Biology Exam 1 Study Guide!
Biology Exam 1 Study Guide! 200001
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This 18 page Study Guide was uploaded by Audrey Notetaker on Wednesday February 10, 2016. The Study Guide belongs to 200001 at Boston College taught by Danielle Taghian in Spring 2016. Since its upload, it has received 49 views. For similar materials see Molecules and Cells in Biology at Boston College.
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Date Created: 02/10/16
EXAM 1 STUDY GUIDE All lectures through lipids 1015 multiple choice 6070% short answer Chapter 2: Solution Chemistry AcidBase Case Study Molecular Weight: sum of all mass numbers of atoms (g/mol) Acid: gives a proton (H+) Base: takes a proton *The body buffers substances to maintain homeostasis * change in pH can denature proteins – cause them to lose function *more H+ = more acidic CO2 + H2O H2CO3 (carbonic acid) HCO3 (bicarbonate) + H+ This reaction lowers pH *Strong acids dissociate completely, weak acids do not *weak acids are used as buffers – a solution of weak acid + its conjugate base that resists changes in pH (maintains homeostasis) Every factor of 2 difference in H+ concentration represents 0.3 pH units Chapter 2: Covalent Bonds and Weak Chemical Interactions Elements in organisms: 99% C, N, O, H Four major small organic compounds in cells (macromolecules) Sugars (carbohydrates) – provide quick energy, structural support and form polysaccharides Fatty acids (lipids) – have long hydrocarbon chains, serve as the cell membrane and have bigger long term energy Amino acids (proteins): form protein Nucleotides: the building blocks of RNA and DNA Macromolecule Monomer unit Covalent bond Nucleic acids (DNA, RNA) Nucleotide Phosphodiester Proteins Amino acids Peptide Carbohydrate Monosaccharides Glycosidic bond Lipids (phospholipids and triglycerides) Fatty acid and Ester bond glycerol Macromolecules: constructed by polymerization of monomers via covalent condensation reactions in which a molecule of water is lost with each subunit added Covalent: sharing of electrons equally electronegative; stable; strongest bond Single bond = free rotation Double bond = no rotation Polar: slight electronegative difference leads to unequal sharing of electrons which results in a dipole (partial charge); the electrons are more towards O in H2O Non polar: electrons equally shared, little electronegativity difference (lipids) Ionic: big electronegative difference (NaCl), transfer of electron(s); ions are formed Non covalent bonds: rely on attractive and intermolecular forces Salt bridges: ionic interaction between salts: strongest Hydrogen: HO. HN, HF / electronegative atom attracted to another electronegative atom o Two strands of DNA interact this way Van der Waals: occasional dipole moments in non polar molecules; weakest Hydrophilic interactions molecules interact with water via hydrogen bonds (polar) Hydrophobic no interaction with water (non polar) Insoluble in water; shields itself from water Lipid bilayer Electronegativity: measure of the tendency of an atom to attract a bonding pair of electrons Chapter 2: Water and Carbon Capillary Action: the ability of liquid to flow up a narrow tube against gravity Adhesive – molecules stick to the wall Cohesive – molecules stick to each other if the adhesive force is greater than the cohesive, then the liquid will creep up the side (i.e. water) if the cohesive force is greater than the adhesive, then the liquid will bulge (i.e. mercury) *water has a high surface tension * Liquid water is more dense than solid ice Ice: Hydrogen bonds are arranged in an open crystal pattern water: fewer hydrogen bonds so liquid can pack more closely together Functional Groups Name & Structure Examples Properties Methyl lipids Nonpolar. Hydroxyl Alcohols and sugars Polar. Hydrogen bonds with water to help dissolve molecules. Enables linkage to other molecules by condensation. Carbonyl Sugars Polar. Contribute to making molecules watersoluble. Can be very reactive. Important in carbohydrates and energy releasing reactions. + Carboxyl In fatty acids and amino Acidic. Ionizes in living tissues to form COO and H . acids Enters into condensation reaction by giving up OH. Some carboxylic acids important in energyreleasing reactions. Amine Basic. Accepts H in living tissues to form NH En3ers + into condenstation reactions by giving up H . Phosphate Negatively charged. Enters into condensation reactions by giving up OH. When bonded to another phosphate, hydrolysis