Flashcards
Biochem exam 1
Cards in this deck (72)
- 1Carbohydrates(CH2O)n
most abundant biomolecules
CO2 + H2O->cellulose, plant products
1)energy-sugar and starch, oxidize carb, energy yielding pathways, NON-photosynthetic
2)structure/protection-formed by glycans: chitin, cell walls, lubricant, recognition/adhehsion between cells - 2Monosaccharidein nature usually 6C sugar (D-glucose), 4C sugars tend to be cyclic
simple sugars, colorless, crystalline, sweet, solids, freely soluble in H2O, insoluble in non polar solvents - 3Disaccharide2 monosaccharide units
sucrose (cane sugar)- D-glucose + D-fructose - 4Oligosaccharides3+ monosaccharides, can be 100s-1000s
cellulose (linear), glycogen (branched), both (D-glucose)n - 5Stereoisomersame atoms, different geometrical/optical positioning
- 6Diastereomerstereoisomers that are not mirror images, have different chemical properties (solubility)
- 7Enantiomersoptical isomers (D/L-glyceraldehyde)
- 8n chiral centers general rule1 C*=2^1---> 2 sterioisomers
4 C*=2^4--->16 stereoisomers
ketoses C*=#Cs-3
aldoses C*=#Cs-2 - 9D (dextro)optical rotation-d/+, Cahn-Ingold-R
if rotation of plane with polarized light is clockwise approaching the observer, most common-humans, depends on C* furthest from carbonyl
if OH is on right/down - 10L (levoro)optical rotation: l/-
cahn-ingold: S
if rotation of plane with polarized light is counterclockwise facing the observer, less common, glycoconjugates in bacteria
If OH is on left/up - 11Fisher Projections2D representation of 3D sugar structures
horizontal bonds projected out of plane towards you (dark)
vertical bonds projected in away from plane (light) - 12Epimerssugars that differ only in configuration around 1 C
- 13Anomersalpha and beta isomers, differ only in configuration about hemiacetal and hemiketal C atom
ANOMERIC C=CARBONYL C - 14Mutarotationalpha and beta can interconvert, ring opens briefly then quickly closes
D glucose- alpha 1/3, beta 2/3 - 15Haworth Projectionmore accurate representation of cyclic sugar structure, ring is titled almost perpendicular to plane of the paper, closer bonds thicker
- 16Pyranoses6 membered rings, prefer chair, 2 possible conformations, can interchange but requires energy (46kJ/mol)
- 17Furanoses5 membered rings, pucker, recall-ribose in DNA/RNA C2 endo (b, Watson crick) or C3 endo (a, RNA)
- 18Homosaccharidespolymer of single monosaccharide subunits
roles 1. storage of monosaccharides--> fuel (glycogen, starch)
2. structure (cellulose, chitin) - 19Heterosaccharidespolymer of 2+ monosaccharide units
roles 1. extracellular support (bacterial cell envelope, peptidoglycan=2 alternating monosaccharides) (animals-form matriculates, hold cells together, protection, maintenance)
2. glycosylation-intracellular targeting protein on/off mechanisms (A/B/O) - 20Glycogenglucose storage in liver and muscle tissue, mainly alpha 1-4 links, alpha 1-6 branches every 8-12 residues. 3D structure-seed protein, glycogenin binds to UDP glucose and acts as a primer for 1st few glucose molecules, then enzymes take over
- 21Starchamylase(unbranched D glucose chains alpha 1-4 only 1000s-millions of Da) + amylopectin(highly branches amylose alpha 1-6)
double helix like structure, H bonds between 2'OH and 3'OH of adjacent glucose molecules-kinks-spirals, digested by amylase-saliva, and glycosylases-sm intestine, both hydrolyze alpha 1-4 links - 22Dextransbacteria and yeast homopolysaccharide--> glucose storage
alpha 1-6 linked D glucose and alpha 1-3 branches, some a1-2/a1-4
used in gel filtration(sizing columns)
dental plaques on teeth - 23CelluloseD glucose homopolymers-exclusively B1-4 links
plants-stem, trunks, woody portion
H bonding between monomers in cellulose keeps it linear - 24Chitinexoskeletons of arthropods (insects, lobsters, crabs) cant be digested by vertebrates, homoploysaccharide of GlcNAc B1-4 links. 2nd most abundant polysaccharide on planet-1 billion tons/year
- 25Glucosaminoglycans- charge, extended, glucaronic acid +SO4 (-2)
- 26Hyaluronic Acid[GlcA (B1-3) GlcNAc]~50,000
clear, viscous soln, lubricant for joints, vitreous humor in eyes, some pathogenic bacteria secrete hydraluronidase which hydrolyzes glycosidic link--> makes tissue more susceptible to bacterial invasion - 27Chondroitin-4-sulfate[GlcA (B1-4)GalNAc]~20-60 (SO4 @ C4)
covalently linked to a protein, tensile strength of cartilage, tendons, ligaments, aortic wall - 28Keratin Sulfate[Gal (B1-4) GlcNAc (SO4 @C4) (B1-3) Gal]~25
cornea, cartilage, bond, hair, nails/claws, hooves - 29Heparin[IdoA25 (a1-4) GlcNs6s]15-90
anticoagulant-inhibits thrombin @C2
most negatively charged density - 30Polysaccharides as information carriersimportant in 1. intracellular info, protein transport and localization-organelles or decision for destruction?
