BIOKMBI - LE3 (di kasama enzyme kinetics only basic info about enzymes)

Denaturation

Denaturation

loss of structural order in a protein

Loss of biological activity

Denaturation’s loss of structural order also leads to

Heat

pH change

Detergents

Urea

Guanidine

Mercaptoethanol

How can denaturation happen?

Detergents

Will disrupt the hydrophobic interactions leading to denaturation

pH change

Will alter the side chains (COO- to COOH or NH2+ to NH2) leading to denaturation

Urea and Guanidine

Will disrupt the hydrogen bonding leading to denaturation

Mercaptoethanol

Will reduce the disulfide bond leading to denaturation

311-314 residue alpha helical rod segments

Sequence of Alpha-Keratin consists of__

non helical N- and C- termini

Alpha Keratin are capped with__

coiled coils

Alpha Keratin promotes association of helices to form__

cysteine residues and disulfide bridges

Alpha Keratin protein is rich in ___ and ___

22% cysteine

Hard and brittle

Alpha Keratin

Characteristics of horns and nails:

14% cysteine

Softer, flexible, elastic

Alpha Keratin

Characteristics of hair, wool, and skin:

Ropes, S-S linkages

In alpha keratin of wools and hair 3-7 alpha helices may be coiled around each other to form ___ held together by ___

antiparallel, Ser-Gly-Ala-Gly

Beta Keratin

In silk fibroin, beta-pleated sheets are ___and contain sequences of ___

Gly on other adjacent sheet

Beta Keratin. Since B sheet extends alternately above and below, the plane of the sheet places all Gly on one side and Ser and Ala on other side. This allows:

Gly on one sheet meshes with ___. Same for Ser and Ala

microcrystalline arrays, amorphous regions

Beta Keratin

The fiber is composed of ____ alternating with ___

H bonding, Van der Waals interactions

Beta Keratin

Fiber strength results from extensive ____ of adjacent chains and the cummulative effect of ____ among stretched chains.

stacked array of B pleated sheets

Beta Keratin

Silk Fibroin comes from a ___

Collagen

Principal componet of connective tissue

Pro and Hyp (Hydroxyproline)

Collagen

30% of amino acids in the chain are ___

Gly, X-Pro-Gly, X-Hyp-Gly

Collagen

Every third position is ____ and repeating sequences are ____ and ____

Collagen Triple Helix

The basic unit of tropocollagen

3 polypeptides chains, triple helix

Collagen Triple Helix consists of ___ wrapped around each other to form and ___

hydroxyproline and hydroxylsine

Collagen Triple Helix

The 3 strands are held together by hydrogen bonding involving ____

Alpha helix

Collagen Triple Helix is a helix but not a ___

crosslinked, His and Lys residues

With age, collagen helices become ____ by covalent bonds formed between ____

Myoglobin

Is a single polypeptide with 153 amino acids. Has 1 heme group in a hydrophobic pocket

8 alpha helix, none beta sheet

Myoglobin

Number of alpha helix regions

Number of beta sheet regions

surface

Myoglobin

Polar side chains are on the

folded to the interior

Myoglobin

Non-polar side chains are

Two His side chains

Myoglobin

Are in the interior, involved with interaction with the heme group

4, 1, 1

Myoglobin

Fe (II) of heme has 6 coordinates:

__ interact with N atoms of heme

__ interact with N of His side chains

__ interact with O2 or N of second His side chains

Hemoglobin

A tetramer of 2 alpha chains (141 amino acids each) and 2 beta chains (153 amino acids each)

Each chain has 1 heme group

4 molecules of O2

Hemoglobin can bind ___

One O2 is bound, next O2 binds easier

Hemoglobin

Binding of O2 exhibited by positive cooperativity which means when

Transport oxygen

Function of hemoglobin

H+, CO2, Cl-, 2,3-biphosphoglycerate

Affect the ability of Hb to bind to oxygen:

Bohr Effect

the affinity of hemoglobin for O2 depends on pH

BPG, O2, maternal hemoglobib.

