MCAT AAMC Content Outline - Science (1) PDF

AAMC Content Outline General Math Recognize and interpret linear, semilog, and log-log scales and calculate slopes from data found in figures, graphs, and tables Semi-log graph or semi-log plot is a...

AAMC Content Outline General Math Recognize and interpret linear, semilog, and log-log scales and calculate slopes from data found in figures, graphs, and tables Semi-log graph or semi-log plot is a way of visualizing data that are related according to an exponential relationship. One axis is plotted on a logarithmic scale. This kind of plotting method is useful when one of the variables being plotted covers a large range of values and the other has only a restricted range o Demonstrate a general understanding of significant digits and the use of reasonable numerical estimates in performing measurements and calculations Use metric units, including converting units within the metric system and between metric and English units (conversion factors will be provided when needed), and dimensional analysis (using units to balance equations) Perform arithmetic calculations involving the following: probability, proportion, ratio, percentage, and square-root estimations Demonstrate a general understanding (Algebra II−level) of exponentials and logarithms (natural and base 10), scientific notation, and solving simultaneous equations Demonstrate a general understanding of the following trigonometric concepts: definitions of basic (sine, cosine, tangent) and inverse (sin‒1, cos‒1, tan‒1) functions; sin and cos values of 0°, 90°, and 180°; relationships between the lengths of sides of right triangles containing angles of 30°, 45°, and 60° Demonstrate a general understanding of vector addition and subtraction and the right-hand rule (knowledge of dot and cross products is not required) Scientific Inquiry and Reasoning Skills 1) Knowledge of Scientific Concepts and Principles Demonstrating understanding of scientific concepts and principles Identifying the relationships between closely-related concepts 2) Scientific Reasoning and Problem Solving Reasoning about scientific principles, theories, and models Analyzing and evaluating scientific explanations and predictions 3) Reasoning about the Design and Execution of Research Demonstrating understanding of important components of scientific research  Reasoning about ethical issues in research 4) Data-Based and Statistical Reasoning Interpreting patterns in data presented in tables, figures, and graphs Reasoning about data and drawing conclusions from them Biological and Biochemical Foundations of Living Systems “This section tests processes that are unique to living organisms, such as growing and reproducing, maintaining a constant internal environment, acquiring materials and energy, sensing and responding to environmental changes, and adapting. It also tests how cells and organ systems within an organism act independently and in concert to accomplish these processes, and it asks you to reason about these processes at various levels of biological organization within a living system” Foundational Concept 1: Biomolecules have unique properties that determine how they contribute to the structure and function of cells and how they participate in the processes necessary to maintain life. 1A. Structure and function of proteins and their constituent amino acids Amino Acids (BC, OC) Description Absolute configuration at the α position Amino acids are all L and have the absolute configuration of S. Cysteine is an exception: it is still L, but its absolute configuration is R. Amino acids as dipolar ions Amino acid in physiological pH exists as a zwitterion Start off positive, become more negative (as pH becomes greater and they lose H + ions Isoelectronic point calculation (average of surrounding pKa’s) Classifications Acidic or basic o Acidic: Aspartic and Glutamic o Basic: Histidine, Lysine, and Arginine ▪ Note: At pH of 7, Histidine is neutral (it’s pKa is 6) ▪ Arginine and lysine have side chains with pH of roughly 10 ▪ Arginine has a “guanidine” group Hydrophobic or hydrophilic o Hydrophobic: GAVLIM PPT Reactions Sulfur linkage for cysteine and cystine Disulfide links are effectively oxidations Peptide linkage: polypeptides and proteins Peptide bond has slight double bond character – prevents bond from rotating freely, affects secondary structure and tertiary structure to some extent Hydrolysis Most macromolecules of living cells are broken apart by hydrolysis o Ex: ATP hydrolysis, digestion Dehydration – two molecules combine to form a larger molecule and water is formed as a byproduct Protein Structure (BIO, BC, OC) Structure (1o to 4o) Primary structure – sequence of amino acids secondary structure - -helix or -sheets o -sheets – can be parallel or antiparallel o reinforced by h-bonds between carbonyl oxygen of one amino acid and the hydrogen on the amino group of another o single protein usually contains both structures at various location throughout Tertiary structure-3D shape formed by curls and folds of the peptide chain o Five forces: o 1. Covalent disulfide bonds between cysteines to form the dimer cysteine o 2. electrostatic interactions (between acidic and basic) o 3. hydrogen bonds o 4. van der Waals o 5. hydrophobic forces o Proline also plays a part – kink o Note: Salt bridges contain both electrostatic interactions and hydrogen bonding (both have to be charged) Quaternary structure o two or more polypeptide chains o same five forces as tertiary Conformational Stability (Denaturing and folding, hydrophobic interactions, solvation layer) Many different conformations available for any one protein, but it will generally exist in one of few possible conformations that have the highest stability The solvation layer (or shell) describes the structured organization of a solvent (e.g. water) around a solute (e.g. a polypeptide or protein). In the case of a protein which displays hydrophobic residues on its surface, the surrounding water will orient into a highly structured organization to optimize hydrogen bonding among water molecules (as hydrogen bonding with the presented hydrophobic side chains is not an option). This highly ordered rearrangement has a much lower entropy and is less favorable than if polar side chains were present on the surface of the protein. Thus, a conformation that buries its hydrophobic residues inside the protein leads to less disruption of water's hydrogen bonding, allowing for less structure and higher entropy, which increases the protein's conformational stability. o results in less entropic penalty Two types of proteins – globular and structural o globular – more diverse, function as enzymes, hormones, membrane pumps, receptors, transport and storage, immune response, etc o Structural – made from long polymers, maintain and add strength to cellular and matrix structure ▪ collagen – most abundant type of protein in the body, adding great strength to skin, tendons, ligaments, and bone Separation techniques Isoelectric point The isoelectric point is influenced by the anionic or cationic character of the protein's amino acid side chains at a certain pH. Separation can be performed by the movement of proteins over a pH gradient in a gel electrophoresis. Proteins at their isoelectric point also have lower solubility and may precipitate out of solution. o The cathode (negative) is at the high pH end, while the anode (positive) is at the low pH end o Proteins moving from left to right get their protons stripped off and become more negative.  ▪ Negatively charged acidic proteins would be found towards the left, closer to lower pH’s (they have lower isoelectric points) ▪ Positively charged basic protons will be found towards the right, closer to higher pH’s (they have higher isoelectric points. Note: the Cathode is always negative in biochemistry, and the anode is always positive (anions flow to the anode) Electrophoresis Electrophoresis focuses on separating proteins mainly by size or charge in the course of moving across an electric field, usually with a support medium (e.g. a gel). At the end of the migration, the proteins can be stained to show the location of various protein samples, and conclusions can be drawn about the characteristics of the protein. For example, a small protein will travel farther than a larger protein, and a positively charge protein will be pulled towards the cathode (-) while a negatively charged protein will be pulled towards the anode (+) SDS-PAGE - used to analyse proteins. As a separation medium (also referred to as matrix) a polyacrylamide-based discontinuous gel is implemented in this type of electrophoresis. In addition, SDS (sodium dodecyl sulfate) is used. This anionic surfactant (detergent) covers the intrinsic charges of proteins. About 1.4 grams of SDS bind to a gram of protein, corresponding to one SDS molecule per two amino acids, so that the proteins have a constant negative charge distribution. Thus, the proteins will be separated out by size only. Reducing SDS Page – cleaves disulfide bonds, destroys quaternary and tertiary structure Non-reducing SDS page – does not cleave disulfide bonds, destroys quaternary and tertiary structure Native Page – keeps quaternary structure Non-Enzymatic Protein Function (BIO, BC) Binding A special feature of some proteins is the capability to bind other molecules with non-covalent interactions. Protein binding can be characterized by its affinity and specificity for the binding target. Affinity describes how readily the protein binds its target, and specificity refers to the preferential binding of the target over other entities. A change in the protein's conformation can alter affinity and specificity as seen in the control of voltage-gated ion channels in cell membranes Immune System The high degree of protein variability allows for a key feature of the adaptive (or acquired) immune system, the production of antibodies. An antibody is a type of protein that has a unique and very specific binding site that will readily bind its target, called an antigen, such that its target is inactivated or tagged for immune response. Motors A motor protein can perform mechanical work by coupling exergonic (energy releasing) ATP hydrolysis to a conformational change that allows for interaction with the protein's target substrate. Muscle contraction, for example, is achieved through a process of the motor protein myosin binding and releasing its microfilament (actin) substrate. Myosin also acts on microfilaments of the cytoskeleton to generate cellular movement. Two other types of motor proteins, kinesins and dyneins, act on microtubules and play a role in transport within the cell. Kinesin walks microtubule "tracks" to deliver cellular cargo (e.g. chromosomes during mitosis, vesicles), generally in an antegrade direction (center to periphery). Dynein is used in retrograde cargo transport in the axons of neurons, and is capable of sliding microtubules in relation to one another, generating the movement of cilia and flagella. Enzyme Structure and Function (BIO, BC) Function of enzymes in catalyzing biological reactions An enzyme is a biological catalyst, in that it accelerates chemical reactions in a biological system. An enzyme accomplishes this acceleration by interacting with the reactants (the enzyme's substrates) in a manner which stabilizes their transition state (‡), which in turn lowers the activation energy (Ea) of the reaction, and a lower activation energy allows for the reaction to proceed faster. Although an enzyme interacts with its substrates, it is not consumed in the reaction like a reactant. Once a reaction completes, the enzyme is again available to process new substrate. In a biological context, the reusable nature of enzymes to catalyze a particular reaction (the enzyme's specificity) offers a mechanism of controlling reactions by directing which enzymes are present and active, and in what quantities. Enzyme classification by reaction type Because of their specificity, a particular enzyme will only catalyze a singular or narrow set of similar reactions, allowing for classification by reaction type. Names for classes of enzymes are generally descriptive of the type of reaction they catalyze and usually end in the suffix -ase. o Major Class Description of reaction activity o Oxidoreductases oxidation of a hydrogen (or electron) donor (loses) and reduction of the acceptor (gains) o Transferases move a functional group from a donor molecule to an acceptor molecule ▪ Ex: protein kinases  o Hydrolases couple breaking a bond with hydrolytic cleavage (breaking water) ▪ Ex: proteases o Lyases breaking a bond with elimination to form a double bond (or ring) or adding to a double bond o Isomerases alter the geometry or structure of the reactant molecule (rearrangements) o Ligases couple forming a bond (joining two molecules) with ATP hydrolysis Reduction of activation energy Over the duration of a reaction, the reactants must move through a high energy transition state before becoming products. The difference between the free energy of the reactant(s) and the free energy of the transition state is called activation energy. When the activation energy required to arrive at the transition state is lower, the reaction will proceed faster. Thus, in stabilizing the transition state, an enzyme reduces activation energy and increases reaction rate. Substrates and enzyme specificity Enzyme specificity describes the highly selective nature of an enzyme for a particular reaction or set of reactions. The reactants for a specific enzyme then are narrowly defined and called its substrates. Active Site Model The active site model describes the location on the enzyme where it interacts with its substrate. The shape and local chemical characteristics (functional groups) of an active site are responsible for the specificity of the enzyme. In their interactive state, the enzyme and its substrate, bound at the active site, are called the enzyme-substrate complex. Induced-fit Model The induced-fit model describes how the interaction of an enzyme and its substrate is often reliant on effects the substrate has on the enzyme as well as effects the enzyme has on the substrate. The binding of an enzyme to its substrate results in a release of free energy called binding energy, with which suitable substrate in close proximity to an enzyme may cause a small change in the shape of the enzyme that is enough to boost the enzyme's affinity for the substrate, a more complementary conformation, thus "inducing" a better fit for the enzyme and its substrate. Mechanism of catalysis A mechanism of catalysis is the way in which the chemical reaction is assisted in moving forward. o Mechanism Description o Approximation simply brings reactants together in proximity and proper orientation o Covalent catalysis a reactive group on the enzyme is temporarily covalently bonded to the substrate o Acid-base catalysis a reactive group on the enzyme acts as a proton donor or acceptor o Metal ion catalysis assists in electrophilic or nucleophilic interactions or binds to substrate (increasing binding energy) Cofactors o Cofactors are inorganic ions that assist an enzyme in its catalytic activity. Examples include Fe2+ and Mg2+. (The term cofactors is sometimes used to describe the superset of non-protein helper compounds with inorganic ions in one subset and organic molecules called coenzymes in another. In this usage, cofactors, inclusive of coenzymes, may be closely or covalently bound to the enzyme as a holoenzyme. Without the required cofactor, an enzyme is in an inactive state, or an apoenzyme.) Coenzymes o Coenzymes are small, organic molecules that assist an enzyme in its catalytic activity. Examples include heme, NAD+, and coenzyme A. Many coenzymes are derived from vitamins. Water-soluble vitamins o Water-soluble vitamins include the series of B-vitamins and Vitamin C and are a dietary requirement as precursors to coenzymes (or as the coenzyme itself in the case of Vitamin C). (ADEK are fat soluble) Effects of local conditions on enzyme activity Enzyme activity can be dramatically affected by changes in temperature and pH. Low temperatures slow reaction rates, and high temperatures may increase reaction rates but also cause denaturing in protein enzymes. Fluctuations in pH can also denature a protein enzyme by disrupting the non-covalent interactions that stabilize its 2°, 3°, and 4° structures. Ideal temperatures of many enzymes is Control of Enzyme Activity (BIO, BC) Kinetics General (catalysis) o Catalysis is the process of accelerating a chemical reaction. As biological catalysts, enzymes speed up the rate of reaction but do not affect the equilibrium (Keq) or the (thermodynamically) favorable direction of the reaction. o A favorable (spontaneous) reaction is one in which the free energy of the products is lower than the free energy of the reactants (ΔG < 0). However, a thermodynamically favorable reaction may not proceed (at a perceptible rate) on account of a kinetic barrier, e.g., activation energy, which is where enzymes come in. Michaelis–Menten  o In general, reaction rate is directly proportional to the frequency of effective collisions between reactant molecules (collision theory). Higher reactant concentrations have a higher probability of collision. Similarly, in an enzyme-catalyzed reaction, an increase in the relative