releases much energy. Sulfyhydryl By giving up H, two SH groups can react to form a disulfide bridge (SS), thus stabilizing protein structure because it's a covalent bond. Chapter 3: Proteins All proteins are made up of amino acids and a central carbon atom that bonds to: 1. H2N (an amino functional group) 2. COOH (a carboxyl functional group) 3. H (a hydrogen atom) 4. R (a variable side chain) *The amino group ionizes to NH3+ and the carboxyl group ionizes to COO this helps the amino acid stay in solution and makes them more reactive Alpha Carbon: central carbon atom that the amino group, H, R, and carboxyl group is attached. Beta carbon is the first carbon on the attached R group. Types of Amino Acid Side Chains *KNOW HOW TO DRAW ONE OF EACH OF THESE The nature of Side Chains: 1. If the side chain is negative then it is acidic 2. If the side chain is positive then it is basic 3. If the side chain in uncharged but has an oxygen and or nitrogen atom then it is uncharged polar 4. If none of the above is correct then it is a nonpolar amino acid (Amine Bond) Peptide bond: condensation reactions bond the carboxyl group of one amino acid to the amino group of another amino acid. This reaction produces the peptide bond and water. The electrons shared between the carbonyl group and the peptide bond allow for some double bonds. *only alpha amino acids can form secondary structures (main/central carbon) Primary Structure unique sequence of amino acids; just the code; determines 3D structure and function. It has an amino end and a carboxyl end, in the middle are amino acids connected with peptide bonds. Changing one of the amino acids in the sequence can completely change the structure and function of the protein. Does not always cause a change, but change can be drastic (cancerous, sickle cell, etc.) Polypeptide: the linking together of amino acids. It is flexible and has directionality. Its side chains extend out from the peptidebonded backbone Secondary Structure local confirmation of polypeptide chain; formed and stabilized by hydrogen bonds. Each 360 turn = 3.6 aa at 1.5 A(angstroms) rise/aa; the peptide bond of every 4th aa interacts via hydrogen bonds which are parallel o the axis of the alpha helix while the aa side chains are perpendicular Alpha helix CO group forms hydrogen bond with NH every 4; mostly found on outside of proteins Beta sheets Consists of beta strands joined by hydrogen bonds formed between carbonyl and imine groups of neighboring backbones. Pleat is caused by the position of the alpha carbons above and below the plane of the sheet. Consists of parallel beta strands joined by hydrogen bonds between carbonyl and amine groups Beta turn: allows peptide chain to reverse direction Random coils: no defined helix or beta sheet Tertiary Structure interactions/intermolecular forces between R groups form to maintain overall structure of protein. Get hydrophobic amino acids to the inside of the protein and get hydrophilic amino acids to the outside so the protein can interact with water Quaternary form follows function; two or more proteins interact with one another *Similar looking proteins may not have the exact same amino acid sequence (primary structure) Chapter 3: Protein Domains and Folding Protein domains: substructures that can fold independently into compact, stable, structures, usually 40350 amino acids that has a specific function and can function independently of the rest of the protein. Posttranslational modification of proteins: proteins are regulated and their function, lifetime, ability to bind with another protein or DNA, etc. is all a result of posttranslated modifications *Phosphorylation (adding phosphate) going from ADP > ATP changes the structure of protein *Protein folding is both spontaneous (selfassembling) and can be often facilitated by other proteins by controlling when/where it’s folded and/or regulates the protein’s activity *Protein misfolding can lead to inactive proteins or proteins that cause diseases (Alzheimer’s and Parkinson’s) Chapter 4: Nucleic Acids and the RNA World Nucleotides: monomers that consist of sugar, phosphate group, and a nitrogencontaining base Evolution of Life: Chemical evolution suggests that the first step in the evolution of life was the formation of a selfreplicating molecule which must have been enclosed in a membrane to make the first cell (first organism) which allowed for all proteins and DNA to be in a smaller space for faster reactions. RNA world hypothesis suggests life started with