Fetal hemoglobin binds less strongly to ___ and has greater affinity for ___ than ___

Enzyme

a biological catalyst

proteins

All enzymes are __

increase a rate of a reaction

enzymes can ___ by a factor of up to 10²⁰ over an uncatalyzed reaction

activation energy

Rate of enzyme reaction depends on ___

specific

some enzymes are so ___that they catalyze the reaction of only one stereoisomer

alternative pathway, lower

an enzyme provides an ____ with ____ activation energy

Oxidoreductases

catalyze oxidation-reduction reactions

Transferases  

catalyze the transfer of functional groups

Hydrolases

catalyze hydrolytic cleavages or their reversible   reactions (split out H₂O and add H⁺ and OH^-   moieties to the substrate)

Lyases

catalyze the cleavage of bonds without hydrolysis   or oxidation-reduction reaction

Isomerases

catalyze isomerization reactions

Ligases

catalyze reactions involving the formation of bonds   between two substrate molecules coupled to the   cleavage of the pyrophosphate bond in ATP or   another high energy compound

Active site

the small portion of the enzyme surface where the substrate(s) becomes bound by noncovalent forces, e.g., hydrogen bonding, electrostatic attractions, van der Waals attractions

Substrate

a reactant (S)

Substrate and Active site

In an enzyme-catalyzed reactions there are:

Lock and Key model

Induced fit model

Binding Models of enzyme substrate complex

Lock-and-key model

substrate binds to that portion of the enzyme with a complementary shape

Induced fit model

binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit

Absolute specificity

catalyzes the reaction of one unique substrate to a particular product

Relative specificity

catalyzes the reaction of structurally related substrates to give structurally related products

Stereospecificity

catalyzes a reaction in which one stereoisomer is reacted or formed in preference to all others that might be reacted or formed

specific rate constant

Where k is a proportionality constant called the

Reversible inhibitor

a substance that binds to an enzyme to inhibit it, but can be released

competitive inhibitor

binds to the active (catalytic) site and blocks access to it by substrate

noncompetitive inhibitor

binds to a site other than the active site; inhibits the enzyme by changing its conformation

Irreversible inhibitor

a substance that causes inhibition that cannot be reversed. Usually involves formation or breaking of covalent bonds to or on the enzyme

Uncompetitive inhibition

inhibitor can bind to the ES complex but not to free E. 

Mixed inhibition

Similar to noncompetitive inhibition, butbinding of I affects binding of S and vice versa.

Holoenzyme

conjugated enzyme

Apoenzyme

the protein portion of a holoenzyme catalytically inactive when alone

prosthetic group

non-protein that is covalently bonded to the protein

conenzyme

non protein that is an organic compound readily dissociable from the protein; many are vitamins or are metabolically related to vitamins

cofactor

non protein that is a substance that takes part in enzymatic reactions but may be regenerated for further reaction e.g.metal ion

Nicotinamide adenine dinucleotide (NAD⁺)

is used in many redox reactions in biology.

nicotinamide ring, Adenine ring, 2 sugar-phosphate groups

NAD+/NADH contains

NADH

NAD+ is a two electron oxidizing agents and is reduced to

Zn²⁺

Metal ions for alcohol dehydrogenase, carboxypeptidase

Mg²⁺

Metal ions for phophotransferase

Fe²⁺, Fe³⁺

Metal ions for cytochromes, peroxidase,   catalase

Mn²⁺

Metal ions for arginase, pyruvate   phosphokinase

Cu⁺, Cu²⁺ 

metal ions for tyrosinase, cytochrome oxidase

metal ions

Some enzymes requires

Availability of substrates and cofactors

What Factors Influence Enzymatic Activity?

how fast the reactio goes

Availability of substrates and cofactors determines

product accumulates

Rate of enzymatic reaction will decrease if

Genetic regulation of enzyme synthesis and decay

determines the amount of enzyme present at any moment

allosterically

Enzyme activity can be regulated

covalent modification

Enzyme activity can be regulated through

reversible phosphorylation

Enzyme activity can be regulated through

protein kinases

Phosphorylation is accomplished by

specific proteins

Each protein kinase targets ___ for phosphorylation

Phosphoprotein phosphatases

catalyze the reverse reaction – removing phosphoryl groups from proteins

targets of regulation

Kinases and phosphatases themselves are

Zymogens

are inactive precursors of enzymes. Typically, proteolytic cleavage produces the active enzyme.

Allosteric effects

Enzymes situated at key steps in metabolic pathways are modulated by