Biochemistry Concepts and Terminology, Exams of Nursing

Download Biochemistry Concepts and Terminology and more Exams Nursing in PDF only on Docsity!

BCH 100 MT 1

Amphipathic - correct answer ✔✔Both hydrophobic and hydrophilic Molecules that contain one or more hydrophobic and one or more hydrophilic regions Hydrophilic - correct answer ✔✔Water-loving -Polar covalent compounds such as low-molecular-weight alcohols and ketones -Sugars -Ionic compounds -Amino acids and phosphate esters Hydrophobic - correct answer ✔✔Water-hating -Nonpolar covalent compunds such as hydrocarbons -Fatty acids and cholesterol Micelle - correct answer ✔✔Spherical arrangment of amphipathic organic molecules in water clustered so that hydrophobic parts are buried inside the sphere and hydrophilic parts are on the surface of the sphere and in contact with the water enviornment Bronsted Acid - correct answer ✔✔A proton donor Bronsted Base - correct answer ✔✔A proton acceptor Strong Acid - correct answer ✔✔An acid that is completely dissociated in aqueous solution -HCl, HBr, HI, HNO3, HClO4, H2SO Strong Base - correct answer ✔✔A base that is completely dissociates in aqueous solution -LiOH, NaOH, KOH, Ca(OH)2, Ba(OH)

Weak Acid/Base - correct answer ✔✔Not completely dissociated in aqueous solution -Carboxylic acids, H2O (acid): low Ka, high pKa Titration Curve - correct answer ✔✔pH vs. equivalents of OH- Used to determine amount of the weak acidic group in the soln = mols of OH- required to completely deprotonate each acidic group Equivalence point: the point in an acid-base titration at which enough strong base has been added to exactly neutralize the weak acid Buffer - correct answer ✔✔Aqueous system that tends to resist changes in pH when small amounts of acid or base are added Why is water a polar molecule? - correct answer ✔✔Because of the difference in electronegativity between oxygen and hydrogen and its asymmetrical shape Why are polar and charged molecules so soluble in water? - correct answer ✔✔Electrostatic attraction of opposing charges Water is an excellent solvent for what? - correct answer ✔✔1. Ions/charged groups

2. Neutral polar compounds 4 Types of Noncovalent Interactions - correct answer ✔✔1. Hydrogen bonds
3. Ionic Interactions
4. Van der Waals Interactions
5. Hydrophobic interactions Hydrogen Bonds - correct answer ✔✔Attractive interaction between dipoles

Donor: Hydrogen bonded to an atom of high electronegativity (N or O) Acceptor: Electronegative atom with a lone pair of electrons (:O or :N) *Hydrogen bonds are directional Van der Waals Interactions - correct answer ✔✔Energy between atoms is related to distance between them (within 4-5 A) Weak and nonspecific individually, but a lot can be important in steric complimentarity Hydrophobic Interactions - correct answer ✔✔Association of nonpolar groups with eachother in aqueous systems Preference of hydrophobic groups and molecules to minimize their exposure to water Why does water have a much higher melting point and a much higher boiling point than methane? - correct answer ✔✔Because it is more cohesive and the molecules stick together more tightly Dissociation of H2O - correct answer ✔✔H2O <--> OH- + H+ Ka= [OH-][H+]/[H2O] Ka= [OH-][H+]/55.5 M Kw= Ka x 55.5 M= [OH-][H+] Kw= 10^-14 M^ In pure water: [H+] = [OH-] = 10^-7 M Explain the relationship between how weakly a proton is bound in a weak acid and the Ka for that acid, and the pKa for that acid. - correct answer ✔✔-Stronger acid, stronger tendency to donate its proton, conj. base binds the proton weakly, lower concentration of conj. acid at equilibrium, higher Ka -Weaker acid, weaker tendency to donate its proton, conj. base binds proton tightly, higher concentration of conj. acid at equilibrium, lower Ka Henderson-Hasselbalch Equation - correct answer ✔✔pH = pKa + log [base]/[acid]

What is the relationship of the 3 parameters of the Henderson-Hasselbalch Equation? - correct answer ✔✔-Higher [H+], lower pH, equilibrium shifts left, lower base/acid ratio -Lower [H+], higher pH, equilibrium shifts right, higher base/acid ratio

