This site is 100% ad supported. Please add an exception to adblock for this site.

BioChem Exam 2


undefined, object
copy deck
Activation vs. Inhibition
activation: process that starts or increases enzyme activity inhibition: process that slows of stops activity
Active Site
-has shape and chemical reactivity
Allosteric Control
"other space" -occurs when a molecule binds at a ite on teh protein and affects binding of another molecule at different site (not active site)
Allosteric enzymes
-contain more than 2 kinds of binding sites, substrates and regulator sites -binding of regulator changes shape, which alters active site and affects activity
Alpha Helix
a single protein chain coiled in a spiral with a right-hand twist (clockwise); stabilized by H-bonds
Amino Acids
- 20 total; build proteins -differ in side chains (R) - Proline is cyclical -has 3-letter abbreviation and 1 letter code -classified based on the nature of their side chains
-substance prevents oxidation -protect aginst oxidizing agents or free radicals which are invloved in aging and neurodegenerative diseases -free radicals are highly reactive
Basic Amino Acid Structure
amine group written on left -NH2, carboxyl group written on right (-COOH),side chain "R" attached to alpha carbon
Beta Sheet
adjacent protein chains in molecules are held in place by H-bonds along the backbone
Biological Roles of Proteins
1)Structural: involved in cell membranes 2)Messengers: hormones, neuropeptides, i.e. insulin 3)Catalyze reactions (enzymes): all enzymes are proteins, not all proteins are enzymes; enzymes catalyze a reaction and can repeatedly do it b/c its not destroy
-accelerate rates of reactions but at the end of reaction as undergone no change
-cannot be superimposed on each other
-breaks down proteins -cleaves peptide bonds on the carbonyl side of amino acid residues that include an aromatic ring
Chymotrypsinogen, trypsinogen, and proelastase
digest proteins in the stomach and intestine; produced in pancrease a zymgens; must be cut to becom active
- most abundant of all proteins in mammals -major constituent of skin, tendons, bones, blood vessels and other connective tissues
Conjugated Proteins
-require non-protein portions known as COFACTORS (metals) -oranic molecules are COENZYMES
Covalent Sulfur-Sulfur Bonds
-disulfide bonds are covalent -play a role in protein shape -cystine contains sulfur atom -if residues invloved in bond are same protein a loop form -if residueis from different protein, the separate chains are linked
Effect of pH on enzyme activity
-depends on pH because on interactions in the active site and enzyme stabilization -extremes of pH will denature enzyme
Effect of Temp on Enzyme Activity
-rates of enzyme reactions do not increase continuously with rising temp; reaches a max then decrease bc the protein denatures -bell shape; temp optimum
in an electric field, a positively charged molecule moves toward a negatively charged electrode -used in basic science and applied health
-also known as optical isomers -two mirrow images of a chiral substance -reflect light different -L (levo) or D (dextrorotatory)
Enzyme Concentration
relationship between enzyme concentration and reaction rate is linear
Enzyme-Substrate Complex
-a substrate in an active site forms this -results in lower activation energy between the substrate and product
-catalyze (control) reactions in living organisms -controlled chemical messengers (hormones, neurotransmitters) -arent changed in reactions -globular proteins
Enzymes as Catalysts
-decrease time it takes for an energetiall favorable reaction to take place by lowering activation energy (amount of energy needed for reactants to react)
Enzymes in Medical Diagnosis
measure blood enzymes to screen for enzymes released as a result of a medical condition
Essential Amino Acids
-nine of twenty amino acids not synthesized by humans -obtained in the diet -COMPLETE protein source provides all 9
-enzymes from extremophiles: organisms that live in conditions hostile to mammalian cells -enzymes from thermophiles "love heat" include the heat stable Taq polymerase
Fat Soluble Vitamins
stored in fat deposits, none of them are known to be a coenzyme -vitamins A, D, E, K
proteins are insoluble and composed of almost all alpha helices
Genetic Control
occurs by regulating the synthesis of the enzyme; molecular control of gene
proteins are water-soluble with chains folded into compact, globe like structures composed of alpha helices and beta sheets
-conjugated protein -composed of 4 polypeptide chains -4 heme groups
How do extremozymes work?
-use proteins (chaperonins) to refold or stabilize denatured enzymes -thermophilic proteins have sticky active sites, tightly folded, highly nonpolar cores that resist denaturation; lack flexible amino acids
Hydrogen Bonds along the Backbone
- h-bonds form between the H in NH and C=O groups along backbone -creates pleated sheets and helical secondary structures
Hydrogen Bonds of R Groups with Each Other or Backbone Atoms
-amino acid side chains for H-bonds nearby or far aprt along protein -if side chain on surface: H bond with H2O