RNA. Viruses show this (virus is a strand of RNA). RNA is less stable than DNA which allows it to react and can catalyze reactions DNA > replication DNA polymerase> transcription (DNA > RNA) RNA polymerase > translation (RNA > protein) ribosome > PROTEIN Nucleic Acids: include DNA and RNA and strands of nucleotide monomers. Functions to store and transmit genetic information and has structural and catalytic roles (RNA). Is a polymer of nucleotides which contain: 1. phosphate group attached to 5’ carbon 2. sugar (deoxyribose, DNA; ribose, RNA) 3. nitrogenous base Purine: a type of nitrogenous base; includes adenine (A) and guanine (G). Found in all nucleic acids Pyrimidine: a type of nitrogenous base; includes cytosine (C), uracil (U), and thymine (T). Uracil is only in RNA and thymine (T) is only in DNA How do nucleotides polymerize to form nucleic acids? Phosphodiester bonds between PO4 group and OH group on sugar of different nucleotide that links the 3' C of one nucleotide to the 5' C of the other. Chapter 4: Directionality of DNA and RNA Directionality: RNA and DNA are writing in the 5’ 3’ direction 5' end has phosphate group 3' end has hydroxyl group *the 3’ and 5’ carbons are joined through phosphodiester linkage Potential energy in the monomer: Addition of phosphate groups raises the potential energy of the monomer (ATP) Watson and Crick – Physical model of DNA: They knew that there was a phosphodiester linkage so DNA must have a sugarphosphate backbone that was on the outside because it is polar and can interact with water while the nitrogenous bases form a hydrophobic interior Ran in antiparallel strands To fit, the nitrogenous bases formed purinepyrimidine pairs Erwin Chargaff’s Rule: Total number of purines = total number of pyrimidines A=T C=G A+T = T+C Rosalind Franklin: Xray crystallography gave dimensions of DNA molecule: 0.34 nm (length of turn, 10 rungs), 2.0 nm (width of helix), and 3.4 nm (distance between bases) Base pairing: The two DNA strands form complimentary base pairs AT and GC through hydrogen bonding. The purine and pyrimidine pair fit just right GC base pair has 3 hydrogen bonds, stronger and harder to break; AT base pair has 2 hydrogen bonds Making a copy of DNA 1 Strand separation – DNA polymerase 2 Polymerization: new nucleotides added through base pairing with templates. Replicated DNA is a semiconservative model. Each copy has one new strand and one old strand 3 Strands rewind into double helix with new SP backbone. Spontaneous reaction because double helix has lowest potential energy Primary Secondary Structure Stability/Reactivity Structure DNA C, A, G, and T TWO DNA strands running in opposite Very stable – more reliable for deoxyribose directions held together by storage of genetic information but not complementary base pairing and twisted a good catalyst (so likely not the first double helix form of life) Not as reactive, but more resistant to degradation RNA C, A, G, and U Short double helices (hairpins) where The OH group on the Ribose makes Ribose the bases on one side of the fold align the molecule less stable and, with an antiparallel segment on the other therefore, more reactive strand through hydrogen bonds More likely to be degraded because Tertiary and quaternary structures allow the hydrophobic nucleotides are it to have multiple functions exposed to water Ribozymes: RNA catalyst. Not as good as a protein because it only has 4 nucleotides while proteins have 20 amino acids *RNA can replicate itself as and catalyze polymerization reactions Chapter 5: Introduction to Carbohydrates Monosaccharides: monomers that polymerize to form polymers called polysaccharides through different types of glycosidic linkages. Vary in structure based on: placement of carbonyl group (aldehyde vs ketone), differences in carbon number, arrangement of hydroxyl group, different alpha and beta ring forms. Carbon atoms are numbered starting at the end closest to the carbonyl group. Carbohydrates: Contains carbonyl and several hydroxyl groups with many carbonhydrogen (C H) bonds Polysaccharides: complex carbohydrates are formed from monosaccharides via condensation reaction between hydroxyl groups to create a glycosidic linkage Multiple hydroxyl groups produce different molecules – different from proteins and nucleic acid polymerization *Beta bond between monosaccharides forms lactose which most animals can't break; only lactose enzyme can break this beta bond which is why most people are lactose intolerant *Can digest 1' 4' alpha linkage