BIO Midterm1- Reading.docx

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University of California - Santa Barbara
Molecular, Cellular & Develop. Biology

Introduction to class and Biochemical Principles Ch.1 (1-20) 1. What is Bio? i. Study of life ii. Cells grow & produce E & raw materials from environ. iii. Evolution-genetic-major unifying principle of bio 1. Natural selection iv. Organisms interact w one another v. Discoveries can be generalized into “model systems” vi. Scientific method= observation & logic vii. Science depends on objectivity & reproducibility b. Living things i. Have 1+ cell ii. Have genetic info & use to reproduce iii. Convert molecules from environment to new molec. iv. Extract E from environ. v. Regulate internal environ. c. Cell Theory i. Cells= basic unit of life ii. Distinct entities & building blocks iii. All cells come from preexisting cells iv. All cells similar in composition v. Chemical rxns occur in aq. Sol’n of cells vi. Genetic info replicated & passed on during cell division vii. Viruses are not alive 1. Viruses lack cellular structure 2. Dependent on other cells d. Evolution (Darwin) 1. Change in genetic makeup over time ii. Natural selection 1. Survival & reproduction in pop. 2. Traits hat improve survival/ reproduction spread -> pop. a. Adaptations: increase chance of survival iii. Species = group that can reproduce w/ one another iv. Genome: blueprint (all genetic info) 1. DNA (made of nucleotides) = long seq. of genetic info 2. Genes: specific info to make proteins 3. Protein molecules control chemical rxns & structure **DNA< Proteins< Combo of Proteins < Structures & Processes< Organism ** **atom products) 4. Water important for life a. Unique structure and properties i. Ice floats: solid water = less dense than liquid ii. Melting freezing & heat capacity 1. High specific heat capacity (much E needed to heat water) 2. High heat of Vaporization (much E needed to evaporate water) 3. Cohesion & surface tension a. Cohesion: strong water, water bond (many H-bonds) b. Surface tension: hard to break surface of water bc H-bonds link water molecules to other water molecules 4. Water can ionize (release H+ ions) b. Water is an excellent solvent i. Solution: produced when substance (solute) dissolved in a liquid (solvent) ii. Aqueous solution: something in water (solvent) 1. Acidic a. Acids release H+ b. Strong acids dissociate completely in water c. Weak acids don’t completely dissociate into ions in water 2. Basic a. Bases accept H+ 3. Acid/base rxns can be reversible a. Ionization of strong acids likely irreversible b. Ionization of weak acids likely reversible c. pH: H+ concentration a. pure water has H+ concentration of 10 M -7 b. a 1 M HCl sol’n has H+ concentration of 1M (everything dissociates) c. 1 M NaOH has H+ concentration of 10 -14 2. pH= -log [H+] a. pH: acid<7 b. pH: base>7 ii. buffers: weak acid & conjugate base 1. resists pH change 2. ex: human blood ______________________________________________________________________________________________________________ Introduction to Macromolecules/ Lipids and Polysaccharides 3 (39-42); 6 (105-109) 1. What kinds of Molecules Characterize living things? a. Polymers (many units) b. Monomers (smaller units) i. Amino acids -> proteins ii. Monosaccharide -> polysaccharides iii. Nucleotides -> nucleic acids iv. Lipids c. Functional groups : certain small group of atom Carboxyl Hydroxyl Aldehyde Amino Keto Phosphate Sulfhydryl i. Isomers have same atoms but arranged diff a. Structural (i.e. branched & unbranched) b. Optical (mirror images) like hands i. when carbon has 4 attachments ii. the carbon called assymetrical carbon 1. other molecules = optical isomers of each other ii. macromolecules (large polymers) are formed by condensation reactions and broken down by hydrolysis a. condensation rxns: loses 1 water molecule for every covalent bond formed b. opposite is called hydrolysis reaction: i. hydrolysis rxns turn polymers-> monomers 51-61 1) Glycosidic linkages bond monosaccharides a) Glycosidic linkage = formed by condensation/dehydration rxn i) Diff linkages make different sugars (alpha and beta) ii) Alpha-D- glucose has “OH” group coming down from C1 (A-down) iii) Beta –D-glucose has “OH” group going up from C1 (B-up) b) Polysaccharides store ENERGY & provide structural materials i) Starch (1)Polysaccharides of glucose w α- glycosidic linkages (a) α-1,4, and α-1,6 glycosidic bonds (b)branching at C1 and C6 (i) some plant starches are unbranched (amylose) ii) Glycogen (1)Water-insoluble (a) Better storage of glucose bc lower osmotic pressure (2)Highly branched polymer of glucose iii) Cellulose (1)Polysaccharide