• [base] = [acid] : pH = pKa
• [base] > [acid] : pH > pKa
• [base] < [acid] : pH < pKa Buffer Range of a Weak Acid - correct answer ✔✔Near its pKa, +- 1 pH unit from the pKa alpha-amino acid - correct answer ✔✔A structure in which the amino group is on the alpha carbon Aliphatic - correct answer ✔✔Side chains that are highly hydrophobic Carboxyl Group - correct answer ✔✔Readily donate their protons, Negatively charged at pH 7 Guanadino - correct answer ✔✔3 N atoms around the terminal C of the side chain Imidazole - correct answer ✔✔2 N atoms in a 5-membered ring structure Thiol - correct answer ✔✔-SH (sulfhydryl group) not very polar Isoelectric pH = pI - correct answer ✔✔The pH at which the overall net charge of all the molecules of a compound in solution is zero pI = the pH halfway between teh 2 functional groups surrounding a net charge of zero Peptide Bond - correct answer ✔✔The special name given to the amide bond between the alpha- carboxyl group of one AA and the alpha-amino group of another

What configuration do the AAs found in proteins have? - correct answer ✔✔L-configuration at the alpha- carbon Nonpolar, aliphatic R groups - correct answer ✔✔Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine Aromatic R Groups - correct answer ✔✔Phenylalanine, Tyrosine, Tryptophan Polar, uncharged R groups - correct answer ✔✔Serine, Threonine, Cysteine, Asparagine, Glutamine Positively Charged R Groups - correct answer ✔✔Lysine, Arginine, Histidine Negatively Charged R Groups - correct answer ✔✔Aspartate, Glutamate Greek Letters - correct answer ✔✔alpha - 1 beta - 2 gamma - 3 delta - 4 epsilon - 5 Primary Structure - correct answer ✔✔Sequence of AAs -determines how proteins will fold in 3D -Read from left to right (N-terminal to C-terminal) Secondary Structure - correct answer ✔✔Regular folding within a polypeptide chain -always have repeating values of phi and psi -results from hydrogen bonding between the amide and carbonal oxygens of peptide backbone -alpha helix, beta conformation, beta turns

Supersecondary Structure - correct answer ✔✔Recognizable patterns/combinations of secondary structural elements -part of tertiary structure -beta alpha beta unit, alpha alpha unit, beta meander Tertiary Structure - correct answer ✔✔Overall folding within a polypeptide chain -conformations of side chairs -relationships between secondary structures -prosthetic groups Quaternary Structure - correct answer ✔✔Interactions between different polypeptide chains -fibrous proteins -globular proteins Globular Proteins - correct answer ✔✔-Compact shape with significantly higher order structure -Includes alpha helices, beta pleated sheets, supersecondary structures, disulfide bridges, etc. -Soluble in aqueous solutions and contain a high percentage of hydrophobic AAs within their interiors -Exterior=mixture of polar and charged AAs Fibrous Proteins - correct answer ✔✔-Shape=long rod -Helical backbone of protein does not fold back on itself -Beta sheets also possible -Mechanically strong -Insoluble in water and dilute salt solutions Examples: alpha-keratin, collagen Alpha-helix - correct answer ✔✔-Right handed coil -1 polypeptide per helix

-Each peptide bond is planar

• C=O: is hydrogen bonded to the N-H of the 4th AA away, linear and parallel to helix axis -R groups point outward from helix -Dipole: N-term end delta+, C-term end delta- -Strong electrostatic repulsion caused by proximity of several side chains of like charge -Steric hinderance Beta-conformation - correct answer ✔✔-Polypeptide chains lie adjacent to one another, may be parallel or anti-parallel -R groups alternate, first above and then below plane -Alpha-carbons are at the creases
• C=O---H-N hydrogen bonds are between adjacent planes and perpendicular to direction of backbones of chains How do disulfide bridges form between cysteine residues? - correct answer ✔✔Oxidation Beta-turns - correct answer ✔✔-Abrupt change in direction of polypeptide backbone, at surface of protein -Stabilized by hydrogen bond across stem of protein -Steric problems with larger AA side chains -Involves Gly, Asn, Ser residues Collagen Helix - correct answer ✔✔-3 ppcs wrapped around each other in a ropelike twist to form a triple helix called tropocollagen -Every 3rd position is Gly: only Gly residues are small enough to fit in the middle -The 3 strands are held together by hydrogen bonding between strands -The presence of hydroxyproline adds stability to the collagen helix Denaturation - correct answer ✔✔Loss of the structural order -Inactivates the protein

Denaturants: heat, large changes in pH, SDS, urea or guanadine Proteins can be purified on the basis of these 4 difference chemical properties: - correct answer ✔✔1. Solubility

