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Biochem 2/3 exam 1

by: Leila HD

Biochem 2/3 exam 1 BIOCHM 307

Leila HD
GPA 3.7

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About this Document

these notes cover the second third of information on exam 1
Intro to biochemistry
Dr. Orla Hart
Study Guide
Biology Chemistry
50 ?




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This 4 page Study Guide was uploaded by Leila HD on Friday February 26, 2016. The Study Guide belongs to BIOCHM 307 at Purdue University taught by Dr. Orla Hart in Spring 2016. Since its upload, it has received 132 views. For similar materials see Intro to biochemistry in Biochemistry at Purdue University.


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Date Created: 02/26/16
2/1  Proteins are polymers of amino acids  3 categories for R groups  hydrophobic have nonpolar R groups and hydrophilic have polar R groups o hydrophilic is either polar uncharged or polar charged  Gly is the simplest amino acid (each aa has full name, 3 letter code, 1 letter code)  Met= 1 of 2 aa with Sulfer in Rgroup  Trp (W)= only aa with fused ring system o Most proteins have at least one Trp o Trp absorbs UV light at 280nm  Pro= only aa whose side chain loops back into its own backbone  Disulfide bonds form intra-strand crosslinks  Ser (S) and Thr (T)= hydroxyl groups in side chain  Phe and Tyr (Y)= precursers of aa derivatives that are neurotransmitters and 1 ring  Gln (Q)(2 methylene) and Asn (N)(1 methylene): polar uncharged  His (H): polar uncharged/ has 5 membered ring system with N’s o Can be charged at certain pH values  Lys (K) and Arg (R): long, positively charged amine group  Asp (D) and Glu (E): carboxylate groups  Aa linked by condensation reactions and peptide bonds link together and form polypeptide  pK reveals the cutoff pH for protonation  primary, secondary, tertiary, quaternary 2/3  Asparagine is hydrophilic uncharged  Valine is hydrophobic  Glutamic acid is polar charged  Tyrosine is polar uncharged  Phenylalanine is non polar  Ser and Thr have hydroxyl groups in side chains  Tyr and Phe are polar uncharged  Asn and Gln are polar uncharged  His is polar uncharged  Lys and Arg are positively polar  Asp and Glu are negatively polar  Condensation rxn removes water  Peptide< oligopeptide< polypeptide  On polypeptide chain, N terminus is on L with ammonia and C terminus is of R with COOH  Primary structure can be predicted  Tertiary structure occurs once all secondary structures get together  Cistine disulfide bonds are vital in maintaining higher levels of structure  Tertiary and quaternary structures cannot be predicted  Secondary structure have alpha helix and beta sheet bonded by hydrogen bonds that form between the carbonyl oxygen and the amino hydrogen  Antiparallel beta sheets align in opposite directions  Parallel beta sheets align in the same direction  Folded polypeptide has hydrophilic surface and hydrophobic core  Protein folding and protein stabilization depends on noncovalent forces  Domain= single chain can form local 3D structure  Subunits= 2 or more separate chains orient in 3D space for quaternary 2/5  Met: contains sulfur and is the start codon  Only cysteine can form disulfide bonds  Tyrosine and phenylalanine only have 1 ring  Aa with 2 fused rings and absorbs light at 280nm= tryptophan  Proline’s R group is bonded to its alpha amino group forming a ring and can form “kinks” in the peptide chain  Hydrogen bonds stabilize secondary structures  Disulfide bonds help stabilize tertiary and quaternary structures  Peptide bonds after the C double bonded to an O  Primary and secondary can be predicted from nucleotide sequence 2/8  Protein functions: o Transport: myoglobin transports O2 throughout muscles/ hemoglobin transports O2 in blood o Structure: actin forms microfilaments in cells/ tubulin dimers constitute microtubules/ keratin filaments constitute animal hair/ collagen in connective tissue o Motor: myosin interacts w actin for muscle movement/ kinesis moves along microtubules to support cells o Catalysis o Immunity o Regulation of gene expression  Heme is a prosthetic group and has iron o Prosthetic group= organic mc bound to protein that aids protein function o Heme is a porphyrin that chelates iron for O2 transport  Myoglobin only has 3 units of structure no quaternary  Hemoglobin and myoglobin are only 18% identical so not a lot alike at all  Myoglobin transports O2 by Fe in heme and binds to O2 in hyperbolic trend  High level of similarity in secondary and tertiary structures  As pH increases, it promotes binding of hemoglobin to O2  As pH increase, O2 affinity increases  Bohr effect o BPG decreases Hb’s O2 affinity 2/10  Ppl with sickle cell disease have 2 copies of mutated gene (carriers have 1 copy) o Recessive disease  Microfilaments are polymers of actin  Globular actin subunits make double chain forming microfilament  Alpha and beta tubulin form dimers  Microtubules are hollow fibers build from tubulin dimers  Cryoelectron microscopy shows tubular structure of microtubule  Keratin is an intermediate filament that forms a coiled coil structure  Collagen is a triple helix and is covalently cross linked  Motor proteins allow you to yawn  Myosin has 2 heads and a long tail and binds to ATP o ATP hydrolysis drives physical movement of myosin on actin filament  Kinesin is microtubule assoc protein o Transports cargo by moving along microtubule track 2/12  Hemoglobin and myoglobin are transport proteins  Actin, collagen, tubulin, and keratin are structural proteins  Myosin and kinesin are motor proteins  Myoglobin is in muscles, saturated with O2  Hemoglobin is in blood, has quaternary structure  Sickle shape of RBCs is due to mutated hemoglobin aggregates end-to-end and distorts the cell shape  His is aa residue in myoglobin alpha helices and plays role in anchoring O2 and iron  Myo and hemo have diff primary and quaternary structures  Hemoglobin is a tetramer  The Bohr effect says as pH decreases, hemoglobin’s affinity for O2 decreases  Actin is a microfilament  The “+” at the end of actin means polymerization  Histodine anchors O2 and Fe  Alzheimers affected by APP protein  PrP protein in spongiform/ mad cow disease  CFTR protein in cystic fibrosis  4 aa on surface of protein: Asn, Lys, (hydrophobic interior, hydrophilic exterior)  Ala interior so is hydrophobic  Globular protein structures stabilized by hydrophobic interactions  Peptide bonds stabilize primary aa structure  Hydrophobic effect: thermodynamically favorable when most environ is aqueous so all hydrophobic things get together so the surface area of the mc involved with water will be less than they all would experience apart


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