catalyze hydrolysis -breaking of bonds with the addition of water -dipeptide bond being broken
-digestion -reverse of protein formation takes place, peptide bonds are hydrolyzed to yield amino acids -takes place in stomach and small intestine
Hydrophobic Interactions between R Groups
-individual attractions are weak between nonpolar side chains -they play a major role n stabilizing folded proteins because of the large numbers of nonpolar interactions
Hydrophobic vs Hydrophilic side chains
phobic: nonpolar Philic: polar, acidic, basic
Induced-fit Model
changes in shapes occur when a substrate enters an active site, these interactions induce the right fit for catalysis
Ionic Attractions between R Groups (Salt Bridges)
attraction between acidic and basic side chains
Irreversible Inhibition
forms a bond that is not easily broken with a group in the active site it will prevent the substrate from binding -poison like lead and mercury bind with -SH
Irreversible inhibitor
remains bound; the enzyme is permanently inactivated
catalyze the isomerization (rearrangment of atoms) of a substrate , there is only 1 reactant and 1 product
-covalent modification -catalyze the addition of -PO3 -phosphatases catalyze its removal
"to tie together" -catalyze teh bonding of two substrates, a reaction which requires energy, typically generated from ATP to ADP
Lock and Key model
substrate fits into the active site as a key fits into a lock -however, substrates and enzymes are not rigid like keys and locks
"to break" -catalyze the addition of a molecule to a double bond of the reverse reaction in which it eliminates a molecule to form a double bond
Negative Regulator
changes the active site so the enzyme is a worse catalyst and the rate decreases
-catalyze oxidation-reduction reactions -commonly the addition/removal of O or H -needs coenzyme that can be oxidized/reduced as a substrate is reduced/oxidized
Positive regulator
changes the active site so teh enxyme is a better catalyst and the rate accelerates
Primary Protein Structure
-crucial to function -backbone is a chain of alternating peptide bonds and alpha carbons -sequence in which amino acids are connected by peptide bonds
Primary Structure
sequence of amino acids in the protein (covalent bonds)
Protein Denaturation
-disruption in shape that does not affect primary structure -physical, chemical, biological changes -solubility decreased, function lost, irreversible
Quaternary Protein Structure
-interaction of two or more polypeptide chains to form a single protein
Quaternary Structure
proteins composed of more than one polypeptide; has sub-units and how they interact (ionic bond)
-between hydrophobic groups and water: results in a protein bein water insoluble -between hydrophilic groups and water: results in a protein being water soluble
Reversible Competitive Inhibitor
binds at active site
Reversible Inhibitor
leaves, the enzyme is restored to its original condition
Reversible Noncompetive Inhibitor
doesn't compete w/ substrate for active site, changes enzyme shape so site is less accessible and reaction occurs less efficintly
Secondary Protein Structure
-spatial arrangement -includes alpha helix and beta sheet - H-bonds hold peptide chain together
Secondary Structure
spatial organization of amino acids (H-bonds)
Separation depends on several variables:
1) strength of electric field 2) charge of biomolecule 3) size of the biomolecule 4) shape of biomolecule 5) medium on which electrophoresis is conducted
Simple vs Conjugated Protein
single: composed of only amino acids conjugated: contains one or more non-amino acid units, also known as moietie, often required for activity
is that fact that it's limit to a certain substrate and type of reaction ex: an enzme may act on A but no A' to produce C
-if a substrate is chiral, an enzyme usually catalyzes the reaction of only one enantiomer becaue only one fits the ative site
enantiomers have the same formula but different arrangement of atoms
Substrate Concentration
-when its less than the amount of enzyme not all catalytic molecules are used -rate increases bc more enzynes catalyze reactions until all active sites are full(enzyme saturation); rate levels off
-reactants -held in place in active site
Tertiary Protein Structure
-overall 3-D that results from being folded -depends on interactions of amino acid side chains
Tertiary Structure
shape of protein (hydrophobic bonds) *when protein is folded how do different chains interact?*
catalyze the transfer a group from one molecule to another
Turnover Number
max number of substrate molecules acted upon by a molecule of enzyme per unit -measures catalytic activity -limited by how fast molecules collide
-coenzymes -dietary necessity because we do not synthesis them -all water soluble, A,B
Water Soluble Vitamins
-contain -OH, -COOH, or other polar groups -vitamin C, biotin
Why are cofactors important?
protein composition is limited to 20 L-amino acids and function groups in their side chains; provide chemically reactive groups not available in side chains -may anchor a substrate in an acitve site and/or stabilize shape
Why does glycine allow flexibility?
it doesn't have a bulky side chain
inactive forms;

Deck Info