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Biochemistry BBMB 301

by: Emily

Biochemistry BBMB 301 BBMB 301


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Week 4 Lecture Notes
Survey of Biochemistry
Robert Thornburg
Class Notes
biochemistry, BBMB
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This 7 page Class Notes was uploaded by Emily on Tuesday February 9, 2016. The Class Notes belongs to BBMB 301 at Iowa State University taught by Robert Thornburg in Spring 2016. Since its upload, it has received 9 views. For similar materials see Survey of Biochemistry in General Science at Iowa State University.

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Date Created: 02/09/16
Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 9 - CHAPTER 9 - HEMOGLOBIN By: Emily Settle  Oxygen needs to be transported from the lungs to the tissues. o The oxygen concentration in the tissues is much lower than the concentration of oxygen in the lungs. o Human bodies use about 55 liters of oxygen daily. o Oxygen can diffuse across 1 to 2 cell layers.  Hemoglobin (Hb) – functions in transportation of oxygen. Binds oxygen. o Structure – 4 subunits (same fold as myoglobin) o α2β2 quaternary structure o four heme groups  bind four oxygens.  Myoglobin (Mb) – functions in storage of oxygen. Binds oxygen. o Structure – 8 α-helices o One heme group  can only bind one oxygen.  Oxygen binds to a heme group – hydrophobic.  Hb picks up at the lungs and drops off at the tissues.  Mb affinity is higher at the tisues than Hb affinity.  Mb stores oxygen until the oxygen concentration gets very low.  Exercise – burn extra oxygen to get more energy -> releases more CO2 -> decreases pH -> Hb binds less O2, releasing O2 more readily.  O2 binding sigmoidal binding o Positive cooperativity - T state to R state (tense to relaxed) o Negative cooperativity – R state to T state (relaxed to tense)  Allosteric Regulation – conformational change at one site in a protein is transmitted to a distant site. O2 binds to one site, causes structural change to other sites.  Deoxyhemoglobin – Fe2+ atom pulled below plane of heme ring  Oxyhemoglobin – Fe2+ moves back into heme plane.  Cooperative Effect: enhanced activity resulting from cooperation between subunits of an allosteric molecule.  Cooperative behavior allows for rapid binding of oxygen by hemoglobin in the lungs and quick release in the tissues.  Cooperative Function: When the Fe2+ atom moves back into the heme plane… o 1. Physical pull of the Fe2+ pulls on the His R group o 2. Pull on the His R group moves α helix towards the heme plane o 3. Pull on the α helix pulls at the contacts between subunits o 4. Pull at contacts in other subunits causes O2 sites to open and become accessible to bind more O2. -> Cooperativity.  Hb is affected by allosteric regulator. o Binds to maternal Hb o Stabilizes T state (deoxy state) o OXYGEN CAN ONLY BIND WHEN REGULATOR IS NOT BOUND TO IT.  Fetal Hb – α2β2 structure  Maternal Hb – α2δ2 structure  δ subunit has a greater affinity for O2 than the β subunit. o Fetal Hb binds oxygen more tightly than maternal.  O2(unbound) + E  EO2(bound) o Maternal Hb continuously releases and re-binds oxygen. o Fetal binds oxygen more easily than maternal.  Babies in the womb… o Mother and baby have different Hb. o fHb has a higher affinity for oxygen than mHb. o fHb is unaffected by BPG . o BPG reduces oxygen binding in mHb.  As [O2] decreases, more O2 is released from the tissues.  pH decreases as [O2] decreases  [CO2] increasescreates negative chargeNew salt bridge forms, stabilizing tense state (deoxy).  [H+] increasescreates positive chargeNew salt bridge forms, stabilizing tense state (deoxy).  