but not the beta 1' 4' linkage in plants Starch: is a polysaccharide found in plants which is a mix amylose and amylopectin and branches when a 1, 6 glycosidic bond forms. It’s harder to digest so we get more energy over time from it Glycogen: found in animals stored in muscles, blood, liver; energy storage in animals. It has a lot of branch points (more than starch) (1 in 10 glucose molecule branch points) so it’s easier to break down to glucose for faster energy. Alpha 1' 4' linkage Cellulose: used as structural support in cell wall in plants. It’s linear not helical; long parallel strands held together by H bonds so much stronger and hard to digest. Chitin (structural cell support in fungi, external skeleton of insects and custaceans). Has linear molecules like cellulose, but glucose monomers have NHCOCH3 (Nacetylglucosamine) Nac subunits form H bonds causing an even stronger bond Peptidoglycan (bacterial cell walls). Glycosidic linkage between glucose and then chain of 4 amino acids forming peptide bond. 4 amino acid chain forms covalent bond (peptide) with other molecule with 4 amino acids Beta 1' 4' glycosidic linkage Two types of covalent bonds *Cellulose, chitin, and peptidoglycan can't be digested because of their strong bonds Function of Carbohydrates: 1. Building blocks and synthesis of other molecules (ribose/deoxyribose; carbon skeletons) 2. Cell identity (attaches to lipid bilayer) a. Glycoprotein doesn't store information but can display it proteins with covalent bond to carbohydrate 3. Chemical energy is stored in H2CO and HCN bonds. The CH bond have high potential energy compared to CO bond because the electrons are shared more equally; more CH bonds = more energy storage a. Glucose produces ATP through cellular respiration b. Starch and glycogen > glucose > energy (ATP) c. A molecule has more free energy if linked together with weak bonds Chapter 6: Lipids, Membranes, and First Cells Plasma membrane: protein containing lipid bilayer surrounding cells that separates life inside the cell from outside of the cell and acts as a selective barrier. Membrane also helps localize and maximize reactions that otherwise wouldn’t occur. Selective Barrier: regulates the passage of molecules and ions into and out of the cell (i.e. lipid bilayer) so that harmful molecules cannot get in. Lipid: a molecule that consists of a major hydrocarbon component which are normally nonpolar and hydrophobic. The length of which varies and impacts the fluidity Isoprene: hydrocarbon chain Fatty Acid: hydrocarbon chain bonded to a carboxyl group. Formed by adding 2 carbon subunits. The carboxyl group is why it’s called a fatty acid Isoprene chains have a methyl group sticking out Steroids (cholesterol): are amphipathic, have a four ring structure made from isoprene subunits, vary by different R groups, cholesterol is important in the plasma membrane. It is also the starting point for the synthesis of estrogen, progesterone, and testosterone Phospholipid: Glycerol group reacts with phosphate group has two isoprene chains or two fatty acids Amphipathic: has a hydrophilic (polar) head, and a hydrophobic (nonpolar) tail Fatty Acid no methyl group Fats: are formed via dehydration synthesis or ester linkages to form three fatty acid chains Ester Linkage: formed between glycerol and a fatty acid, releases water Bonding: carbon double bonds create cis and trans molecules Cis has kinks in it which helps the fluidity of the membrane Trans all hydrogens are on opposite side; not many kinks Unsaturated/short: have double bonds (oil) and are permeable and liquid at room temperature. Better for membranes because it has better fluidity Saturated/long: max amount of hydrogens attached to carbon (butter). Are less permeable, solid at room temperature Membranes form spontaneously because of entropic forces (hydrophobic force) which is the energy that causes the bilayer so nonpolar part is away from the polar water and polar head group is by water. The nonpolar acyl chains are then further stabilized by van der Waals between the closely packed acyl chains (stronger forces with longer/larger molecule) Liposome: bimolecular phospholipid layer with fluid filled inner cavity, like a sphere Micelle: single layer, all chains are in the middle with phosphate on the outside (detergent); long single fatty acid chain; has a single fatty acid chain vs two Permeability: tendency to let a substance cross. The size and charge of a molecule affect the rate of diffusion across the membrane High to low