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BCHM 307 Quiz 1 Material

by: Sean Anderson

BCHM 307 Quiz 1 Material BCHM 307

Marketplace > Purdue University > BCHM 307 > BCHM 307 Quiz 1 Material
Sean Anderson
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These notes and images cover the material we have covered thus far in class for quiz 1.
Dr. Stefan Paula
Class Notes
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This 13 page Class Notes was uploaded by Sean Anderson on Thursday October 6, 2016. The Class Notes belongs to BCHM 307 at Purdue University taught by Dr. Stefan Paula in Fall 2016. Since its upload, it has received 3 views.


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Date Created: 10/06/16
Sean Anderson Professor Paula BCHM 307 10/31/16 BCHM 307 Exam 2 Study Guide Lipids  Lipids—biological molecules that are soluble in nonpolar solvents and poorly soluble in water o They are predominantly hydrophobic molecules o They do not form polymers and aggregate to form bilayers and micelles o Glycerophospholipids and sphingolipids  Lipid classes o Fatty acids o Triacylglycerol o Glycerophospholipids o Sphingolipids o Cholesterol  Fatty acids o Amphiphilies o Polar head group: Carboxylic acids o Nonpolar tail: Hydrocarbon tail o Fatty acids can be saturated, unsaturated, or polysaturated  Unsaturated fatty acids o Double bonds are usually in the cis-conformation  Triacylglycerol “triglycerides” o Function: energy storage in fat cells (adipocytes)  Glycerophospholipids o Function: major component of biological membranes  Lipid bilayers o Three common head groups on Glycerophospholipids  -Choline (no charge)  -Serine (- charge)  -Ethanolamine (no charge)  Phospholipases o They cleave phospholipids at specific sites o  Sphingolipids o Instead of glycerol, sphingolipids have sphingosine as their backbone o  Sphingomyelins o Function: sphingomyelin is found in the myelin sheath around nerves o Head group is a phophocholine or phosphoethanol group  Cerebrosides o Similar to sphingolipids, but carry a monosaccharide in their head groups (instead of phophocholine or phosphoethanolamine)  Gangliosides o A ganglioside is a sphingolipid with an oligosaccharide head group o Function: gangliosides are found on cell surfaces are involved in cell/cell recognition  Steroids: cholesterol o Cholesterol is derived from isoprene o Has a weak amphiphilic character o Cholesterol is found in the biological membrane o Cholesterol is a metabolic precursor of steroid hormones  Estrogen, testosterone, cortisol, aldosterone  Characteristics of a lipid bilayer o Fluid: no clearly defined geometry, head groups move up and down o Hydrocarbon tails wave o Asymmetric: different lipids are found in each leaflet  Only certain lipids can from bilayers o Fatty acids 1 hydrocarbon tail o Glycerophospholipids  2 hydrocarbon tails o Triacylglycerol’s  3 hydrocarbon tails o  Melting points of lipids o Double bonds put kinks into the acyl chain o The melting point of an acyl chain decreases as the degree of unsaturation increases  More double bonds = lower melting point –highly saturated  Less double bonds = higher melting point –highly unsaturated  Lipid motions in a bilayer o Transverse diffusion  Polar head group has to travel through the hydrophobic tails o Lateral diffusion  Polar head group travels along the hydrophilic membrane o  Three types of membrane proteins o Integral membrane protein o Peripheral membrane protein o Lipid-linked protein o  Lipids can be covalently linked to proteins in a variety of ways o Myristoylation o Palmitoylation o Prenylation o  Transmembrane proteins span the bilayer o Bacteriorhodopsin: 20 AA/helix o Beta Barrel: 8 strand minimum o  The Fluid Mosaic Model o Membrane proteins float in a sea of lipids and do not transverse the bilayer (= lateral diffusion) o Carbohydrates   Carbohydrates o They are formed from CO a2d H O 2 o Carbohydrates have the generic formula: (CH 2) n  Where n > 3 o Their roles:  Energy source in metabolism  Mediation