Unit 1 Biochemistry SG PDF

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This is a compilation of notes from the Biochemistry Unit of AP Biology (Can be used to study for one particular test and for the AP as a whole)...

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Unit 1: Biochemistry Study Guide experimental design and variables - independent variables: the variable that you change - dependent variables: the variable that you measure based on the changes in the independent variable - good experimental design - controlled experiments - you should only change one variable and measure one variable - all other variables should be kept the same (control group) - the assumption is that random variables are the same in both groups - control group vs. experimental group - control group: negative control - no response is expected - experimental group: positive control - expected response - factors to consider - outside variables - sample size - larger size means narrower chance of error, but too large a size causes inefficiency - scientific method - make an observation and ask a question about it - come up with a hypothesis - a proposed explanation for a set of observations - good hypothesis: allows you to make predictions, is testable, and is falsifiable - you can’t prove a hypothesis, you can  only support or fail to support it with evidence - make predictions based on your hypothesis - do experiments and make observations to gather info - draw a conclusion about your hypothesis based on that info - share findings with others - repeat data in biology - data set

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- mean, graph, etc - reliability of data sample population vs. actual population - infer stats about the actual population from the sample population

- sample should be a reflection of the actual population - calculating the mean value, the median, and the mode of a set of data - SEM - S/√n - 95% interval (2 SEM): there is a 95% chance that the actual population falls into that interval - standard deviation: the spread of the data - hypothesis - statistical hypothesis: null hypothesis (there is no statistical difference between the two groups) - experimental hypothesis: one that where you predict the differences between the groups - ex. are people who pay fall sorts taller than people that don’t? - exp hyp: fall sports people are taller - stats hyp: no difference between the groups - result: we support our stats hyp and not our exp hyp - p-value is the percentage probability that the two groups are not significantly diff. (0.15 means 15% chance that the two groups are not really different) - it must be under 5% to neglect the statistical hypothesis basic chemistry vocabulary - vocab - covalently bonded molecules - electronegativity: attraction pull for shared electrons - non polar: the distribution of electrons is equal (symmetrical) - polar: the distribution of electrons is unequal - concepts - 96% of living organisms are made up of Nitrogen, Carbon, Oxygen, and Hydrogen - polarity of bonded molecules water properties and hydrogen bonds - polar molecules stick together - if the ends contain hydrogen → hydrogen bonding - properties - water’s polarity makes it extremely cohesive (molecules stick together) - surface tension: a measure of how difficult it is to break the surface of a liquid - capillary action: the use of adhesion and cohesion together to climb up narrow areas

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resistance to temperature and state changes (high specific heat and high latent heats of fusion/vaporization) ice is less dense than liquid water - molecules are less densely packed than in liquid form → floats is a very good solvent - polar solutes dissolve when water surrounds them (like dissolves like) - can pull ions apart (like nacl) - hydration shell → disrupts IMFs → solute dissolves

interactions of polar/nonpolar/hydrophobic/hydrophilic molecules. - hydrophilic: one that has an affinity for water (polar substances) - like dissolves like / like interacts with like - hydrophobic: one that does not have an affinity for water (nonpolar substances) - ex: oil and water key roles of carbon, sulfur, nitrogen, and phosphorus - 96% of living organisms are made up of Nitrogen, Carbon, Oxygen, and Hydrogen - sulfur and nitrous oxides react with water in the air to form acids - macromolecules are made of carbon (only element that can make extremely complex molecules - carbon-based → organic compounds - can bond to four other atoms, branch up to four directions - carbon skeleton: chain of carbon atoms - hydrocarbons: molecules consisting of only carbon and hydrogen functional groups - seven functional groups (have to memorize the structures of them) - hydroxyl group

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carbonyl group carboxyl group