concentration of substrate will increase the reaction rate up to a maximum rate (with enzyme concentration held constant). o At the point where an enzyme is catalyzing reactions as fast as it can (maximum turnover), adding more substrate will not make any difference and the reaction rate is at its maximum, Vmax. Adding more enzyme at this point will allow reaction rate to continue to increase and define a new Vmax. (That is, Vmax is defined for a specific enzyme concentration.) o The Michaelis-Menten equation calculates the rate of reaction (v) using Vmax, the substrate concentration ([S]), and the Michaelis constant (Km). Km equals the substrate concentration required for the reaction rate to reach ½Vmax. As a constant, Km does not fluctuate with changes in enzyme concentration and is indicative of enzyme- substrate affinity. Enzyme-catalyzed reactions with high enzyme-substrate affinity will reach the ½Vmax benchmark at a lower substrate concentration (have a lower Km), whereas lower enzyme-substrate affinities will result in needing a higher substrate concentration to reach ½Vmax (have a higher Km). o o Catalytic Efficiency: kcat = Vmax / [Et] o catalytic efficiency is Kcat / Km (Makes intuitive sense Cooperativity o An exception to the Michaelis-Menten equation are enzymes with multiple binding sites (often over multiple subunits) that undergo cooperativity, a case in which the binding of one ligand will increase the affinity for binding another ligand at a different site. Binding sites that are not substrate active sites are called allosteric sites, and enzymes that undergo a change in catalytic activity on account of a molecule binding at an allosteric site are referred to as allosteric enzymes. o If the Hill coefficient is greater than 1, enzymes express cooperativity o Sigmoidal curves (the steeper, the more cooperative) Feedback regulation Feedback regulation of an enzyme occurs when a product of the reaction binds to an allosteric site on the enzyme, affecting its catalytic activity. This effect can be positive, producing a change that increases enzyme-substrate affinity, or inhibitory, reducing the activity at the active site or inactivating it completely. Binding molecules in feedback regulation may also extend to other reactants and products in an enzyme's metabolic pathway, producing upstream or downstream effects. Inhibition – types Competitive o A competitive inhibitor is a molecule that is similar enough to an enzyme's substrate that it can compete for the space occupying the active site. While a competitive inhibitor is bound to the active site, substrate cannot be processed. Non-competitive o A non-competitive inhibitor is a molecule that binds to an allosteric site on the enzyme, causing a conformational change that decreases catalytic activity at the active site regardless of whether a substrate is already bound. Mixed (BC) o A mixed inhibitor is a molecule that binds to an allosteric site on the enzyme, causing a conformational change that decreases catalytic activity at the active site. Mixed inhibitors generally have a preference towards binding either the enzyme-substrate complex or the enzyme alone Uncompetitive (BC) o An uncompetitive inhibitor is a molecule that binds only to the enzyme-substrate complex, rendering it catalytically inactive. o It is important to note that this does not change the slope of the lineweaver-Burke plot: the ratio of KM / Vmax is the same Binding Blocks Effect on Overcome by Inhibition type state Binding site substrate Effect on Km Vmax ↑[S] Competitive E active site yes increases no effect yes  Binding Blocks Effect on Overcome by Inhibition type state Binding site substrate Effect on Km Vmax ↑[S] Noncompetitive E or ES allosteric no no effect decrease no site Mixed E or ES allosteric no increases or decrease partially site decreases Uncompetitive ES allosteric no decreases decrease no site Regulatory enzymes Enzymes often work in concert, forming biochemical pathways that use sequences of enzyme-catalyzed reactions to achieve an overall goal (e.g. glycolysis). Enzymes along a pathway that are specifically targeted for regulation of the pathway are referred to as regulatory enzymes. Allosteric enzymes o The catalytic activity of an allosteric enzyme is regulated by an effector molecule (acting as an activator or inhibitor) that binds an allosteric site, resulting in a conformational change to the enzyme that either activates or inhibits the active site on the enzyme. In homotropic allosteric regulation the effector molecule is also the enzyme's substrate, while the effector in heterotropic allosteric regulation is not a substrate of the enzyme. Covalently-modified enzymes o Covalent modification can either activate or deactivate an enzyme through the addition or removal of a modifier using a reversible covalent bond (e.g. phosphorylation). Zymogen o A zymogen (or proenzyme; generally indicated by the suffix -ogen) is an inactive precursor that will undergo irreversible conversion to the final active form of an enzyme. Activation triggers include proteolytic cleavage of an activation segment, change in environmental pH, or cofactors. Content Category 1B: Transmission of genetic information from the gene to the protein Nucleic Acid Structure and Function (BIO, BC) Description Nucleic acids are organic macromolecules composed of a limited variety of monomers (nucleotides) linked together into polymer strands (DNA, RNA) with characteristic stability (DNA more stable; RNA less stable). Nucleotides and nucleosides The monomeric unit of nucleic acid is a nucleotide, which in turn is composed of three parts: a sugar ring, a heterocyclic base, and a phosphate group. A corresponding nucleoside is structurally similar with a sugar ring and heterocyclic base but lacks a phosphate group. The sugar ring can be either a ribose (found in RNA) or 2′-deoxyribose (found in DNA). Sugar phosphate backbone In the structure of a nucleotide, the sugar subunit is situated as a hub, linked on one side to the phosphate group and, on another side, to the base. This arrangement lends itself to the polymer construction of nucleic acids by the formation of phosphodiester bonds that connect the sugar of one nucleotide to the phosphate group of the next nucleotide in the strand. Following these sugar-phosphate linkages down the length of the nucleic acid polymer gives the impression of a backbone with a variety of bases, each extending from its sugar link.  Pyrimidine, purine residues The five common nucleotides found in DNA and RNA are divided in to purines (double ring structure) and pyrimidines (single ring structure). Base Ring structure Found in DNA Found in RNA Adenine purine Yes Yes Guanine purine Yes Yes Cytosine pyrimidine Yes Yes Thymine pyrimidine Yes No Uracil pyrimidine No Yes Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure The Watson-Crick model of the structure of DNA elucidated a double stranded composition with the two strands wound into a double helix. In addition to the helical formation, each strand runs antiparallel (its nucleotides oriented in the opposite direction of its partner strand), with the sugar-phosphate backbone running along the outside and bases projected into the center of the helix where they hold the formation by hydrogen bonding to the bases projected inward from the other strand. Base pairing specificity: A with T, G with C The hydrogen bonding between bases on each strand of a double stranded molecule of DNA is arranged with specificity between certain base pairs with each pair composed of a purine and a pyrimidine. Purine Pyrimidine Number of hydrogen bonds Adenine Thymine 2 Guanine Cytosine 3 Function in transmission of genetic information (BIO) The structure of nucleic acids as polymers with unique sequences of bases (by way of their nucleotide residues) gives way to a high fidelity means of transmitting genetic information by reading and replicating the base sequence for a strand of DNA. This process is performed in DNA replication, whereby each strand of the double-stranded DNA molecule is introduced to a new partner strand by matching new nucleotides with the correct base pairing, and in transcription, where a new molecule of RNA is created by linking nucleotides that pair with the sequence of bases on a template strand of DNA. DNA denaturation, reannealing, hybridization The double helix of double-stranded DNA is stabilized by the hydrogen bonding between base pairs along the length of the molecule. Disruption of the hydrogen bonds, such as in the case of high temperature, can cause the unwinding of the two strands (denaturation), which can then also be brought back together when proper conditions return (reannealing). A single strand of DNA will readily bind to another single strand of DNA in the process of hybridization where there is a significant amount of base pair matching between their sequences (in conditions conducive to its hydrogen bonds). DNA Replication (BIO) Mechanism of replication: separation of strands, specific coupling of free nucleic acids  Replicating a molecule of double-stranded DNA involves unwinding its helical structure, separating its two strands, and filling in new partner strands from free nucleic acids (nucleotides). Specific coupling assures that nucleotides are incorporated with correct base-pairing along the length of each of the separated strands (A with T, G with C). Each of the separated strands is read and matched with appropriate nucleotides to create a newly synthesized partner strand. Nucleotides are added by attaching the phosphate group of the nucleotide (found on its 5′ carbon) to the open 3′ carbon on the end of the elongating strand. Thus replication proceeds by reading the original strand 3′ → 5′ and elongating the new strand 5′ → 3′. Because the strands of double-stranded DNA run antiparallel, replication is performed in opposite directions, with one side extending its newly synthesized strand towards the replication fork and one side away. Only short portions (Okazaki fragments) can be synthesized in the direction away from the fork as it unzips, making this side the lagging strand. Replication on the leading strand, by contrast, is continuous into the direction of the replication fork as it unzips. Semi-conservative nature of replication DNA replication is semi-conservative on account of its two resulting molecules of double-stranded DNA each having retained a strand from the original molecule in addition to the newly synthesized strand. Specific enzymes involved in replication Enzyme Role DNA helicase works at the replication fork to unwind the helix (unzips DNA) Topoisomerases, including relax super-coiling that results from unwinding the helix DNA gyrase Single-stranded binding bind to the separated strands of DNA to keep them from reannealing proteins (SSBPs) Primase creates short RNA primer that is temporarily attached for DNA polymerase to extend from DNA polymerase follows the replication fork, working to add new nucleotides in 5′ → 3′ direction; proofreads and removes incorrect nucleotides DNA ligase helps to anneal strands; joins Okazaki fragments Telomerase lengthens telomeres of linear eukaryotic DNA Note: DNA polymerase 3 is essential for the replication of the leading and the lagging strands whereas DNA polymerase 1 is essential for removing of the RNA primers from the fragments and replacing it with the required nucleotides. Origins of replication, multiple origins in eukaryotes The process of DNA replication begins at an origin of replication, where the molecule's two strands are separated, producing a replication bubble with two replication forks unzipping the DNA bidirectionally away from the origin. Prokaryotes usually have a single origin of replication for their single, circular DNA. Eukaryotes, however, have multiple origins of replication across their numerous linear chromosomes. Replicating the ends of DNA molecules Linear chromosomes will arrive at an issue with replication at the ends of their lagging strands by which a portion of the strand at the very end (located in the telomere, a region of repetitive sequences at the end of the chromosome) is unable to be synthesized due to the lack of a 3′ end of a nucleotide to extend from. This issue results in the progressive shortening of the telomeres in linear chromosomes after numerous rounds of replication. The issue is resolved in presence of telomerase which acts to lengthen the telomeres with repetitive sequences, thereby protecting them from loss during replication. Repair of DNA (BIO) Repair during replication In replicating the DNA, there is the possibility of introducing mutations through errors in base-pairing. To limit this possibility, mismatched bases can be detected and repaired during replication. In prokaryotes, DNA Polymerase III, which is responsible for the 5′ → 3′ elongation of the newly synthesized strand, can exercise 3′ → 5′ exonuclease activity. That is, DNA Pol III can proofread upstream (3′ → 5′; the opposite direction of elongation) the last nucleotide added and, if an error is found, excise and correct it. DNA Polymerase I, which is also responsible for removal and replacement of the RNA primer, provides 5′ → 3′ exonuclease activity to repair mismatches in the direction of elongation. Repair of mutations Errors that escape correction during replication can still be identified and repaired later by a mismatch repair mechanism, a concert of mismatch repair proteins that identify mismatched bases by way of characteristic distortion of the sugar- phosphate backbone. Once mismatches are found, the incorrect match is excised (via exonuclease), replaced (via polymerase) with the correct nucleotide, and joined (via ligase) to its adjacent nucleotides in the strand. More complex but similar processes of DNA repair during and after replication take place in eukaryotes. Genetic Code (BIO) Central Dogma: DNA → RNA → protein The triplet code allows for 64 different combination unambiguous – any single series of 3 nucleotides codes for only one amino acid nearly universal Codon–anticodon relationship Degenerate code, wobble pairing mRNA – template tRNA – plays a vital role in actually rendering the triplet code of the mRNA into a specific amino acid sequence has two ends: one end: anticodon – will bind to complementary codon sequence on mRNA other end: carries the amino acid that corresponds to that codon the first two base pairs in codon and anticodon must be complementary however, there is some flexibility in bonding at the third base pair position wobble pairing – helps explain why multiple codons can code for the same amino acid Missense, nonsense codons ▪ A base substitution may have three different effects on an organism's protein. It can cause a missense mutation, which switches one amino acid in the chain for another. It can cause a nonsense mutation, which results in a shorter chain because of an early stop codon. Initiation, termination codons ▪ Start Codon – AUG - Methionine ▪ (school starts in august) ▪ Stop codons: UAA, UAG, UGA Messenger RNA (mRNA) Transcription (BIO) 1) Initiation o group of DNA binding proteins called transcription (nuclear) factors identify a promoter on the DNA strand ▪ promoter – sequence of DNA nucleotides that designates a beginning point for transcription ▪ at the promoter, the transcription factors (nuclear factors) assemble into a transcription initiation complex, which includes the major enzyme RNA polymerase ▪ consensus sequence – most commonly found promoter nucleotide sequence recognized by a given species of RNA polymerase variation from the consensus sequence causes RNA polymerase to bond less tightly and less often to a given promoter, which leads to the associated genes being transcribed less frequently o RNA polymerase unzips DNA double helix, creating the transcription bubble 2) Elongation – RNA polymerase transcribes only one strand of the DNA sequence into complementary strand o transcribed strand = template strand, or antisense (-) strand o Coding strand = (+) sense strand o RNA polymerase moves in the 3’→ 5’ direction, building new RNA strand in the 5’→3’ direction o there is no proof-reading mechanism that corrects for errors in the transcription process ▪ errors in RNA are just not transmitted to progeny 3) Termination – occurs when termination sequence is reached o can also involve special proteins, known as Rho proteins, that help to dissociate RNA polymerase from the DNA template Transcription is the main level of activation or deactivation of genes o activators and repressors (proteins) bind to DNA close to promoter and either activate or repress the activity of RNA polymerase ▪ often allosterically regulated by small molecules such as cAMP o Enhancers – short, non-coding regions of DNA found in eukaryotes, function similarly to activators but act at a much greater distance from the promoter Transfer RNA (tRNA); ribosomal RNA (rRNA) Mechanism of transcription mRNA processing in eukaryotes, introns, exons Modification of RNA o post-transcriptional processing occurs both in eukaryotes and prokaryotes o In Eukaryotes ▪ primary transcript must under modifications that include: helping the molecules that initiate translation recognize the mRNA, protect the mRNA from degradation, eliminate extraneous sequences of nucleotides, and provide a mechanism for variability in protein products from a single transcript ▪ 5’ cap – serves as an attachment site in protein synthesis during translation and as a protection against degradation by enzymes that cleave nucleotides, called exonucleases ▪ poly A tail – added at 3’ end to protect form exonucleases o Splicing – removes introns, exons remain ▪ joins the ends of exons together ▪ involves snRNPs, which contain assortment of proteins and snRNA snRNA acts as a ribozyme—an RNA molecule capable of catalyzing chemical reactions snRNPs recognize nucleotide sequences at the ends of introns, pulls the ends together (forming an intron loop of lariat), then excises the introns and joins the ends of exons ▪ spliceosome – complex formed from the association of the snRNPs and additional associate proteins o alternative splicing – allows cell to incorporate different coding sequences into mature mRNA ▪ introns may play an important function in gene expression ▪ alternative splicing, together with other eukaryotic techniques such as the use of alternative promoter sites or terminating transcription at different sites, allows the cell to create vast diversity of proteins o Takes place in nucleus of eukaryotes ▪ in contrast, prokaryotes can carry out transcription and translation concurrently, and they do not modify RNA transcripts prior to the start of translation Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNAs (snRNAs) Functional and evolutionary importance of introns ▪ While introns do not encode protein products, they are integral to gene expression regulation. Some introns themselves encode functional RNAs through further processing after splicing to generate noncoding RNA molecules (RNA that is not translated into a protein) ▪ Alternative splicing is widely used to generate multiple proteins from a single gene. Furthermore, some introns play essential roles in a wide range of gene expression regulatory functions such as non-sense mediated decay and mRNA export Translation (BIO) Roles of mRNA, tRNA, rRNA Role and structure of ribosomes Initiation, termination co-factors Post-translational modification of proteins takes place on ribosome (Note: the chemical composition of ribosomes on eukarya and Bacteria are slightly different) o small subunit and large subunit, made from rRNA and many separate proteins o Prokaryotic ribosomes – 30S and 50S, combined sedimentary coefficient of 70S o Eukaryotic ribosomes – 40S and 60S, combined sedimentary coefficient of 80S o assembled in the nucleolus ▪ small and large subunits exported separately to the cytosol Same steps as transcription – initiation, elongation, and termination o initiation ▪ initiation factors help attach 5’ end to small subunit of ribosome ▪ a tRNA containing the 5’-CAU-3’ anticodon sequesters methionine and settles into the P site signal for the large subunit to join and form the initiation complex o Elongation ▪ ribosome slides down mRNA one codon at a time in the 5’→3’ direction, matching each codon to a complementary tRNA anticodon ▪ the corresponding amino acids attached to these tRNAs are bound together into a growing polypeptide ▪ requires the input of energy ▪ C-terminus of methionine attaches to the N-terminus of the amino acid at the A site in a dehydration reaction, forming a peptide bond takes place through peptidyl transferase activity, which is catalyzed by rRNA in the ribosome o another example of ribozyme function the tRNA that carried methionine moves to the E site (for exit) ▪ E- exit, P – Peptide bond, A – accept o Termination ▪ stop codon is reached ▪ proteins known as release factors bind to A site ▪ allows water molecule to add to the end of the polypeptide chain ▪ polypeptide is freed, ribosome breaks up Even as the polypeptide is being translated, it begins folding After translation o post-translational modifications – affect which products of translation ultimately become functional proteins ▪ sugars, lipids, or phosphates can be added to amino acids to influence functionality ▪ cleavage can occur ▪ formation of quaternary structure o Final destination ▪ proteins translated by free-floating ribosomes function in the cytosol ▪ proteins synthesized by ribosomes that attach to the rough ER during translation are injected to the ER lumen can become membrane-bound proteins of nuclear envelope, ER, golgi, lysosomes, plasma membrane, or can be secreted from the cell  the growing polypeptide itself may or may not cause the ribosome to attach to the ER, depending upon the polypeptide o a 20 aa sequence called a signal peptide near the front of the polypeptide is recognized by protein-RNA signal-recognition particle (SRP) that carries the entire ribosome complex to a receptor protein on the ER o signal peptide is usually removed by an enzyme o signal peptide can also target to mitochondria, nucleus, or other organelles Eukaryotic Chromosome Organization (BIO) Chromosomal proteins Single copy vs. repetitive DNA - The vast majority of the genome consists of non-coding DNA sequences, much of which is repetitive Supercoiling Heterochromatin vs. euchromatin Telomeres, centromeres ▪ sister chromatids joined together at centromeres kinetochore – structure of protein and DNA located at the centromere of joined chromatids of each chromosome Chromosomes o consists of compactly wrapped DNA and protein in a hierarchy of organizational levels o proteins – histones ▪ have basic functional groups, which give net positive charge that attracts the negatively charged DNA strands ▪ 8 histones – nucleosome ▪ nucleosomes wrap into coils, which wrap into supercoils ▪ cannot be transcribed Chromatin – entire DNA/protein complex, and a small amount of RNA o Tightly condensed = heterochromatin ▪ constitutive heterochromatin – permanently coiled o Euchromatin – uncoiled, able to be transcripted (“YOU”-Chromatin) ▪ is only coiled during nuclear divisions o Nucleotide sequences that code for protein products often contain single copy DNA ▪ as opposed to repetitive DNA, which makes up non-coding regions DNA methylation o involves the addition of an extra methyl group to particular cytosine nucleotides o causes DNA to be wound more tightly—methylated sections are thus inaccessible to transcription machinery o If methylation is in the repressor region of a gene, it can increase activation of that gene Chromosomal Vocabulary o inside human somatic cell, ▪ 46 double-stranded DNA molecules ▪ chromatin associated with each one is wound into chromosome ▪ in human cells, each chromosome possess a partner that codes for the same traits— homologues o Diploid – contains homologous pairs o Haploid – does not contain homologues o There are 46 chromosomes before replication, and 46 chromosomes after replication ▪ the replicated and un-replicated versions of a chromosome are each considered to be a single chromosomes ▪ the duplicates can be referred to separately as sister chromatids Control of Gene Expression in Prokaryotes (BIO) Operon Concept, Jacob–Monod Model ▪ The model proposed by Jacob and Monod predicted that a specific DNA sequence near the transcription start site of the lac operon is a binding site for lac repressor. Gene repression in bacteria Positive control in bacteria In Prokaryotes o primary function of gene regulation is to respond to changes in the environment ▪ in contrast, the maintenance of homeostasis is the hallmark of multicellular organisms o Prokaryotic mRNA typically include several genes in a single transcript (polycistronic), whereas eukaryotic mRNA includes only one gene per transcript (monocistronic) o Operon – genetic unit consisting of operator, promoter, and genes that contribute to a single prokaryotic mRNA ▪ Lac Operon in E. Coli E coli generally prefers to use glucose when it is present lac operon codes for enzymes that allow E. coli to import and metabolize lactose when glucose is not present in sufficient qualities o the lac operon is thus only activated if two conditions are met: if glucose is scarce and lactose is present o low glucose → high cAMP levels o cAMP binds to and activates Cap, which binds to a CAP site located adjacent and upstream to promoter on lac operon o CAP activates promoter, allowing transcription second regulatory site –operator, located adjacent and downstream to the promoter o when lactose is not present in the cell, repressor protein binds to the operator site and prevents transcription of lac genes, thereby preventing gene expression o when lactose is present, it binds to lac repressor protein, making that protein unable to bind to the repressor site ▪ No glucose → activation, lactose → lack of repression presence of lactose can induce the transcription of lac operon only when glucose is not present Control of Gene Expression in Eukaryotes (BIO) Transcriptional