of intercellular communication  Structural support (cell walls)  Carbohydrate classification o Monosaccharides  Glucose, fructose, ribose o Small polymers  Disaccharides – two sugars bound  Sucrose, lactose, maltose  Trisaccharides—three sugars bound  Oligosaccharides—several sugars bound o Polysaccharides—large polymer of sugars  Starch, glycogen, cellulose  Carbohydrate naming o Pent—5 o Hex—6 o Aldoses: monosaccharides made from aldehydes  Glyceraldehyde is the simplest aldose o Ketoses: monosaccharides made from ketones  Dihydroxyacetone is the simplest ketone  Isomers o Most carbohydrates are chiral o (picture)  Rules for designating D and L notation 1. Draw aldehyde or ketone group at the top—Fischer Projection 2. Identify lowest chiral center in molecules 3. Classify configuration based on position of the OH group  If OH is on the right, D form  If OH is on the left, L form o Most sugars in nature are in D form o Biological systems can distinguish D and L sugars  Plenty of isomers possible –be able to sketch them o Aldopentoses  D-Ribose o Aldohexoses  D-Glucose  D-Galactose  Ring formation o Same sugar can be sketched in different ways  Fisher projection  Haworth projection o  Cyclization of glucose o Since the aldehyde group has rotational freedom about the C1-C2 bond, two anomers are possible  α-anomer (-OH down)  β-anomer (-OH up) o α-D-Glucose is most prevalent in biochemistry  Bond formation between monosaccharides and other molecules o Glucose methylated at the hydroxyl group at C1 o The C1O bond is called a glycosidic bond (keeps monosaccharides together) o  Some more monosaccharide derivatives o Glucosamine—an amino group has replaces the OH substituent o Glucuronic acid—a carboxyl group has replaces the terminal CH OH 2 o Glyceraldehyde-3-phosphate—a phosphate group has replaced an OH substituent  Disaccharides: o Sucrose  Sucrose is table sugar  Sucrose has an α(12)β glycosidic bond  Sucrose is the most abundant sugar in nature  o Lactose  Lactose is milk sugar  Lactose has a β(14) glycosidic bond  Breakdown enzyme: lactose  (lactose intolerance)  o Cellulose  Structural support of plants  β-1,4 glycosidic bond  o Starch  α-amylose (100-1000 glucose units)  α-1,4 glycosidic bond   Amylopectin  α-1,6 glycosidic bond  branching   Polysaccharides o Starch  Long chain polymer with many glucose units is the principle store of carbohydrates in plants  Used as food by young plants until leaves grow  Animals use starch as an energy source by ingesting plants  Mixture of α-amylose and amylopectin o Glycogen  Found in animals, not plants  Similar to amylopectin (but higher degree of branching)  Glucose is needed by the body  quick removal of glucose monomers from multiple branch ends  Straight chains like amylose provide only one glucose molecule at a time (slower)   Glycoproteins o Glycoproteins are N-linked via—Asn o Glycoproteins are C-linked via—Ser or Thr o o ABO blood types:  Oligosaccharides on surface of red blood cells  Type Aantibodies against B  Type B antibodies against A  Type AB  no antibodies  Type O  antibodies against A and B o  Artificial sweeteners o Very sweet compounds o Compounds that cannot be metabolized  Aspartame DNA  DNA: general o Carrier of genetic information o Chromosomes: DNA and proteins o Virus: encapsulated DNA  DNA structure o DNA and RNA contain nitrogenous bases –learn to draw purines and pyrimidines  Purines – Adenine and Guanine  2 ring structures  Pyrimidines—Thymine and Cytosine  1 ring structures  RNA: uracil o RNA: uracil instead of thymine  Absence of methyl group  DNA/RNA: ribose o Bases are linked to a sugar via a N-glycosidic bond o Ribose: 2’ –OH group o Deoxyribose: 2’ –H group o Ring numbering on the sugars contains primes  Nucleotides o Add 1-3 phosphate groups at 2’ carbon atoms o Nucleoside = base + sugar o Nucleotide = base + sugar + phosphate  Some nucleotides have functions other than being part of DNA/RNA o Coenzyme A (CoA)  -SH at top of structure is the only active part of the molecule o Nicotinamide