2. extracellular signal molecules-growth factors, parasites - 31Glycoconjugateinformational carbohydrate covalently joined to protein or lipid
- 32Peptidoglycanimportant in bacterial cell walls
recall: lysozyme hydrolyzes Nac Muramic Acig (B1-4) GlcNAc (NAM-NAG)
NAM 3'OH attached to L-ala-D-glu-L-lys-D-ala-peptidoglycan crosslinker - 33Proteoglycansmacromolecules on cell surface or extracellular matriculates w >1 glucosaminoglycan chain attached via membrane/secreted protein (syndecan-single transmembrane protein 3-5 heparins (sometimes chondroitin sulfate)
- 34Glypicanprotein attached by lipid anchor (phosphatidylinosital PIP) cleavage of proteins from surface of membranes-> quick protein change->response
(cell recognition, proliferation, differentiation) - 35GlycoproteinsN and O linked glycosylation (PTM) in Golgi
(antibodies w N linked-etanercept and inflizimab-treat autoimmune diseases- psoriases, arthritis, chrohns
rituximab(monoclonal antibody)kills B cells, treats leukemias, lymphomas, and transplant rejection - 36Type A (RBC)[Ser-Gal-GlcNAc-Gal-Fuc-GalNAc]
- 37Type O (RBC)[Ser-Gal-GlcNAc-Gal-Fuc]
- 38Type B (RBC)[Ser-Gal-GlcNAc-Gal-Fuc-Gal]
- 39Glycosphinolipidshydrophilic head group=oligosaccharides, recognition of lectins, rich in brain and neurons-nerve conduction and myelin formation
- 40Lipopolysaccharidessurface of gram - bacteria (E. coli and Salmonella), usually recognized by antibodies-immune response
salmonella enterotoxin release (depending on specific species)-typhoid, food poisoning, toxic shock syndrome - 41Carbohydrates Informational Codesugar code: 1. intracellular targeting of proteins 2. cell cell interaction 3. cell differentiation and tissue development 4. extracellular signaling
unique from proteins/DNA 6C sugars cant branch 20 dif monosaccharide building blocks for hexameric oligosaccharides
20^6=6.4x10^7 vs DNA 4^6=4096 - 42Lectinsproteins that bind carbohydrates, high specificity and moderate/high affinity
found in all organisms 1. cell cell recognition 2. signaling and targeting 3. adhesion, lectin sugar binding protein site specific for certain sugars (galactose hydrophilic and hydrophobic) - 43Plant Lectinsdetterents to insects and predators (protective role) useful in molecular biology, separate glycan and glycoproteins w different oligosaccharide moieties. a. concanavalin a. binds to alpha mannose residues, binds antibodies b. clover lectin (in roots) binds to polysaccharides on surface of N2 fixing bacteria
- 44Neisseria gonorrhaeaehave carbohydrates that bind to receptors on surface of genital/oral epithelial cells
- 45Influenza virushas hemoglutinin, binds to sialic acid (SA) on surface of cells, aka N acetyl neuraminic acid
H1N1
H=hemoglutinin (binds to SA)
N=neuraminidase (cleaves SA) - 46Inflammation-selectinsplasma membrane mediated cell cell recognition and adhesion
(leukocytes (WBCs) slow rolling T cells through capillary, as T cells get closer to injury lectin ligand affinity rises, localization of T cells-extravasculation event) - 47Neural adhesionhelps to cause a target cell to adhere to neuron, lectin->neural cell->adhesion molecule (NCAM) aka CDS6, member of Ig family, expressed on surface of neurons, glia, skeletal, muscle, and killer cells
important in neurotransmission (learning and memory), synaptic plasticity, neuritis out growth (projection from neuron cell) - 481. Methods to analyze carbohydratesendoglycosidase
release oligosaccharide from glycoprotein or glycolipid
(N or O linked glycosidase) - 492. Methods to analyze carbohydrateschromatography
(IE, gel filtration, lectin affinity) - 503. Methods to analyze carbohydratesw released and isolate oligosaccharides
4 experiments
a. comp of mixture: hydrolysis w strong acid, breakdown into monosaccharides
b. positioning of glycosidic bonds: methylate all free OH groups w CH3I, hydrolyzes w SA
c. sequence of monosaccharides and/or position and configuration of glycosidic bonds
d. oligosaccharide microarray: very similar to DNA microarray but more difficult - 51Bioenergeticsquantification study of energy transductions (changes of one from of energy into another) in living cells--> nature and function of chemical processes underlying these processes
- 52Energy in bondsvibration, rotation, storage
- 53Energy in system depends on...temperature, pressure, volume, CONCENTRATION!