Sickle Cell Anemia – disease caused by a single amino acid substitution. o Glu residue (negatively charged) replaced by a Val (nonpolar) o Nonpolar Val can fit into a hydrophobic pocket of other Hb moleculesHydrophobic effectsticky patch. o Forms protein fibers of Hbred blood cell lysis, anemia – poor delivery of oxygen to tissues. o Can cause blockage of capillaries due to abnormal sickle-like shape. o Positive effect – provides resistance to malaria in heterozygotes.  Malaria parasite persists for a long time in sickle shaped cells allowing for a more effective immune response.  Bohr Effect – observation made by Christian Bohr that H+ and CO2 promote the release of oxygen from oxyhemoglobin.  The activity of hemoglobin can be used to measure brain activity. o Blood vessels relax to allow more blood flow to an active region of the brain. o This can allow us to map the brain and track pathways. Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 10 – CHAPTER 10 – CARBOHYDRATES By: Emily Settle  Saccharides: o Mono – one o Oligo – several o Poly – many  Types of carbohydrates o Cellulose  Plant cell walls and fibers  Ex  cotton – almost pure cellulose o Starch  The major energy source in most diets  Ex  potatoes, rice, bread, pasta, tortillas, noodles o Glycogen  Major energy source in the animal bodies o Chitin  Arthropod exoskeletons, fungal cell wall o Murein  Bacterial slime layer  Monosaccharide Terms o Polyhydroxy aldehydes – aldoses o Polyhydroxy ketones – ketoses o Carbon number  Triose (3)  Tetrose (4)  Pentose (5)  Hexose (6)  Heptose (7) o Carbons numbered starting from the end closest to the carbonyl  Glyceraldehyde Enantiomers o Glyceraldehyde (triose) – one chiral center o Monosaccharides in nature resemble the D stereoisomer of glyceraldehyde  Carbonyl on top  Chiral center furthest from carbonyl has secondary alcohol on the right  D- and L- are based upon the rotation of polarized light  Hexose Monosaccharides o To construct D-hexoses, instert three secondary alcohol groups into D- glyceraldehyde immediately following the carbonyl group  These become carbons 2, 3, and 4.  Each a new chiral center  Eight possible configurations  Three configurations are frequently found in biological systems  Glucose  Mannose  Galactose  “D” notation refers to the chiral center furthest away from the carbonyl, which matches D-glyceraldehyde  Ribose Monosaccharides o Two secondary alcohols inserted into D-glyceraldehyde o D-ribose (RNA) and D-deoxyribose (DNA) are components of nucleic acids o D-deoxyribose formed by converting –OH at C-2 to a proton  D-fructose – a ketohexose o Converting D-glucose from an aldhexose (aldehyde (6)) to a ketohexose (ketone (6)) generates D-fructose.  Cyclic forms o Aldehyde or ketone groups are free to react  Reaction of aldehyde with hydroxyl forms hemiacetal  reaction of ketone with hydroxyl from hemiketal o can occur within a single molecule, to form a 5- and 6- membered rings  Cyclization of D-glucose o New chiral center is formed at C-1 when the aldehyde is converted to a hemicetal  Stereochemical forms are denoted “α” and “β”  New chiral center is the anomeric carbon - only carbon bound to two oxygen atoms o Pyranose notation indicates a six-membered ring o Furanose notation indicates a five-membered ring  Haworth Projections o Represent ring forms of monosaccharides  Drawn flat  Bonding around each carbon is sp3, tetrahedral shape, puckered rings o Several possible conformations  Prevalent ones have least steric hinderance  Protons axial, hydroxyls equatorial  Monosaccharide Derivatives o Amide or amino groups can replace –OH  N-acetylglucosamine, N-acetylgalactosamine, glucosamine, galactosamine o Phosphate esters  Often at C-1 or C-6  O-Glycoside Bonds o Glycoside bond formation  Anomeric carbon of a monosaccharide condenses with an alcohol  Bound to two O atoms  Linkage called an O-glycoside bond  Can occur between two monosaccharides  N-Glycoside Bonds o Condensation between anomeric carbon and amino or imino group  Similar to O-glycoside bond formation  Linkage is a N-glycoside bond  