AP Biology SG PDF

Preview

Summary

This is a compilation of all notes needed for the 2019 AP Biology exam (note: this was taken online, so some information that may be in future exams is not present)...

Description

AP Biology Full Study Guide units 1–6 unit 1: scientific method - hypothesis: prediction of the relationship between two variables - dependent: the variable you measure - independent: the variable you change - control: positive (expected response), negative (no response is expected) - null hypothesis: predicts that there will be no effect of the independent variable on the dependent variable (n o statistical difference between the experimental and control group) - standard error of mean: determining how much error there is in our estimation of the true mean of a population - using a sample population to determine estimation of true population - SEM (+- 2 SEM for 95% range) - there is a 95% chance that the true population falls within the 95% confidence interval - chi-squared: how likely the deviation of our observed values from the expected values is due to random sample error - if there is a g reater than 5% c hance that the results are due to sample error, then we accept the null hypothesis - if there is a l ess than 5% c hance that the results are due to sample error, then we reject the null hypothesis unit 2: cell biology - polar molecules: positive ends of polar molecules containing hydrogen can stick very well to the negative ends of other polar molecules (hydrogen bonds) - water properties - cohesion: tendency of molecules of the same kind to stick together - resistance to temperature change: water’s hydrogen bonds moderate temperature - stabilizes internal and external environments - water cools things when it evaporates - ice is less dense than water: hydrogen bonding (less densely packed) - solvent of life - hydrophilic vs. hydrophobic - hydrophilic: affinity to water - hydrophobic: no affinity to water - macromolecules - carbon-based (organic compounds) - carbon: can bond to four atoms (big variety of molecules) - dehydration reactions: take monomers and form them into polymers by removing water - hydrolysis: polymers are broken down by the addition of water - carbohydrates - general chemical formula: CH2O - monosaccharide pairs → disaccharides - lactose and sucrose

-

-

-

-

-

-

-

polysaccharides - starch, cellulose, glycogen proteins - polymers consisting of amino acids bound by dehydration reactions - amino acids - amino group - carboxyl group - r group - protein function is the result of protein structure - denaturing = loss structure = loss of function - four levels of protein structure - primary structure - secondary structure - tertiary structure - quaternary structure - recognize different types of amino acids - nonpolar side chains (CH2) - polar side chains (OH, SH, NH) - electrically charged side chains (hydrophilic, charged at the end) - different types of bonds - hydrogen bond: OH - O - hydrophobic interactions - disulfide bridge - ionic bond three general parts of the nucleotide (phosphate, sugar, nitrogenous base) nitrogenous base - AG - purines (double ring structures) - CU/T - pyrimidines (single ring) RNA is unlike DNA in - uses sugar ribose instead of deoxyribose - rna has the nitrogenous base U - rna is single stranded elements in macromolecules - carbohydrates only have H, C, and O - nucleotides only have N and P - proteins only have S and N identifying macromolecules - carbohydrates have H and OH - lipids are long fatty acid chains of C and H (not much OH) - proteins = amino acids (NH2 and COOH) - nucleic acids are super complex (multiple rings) enzymes: speed up metabolic reactions by lowering energy barriers

-

catalyst: chemical agent that speeds up a reaction without being consumed by the reaction (by lowering the activation energy) - enzyme is a catalytic protein - some ncRNAs have catalytic function - active site: where the substrate binds - induced fit: enzyme changes shape when the substrate bonds to it - denaturing: can be affected by general environmental factors or chemicals (change the shape of the active site so the substrate can’t bind to it) - inhibitors - competitive: bind to the active site (competing with the substrate) - noncompetitive: bind to another part of the enzyme (changing the shape of the active site so the substrate can’t bind to it) - diffusion and osmosis - isotonic: the concentration of the solute is the same on both sides - hypotonic: the concentration of the solute is lower outside - hypertonic: the concentration of the solute is lower inside - cell size - be large enough to house DNA, proteins, ad structures needed to survive - be small enough to allow for large SA to V ratio (exchange with the environment) - cell membrane permeability - hydrophobic core - what CAN pass: small non polar molecules, some large hydrophobic molecules, water - what CANNOT pass: ions and charged particles, polar molecules larger than water - exocytosis: export bulky molecules (proteins, polysaccharides) - endocytosis: import substances - cell communication - reception (detection of a signal molecule), transduction (convert signal to a form that can bring about cellular response), response (cellular response to the signal molecule) - animal cells communicate by direct contact, secreting local regulators, long distance - phosphorylation cascade: amplifying signals through transduction - response: regulate protein synthesis through gene expression (regulate activity of proteins in the cytoplasm) - autoimmune diseases, cancer - apoptosis: programmed cell death unit 3: energy and cell - big idea 2: living systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis - autotrophs: producers - able to capture energy from light and store that energy by creating large molecules like sugar from smaller molecules like CO2 and H2O (ex. photosynthesis) - *still do cellular respiration, break down the large molecules that they make* - base of the food chain - heterotrophs: consumers