permeability: hydrophobic, small uncharged, large uncharged, ions Phospholipids have selective permeability Small/nonpolar molecules move across quickly/easily without much if any help while charged, large, or polar molecules cross slowly and need help (facilitated transport) *Temperature decreases membrane fluidity and permeability because it causes the molecules to move more slowly. Not capable of supporting biochemical reactions at too low of a temperature Fluidity: phospholipids are in constant lateral motion but rarely flip to the other side of the bilayer, movement laterally is fluidity *Kinking in fatty acid chain pushes things away, opening more space, allowing for more fluidity *In eukaryotic cells, cholesterol influences permeability by reducing membrane fluidity because the increase in CH bonds causes more intermolecular forces (van der waals) making the fatty acids stick more to each other. Fluid mosaic model: a structure of the membrane that is composed of phospholipids that contribute to the fluid and dynamic membrane and also proteins which are either attached or are imbedded within the membrane (i.e. transmembrane proteins span the bilayer). 1. Bimolecular sheet of 2 monolayers of lipid. Hydrophobic chains inside and hydrophilic on the outside 2. Fluidity (mobility of lipids) is only lateral and rotational; lipid cannot flip from one monolayer to the other because of the polar head. Low temperature decreases fluidity. Scientists track this movement by tagging proteins, or by mixing two types of cells (mouse vs human) and seeing if they mix. 3. Bilayers are asymmetric in nature different on both sides depending on what is attached to the bilayer (different proteins and lipids) 4. Membrane proteins are either integral (through and through) or peripheral (only on the outside) Membrane proteins: are the proteins either attached or embedded within the membrane; tend to be heavily glycosylated. They are integral so they span the lipid bilayer and include, transmembrane, membrane associated, lipid linked, and protein attached. Similar to phospholipids, they can only move laterally in the membrane (cannot flip from one side to the other) but they move more slowly due to their size. Extracellular (polar and charged amino acids) Intracellular (nonpolar and small charge amino acids) Transmembrane composed of at least 20 nonpolar amino acids and adopts an alpha helix Glycoproteins: carbohydrates attached to protein. Include Olinked (carbohydrate attached to oxygen, ser/thr), and Nlinked (carbohydrate attached to N, asn). Glycophorin A is a glycoprotein in red blood cells Passive Transport: does not require an input of energy, can be diffusion or proteinfacilitated down a concentration gradient (goes from high concentration to low concentration). It is dependent on the concentration difference across the membrane (inside vs outside cell); distribution ratio is less than 1. The proteins are specialized for specific compounds and faster than simple diffusion with no protein. Ion channels: specialized membrane proteins for specific ions which allow small, charged compounds allowing them to diffuse through membrane. Different channels for different ions Gated channels: open or close in response to binding of a specific molecular or to an electric charge Aquaporins/water channels: open/close in response to membrane depolarization or binding of a regulatory molecule. Only moves water Carrier proteins: “carry” solutes through membrane. Highly stereospecific/highly selective for substrate recognition. Ex. Glucose carrer recognizes Dglucose, but not Lglucose, and transports D mannose or Dgalactose to a minor degree *Saturation is a sign of the use of facilitated diffusion (can only go at a certain rate) Active Transport: requires energy across membrane against a concentration gradient (going from low to high concentration). SodiumPotassium pump: pumps sodium ions out and brings potassium ions in using ATP. 1. Maintains resting potential across membrane; electrochemical gradient of sodium and potassium across membrane 2. Regulates cell volume 3. Contributes to active transport of solutes 4. Needs 1/3 of ATP to function and 2/3 of ATP for neurons *"pump" is only used for active transport; passive transports are "channels" Diffusion: molecules or ions diffuse across a phospholipid bilayer from an area of high to low concentration (down concentration gradient). Will always be linear with respect to concentration
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