- 541. EfEi1. change in E-negative, favorable
2. change in E-positive, requires energy - 552 ways a system can exchange energy1. heat energy (q) works only by surroundings, q leaving system (-) q entering system (+) change in E=q-w
1st law of thermodynamics - 56Variables of thermodynamicsT-temp (K)
P-pressure
V-volume
R-gas constant (8.315 J/mol K)
n=# moles
PV=nRT - 57w=oreaction @ constant volume- not expanding- no work can be done, only pressure can change, all energy change is heat, called "constant volume energy change"
- 58Reaction at constant Penergy changes in work and hehat
PV=nRT-->V=nRT/P
w=PdeltaV sub in w=PdeltanRT/P - 59Enthalpy (H)heat change at constant pressure (q @ constant P)
E of making and breaking bonds - 60Entropy (S)measure of disorder (J/degree/mol)
2nd law of thermodynamics=CHAOS RULES
deltaS=chhange in entropy, >0 is favorable - 61Gibbs free energy of a systemG=H-TS heat and orderness
if deltaH so big, deltaS doesn't matter
deltaG=deltaH-TdeltaaS
deltaG=Gf-Gi if deltaG<0 (-) exergonic (release E, favorable) deltaG=0 equilibrium-nothing happens, deltaG>0 (+) endergonic (requires E, unfavorable) - 62Metastable Statewhen molecule/system spends extensive amount of time in a certain state other than systems least favorite energy state. kinetic variables can alter process rates-enzymes speed rxn, cold temps slow rxn
- 63Standard state25C (298K), 1atm, 1M conc
aA + bB --> cC + dD
deltaGknot(standard state)
deltaG=-RTlnKeq @ equilibrium
Keq=products/reactants, e^-deltaGknot/RT - 64Biological Standard StatepH=7
[H+]=10^-7M
[H2O]=55.5M
if Mg (+2) involved, [ ]=1mM - 65Keq and Qequilibrium constant and expressing relative ratio of protucts at a given instant-mass action ration, Q wants to go to Keq
[C]c[D]d/[A]a[B]b - 66@ equilibriumQ=Keq, deltaG=0, in lab allow reactants to reach equilibrium and measure Keq by determining conc of reactants and products, only need to know Keq, sub into deltaG'knot=-RTlnQ, get deltaG'knot @ pH 7
- 67Le Châtlier's Principleincrease [reactants] Q and deltaG get smaller
increase [products] Q and deltaG get larger
if Q>K, deltaG>0
if Q - 68Other ways to couple a reaction1. other NTPs (GTP, CTP, UTP)
2. Other phosphomolecules (PEP, 1,3 BPG, P. creatine)
3. Thiolesters (acetyl CoA, ubiquitin w E1 E2 E3s.
4. ion gradients
5. protein conformation - 69ATPvery energetic-really eager to hydrolyze, hard to go backwards, has to cram 2 anions together
1. charge of products (-3/-2)hinder reverse reaction (repulsion)
2. better hydration of phosphates--stability of phosphate
3. buffering of protons given off by rxn--recall Pi is good buffer
4. more resonance stabilization in products than reactants
all 4 of these favor products - 70Nucleotide diphosphate kinaseenzyme that can carry phosphate groups from ATP to the nucleotides
- 71Redox pairse- transfer form donor to acceptor-may be spontaneous, depends on relative affinity of the e- acceptor in redox pair (leoger)
e- transfer one was when potential is large - 72deltaGredox cell=-nFdeltaEcell
Information
- Description
- Flashcards on Biochem exam 1, created by Cammi MacKenzie on 07/02/2020.
- Created by
- Cammi MacKenzie
- Views
- 11
- Rating