-

-

-

-

must eat other organisms to acquire their free energy. the energy is stored as large, energy storing molecules like sugar, fat, ad protein 1st law of thermodynamics: energy in the universe is constant 2nd law of thermodynamics: energy conversions increase the disorder of the universe free energy (ΔG) - ΔH - TΔS - negative for all spontaneous processes exergonic reactions: net release of free energy and is spontaneous endergonic reactions: absorbs free energy and is nonspontaneous energy coupling: the use of an exergonic process to fuel an endergonic one (usually mediated by ATP) anabolic v catabolic v metabolic - metabolism: the sum of all the chemical processes that maintain life - anabolic: building big molecules from small ones (endergonic) - catabolic: breaking apart big molecules into small ones (exergonic) cellular respiration: - C6H12O6 + 6O2 → 6CO2 + 6H20 + ATP - high energy reactants produce low energy products (exergonic) - glycolysis + citric acid cycle (produce some ATP, CO2 released) → high energy electrons are used during oxidative phosphorylation to make ATP - glycolysis - breaking the glucose → electrons are shuttled to the mitochondria by NADH, leaving 2 pyruvates - fermentation: cell unloads NADH → electrons go to the pyruvate molecules - frees up NAD+ so that another glucose can be broken - converts pyruvate into a less energetically useful molecules (lactic acid or ethanol) → stops cellular respiration at 2ATP - pyruvate oxidation - pyruvate loses a carbon, drops electrons on a NAD+ bus, and combines to coenzyme A → Acetyl CoA - citric acid cycle - two carbons from Acetyl CoA get ejected as CO2, some ATP gets made, more electrons go on NAD and FADH busses - H+ concentration gradient - H+ wants to flow into the matrix - electrons reduce oxygen, forming H2O - electron transport chain: series of redox reactions which move electrons from molecule to molecule - oxidative phosphorylation: phosphorylation is adding P to ADP to make ATP - chemiosmosis: facilitated diffusion of H+ back into the matrix (plus the ATP production) - ATP is generated using carbohydrates, fats and proteins - fats make excellent cellular fuel because they contain many hydrogen atoms and many energy-rich electrons

-

photosynthesis - stage 1: store light energy in ATP and NADPH - light energy is captured by photosystem I (extract electrons from H2O and energize them) - electrons are passed through the electron transport chain that pumps hydrogens out using the energy from the electrons - the now low-energy electrons are reenergized by PSI using light energy - PSI uses the electrons to reduce NADP+ to NADPH → calvin cycle - stage 2: use energy from stage 1 to bind CO2 into sugar - the calvin cycle makes sugar with a chloroplast - CO2 - ATP and NADPH generated by the light reactions unit 4: cell division and patterns of inheritance - cell cycle (driven by specific chemical signals + specific checkpoints) - interphase: - G1: growth in cell size - S: cell will replicate its DNA - G2: cell grows again to prepare for division - mitotic phase: mitosis, cytokinesis - chromosomes → sister chromatids → chromosome division to daughter cells - stages of mitosis - mitosis begins and ends with diploid cells (meiosis begins with diploid and ends with haploid) - cancer cells do not respond normally to the body’s control mechanisms - divide rapidly - spread to other tissues throughout the circulatory system - grow without being inhibited (tumor growth) - cell division is controlled by genes - oncogenes stimulate cell division - tumor suppressor genes inhibit cell division - failure of both → uncontrolled division + development of cancer cells - meiosis: converts diploid nuclei to haploid nuclei - reduction division: reduces the number of chromosomes in each new cell - the conversion happens in meiosis I (separation of homologous pairs) - crossing over - exchange of corresponding segments between homologous chromosomes (during prophase I of meiosis) - sister chromatids are joined and are not yet lined up to separate into two cells - independent assortment: the allele determined in one gene of a cell does not affect the allele determine in another gene - random fertilization - patterns of inheritance - key probabilities to know:

- there is a 50% chance of a gamete inheriting a given allele from a parent - Aa x AA and aa x AA both produce 100% dominant offspring - Aa x Aa produces a 3:1 ratio of D/R - Aa x aa produces a 1:1 ratio of D/R - a dihybrid cross - AaBb x AaBb always produces a 9:3:3:1 phenotype ratio - sex linked genes will have different ratios in males and females - crossing over problems - you know you have linked genes crossing over if you have four offspring phenotypes but not a 9:3:3:1 ratio - non-dominant/recessive inheritance patterns - incomplete dominance: red + white = pink (Aa is different from AA and aa) - codominance: heterozygotes show both traits (red and white flowers) - pleiotropy: one gene affects many traits (sickle cell anaemia mutation) - polygenic inheritance: one trait affected by many genes (skin color) - epistasis: one gene affects the phenotypic expression of another gene (albinism one gene mutation turns off the ability of other genes to make color) unit 5: molecular genetics - DNA is a molecule that contains genetic information as a series of nucleotide bases (double helix) - all of your DNA is your genome - chromosome: a single long DNA molecule - gene: section of the chromosome that encodes a specific polypeptide - alleles: slightly different version of the same gene (produce different phenotypes) - chromosome structure - DNA is wrapped around histones (but not tightly wrapped) → chromatins - at prophase of mitosis/meiosis, the chromatin condenses into tightly packed, visible structures known as chromosomes - replication vs transcription vs translation - replication - ‘semiconservative’ (retains one strand of old DNA and has one strand of new DNA) - 5’ to 3’ synthesis - leading vs lagging strand - DNA polymerase, DNA ligase, Helicase, Topoisomerase - the ends of DNA molecules: the ends of eukaryotic chromosomal DNA gets shorter with each round of replication because cells are unable to replace RNA primers at the 5’ end of the chromosomes - transcription - transcription unit, promoter/terminator - coding vs template strand - the difference between mRNAs and ncRNAs - introns, exons, and alternative splicing - trp and lac operon functions (repressive vs inducible systems)

-

-

*eukaryotic mRNA undergoes significant modifications before it is shipped out to the ribosomes* - addition of polyadenylated tail and a 5’ nucleotide cap post transcriptional modifications - splicing non-coding sequences (introns) out → increases variation of multiple proteins from the same gene codons, anticodons, start codons, and stop codons initiation, elongation, termination

unit 6: modern genetics - gene expression: ability to selectively use only certain genes (o ften occur in response to environmental factors and cell signaling) - prokaryotic vs. eukaryotic genomes/genes - lac operon/trc operon - lac operon: a regulatory gene in the lac operon continuously produces a repressor protein that binds to the operator (the genes can’t be transcribed), when lactose is not present, the proteins needed to deal with lactose are not made - when lactose is present, it blocks the repressor from binding to the operator → genes get transcribed and lactose is not used by the cell - lactose: inducer (molecules that turns on the gene expression of a cell) → inducible system - trc operon: prokaryotes have the ability to make their own amino acids, like tryptophan (the trp operon is turned off by tryptophan because the cell won’t make it if it can get enough of it from its environment) → repressible system - promoter, operator, inducer, repressor, and regulatory proteins - promoter: where RNA polymerase attaches - operator: “on/off” controls access of RNA polymerase - DNA methylation, transcription factors, RNAi, and gene packing - transcription factors: bind to specific DNA sequences to either activate or repress gene expression - this allows cells to simultaneously turn on/off many genes whose proteins work together under a given environmental condition - DNA packing: can prevent gene expression by preventing RNA polymerase and other transcription factors from contacting the DNA - heavily packed regions of DNA are essentially inactive - methylation: cells can selectively add methyl groups to the cytosine nucleotides in a gene → correspond to “turned off” genes - can cause long-term inactivation of genes in cellular differentiation - RNAi (non-transcriptional): cells produce short, targetec ncRNA molecules → bind to mRNA and/or DNA directly to block transcription, degrade mRNAs, block translation of mRNAs - gene expression and the environment - cell-cell signaling: hormones, growth factors, etc. - direct environmental factors

-

-

- exposure to UV light - genes being turned on/off by cold - environmental gene expression: siamese cats (cold parts have color, warm parts are albino) - the turning on/off of genes in development guides cell differentiation - homeotic genes (drive big-picture development) - cellular signaling in embryonic development - pluripotent cells (can develop into any kind of cell depending on the stimulus) - different parts of embryo exhibit different gene expression in response to signals from either the mother or the surrounding cells - signals put the cells in dedicated, non reversible gene expression sequences - gene expression and apoptosis - apoptosis: programmed cell death (result of altered gene expression (cells produce proteins that result in their own death) - phenotypic complexity: a single gene can produce multiple protein products - alternative splicing - heterozygosity (can be beneficial sometimes) - sickle cell anemia (resistant to malaria) - cystic fibrosis (resistance to diarrheal dehydration) restriction enzyme - enzyme that cuts DNA at specific nucleotide sequences - sticky ends: allows another fragment of DNA to be “glued” - uses? - making recombinant DNA (genetic engineering) → cut and splice new DNA - identifying SNPs: key to identifying carriers of recessive alleles + DNA fingerprinting techniques - PCR (how it works will not be tested) - allows copying/amplification of specific DNA sequences/genes - exponentially replicating one DNA sequence to analyze it epigenetic inheritance biotech techniques - RFLP (how it works?) - identify a SNP (mutation in gene of interest) - find a restriction enzyme that cuts the DNA differently when it has the mutation vs. when it doesn’t - make many copies of that gene (PCR - polymerase chain reaction) - “amplifying the gene” - mix the gene with the enzyme so they can cut them - separate the resulting fragments to see which length fragments you end up with...