Found in nucleotides  Ribose or 2-deoxyribose as the carbohydrate portion  Biologically important disaccharides (two monosaccharides) o glucose to glucose by α(14) glycoside bond  maltose  anomeric forms possible at reducing end o galactose to glucose by β(14) glycoside bond  lactose  anomeric forms possible at reducing end o glucose α1 to fructose β2 to form a α,β(12) glycoside bond o sucrose o non-reducing sugar  both anomeric carbons involved in glycoside bond  not “free” to reduce indicator compound  Starch and Glycogen o Homopolysaccharides: only one type of monosaccharide  Repeating unit is a α-D-glucopyranose o Starch occurs in plants  Two forms – amylose and amylopectin  These two polymers assemble into insoluble granules o Glycogen occurs in animals, fungi, bacteria  Soluble polymers  Amylose o Linear chain of glucose, only α-(14) glycoside bonds  Reducing end (free hemiacetal)  Non-reducing end o Many hydroxyl groups available for hydrogen bonding o Rotation about glycoside bonds allow many potential conformations  Most stable conformation is a coil  Stabilized by intramolecular H-bonds  Cellulose o Homopolymer of β-D-glucopyranose  Linked by β-(14) glycoside bonds o Each monosaccharide unit is flipped 180 degrees relative to its two neighbors  Stabilized by H-bonds between adjacent units o Chain is extended in a linear form o Many chains associate by intermolecular H-bonds  Forms cellulose fibers o Only difference between amylose and cellulose is the glycoside bond  α-(14) in amylose  β-(14) in cellulose  results in very different structures and functions.  Amylopectin o Homopolymer of α-D-gludopyranose  Mostly α-(14) bonds  Some α-(16) bonds  Create branches in the polymer o Many non-reducing ends  1 per α-(16) branch linkage  Only one reducing end  Glucose Polymers as Food o Starches are degraded to glucose, which starts the energy production pathway  Enzymes called α-amylases hydrolyze α-(14) glycoside bonds  Do not act on β-(14) glycoside bonds o Mammals do not possess β-amylases, so mammals cannot digest cellulose however, termites can – dietary fiber o Ruminants (grass eaters) harbor bacteria that produce β-amylases  Chitin o Monomer is a substituted monosaccharide  N-acetylglucosamine o Same glycoside linkages as cellulose o Amide group provides more H-bonds  Chitin is even stronger and more insoluble than cellulose  Forms arthropod exoskeletons  Glycoproteins o Polysaccharide or oligosaccharide linked to protein or lipid o <50% carbohydrate by weight o Oligosaccharides linked to protein by glycoside bonds  O-linked to threonine or serine R groups  O-glycoside bonds  N-linked to asparagine R groups  N-glycoside bonds  10-20 monosaccharides in each chain  Many types of glycoside bonds  Proteoglycans o Carbohydrates make up about 95% of molecule by weight, protein is about 5% o Carbohydrate portions are heteropolysaccharides called glycosaminoglycans  Repeating disaccharide units  Repeated patterns of glycoside bonds  Highly polar and charged modifications of the monosaccharide components o Primary constituents of the extracellular matrix making up bond and cartilage  Provide tensile strength, stretchiness, lubrication  Mucins o Protein carbohydrate conjugates where many closed located amino acids are all glycosylated o Small carbohydrate groups compared to proteoglycans o Make up mucous material that lines intestinal epithelia  Cell Surface o Covered with oligosaccharide part of glycoproteins o Oligosaccharides mediate cell-cell interactions  Configuration and conformation provide specific structures  Receptor proteins bind to those oligosaccharide structures  “lock and key” interactions allow specific cell-cell contacts  Molecular recognition at the cell surface o Lectins are carbohydrate binding proteins  Specific lectins bind specific carbohydrate structures


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