- 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 - Antioxidants
- -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 - Catalysts
- -accelerate rates of reactions but at the end of reaction as undergone no change
- Chiral
- -cannot be superimposed on each other
- Chymotrypsin
- -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
- Collagen
- - 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 - Electrophoresis
- in an electric field, a positively charged molecule moves toward a negatively charged electrode
-used in basic science and applied health - Enatiomers
- -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 - Enzymes
- -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 - Extremozymes
- -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 - Fibrous
- proteins are insoluble and composed of almost all alpha helices
- Genetic Control
- occurs by regulating the synthesis of the enzyme; molecular control of gene
- Globular
- proteins are water-soluble with chains folded into compact, globe like structures composed of alpha helices and beta sheets
- Hemoglobin
- -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 - Hydrolases
- catalyze hydrolysis
-breaking of bonds with the addition of water
-dipeptide bond being broken - Hydrolysis
- -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
- Isomerases
- catalyze the isomerization (rearrangment of atoms) of a substrate , there is only 1 reactant and 1 product
- Kinase
- -covalent modification
-catalyze the addition of -PO3
-phosphatases catalyze its removal - Ligases
- "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 - Lyases
- "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
- Oxidoreductase
- -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)
- Repulsion
- -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 - Specificity
- 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 - Stereochemistry
- -if a substrate is chiral, an enzyme usually catalyzes the reaction of only one enantiomer becaue only one fits the ative site
- Stereoismoers
- 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 - Substrates
- -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?* - Transferases
- 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 - Vitamins
- -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