2. Size
3. Charge
4. Binding affinity Gel-filtration Chromatography - correct answer ✔✔Size exclusion -Minimal sample loss Ion-exchange Chromatography - correct answer ✔✔Proteins with the same charge as the column beads flow through unimpeded Affinity Chromatography - correct answer ✔✔Specific binding interactions SDS-Page - correct answer ✔✔Allows a visual evaluation of the purification scheme Hemoglobin - correct answer ✔✔A red blood cell protein that carries oxygen from the lungs to the tissues -Allosteric protein that displays cooperativity in oxygen binding and release -Four O2 binding sites -Binding curve=sigmoidal Myoglobin - correct answer ✔✔Binds oxygen in muscle cells -Not cooperative -One O2 binding site -Binding curve=hyperbola Prosthetic Group - correct answer ✔✔Tightly bound non-AA component of a protein

Ligands that affect the ability of Hb to bind to O2 - correct answer ✔✔H+ CO 2,3-bisphosphoglycerate (BPG) Quaternary structure of Hemoglobin - correct answer ✔✔Noncovalent bonds (no disulfide bonds) Conformational changes affect Hb affinity for O R State - correct answer ✔✔High O2 affinity -Lower H+, CO2, and 2,3-BPG binding affinity T State - correct answer ✔✔Low O2 affinity -Higher H+, CO2, and 2,3-BPG binding affinity The Bohr Effect - correct answer ✔✔Effect of pH on the oxygen-binding affinity of Hb -As pH decreases, there's more T state, so O2 is bound more weakly, so more O2 is released Basis: A protonation of a His residue on the beta1 chain 2,3-BPG - correct answer ✔✔An allosteric regulator that stabilizes the T state of Hb and thus facilitates the release of O -shifts conformation towards T state, so promotes Os dissociation -shifts oxygen-binding curve to the right Fetal Hemoglobin - correct answer ✔✔Alpha chain replaced with gamma chain The higher curve Higher affinity for oxygen Free Energy (G) - correct answer ✔✔A measure of energy capable of doing work The change in free energy yields information about the spontaneity but not the rate of reaction

Enzymes - correct answer ✔✔Protein catalysts that can accelerate the rate of a reaction by factors of as much as a million or more -Facilitate the formation of the transition state -Bring substrates together to form an enzyme-substrate complex on a particular region of the enzyme called the active site -Induced fit -Specificity for reactants Rate of Reaction - correct answer ✔✔fA + gB -> P Rate = k[A]^f[B]^g Order of reaction - correct answer ✔✔The sum of the exponents in the rate equation Enzyme Assays - correct answer ✔✔Designed to measure appearance of P or disappearance of S for that specific reaction Sickle-cell Anemia - correct answer ✔✔A genetic disease cause by a mutation resulting in the substitution of valine glutamate at position 6 on the beta chain -Can be fatal when both alleles of the beta chain are mutated Michaelis-Menten Equation - correct answer ✔✔Hyperbolic form: Vo = Vmax * [S]/([S]+Km) ** Km = [S] at 1/2 Vmax Lineweaver-Burk Equation - correct answer ✔✔1/Vo = (Km/Vmax * 1/[S]) + 1/Vmax ** y = mx + b** What general types of reactions are catalyzed by chymotrypsin? - correct answer ✔✔Chymotrypsin catalyzes hydrolysis of the carboxyl side of the peptide bonds that contain large hydrophobic AAs with aromatic groups or other bulky hydrophobic AAs at lower rates

-Activity in samples can be assayed because it also catalyzes the hydrolysis of ester bonds of chromogenic substrates such as p-nitrophenyl esters: the hydrolysis of the ester results in appearance of yellow color proteolytic cleavage, irreversible inhibition, specificity, overall enzyme kinetics Reversible Inhibiton - correct answer ✔✔Something binds to the enzyme, but can be unbound -Competitive, Uncompetitive, and Noncompetitive Irreversible Inhibiton - correct answer ✔✔Something binds to the enzyme, but stays bound or is released very slowly -Bind tightly Examples: Penicillin, DIPF, Chymotrypsin 4 Different ways to regulate enzyme activity - correct answer ✔✔1. Allosteric regulation