adenine dinucleotide (NAD)  nicotinamide structure at top is the only active part of the molecule  DNA: polymer formation o Nucleotides are connected by phosphodiester bonds o Direction: read sequence of bases 5’ 3’  DNA: 3D structure o Pauling model for DNA (incorrect) o Triple helix: phosphates and ribose in core with bases periphery o Watson and Crick model for DNA (correct) o Double helix—strands are antiparallel  DNA: the double helix o Base pairs come from the core of the double helix o Phosphate backbone forms the periphery o Structural features:  2 antiparallel strands  Bases in center, sugars and phosphates in periphery  Bases stacked on top of each other  Places of bases roughly perpendicular to axis  H-bonding between base pairs in a complementary fashion  2 grooves (major and minor) o Stabilizing forces:  Hydrophobic interactions  bases buried inside  H-bonds  between base pairs  Van-der-Waals interactions  core densely packed  Ionic interactions  cations around the phosphate groups reduce electrostatic repulsion  Base pairings in a double helix o Pyrimidines form 2 H-bonds o Purines form 3 H-bonds o Base pair width is similar o Chargaff’s rule provided initial evidence for base pairing  A + G = T + C or A = T and C = G  Complementary  DNA denaturing o DNA (like proteins) can denature (unfold, melt) o Monitor denaturing by measuring the absorbance at 260nm o T m melting point o  DNA renaturing o DNA can renature (refold, annealing) o Central Dogma of Central Biology   Central dogma o DNA  RNA  protein o Genes: sequences of DNA o Replication: copying DNA o Transcription: making RNA and DNA template o Reverse transcription: making DNA from RNA template o Translation: making proteins from an RNA template  Replication o Replication is semi-conservative  DNA is supercoiled o Topoisomerases: enzymes that alter supercoiling  Replication fork o A replication for is the site where DNA strands separate and 2 new strands are synthesized  Several proteins participate in DNA replication (“Replisome”) o Helicase o Single-stranded binding proteins o Primase o DNA polymerase o Sliding clamp o RNase o DNA ligase  Helicase o Helicases convert double-stranded DNA (dsDNA) to single-stranded DNA (ssDNA)  Single-stranded binding proteins (ssBP) o Single-stranded DNA is bound by single-stranded binding proteins  Protection from nucleases  Prevention of annealing  DNA polymerase o DNA polymerase faces two problems:  DNA polymerase can only extend a pre-existing chain  DNA polymerase cannot initiate polynucleotide synthesis  RNA polymerase (primase) can  Primase makes an RNA primer (10-60 nucleotides)  The RNA primer will be replaced by DNA later  DNA synthesis occurs in the 5’3’ direction o Antiparallel strands of DNA need to be replicated simultaneously  A DNA polymerase binds to each strand  The two polymerases work side-by-side  One strand must loop out  Lagging strand is synthesized in a discontinuous fashion o Okazaki fragments (100-2000 nucleotides long) o  Sliding clamp o Most DNA polymerases are processive (hold on to substrate for several catalytic cycles) because the sliding clamps holds the DNA and the DNA polymerase in place  3D structure of DNA polymerase o “Klenow” fragment of DNA polymerase I o  DNA polymerase: proofreading o DNA polymerase proofreads newly synthesized DNA:  Base pair mismatch  Local distortion of in helix sense by DNA polymerase  Hydrolysis of wrong nucleotides o 3’5’ exonuclease activity o  RNase and ligase o RNase: removal of primer o Ligase: sealing gaps  Replication: a potential problem at the 3’end o 2 replication forks moving in opposite directions o 3’ overhang of parent strand  Daughter strand shorter o Implication of problem:  Each round of DNA replication would lead to chromosome shortening  Telomeres o Solution:  Telomerase repeatedly adds nucleotide segments (“telomeres”) to the 3’ end of parent DNA strand  DNA polymerase can then complete the other DNA strand  DNA packing o


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