outside, skinny cell
    • Isotonic: equal concentration
    • Hypotonic: higher concentration on inside, fat cell

    Pinocytosis- Cell Drinking

    • Non-selective uptake of water and macromolecules
    • Constant inward budding of plasma membrane to form endocytic vesicles
    • Eventually to be delivered to lysosomes

    Receptor-Mediated Endocytosis

    • Receptor protein binds specific molecule (target)
    • Receptor and target are collected in clathrin-coated vesicles
    • Provides selective uptake of necessary molecules

    Phagocytosis- Cell Eating

    • Selective engulfment of another cell
    • Not all cells capable of this
      • Example: white blood cells destroying invaders

    Energy Basics

    • Flows into the world from the sun
    • Forms: mechanical, heat, sound, electric current, light, radioactivity
    • Two states:
      • Kinetic- energy of motion
      • Potential- stored energy
    • Energy- ability to do work (measured in joule)
    • Reduction- gain of electrons (negative charge)
    • Oxidation- loss of electrons (positive charge)

    First Law of Thermodynamics

    • Energy cannot be created or destroyed
      • Can only change from one form to another
      • Some energy is lost as heat during energy conversion
      • Total amount of energy in the universe is constant
    • Energy continuously flows thru biological systems from sun to heat

    Second Law of Thermodynamics

    • Entropy (disorder) is continuously increasing
    • Energy transformations proceed spontaneously to convert matter from a more ordered/ less stable form to a less ordered/ more stable form

    Free Energy (Gibbs Free Energy)

    • G= energy available to do work
    • G= H-TS
      • H: enthalpy- energy in a molecule's chemical bonds
      • T: absolute temperature (degrees C+273)
      • S= entropy
    • Delta G= change in free energy
    • Delta G= delta H- T delta S

    Endergonic (Positive) Reactions

    • Products of reaction have more free energy than the reactants
    • Not spontaneous
    • Require input of energy (endergonic)
    • Bond energy H is higher, entropy S is lower
    • Energy level of reactions less than products

    Exergonic (Negative) Reactions

    • Proceed spontaneously
    • Contain less free energy than the reactants
    • Lower bond energy H, higher entropy S, or both
    • Exergonic- release energy
    • Not instantaneous- may still need energy input to start
    • Energy level of reactants greater than products

    Activation Energy

    • Extra energy required to destabilize existing bonds and initiate a chemical reaction
    • An exergonic reaction rate depends on the activation energy required
      • To increase reaction rate, either increase energy of reacting molecules (heating) or use a catalyst to lower activation energy

    Catalysts

    • Substances that influence chemical bonds in a way that lowers activation energy of a reaction
    • Cannot violate laws of thermodynamics
    • Cannot make an endergonic reaction
    • Do not alter the proportion of reactant turned into product

    Enzymes are Biological Catalysts

    • Many proteins and some RNA molecules act as enzymes
    • Enzyme shape stabilizes transient association between substrates
    • Enzyme is not changed or consumed in reaction
      • Can be used again and again
    • Different types of cells contain different enzymes: enzymes specify cell structure and function
    • Enzymes may be soluble or associated with membranes

    The Active Site

    • A pocket or cleft for substrate binding
    • Allows precise fit of substrate
    • Applies stress to distort bond(s) to lower activation energy
    • Enzymes may change shape to maximize contact with the substrate (induced fit)

    Factors That Influence Enzyme Function

    • Concentration of substrate
    • Concentration of enzyme
    • Any chemical or physical condition that impacts enzymes structure
      • Temperature
      • pH
    • Regulatory molecules

    Enzyme Regulatory Molecules

    • Allow cells to control enzyme activities (for allosteric enzymes)
    • Inhibitors- molecule that binds to and decreases the activity of an enzyme
    • Competitive inhibitor: competes with substrate for active site
    • Noncompetitive inhibitor: binds the enzyme at a site (allosteric site) other than active site
      • Causes shape change that makes enzyme unable to bind to substrate

    Metabolism

    • Total of all chemical reactions carried out by an organism
    • Anabolic reaction (anabolism)- expand energy to synthesize molecules
    • Catabolic reaction (catabolism)- harvested energy by the breakdown of molecules