2. Feedback inhibition
3. Covalent modification
4. Proteolytic activation Why is proteolytic cleavage necessary? - correct answer ✔✔Chymotrypsin is made in the pancreas, but activated in the stomach. If it were activated when it was made, it's cleave the pancreatic proteins instead of the food 5 Classes of Lipids - correct answer ✔✔1. Free fatty acids
5. Triacylglycerides
6. Phospholipids
7. Glycolipids
8. Steroids Fatty Acids - correct answer ✔✔Chains of H-bearing C atoms that have a carboxylic acid at one end and a methyl group at the other end

-The positions of double bonds are indicated with the symbol delta, with the first atom of the double bond indicated by superscript number -The properties are dependent on chain length and degree of unsaturation (short chain length and the presence of cis bonds enhances the fluidity of fatty acids) -Stored as triacylglycerols in which 3 fatty acids are esterified to one molecule of glycerol Glycolipids - correct answer ✔✔Carbohydrate-containing lipids (Cerebrosides are the simplest) Steroids - correct answer ✔✔Built on a tetracyclic platform, consisting of 3 cyclohexane rings and a cyclopentane ring fused together (Cholesterol is the most common) Hutchinson-Gilford progeria syndrome - correct answer ✔✔A disease of premature aging -Inappropriate farnesylation -Failure to remove a farnesyl group from the nuclear protein lamin results in a deformed nuclear membrane and impaired nuclear function Melting Point Dependency - correct answer ✔✔The melting temp is dependent on the length of the fatty acids in the membrane lipid and the degree of cis unsaturation Passive Transport - correct answer ✔✔Driven by a concentration gradient -Simple diffusion -Facilitated diffusion Simple Diffusion - correct answer ✔✔A solute moves directly through the membrane, small nonpolar molecules Facilitated Diffusion - correct answer ✔✔A solute is carried across a membrane by a carrier protein, no energy input required Ex: glucose permease

Active Transport - correct answer ✔✔Compound is transported against its concentration gradient, driven by some source of free energy input Primary Active Transport - correct answer ✔✔Transport is linked to the hydrolysis of ATP or other high- energy molecule; or by oxidation reactions as in electron transport chain Secondary Active Transport - correct answer ✔✔Driven by gradient of some other solute Insulin Receptor - correct answer ✔✔Insulin binding to specific receptor on target cell surface causes conformational change that activates the protein kinase enzymatic activity of intracellular portion of receptor protein Kinase transfers phosphate groups to Tyr residues on itself, and on Insulin Receptor Substrate (IRS) proteins, which carry the message to other intracellular processes Monosaccharide - correct answer ✔✔A carbohydrate that cannot be hydrolyzed to a simpler carbohydrate Enantiomers - correct answer ✔✔Stereoisomers that are complete mirror images Diastereomers - correct answer ✔✔Stereoisomers that are not mirror images Anomers - correct answer ✔✔Carbohydrates that differ in configuration only at the anomeric carbon Pyran - correct answer ✔✔A 6-membered hemiacetal ring Furan - correct answer ✔✔A 5-membered hemiacetal ring Oxidation of Monosaccharides - correct answer ✔✔Carbonyl group of a monosaccharide can be oxidized to a lactone by oxidizing agents -Requirement for a sugar to be oxidizable is to be a "reducing sugar": a free anomeric carbon-can be in form of hemiacetal or hemiketal

Oligosaccharides - correct answer ✔✔Contain 2 or more monosaccharides linked by O-glycosidic bonds -Large polymeric oligosaccharides are called polysaccharides -If all the monosaccharides in the polysaccharide are the same, the polysaccharide is called a homopolymer Storage Polysaccharides - correct answer ✔✔Starch (plants) and glycogen (animals) -Nonreducing ends -Branched Glycoproteins - correct answer ✔✔The protein is the largest component by weight -Play a variety of roles including as membrane proteins -In all classes of glycoproteins, carbohydrates are attached to the nitrogen in the side chain of Asn (N- linkage) or to the oxygen of the side chain of Ser or Thr (O-linkage) Proteoglycans - correct answer ✔✔The protein is attached to a particular type of polysaccharide called a glycosaminoglycan -Play a structural role or act as lubricant Mucins - correct answer ✔✔Predominantly carbohydrate The protein is characteristically attached to the carbohydrate by N-acetylgalactosamine Often lubricants Lectins - correct answer ✔✔A particular class of glycan-binding protein -The lectins on one cell recognize and bind to carbohydrates on another cell with multiple weak interactions -Cell-cell interaction FRAP - correct answer ✔✔Fluorescence recovery after photobleaching A technique that allows the measurement of lateral mobility of membrane components

How rapidly the bleached area recovers fluorescence