of glucose (2) β- glycosidic linkages (a) more stable (b)has “armor” c) Modified carbs have additional functional groups i) C6 in glucose can be oxidized to a carboxyl group (1)Makes glucuronic acid ii) Amino group can sub for an OH- group (1)Forms amino sugars (a) Important for extracellular matrix (b)Ex: chitin (i) Polysaccharide in skeleton of skeletons & crabs Summary of CELLULOSE, STARCH & GLYCOGEN CELLULOSE STARCH GLYCOGEN Linear Branched Highly branched Parallel cellulose form H- Branching limits H-bonds Branching makes its deposits bonds= think fibrils making them less compact more compact than starch than cellulose Unbranched Branched Branched Polymer of glucose w β- 1,4- Polymer of glucose wα-1,4, Polymer of glucose wα-1,4, glycosidic linkages and α-1,6 glycosidic bonds and α-1,6 glycosidic bonds Chemically very stable Branching at C6 Branching at C6 Lipids 1) Chemical structures & functions of lipids a) Lipids= fats (1)Insoluble hydrocarbons (2)Nonpolar covalent bonds (3)Many weak van der Waals forces hold them together ii) Functions: (1)Store ENERGY (2)Cell membranes (3)Steroids & modified fatty acids regulate (i.e. hormones & vitamins) (4)Thermal insulation (5)Lipid coating around nerves = electrical insulation (6)Repels water on skin b) Fats & oils are hydrophobic (1)Fats = solid triglyceride at room temp (2)Oils= liquid triglyceride at room temp ii)Triglyceride made up of 3 fatty acids & 1 glycerol (1)Glycerol (an alcohol) (a) Small molecule w/ 3 OH groups (2)Fatty acid (a) Long nonpolar hydrocarbon chain & polar carboxyl group (COOH-) (b) Chains are hydrophobic iii) TRYGLYCERIDE synthesis requires 3 condensation/dehydration reactions (a) In each rxn, carboxyl group bonds w/ hydroxyl group of glycerol (b)Results in ester linkage (covalent bond) (c) Releases water molecule (2)unsaturated fatty acids (a) hydrocarbon chain contains 1+ double bonds (b)KINKS in molecule (prevents tight packing) c) Phospholipids form biological membranes i) Amphiphatic- both polar and nonpolar properties (has polar head and nonpolar tails) ii) Contain fatty acids bound to glycerol by ester linkages iii) Phospholipid bilayer (1)Head face outwards into solution (2)Tails turn inward (hydrophobic) (3)Cell membrane d) PHOSPHOLIPIDS important for ENERGY CONVERSION, REGULATION, & PROTECTION (1)Carotenoids (a) Light-absorbing pigments (b)i.e. β- carotene that traps light energy in leaves during photosynthesis (i) color in carrots, egg olds, pumpkins (2)steroids (a) organic compounds where multiple rings share carbons (b)i.e. cholesterol (c) i.e. estrogen (3)vitamins (a) vitamin A, D, E, K… (4)waxes (a) sheen on human hair (b)formed by ester linkage between saturated, long- chain fatty acid & saturated long-chain alcohol 6 (105-109) 1) Biological membrane a) Fluid mosaic model i) Proteins non-covalently embedded in phospholipid bilayer by hydrophobic regions ii) In plasma membranes, carbs are located on outside of cell (1) Recognize specific molecules on surface of other cells iii) During winter (cold enviro) organisms change lipid composition (1) Change saturated fatty acids with fatty acids with shorter tails b) Membrane proteins are asymmetrically distributed i) Peripheral membrane proteins (1) Lack exposed hydrophilic groups & aren’t embedded in bilayer ii) Integral membrane proteins (1) Partly embedded in bilayer iii) Trans-membrane proteins (1) Extend all the way through the bilayer & protrudes on both sides Macromolecules: Proteins and Polysaccharides 3 (42-51) 1) Protein chemical structure & Functions i) Catalytic proteins (enzymes) speed up biochemical rxns ii) Defensive proteins (antibodies) recognize & respond to non-self invaders iii) Hormonal & regulatory proteins (i.e. insulin) control physiological processes iv) Receptor proteins receive & respond to molecular signals inside & outside organism v) Storage proteins store chemical building blocks- amino acids- for later use vi) Structural proteins (i.e. collagen) provide physical stability & movement vii)Transport proteins (i.e. hemoglobin) carry substances within organism viii) Genetic regulatory proteins regulate when & how & to what extent a gene is expressed 2) a) Proteins made of amino acids (20 kinds) i) Polypeptide chains (linear polymer of covalently linked aa’s) ii) Sequence of aa’s determines function & structure iii) Have 1 amine group (NH +3 & 1 carboxyl group (COO-) (1)5 amino acids have electrically charged side chains (+1/-1) (a) attract water (b)hydrophilic (c) attract charged ions (2)5 amino acids have polar side chains (δ- or δ+) (a) form H- bonds with water (b)H- bond with other charged substances (polar & nonpolar) (3)7 amino