regulation DNA binding proteins, transcription factors Gene amplification and duplication Post-transcriptional control, basic concept of splicing (introns, exons) Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes Regulation of chromatin structure DNA methylation Role of non-coding RNAs  Epigenetics – the changes made around the genome that do not alter actual nucleotide sequence o these changes instruct the cellular machinery how to read the genome, thereby altering gene expression o include changes such as the attachment of chemical markers to the genome, histone protein modification, and use of non-coding RNAs to influence gene expression o Epigenetic markers and histone modifications can be passed down from one generation to the next Histone acetylation typically promotes transcription by modifying chromatin structure, decreasing its condensation. Cancer o proto-oncogenes can be converted to oncogenes, genes that cause cancer, by mutagens such as UV radiation or chemicals, or simply by random mutations o carcinogens – mutations that cause cancer o mutagens may also inactivate tumor suppressor genes Recombinant DNA and Biotechnology (BIO) Gene cloning o Cloning ▪ Recombinant DNA placed within a bacterial genome using a vector (typically a plasmid) ▪ bacteria then grown in large quantities not all bacteria take up the vector o include a gene in original vector that lends resistance to a certain antibiotic ▪ screens for bacteria that does not take up the vector o include lacZ gene in original vector—an endonuclease with a recognition site that cleaves the lacZ gene can then be used to place the DNA fragment into the vector ▪ we can thus screen out the vectors that don’t have our GOI, as they will still have the lacZ gene and will turn blue in the presence of X-gal o Eukaryotic DNA contains introns, and since bacteria have no mechanism for removing introns, it is useful to clone DNA with no introns ▪ mRNA produced by DNA is reverse transcribed with reverse transcriptase, forming cDNA ▪ adding DNA polymerase to cDNA produces a double strand of desired DNA fragment Restriction enzymes o Restriction Enzymes – cut only at specific sequences – restriction site ▪ palindromic sequence 4-6 nucleotides long Ex: GGATCC ▪ most restriction endonucleases cleave DNA strand unevenly, leaving complementary single-stranded ends can reconnect through hybridization and are termed sticky ends phosphodiester bonds of fragments can be joined by DNA ligase o we take advantage of the fact that two DNA fragments cleaved by the same endonuclease can be joined together ▪ recombinant DNA ▪ can be used to generate a DNA library for the purpose of DNA cloning DNA libraries ▪ A DNA library is a collection of DNA fragments that have been cloned into vectors so that researchers can identify and isolate the DNA fragments that interest them for further study. There are basically two kinds of libraries: genomic DNA and cDNA libraries. Genomic DNA libraries contain large fragments of DNA in either bacteriophages or bacterial or P1-derived artificial chromosomes (BACs and. PACs). cDNA libraries are made with cloned, reverse-transcribed mRNA, and therefore lack DNA sequences corresponding to genomic regions that are not expressed, such as introns and 5′ and 3′ noncoding regions. cDNA libraries generally contain much smaller fragments than genomic DNA libraries, and are usually cloned into plasmid vectors. Generation of cDNA Hybridization ▪ hybridization – can be used as a technique to find a particular gene in a library fluorescently or radioactively labeled complementary sequence of the desired DNA fragment (probe) is used to search the library Expressing cloned genes Gene A → isolate mRNA → reverse transcriptase → cDNA → amplify by transforming into a plasmid (containing Antibiotic resistant genes for marker → incorporate into bacteria → bacteria replicate Polymerase chain reaction Polymerase Chain Reaction o much faster way of cloning o developed using a specialized polymerase enzyme found in a species of bacterium adapted to life in nearly boiling waters o the double strand of DNA to be cloned is placed in a mixture with many copies of two DNA primers, one for each strand ▪ heating to 95 – denature ▪ cool to 60 – primers anneal ▪ 72 – heat resistance polymerase added with supply of nucleotides o 2n copies o quantitative PCR – used to quantify the amount of DNA in each cycle Gel electrophoresis and Southern blotting o gel electrophoresis ▪ nucleic acids are negatively charged, migrate through gel ▪ larger particles move more slowly ▪ Proteins are separated by a different type of gel usually denatured in the presence of a detergent before they are placed in the gel detergent coats each protein with negative charge proportional to its length proteins can also be separated based on isoelectric points ▪ Ladder – mixture of DNA, RNA , or polypeptide fragments of known sizes or quantities used for comparison o Blotting – after gel electrophoresis, for visualization purposes ▪ molecules transferred from gel onto membrane, allowing for easier manipulation or visualization ▪ Southern Blotting – target fragments of known DNA sequence in a large population of DNA gel placed in basic solution to denature DNA fragments (double to single strand) nitrocellulose placed on top or below gel, transferred to this membrane labeled probe with complementary nucleotide sequence is added visualize ▪ Northern Blot – identifies RNA fragments ▪ Western blot – detect a particular protein in a mixture of proteins visualization usually occurs through antibodies o primary antibody specific to protein in question used first o secondary antibody-enzyme conjugate added ▪ recognizes and binds the primary antibody and marks it with an enzyme for visualization ▪ reaction catalyzed by enzyme attached to the secondary antibody produces color or something DNA sequencing o Sanger Sequencing o ddNTPs incorporated, results in termination of replication o For example: one tube contains both adenine and ddATP ▪ there would be some DNA strands that terminated at every adenine o use Gel electrophorsesis to compare the relative lengths of these strands  o Analyzing gene expression o gene chip – microarray o two different conditions (often the same cell type before and after a stimulus, or cancer cell) o mRNA from first situation labeled in red, while mRNA from second is labeled in green ▪ genes that are downregulated from situation 1 to 2 appear as red dots in the appropriate area of the gene chip ▪ genes that are upregulated appear green ▪ if gene’s expression levels are unchanged, there will be an equal amount of green and red mRNA, creating a yellow spot o Wells are labelled with complementary strands of RNA  ▪ Determining gene function o usually through knockouts ▪ to make a knockout animal, it is necessary to knock out the genes from gametes or from embryonic stem cells and to grow the animal from a zygote o alternatively, gene expression can be reduced by the use of RNA interference – prevents translation of mRNA ▪ does not result in as complete of a knockout as stem cells Stem cells Stem cells are undifferentiated biological cells that can differentiate into specialized cells and can divide (through mitosis) to produce more stem cells. They are found in multicellular organisms. In mammals, there are two broad types of stem cells: embryonic stem cells, which are isolated from the inner cell mass of blastocysts, and adult stem cells, which are found in various tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenishing adult tissues. In a developing embryo, stem cells can differentiate into all the specialized cells—ectoderm, endoderm and mesoderm (see induced pluripotent stem cells)—but also maintain the normal turnover of regenerative organs, such as blood, skin, or intestinal tissues. Practical applications of DNA technology: medical applications, human gene therapy, pharmaceuticals, forensic evidence, environmental cleanup, agriculture Identification o Restriction fragment length polymorphism (RFLP) identifies individuals ▪ genomes of different individuals possess different restriction sites and varying distances between them ▪ produces unique band pattern after fragmenting the DNA sample with endonucleases o Single nucleotide polymorphisms ▪ the genome of one human differs from the genome of another at about one nucleotide in every 1000 human gene therapy o genetic manipulation of an affected individual’s DNA, in which the defective allele of the gene is replaced by the correctly functioning one o theoretically can be accomplished through viral vector or altering the genome of stem cell and letting it replicate Safety and ethics of DNA technology