    Biochemical Pathways

    • Reactions occur in a sequence
    • Product of one reaction is the substrate for the next reaction
    • Many occur within organelle or within certain membranes
      • Example: inner mitochondrial membrane needed for ATP synthesis

    Feedback Inhibition

    • End product of pathway binds allosteric site on first enzyme in pathway
    • Shuts off pathway so raw materials and energy are not wasted

    The ATP Cycle

    • Is main energy currency for all cells (stored in muscles)
    • ATP is constantly synthesized and used
    • Cells only store ATP for a few seconds (Coupled ATP reactions)
    • Overall net negative delta G
    • ATP synthesis depends on energy from exergonic cellular reactions
    • ATP hydrolysis provides energy for endergonic cellular processes.

    ATP is Also Used to Control the Activity of Proteins

    • Phosphorylation/ dephosphorylation is a molecular light switch.
    • To turn on
      • Enzyme kinase binds and hydrolyzes ATP, target protein attaches the released phosphate group to protein
    • To turn off
      • Enzyme phosphatase removes phosphate group from relevant amino acid side chain.

    How Organisms Obtain Energy

    • Autotrophs: produce own ATP and organic molecules through photosynthesis (plants, algae, photosynthetic bacteria)
    • Heterotrophs (95% species): Live on organic molecules made by autotrophs; convert that energy into ATP (animals, fungi, most protists)

    Transfer Often Involves Cofactors Working as Electron Carriers

    • Transfer of electrons always has some energy loss.
    • All are easily and reversibly oxidized and reduced.
    • NAD+ accepts 2 electrons and 1 proton to become NADH, NADH donates 2 electrons and loses 1 proton to become NAD+.
    • NADH has higher energy than NAD+, more electrons and carrying more energy is present in NADH.

    The Aerobic Respiration of Glucose

    • Glucose is oxidized in the presence of molecular oxygen (O2)
    • Final electron acceptor is oxygen (O2)
    • Energy must be harvested in small steps (involve electron carriers)
    • Convert half of energy stored in glucose to ATP
      • C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

    Glucose Oxidation Proceeds in Four Stages

      1. Glycolysis (in cytosol)
      1. Pyruvate oxidation (in matrix)
      1. Krebs cycle (in matrix)
      1. Electron transport chain and chemiosmosis (inner membrane)
      • Bulk of ATP synthesis occurs
      • Cytoplasm or plasma membrane for prokaryotes
      • Steps 2, 3, 4 require oxygen to work

    Glycolysis Converts One Glucose to Two Pyruvates

    • Multi-step biochemical pathway
    • Two phases
      • Energy input (requires ATP)
      • Energy production (produces ATP and NADH)
    • Glucose is converted into 2 G3P molecules, each G3P molecule is converted into pyruvate.

    Glucose in First Converted into Two G3P Molecules

    • Generation of glyceraldehyde-3-phosphate (G3P) (split of glucose) requires energy input
    • Endergonic process
      • Hydrolysis of 2 ATP molecules
      • Needed to prime cleavage of glucose backbone
      • Split into 2, 3-carbon molecules

    Each G3P Molecule is Converted into Pyruvate

    • G3P is oxidized- NAD+ into NADH (Transfers 1 proton and 2 electrons)
    • NAD+ is reduced to NADH
    • Substrate level phosphorylation- transfer of Pi from ADP to form ATP
    • Products of glycolysis: 2 ATP (net), 2 NADH

    Pyruvate Oxidation During Aerobic Respiration (Oxygen)

    • Occurs in: mitochondrial matrix of eukaryotes, plasma membrane of prokaryotes
    • Catalyzed by pyruvate dehydrogenase
    • Causes the removal of CO2 from pyruvate
    • Coenzyme- small organic molecule used as cofactor
      • 1 CO2 (x2), 1 NADH (x2), 1 acetyl-CoA (x2)