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amino group

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sulfhydryl group

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phosphate group

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methyl group

structural isomers, cis-trans isomers, and enantiomers - isomers: compounds with the same molecular formula but different structures → different properties - structural isomers: have different covalent arrangements of their atoms - cis-trans isomers: have the same covalent bonds but differ in spatial arrangements - enantiomers: isomers that are mirror images of each other - two enantiomers of a drug make have different effects (usually only one isomer is active) → organisms are sensitive to even subtle variations in molecules macromolecules - polymers - made from monomers (small molecules) strung together by covalent bonds - are linked through dehydration reactions] (condensation reactions) - removal of water - are broken apart by hydrolysis - addition of water - all biological reactions are mediated by enzymes - sugars and starches - sugars are monomers of carbohydrates → a lot bonded together is a complex carbohydrate called starch proteins - proteins are polymers that consist of long chains of amino acids (a set of 20 different amino acids) - when a protein is broken down, it breaks into amino acids which are delivered to the cells (can be used to build other proteins) - monomers are linked through dehydration reaction (carboxyl group and amino group → peptide bond) - a chain of amino acids is called a polypeptide - the sequence determines the shape → determines the function - proteins can be denature causing it to lose shape and function - amino acids have an amino group, a carboxyl group, and an R group - three types of side chains (remember one from each group) - nonpolar (glycine)

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polar (serine)

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electrically charged (aspartic acid)

4 types of structures - primary structure: the sequence of the amino acids - determined by cell’s genetic information - slight changes could cause changes in function - example of a change in primary structure: sickle cell disease (a single change in amino acid → change in function) - secondary structure: interior shapes that result from folding or coiling - caused by hydrogen bonding - could be alpha helix or beta pleated sheet - tertiary structure: 3d shape of the polypeptide - interactions between R groups - bonds - hydrogen bonds - disulfide bridge - hydrophobic interactions - ionic bonds - quaternary structure: interaction between two polypeptides to function functions of proteins - the most important: an enzyme to catalyze reactions (pick three others to memorize)

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- receptor proteins transmit signals into cells - transport proteins carry oxygen - contractile proteins are found within the muscle proteins have two ends, N-terminus (amino) and C-terminus (carboxyl) - new amino acids can only be added to the C-terminus

lipids - consist of mainly hydrogen and oxygen atoms - is water insoluble (hydrophobic) - fats: oils, waxes fats - consist of a glycerol molecule bound to three long fatty acid chains - triglycerides/triglycerols - saturated vs unsaturated vs trans - saturated: solid at room temp - unsaturated: liquid at room temp (has a double bond) which prevents from them packing solidly together - trans: saturated facts created by hydrogenating unsaturated plant oils - steroids: ring structure that includes cholesterol and steroid hormones - cholesterol is a lipid that transports fats through your bloodstream and maintains fluidity in the cell membrane - steroid hormones: estrogen and testosterone - phospholipids: specials lipids that are involved in cell membranes - consists of a charged phosphate head (hydrophilic) and a fatty acid tail (hydrophobic) carbohydrates - general chemical formula for carbohydrates is CH2O (only contains C, H, and O) - monomers of carbohydrates are called monosaccharides - are bound into pairs to make disaccharides (ex. lactose, sucrose) - are bound into thousands to make polysaccharides (ex. starch, cellulose, glycogen) - polysaccharides store sugar when it isn’t needed (for plants it is starch, and for animals it is glycogen) - dehydration reaction joins them, hydrolysis divides them - sugars are the primary source of energy - carbohydrates are also used for structure (cellulose for plants) - starches use alpha glycosidic bonds, so they can be broken down - cellulose uses beta glycosidic bonds, so they cannot be broken down

nucleic acids - genes consist of DNA (deoxyribose nucleic acid) - inherited from an organism’s parents - provides direction for its own replication - programs cell activities through directing the synthesis of proteins - does NOT build proteins directly - DNA utilizes RNA - DNA is transcribed into RNA - RNA is translated into proteins - nucleotides - five-carbon sugar called ribose in RNA and deoxyribose in DNA - phosphate group - nitrogenous base - DNA: adenine, guanine, cytosine, thymine - RNA: adenine, guanine, cytosine, uracil...