Content Category 1C: Transmission of heritable information from generation to generation and the processes that increase genetic diversity Evidence that DNA is Genetic Material (BIO) Griffith Experiment – injecting mice with heat-killed S (did not cause disease) Harmless R bacteria combined with harmless heat-killed S bacteria injected – killed mouse, found living S bacteria Hersey-Chase – bacteriophage (protein and DNA Mendelian Concepts (BIO) Phenotype and genotype Gene Locus Allele: single and multiple Homozygosity and heterozygosity Wild-type Recessiveness Complete dominance Co-dominance Codominance is a form of dominance wherein the alleles of a gene pair in a heterozygote are fully expressed. This results in offspring with a phenotype that is neither dominant nor recessive. A typical example showing codominance is the ABO blood group system. Incomplete dominance, leakage, penetrance, expressivity Incomplete dominance is a form of intermediate inheritance in which one allele for a specific trait is not completely expressed over its paired allele. This results in a third phenotype in which the expressed physical trait is a combination of the phenotypes of both alleles. Leakage – gene flow from one species to another Penetrance – frequency that a genotype will result in the phenotype (even if you have the genotype, you might not have the phenotype – percent of people that have the phenotype with the genotype Expressivity is to what degree a penetrant gene is expressed. Constant expressivity means that if your genes for being smart manages to penetrate (show up as a trait), then your IQ is 120. Variable expressivity means that your IQ doesn't have to be 120, it could be somewhat lower or somewhat higher Hybridization: viability Genetic hybridization is the process of interbreeding individuals from genetically distinct populations to produce a hybrid. A genetic hybrid would therefore carry two different alleles of the same gene. The process of two complementary, single-stranded DNA or RNA combining together, producing a double-stranded molecule through base pairing. This technique is used for interbreeding between individuals of genetically distinct populations. In summary, a postzygotic reproductive barrier is a mechanism that reduces the viability or reproductive capacity of hybrid offspring. Hybrid zygote abnormality is a type of postzygotic barrier in which hybrid zygotes fail to mature normally. Gene pool The gene pool is the set of all genes, or genetic information, in any population, usually of a particular species. o In biology, a population is all the organisms of the same group or species, which live in a particular geographical area, and have the capability of interbreeding.[ Meiosis and Other Factors Affecting Genetic Variability (BIO) Significance of meiosis Meiosis only in spermatogonium and oogonium Meiosis I – reductional division to make two haploid cells o Prophase I ▪ homologous chromosomes line up alongside each other crossing over – at synaptonemal complex o creates X shape – Chiasma o genes on same chromosomes closer together are more likely to cross over together, and are said to be linked ▪ gene mapping o single and double crossovers possible appears as tetrads – total of four chromatids o Metaphase I ▪ the two homologues remain attached, move to metaphase plate ▪ 23 tetrads lined up (as opposed to 46 chromosomes lined up in mitosis) o Anaphase I ▪ homologous chromosomes separate (as opposed to mitosis, where sister chromatids separate o Telophase I ▪ nuclear membrane may or may not reform, and cytokinesis may or may not occur ▪ When cytokinesis occurs, the new cells are haploid with 23 replicated chromosomes ▪ are called secondary spermatocytes or secondary oocytes Meiosis II – proceeds through prophase II, metaphase II, anaphase II, and telophase II, appearing much like mitosis Nondisjunction o primary nondisjunction (anaphase I)  ▪ one of the cells will have two extra chromatids (which make up a complete chromosome), and the other will be missing a chromosome o Secondary nondisjunction ▪ one cell has an extra chromatid, another lacks a chromatid Meiosis as Gamete Production Important differences between meiosis and mitosis Segregation of genes o When an organism makes gametes, each gamete receives just one gene copy, which is selected randomly. This is known as the law of segregation  ▪ results from alleles splitting in Meiosis II Independent assortment o The Principle of Independent Assortment describes how different genes independently separate from one another when reproductive cells develop Linkage o Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Recombination o Single crossovers o Double crossovers ▪ Say you have DNA strand C and DNA strand D ▪ CCCCCCCCCCCCCCCCCCCCCCCCCC ▪ DDDDDDDDDDDDDDDDDDDDDDDDDD ▪ single crossover yields ▪ CCCCCCCCCCCCCCCCCCDDDDDDDD ▪ DDDDDDDDDDDDDDDDDDCCCCCCCC ▪ double crossover yields ▪ CCCCCCCCDDDDDDDCCCCCCCCCCC ▪ DDDDDDDDCCCCCCCDDDDDDDDDDD o Synaptonemal complex ▪ homologous chromosomes line up alongside each other crossing over – at synaptonemal complex o creates X shape – Chiasma o genes on same chromosomes closer together are more likely to cross over together, and are said to be linked ▪ gene mapping o single and double crossovers possible appears as tetrads – total of four chromatids ▪ The synaptonemal complex (SC) is a protein structure that forms between homologous chromosomes (two pairs of sister chromatids) during meiosis and is thought to mediate chromosome pairing, synapsis, and recombination. ▪ o Tetrad Sex-linked characteristics Very few genes on Y chromosome Sex determination o A baby's sex is determined at the time of conception. When the baby is conceived, a chromosome from the sperm cell, either X or Y, fuses with the X chromosome in the egg cell, determining whether the baby will be female (XX) or male (XY). Cytoplasmic/extranuclear inheritance  o Extranuclear inheritance or cytoplasmic inheritance is the transmission of genes that occur outside the nucleus. It is found in most eukaryotes and is commonly known to occur in cytoplasmic organelles such as mitochondria and chloroplasts or from cellular parasites like viruses or bacteria. o The extranuclear genomes of mitochondria and chloroplasts however replicate independently of cell division. They replicate in response to a cell's increasing energy needs which adjust during that cell's lifespan. Since they replicate independently, genomic recombination of these genomes is rarely found in offspring contrary to nuclear genomes, in which recombination is common. o Mitochondrial disease are received from the mother, fathers don't as sperm do not contribute Mutation General concept of mutation — error in DNA sequence Types of mutations: random, translation error, transcription error, base substitution, inversion, addition, deletion, translocation, mispairing Advantageous vs. deleterious mutation Inborn errors of metabolism o Inborn errors of metabolism are rare genetic (inherited) disorders in which the body cannot properly turn food into energy. The disorders are usually caused by defects in specific proteins (enzymes) that help break down (metabolize) parts of food Relationship of mutagens to carcinogens The Ames test is a widely employed method that uses bacteria to test whether a given chemical can cause mutations in the DNA of the test organism. More formally, it is a biological assay to assess the mutagenic potential of chemical compounds. A positive test indicates that the chemical is mutagenic and therefore may act as a carcinogen, because cancer is often linked to mutation. The test serves as a quick and convenient assay to estimate the carcinogenic potential of a compound because standard carcinogen assays on mice and rats are time-consuming (taking two to three years to complete) and expensive. However, false-positives and false-negatives are known. carcinogen is an agent that induces neoplasia, i.e. cancer. o What’s an agent? Chemicals, radiation, and viruses are among the agents implicated in causing cancer. A mutagen is a chemical that can cause changes (mutations) to the genetic material of a cell (DNA). o A mutagen is one possible pathway to carcinogenesis. o When mutations occur in germ cells (i.e. sperm or ova) it is possible for the mutation to be transmitted to offspring. A mutagen may be a carcinogen, but the link is not absolute. That is, not all chemicals shown to be mutagens are necessarily carcinogens. o Conversely, not all carcinogens are mutagens. o There are nongenotoxic carcinogens—chemicals that cause cancer by several mechanisms including by inducing sustained cell injury. Genetic drift Genetic drift is a mechanism of evolution in