    Krebs Cycle

    • Oxidizes the acetyl group generated by pyruvate oxidation
    • Occurs in the matrix of the mitochondria
    • Pathway of 9 steps divided into 3 parts
      • Acetyl-CoA + oxaloacetate to citrate
      • CoA cycles out and can be reused by oxidation
      • Citrate rearrangement and decarboxylation (2 CO2 released)
      • Regeneration of oxaloacetate

    Krebs Cycle Summary

    • For each acetyl-CoA entering:
      • Release 2 molecules of CO2
      • Reduce 3 NAD+ to 3 NADH
      • Reduce 1 FAD (electron carrier) to FADH2
      • Produce 1 ATP
      • Regenerate oxaloacetate
    • Cycle always happens twice (4 CO2, 6 NADH, 2 FADH2, 2 ATP)

    After the First 3 Stages of Aerobic Respiration

    • One glucose molecule has been oxidized to

      • 6 CO2
      • 10 NADH
      • 2 FADH2

    • Oxidative phosphorylation- produces ATP derived from glucose oxidation

    Electron Transport Chain

    • Three transmembrane enzyme complexes harvest some energy from electrons and pass lower-energy electrons onward
    • Complexes use energy harvested from electrons to pump protons (H+) from matrix to intermembrane space.
    • Creates concentration gradient- higher proton concentration in intermembrane space compared to matrix

    Explaining the Image (Electron Transport Chain)

    • NADH delivers electrons to NADH dehydrogenase enzyme, extracts energy to power proton movement across membrane
    • Carrier Q gives energy to bc1 complex, extracts energy to power proton movement across membrane
    • Cytochrome c catalyzes reduction of molecular oxygen
    • FADH2 electrons bypass first step in inner membrane

    Chemiosmosis

    • The proton gradient represents potential energy
    • Only way for protons to move into matrix is thru proton transporter
    • ATP synthase uses energy released by movement of protons to synthesize ATP from ADP and Pi
    • Movement of 4 H+ thru ATP synthase powers the synthesis of 1 ATP molecule from ADP and Pi

    Calculating the Energy Yield of Respiration

    • Number of ATP molecules produced by ATP synthase depends on
      • Number of protons transported across inner membrane
      • Number of protons needed for ATP synthesis • NADH: 10 protons transported = 2.5 ATP/NADH • FADH2: 6 protons transported = 1.5 ATP/FADH2

    Final Electron Acceptors

    • For aerobic organisms:
      • With O2 (respiration)
      • Without O2 (fermentation): organic molecules (pyruvate), incomplete oxidation
    • For anaerobic organisms
      • Respiration: S or CO2 or inorganic metal, inorganic molecules (sulfate and nitrate)

    Fermentation Differences

    • Lactic acid fermentation produces lactic acid from electron transfer from NADH to pyruvate
    • Ethanol fermentation produces ethyl alcohol and carbon dioxide

    Extraction of Energy from Macromolecules

    • Cell building blocks, Oxidative respiration, Key intermediates: glucose is not the only source of energy

    Catabolism of Proteins

    • Proteins are broken down into individual amino acids subunits
    • Amino groups removed thru deamination reaction
    • Remainder is converted into molecule ready for glycolysis or Krebs cycle

    Catabolism of Fats

    • Fats are first broken down to fatty acid and glycerol
    • Fatty acids are converted to two-carbon acetyl groups by beta-oxidation
    • Each acetyl group is combined with coenzyme A to form acetyl-CoA, then acetyl-CoA enters Krebs cycle

    Photosynthesis Overview

    • Energy for almost all life on earth comes from photosynthesis
    • Carbon dioxide is reduced to glucose using electrons gained from oxidation of water, driven by sun's energy
    • Photosynthesis and respiration use the products of each other as starting substrates
      • 6CO2 + 12H2O → C6H12O6 + 6O2 + 6H2O

    Chloroplasts and Mitochondria Form an Energy Cycle

    • Photosynthesis uses products of respiration as starting substrates.
    • Respiration uses products of photosynthesis as starting substrates
    • Evolutionary related