acids have nonpolar hydrocarbon side chains (a) hydrophobic (b)hydrophobic side chains cluster together in interior of protein (4)3 amino acids (a)cysteine (i) side chain has –SH group (ii)can react with another cysteine side chain in oxidation rxn 1. forms disulfide bridge a. determines how polypeptide chain unfolds (b)glycine (i) side chain has single H atom & is small enough to fit into tight corners of protein (c) proline (i) has modified amino group (ii)often found at protein bends or loops 1. due to ring structure 2. limits H-bonding ability 3. limits ability to rotate about α carbon b) Polypeptide links form backbone of a protein i) Peptide bonds hold together amino acids ii) 3-D structure of proteins (1)C—N linkage limits rotation & folding of polypeptide (2)H-bonding within the protein (a) O (δ-) of carboxyl group (b)N (δ+) of carboxyl group 1. Primary structure of protein is aa sequence a. aa monomers joined by polypeptide bonds 2. Secondary structure a. Alpha helix i. H-Bond ii. Right-handed coil iii. R- groups extend outward from peptide backbone of helix iv. Coiling= result from H-bonds that form between N—H of 1 aa & C=O of another b. Beta pleated sheet i. H-Bond ii. 2+ polypeptide chains stabilized by H-bonds between N—H of 1 chain & C=O of another 3. Tertiary structure a. Polypeptides fold, forming specific 3-D shapes b. Folds stabilized by bonds (H-bonds & disulfide bridges) c. Folding both has α-helix & β-pleated sheet d. **Rxns between R-groups (amino acid side chains** i. covalent disulfide bridges form between cysteine side chains ii. H-bonds between side chains stabilize folding iii. Hydrophobic side chains cluster together insdie & fold iv. Van der Waals forces stabilize close interactions between hydrophobic sc’s v. Ionic bonds form between + & - charged side chains 1. Salt bridges form between aa’s 2. Ionic bonds can also be deep within protein w/in water 4. Quaternary structure (ex. Hemoglobin) a. 2+ polypeptides assemble to form larger proteins b. tetramer has 4 polypeptide subunits c. the ways subunits bind together & interact i. weak interactions 1. hydrophobic 2. van der Waals 3. H-bonds 4. Ionic bonds 5. protein denaturation a. heat can disrupt weak interactions (2° & 3° structures to break) 6. protein fxn affected by shape & surface a. shape i. there needs to be a “fit” for protein to bind to other protein b. chemistry i. exposed aa R-groups on surface on protein permit chemical rxns w other substances 1. interactions can be a. ionic b. H-bond c. Hydrophobic 7. Environmental conditions affect protein structure a. Increase temp i. Rapid molecular movement can break H-bonds & hydrophobic b. Alterations in pH i. Can change pattern of ionization of carboxyl & amino groups ii. Can disrupt pattern of ionic attractions & repulsions c. High [polar substances] i. Can disrupt H-bonding d. Nonpolar substances i. Can disrupt protein structure 8. Molecular chaperones help shape proteins a. “molecular caretakers” i. prevent inappropriate interactions & enhance appropriate ones ii. after denaturation: environment can cause incorrect folding iii. after protein synthesis: surface can cause wrong binding b. Heat shock proteins (HSPs) i. Stress-induced chaperone proteins ii. Bound to target proteins & kept them from being denatured CARBOHYDRATES 1. Carbs: large group of molecules a. General formula: C nH 2) n b. Three major roles i. Store ENERGY ii. Transport ENERGY iii. Carbon skeletons for new molecules 2. 4 types of carbs a. Monosaccharides: simple sugars 1. Monomers of larger carbs 2. i.e. glucose, ribose, fructose ii. α-glucose has OH group “down” on C1 iii. β-glucose has OH group “up” on C1 iv. Pentoses: 5 carbon sugars 1. Backbones of DNA &RNA a. Oxygen missing from C2 in deoxyribose v. Hexoses: six C sugar b. Disaccharides 1. two monosaccharides linked by covalent bonds 2. i.e. sucrose (glucose & fructose) c. Oligosaccharides 1. 3-20 monosaccharides d. Polysaccharides 1. Hundreds or thousands of monosaccharides 2. i.e. cellulose, starch, glycogen 3. Glycosidic linkages bond monosaccharides a. Glycosidic linkages i. Covalent bonds ii. Formed by condensation/dehydration rxns Macromolecules: Proteins and Nucleic Acids 4 (62-67);
 1. Nucleic acids : polymers for storage of genetic info i. DNA 1. Macromolecule that encodes hereditary info & passes it -> generations ii. RNA 1. Intermediate to flow encoded info from DNA b. Nucleotides = building blocks 1. Has base a. Pyrimidine b. Purine 2. Has sugar a. Ribose b. Deoxyribose ii. Nucleotides joined by posphodiester linkages 1. Between sugar of one nucleotide & phosphate of next 2. C
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