which allele frequencies of a population change over generations due to chance (sampling error). Genetic drift occurs in all populations of non-infinite size, but its effects are strongest in small populations. Genetic drift can have major effects when a population is sharply reduced in size by a natural disaster (bottleneck effect) or when a small group splits off from the main population to found a colony (founder effect). Synapsis or crossing-over mechanism for increasing genetic diversity Analytic Methods (BIO) Hardy–Weinberg Principle Hardy-Weinberg Principle o gene pool – total collection of all alleles in a pool ▪ any change in the gene pool constitutes evolution (not phenotype) Can be defined on the individual level when a change occurs in genes that can be passed down to subsequent generations, or at the level of the population where a change in the total gene pool (allelic frequencies) constitutes evolution. During speciation, new species evolve from older species, which illustrates the process of evolution on a macro scale. Things that deal with phenotypic shift, or change in the frequencies of phenotypes, without changing the overall allelic frequencies of that population, do not count. o 5 conditions ▪ no selection for the fittest organism ▪ Random mating ▪ Large population ▪ Immigration/emigration must not change the gene pool ▪ Mutational equilibrium o If population approximates Hardy-Weinberg equilibrium, the following equation can be used to predict the frequencies of genotypes and phenotypes from allelic frequencies within a population ▪ p2 +2pq + q2 ▪ p2 = homozygous dominant, 2pq = heterozygous, q 2 = homozygous recessive ▪ p+q = 1 Testcross (Backcross; concepts of parental, F1, and F2 generations) To identify whether an organism exhibiting a dominant trait is homozygous or heterozygous for a specific allele, a scientist can perform a test cross. The organism in question is crossed with an organism that is homozygous for the recessive trait, and the offspring of the test cross are examined. Gene mapping: crossover frequencies Biometry: statistical methods Biometric identifiers are often categorized as physiological versus behavioral characteristics. Physiological characteristics are related to the shape of the body. Examples include, but are not limited to fingerprint, palm veins, face recognition, DNA, palm print, hand geometry, iris recognition, retina and odour/scent. Behavioral characteristics are related to the pattern of behavior of a person, including but not limited to typing rhythm, gait, and voice.[note 2] Some researchers have coined the term behaviometrics to describe the latter class of biometrics. Biometrics is the technical term for body measurements and calculations. It refers to metrics related to human characteristics. Biometrics authentication (or realistic authentication)[note 1] is used in computer science as a form of identification and access control. It is also used to identify individuals in groups that are under surveillance. Evolution (BIO) Natural selection Fitness concept Reproductive success, contribution to the gene pool Selection by differential reproduction Concepts of natural and group selection o Group selection is a proposed mechanism of evolution in which natural selection acts at the level of the group, instead of at the more conventional level of the individual o The behavior of animals could affect their survival and reproduction as groups, speaking for instance of actions for the good of the species. Evolutionary success as increase in percent representation in the gene pool of the next generation Speciation Polymorphism o Polymorphism is common in nature; it is related to biodiversity, genetic variation, and adaptation; it usually functions to retain variety of form in a population living in a varied environment.:126 The most common example is sexual dimorphism, which occurs in many organisms. Other examples are mimetic forms of butterflies (see mimicry), and human hemoglobin and blood types. Adaptation and specialization Inbreeding o Inbreeding is the production of offspring from the mating or breeding of individuals or organisms that are closely related genetically.[  o Inbreeding results in homozygosity, which can increase the chances of offspring being affected by recessive or deleterious traits. This generally leads to a decreased biological fitness of a population (called inbreeding depression), which is its ability to survive and reproduce Outbreeding o Breed from parents not closely related Bottlenecks Evolutionary time as measured by gradual random changes in genome Random genetic mutations (drift) that are not acted on by natural selection (neutral) occur at a constant rate. By measuring the amount of these neutral mutations, you can find out how much time has passed. You can compare genome differences between two species to find out how long ago they diverged. Another name for this concept is the Molecular Clock. Content Category 1D: Principles of bioenergetics and fuel molecule metabolism Principles of Bioenergetics (BC, GC) Bioenergetics/thermodynamics Free energy/Keq o Equilibrium constant o Relationship of the equilibrium constant and ΔG° Spontaneity of a reaction under specific conditions can be predicted using the relationship between the equilibrium constant K and G The difference between Go and G o Go – under specific case of standard state conditions o G – far less specific, represents the energy change for any given reactions under any attainable conditions Relationship between K and G: o if K = 1, then Go = 0 o if K > 1, then Go < 0 o if K < 1, then Go > 0 ▪ This does not mean that a reaction is always spontaneous if it has an equilibrium constant greater than one spontaneity of a reaction depends on starting concentrations of products and reactants ▪ The relationship between K and Go does say that if a reaction has an equilibrium constant greater than one, the reaction is spontaneous at the temperature used to derive that particular equilibrium constant and standard state Concentration o Le Châtelier’s Principle Le Chatelier’s Principle When a system at equilibrium is stressed, the system will shift in a direction that will reduce that stress o Three stresses ▪ addition or removal or product or reactant ▪ changing the pressure or volume of the system ▪ heating or cooling the system o The Haber Process: N2(g) + 3H2(g) → 2NH3(g) + Heat ▪ If we add N2, the reaction is pushed to the right ▪ If we add heat (analogous to adding more product), then the reaction is pushed to the left ▪ If pressure is increased, equilibrium shifts to the right there are four gas molecules on the left side and two on the right A similar effect is found when a solution in equilibrium is concentrated or diluted o equilibrium shifts to the side with fewer moles when the solution is concentrated Endothermic/exothermic reactions Endothermic – reaction with positive enthalpy change o produces heat flow to the system o Anabolic reactions (building a large molecule from several smaller ones) are usually endothermic ▪ photosynthesis – uses energy to build glucose  Exothermic – reaction with negative enthalpy change o produces heat flow to the surroundings o Catabolic reactions (breaking down a large molecule into several smaller molecules)) are usually exothermic ▪ cellular respiration – breaks down glucose to release energy Free energy: G Spontaneous reactions and ΔG° G = H - TS o all three state functions refer to the system, but the equation also provides information about the surroundings ▪ Heat transferred into the surroundings (exothermic) increases entropy of surroundings ▪ Heat transferred into system (endothermic) increases entropy of system thus, accounts for entropy change of both system and surroundings o Algebraic manipulation to G = -TS ▪ S must be positive for G to be negative – both required for spontaneous reaction ▪ Both S and G must be 0 at equilibrium Extensive property and a state function Not conserved – can change for an isolated system represents maximum non-PV work available for a reaction o contracting muscles, transmitting work, batteries Phosphoryl group transfers and ATP ATP hydrolysis ΔG K, reverse reaction rate will be greater than the forward rate o if Q 1, then Go < 0 o if K < 1, then Go > 0 ▪ This does not mean that a reaction is always spontaneous if it has an equilibrium constant greater than one spontaneity of a reaction depends on starting concentrations of products and reactants ▪ The relationship between K and Go does say that if a reaction has an equilibrium constant greater than one, the reaction is spontaneous at the temperature used to derive that particular equilibrium constant and standard state