    Photosynthesis Occurs in Chloroplasts

    • Triple membrane structure
      • Outer membrane interacts with cytosol
      • Inner membrane encloses internal compartment (matrix- stroma)
      • Thylakoid disks stacked in columns (granna).
        • Contains chlorophyll and protein complexes
    • Convert light energy to chemical energy

    Two Stages of Photosynthesis

    • Light-dependent reactions:
      • Require light
      • Occur in the thylakoid
      • Capture energy from sunlight
      • Make ATP and reduce NAD+ to NADPH
      • Products O2 as a byproduct.
    • Light-independent reactions (carbon fixation)
      • Does not require light
      • Occur in the stroma
      • Use ATP and NADPH to synthesize organic molecules from CO2

    Pigments Absorb Photons of Visible Light

    • Photons: particle of light that acts as discrete bundles of energy
    • Energy is inversely proportional to the wavelength of the light
      • Shorter wavelength = more energy (Blue > Red)

    Photoelectric Effect

    • When a photon strikes a molecule with the correct amount of energy, the molecule absorbs the photon and raises an electron to a higher energy level
      • Excited electron: Chloroplasts in photosynthesis

    Pigments Have Characteristic Absorption Spectra

    • Chlorophyll a: Main pigment in plants (absorbs violet-blue and red light - directly converts light energy into chemical energy)
    • Chlorophyll b: Accessory pigment (absorbs blue and red-orange light)
    • Carotenoids: Accessory pigments (absorbs blue and green light, function as antioxidants, reflects orange and red)

    Chloroplasts Have Two Linked Photosystems

    • Oxygenic photosynthesis: oxygen generation
    • Photophosphorylation: production of NADPH from NADP+ and ATP from ADP

    Light-Dependent Reactions

    • Overall goal: creation of proton gradient across the thylakoid membrane where the concentration is greater in thylakoid space than stroma.
    • Water is electron donor- replaces electrons pairs that reaction center donated to electron acceptor

    ATP is Produced Via Chemiosmosis

    • ATP synthase uses proton gradient to produce energy for ATP synthesis
    • Low protons (high pH)
    • High protons (low pH)

    Noncyclic Photophosphorylation

    • Noncyclic photophosphorylation generates NADPH and ATP but building organic molecules requires more energy.
    • Occurs in both photosystems

    Cyclic Photophosphorylation

    • Cyclic photophosphorylation allows cells to produce additional ATP by "short-circuiting" photosystem I to create a larger proton gradient.
    • High-energy electrons leave photosystem I and are used to make ATP instead of NADPH.
    • Cycle occurs between photosystem I and b6f complex (infinite loop)

    Light-Independent Reactions: The Calvin Cycle

    • Biochemical pathway that allows for carbon fixation
      • Uses ATP as an energy source
      • Uses NADPH as a source of protons and electrons
      • Converts inorganic CO2 into organic carbohydrates
    • Also called C3 photosynthesis
    • Occur in the stroma

    The Calvin Cycle Has Three Phases

      1. Carbon fixation
      • Key step: RuBP+CO2= 2PGA
      • Uses enzyme ribulose bisphosphate carboxylase/oxygenase (Rubisco)
      1. Reduction
      • PGA is reduced to G3P
      1. Regeneration of RuBP
      • G3P is used to regenerate RuBP
      • 3 turns (3 CO2) to make enough carbon to make new G3P)
        • 6 turns to incorporate enough carbon for 1 glucose molecule

    Photorespiration

    • Rubisco has 2 enzymatic activities:
      • Carboxylation: leads to carbon fixation, addition of CO2 to RuBP, favored under normal conditions
      • Oxidation: leads to photorespiration, addition of O2 to RuBP leads to CO2 release, favored in hot and dry conditions
    • CO2 and O2 compete for active site on Rubisco, problems for C3 plants

    C4 and CAM Pathways Minimize Photorespiration

    • Some plants have evolved capture CO2 by another mechanism (C4 and CAM)
      • Add CO2 to PEP to form a 4-carbon molecule
      • Use PEP carboxylase instead of rubisco, has greater affinity for CO2 and no use for oxidase activity
      • Minimizing impact of photorespiration
    • C4 plants use a spatial solution, CAM plants use a time-based solution

    Nucleic Acids are Assembled from Nucleotides

    • DNA is a nucleic acid composed of nucleotides
      • Nucleotides consist of a 5-carbon sugar(deoxyribose), each carbon is bound to different functional groups, nitrogenous base (adenine, thymine, cytosine, guanine, determines identity of nucleotide), phosphate group (PH4).
        • Attached to 5" carbon of the sugar
        • Free hydroxyl group (-OH) attached at the 3" carbon of the sugar)
        • Attached to daughter during replication.

    DNA and RNA Differences

    • DNA: Deoxyribose sugar, Thymine base pairs with adenine, Double strand
    • RNA: Ribose sugar, Uracil base pairs with adenine, Single strand
    • Formed between the phosphate group of one nucleotide and the 3' (-OH) of another
    • Form long chains of DNA thru dehydration synthesis reactions
    • Phosphate group is linked to two sugars by ester bonds
    • Will always have free 5' and 3' at different ends
    • The chain of nucleotides has intrinsic polarity (5'-3' orientation)

    Chargaff's Rules

    • Amount of adenine = amount of thymine
    • Amount of cytosine = amount of guanine
    • Proportion of purines (A and G) = proportion of pyrimidines (C and T)
      • Or add to 50%

    The Watson-Crick Model of DNA

    • Proposed a double helix structure
    • Two nucleotide strands
      • Backbone made of repeating phosphate and sugar units joined by phosphodiester bonds
      • Nitrogenous bases on each nucleotide pair with nitrogenous bases on the opposing strand through hydrogen bonds
    • Strands are antiparallel
      • Can deduce sequence of one strand from the other

    Complementary Base Pairs

    • G forms 3 H bonds with C
    • A forms 2 H bonds with T
    • Gives consistent diameter

    An Introduction to DNA Replication

    • Semi-conservative: one strand from parent model remains intact
    • DNA replication requires:
      • Something to copy (parental DNA molecule, template)
      • Something to do the copying (enzymes, DNA polymerase)
      • Building blocks to make a new copy (nucleoside triphosphates)
      • Only pentose sugar and nitrogenous base.
    • DNA replication occurs in 3 stages: Initiation, elongation, Termination

    DNA Polymerase

    • Matches template base with complementary nucleotides and link incoming nucleotide to daughter strand
    • Several types: all have several common features
      • Add new bases to 3' end of existing strands
      • Synthesize in 5' to 3' direction.
      • Require a primer of RNA
    • Reading in 3' to 5'
    • Writing in 5' to 3'

    Prokaryotic Replication

    • E. coli contains a single circular molecule of DNA (chromosome)
    • Begins at one origin of replication- particular genome where replication is initiated.
    • Catalyzed by replisomes (contains DNA polymerase)
    • Proceed in both directions around the chromosome

    The E. Coli Replication Fork

    • Helicase and primase (replisome): unwinding DNA and synthesizes new primer for lagging strand
    • DNA gyrase: relieve torsional strain in DNA
    • SSBs: maintains template DNA as single strand
    • DNA polymerase III (2): keep strand separate
      • Use clamp molecule to keep DNA on track.
    • Carry out simultaneous synthesis of both leading and lagging strands
    • Looping in lagging strand: polymerases can move together in direction of replication fork
    • Fork moves in direction of parent DNA

    Replication is Semi-Discontinuous

    • DNA is composed of two antiparallel strands
    • DNA polymerase can only synthesize in 5' to 3' direction
      • Problem: how can both strands be synthesized simultaneously?
      • Solution: replication is semi-discontinuous; synthesis occurs continuously on one strand and discontinuously on the other.

    Okazaki Fragments

    • Leading strand is synthesized continuously from an initial primer
    • Lagging strand is synthesized discontinuously w/ multiple priming and synthesis events
    • Creates Okazaki fragments
    • Synthesized in the opposite direction of fork movement

    Eukaryotic Replication

    • Basic mechanisms similar to prokaryotes
    • Complicated by
      • Larger amounts of DNA
      • Multiple chromosomes (can occur simultaneously)
      • Linear chromosomes (must deal w/ replication of ends, need special mechanisms to ensure ends are copied)

    Telomeres

    • Specialized structures found at the ends of eukaryotic chromosomes
    • Composed of short repeated DNA sequences
    • Protect ends from nucleases and maintains chromosome integrity

    Telomerase

    • Allows for replication of lagging strand ends
    • Contains RNA template (matches repeating sequence)
    • Synthesizes last segment of DNA
    • Can base pair to telomere DNA and synthesizes short stretches of DNA at the end
    • Connection between senescence (cell aging) and telomere length (expressed in embryos and childhood; not expressed in adults, only stem cells)
    • Stop dividing when lose telomerase activity
    • Cancer cells generally show activation of telomerase.

    Cells Contain Multiple DNA Repair Mechanisms

    • Mistakes may occur during replication
      • DNA polymerase has “proofreading” ability to fix mistakes
      • Some mistakes remain and maintain genetic variation
    • Mutagens (radiation and chemicals)
      • Increase the number of mutations above the background level Two general categories for DNA repair systems
      • Specific repair: targets a single type of DNA damage and repairs only that damage.
      • Nonspecific repair: use a single mechanics to repair multiple types of DNA

    Photorepair Removes Thymine Dimers

    • UV light induces thymine dimers
    • Covalent link of adjacent thymine bases
    • Photorepair by photolyase
      • Absorbs light in visible range, uses energy to cleave thymine dimer

    Excision Repair

    • Nonspecific repair mechanism
      • Steps: recognition of damage, removal of damaged region, re-synthesized using undamaged strand as template

    Gene Expression and the Central Dogma

    • Transcription: RNA synthesis
    • Translation: protein synthesis
    • DNA to RNA to protein
    • Gene: discrete nucleotide sequence on a chromosome that codes for an RNA or protein

    Types of RNA

    • Messenger RNA (mRNA): codes for proteins
    • Ribosomal RNA (rRNA): components of ribosome, catalyze protein synthesis
    • Transfer RNA (tRNA): adaptors between mRNA and amino acids
    • Small nuclear RNA (snRNA): pre-mRNA splicing
    • Non-coding sequences are removed
    • Micro-RNA (miRNA): regulates gene expression

    RNA Polymerase

    • Enzyme of synthesis- catalyzed phosphodiester bond formation
    • Makes a single-stranded RNA copy of template DNA strand
    • Made of multiple subunits which form the core enzyme
    • Synthesizes in 5' to 3' direction
    • Does not need primer
    • Must be position on promoter sequence upstream of the gene to be transcribed
    • Key regions: -35 (AACTGT) and -10 (ATATTA)
    • Starts at and follows green arrow

    Sequence Process Review of Initiation

    • RNA pol opens DNA and inserts 1st subunit

    Initiation of Transcription

    • Sigma subunit recognizes promoter
    • DNA unwound ahead of start site
    • Sigma subunit released after around 10 subunits

    Termination of Transcription

    • Terminator sequence: RNA base pairs with itself to create hairpin.
    • Disrupts DNA/RNA/RNA polymerase interaction

    Eukaryotic Transcription

    • Occurs in the nucleus
    • Three different types of RNA polymerase
      • Prokaryotes only have one
      • RNA polymerase II transcribes mRNA
    • Promoter position and sequence differs from prokaryotes
    • A series of transposition factors are needed that recruit and activate RNA pol II
    • Termination sites are not well defined
    • Primary transcripts are processed to produce mature mRNA

    Processing of Eukaryotic mRNA

    • Primary transcript modified to mature mRNA by
      • Addition of 5' cap, protects mRNA from degradation, helps align mRNA for translation
      • Addition of 3' poly-A tail, protects mRNA from degradation
      • Removal of non-coding regions (introns) by spliceosome

    Alternative Splicing

    • Exons- coding regions that specify amino acids
    • Introns- non-coding regions that don't need to be translated
    • Single primary transcript may be spliced into different mRNAs by the inclusion of exons

    Translation

    • Process of protein synthesis
      • Convert RNA sequence into polypeptide sequence
      • Basics

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