BMS 124: Enzymes

20 AA

how many amino acids are in the universe

Amino acids that we cannot produce ourselves and must get from environment

What are essential amino acids

Amino acids that we produce ourselves

What are non essential amino acids

Amino acid

The ionizable groups (amino, carboxyl, R groups) and pH of environment

What influences amino acid charge

the presence of a central carbon (the alpha carbon) bonded to four different groups, making the molecule non-superimposable on its mirror image.

What is chirality in amino acids

Covalent bond between two amino acids

What is peptide bond

Primary structure

linear sequence of amino acids (unable to be changed by heat, acid etc)

Secondary structure

the folding of polypeptide chain as a result of hydrogen bonding between peptide groups along its length (alpha helix beta sheet)

Tertiary structure

the further twisting, folding and coiling of polypeptide chain as a result of interactions between the R group, result of intramolecular forces

Quaternary structure

The particular shape of a complex, aggregate protein, defined by the characteristic three-dimensional arrangement of its constituent subunits, each a polypeptide.

covalent bond

Bonds in primary structure

Hydrogen bond

Bonds in secondary structure (backbone of carbonyl and amide groups)

Hydrogen bonds - between side chains.

Ionic bonds (salt bridges) - between charged side chains (e.g. Lys⁺ and Asp⁻).

Hydrophobic interactions - nonpolar side chains cluster away from water.

Van der Waals forces - weak attractions between closely packed atoms.

Disulfide bonds (covalent) - between cysteine residues (S-S linkages).

Bonds in tertiary/quaternary structure

Alzheimer's disease

Accumulation of insoluble and neurotoxic Aβ peptides in the brain is the pathogenic event in

Prion disease

Normal prion protein (PrPc) contains α-helix while

Infectious PrPsc contains β-sheets, which resists to proteolytic degradation and form insoluble aggregates.

α-helix, β-sheets

Normal prion protein (PrPc) contains ____ while

Infectious PrPsc contains ______, which resists to proteolytic degradation and form insoluble aggregates.

What is an enzymes major role in biochemical reaction

An enzyme speeds up a biochemical reaction by lowering its activation energy.

What are properties of an enzyme

Enzymes are highly specific, reusable, work best at optimal pH and temperature, and speed up reactions by lowering activation energy without being consumed.

Transition state of uncatalyzed reaction

Red

Transition state of catalyzed reaction

Blue

Substrate

Purple

Product

Pink

Activation energy for uncatalyzed

Green

Activation energy for catalyzed

Yellow

Reaction energy

Brown

Active site

a region on an enzyme that binds to a protein or other substance during a reaction.

catalytic efficiency

Kcat/Km

Kcat

turnover number (molecules catalyzed per second in optimal conditions)

Vmax / [E]

Km

Substrate concentration at 1/2 Vmax

Exothermic reaction

Endothermic reaction

Specificity

The ability of an enzyme to choose the exact substrate from a group of similar chemical molecules.

• Only one substrate is complementary to the active site.

Holoenzymes

enzymes with their cofactors

Regulation of enzyme

-enzymes can be activated or inhibited so the rate of product formation responds to the need of the cell

-feed back inhibition of metabolic pathway

-most rate limiting steps are at the beginning

Cytoplasm

Enzymes are located in the

Enzyme Kinetics

The study of how fast enzyme-catalyzed reactions occur and how they're affected by factors like substrate or enzyme concentration.

Michalis-Menten Equation

Vo = (Vmax x [S])/(Km + [S])

Km

Substrate concentration at 1/2 Vmax

V max

The maximum rate of the reaction when all enzyme active sites are saturated.

Lower

____ Km means higher affinity between enzyme and substrate

Lineweaver-Burk Plot

the double reciprocal graph of the Michaelis-Menten equation

Reaction rate

The MM equation solves for the _____ (v) of an enzyme-catalyzed reaction based on substrate concentration, Km, and Vmax.

Competitive inhibition

Km increases, Vmax stays the same

Increases

Increasing enzyme concentration _________ Vmax but does not change Km.

Non competitive inhibition

Km unaffected, Vmax reduced

Uncompetitive inhibition

inhibitor binds only to enzyme-substrate complex

Lower Km and vmax

-1/Km

What is the x-intercept of a Lineweaver-Burk plot?

1/Vmax

What is the y-intercept of a Lineweaver-Burk plot?

Allosteric control, covalent modification, feedback inhibition

Enzyme activity is regulated through ______, _________(like phosphorylation), __________, and changes in gene expression.

Competitive and noncompetitive inhibition

What are the two most common types of reversible enzyme inhibition?

Michaelis Menten graph

hyperbolic

Competitive inhibition

Km increases (lower affinity), Vmax stays the same.

Noncompetitive inhibition

Vmax decreases, Km stays the same

[S] in enzyme kinetics

concentration of substrate

Allosteric regulation

The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.

Homotropic/heterotropic effectors

What are types of allosteric regulation

Homotropic effectors

when the substrate itself serves as an effector (oxygen binds to hemoglobin)

Heterotropic effector

effector is different from substrate (PFK1 is inhibitated by citrate)

Covalent modification

phosphorylation and dephosphorylation by ATP or other enzymes

Beta-lactam antibiotics

Penicillins and amoxicillin act by inhibiting enzymes in bacterial cell wall synthesis

Angiotensin-converting enzyme (ACE) inhibitors

lower blood pressure by inhibiting the conversion of angiotensin I (an inactive enzyme) to angiotensin II (a potent vasoconstrictor) drugs include captopril, enalapril, and lisinopril

Plasma enzymes

Active secreted into blood like clotting factors and released during cell turnover (indicate tissue damage)

Alanine Aminotransferase (ALT)

Liver function test panel (type of plasma enzyme)

Creatine Kinase (CK)/Cardiac troponin I (cTnI)

Myocardial infarction test (type of plasma enzyme)

Glucose meter

Provide fast analysis of blood glucose levels and allow management of both hypo/hyperglycermic disorders to adjust glucose to normal level

Enzymatic reaction and detector

What are the two parts of a glucose meter

Enzymatic reactions

Glucose oxidase, glucose dehydrogenase, hexokinase

Biosensor

Those meters incorporate the enzymes into a ______ that generates an electron that is detected by the glucose meter

PCR

detects the presence of viral genetic material (RNA or DNA)—during COVID-19, RT-PCR was used to amplify and identify SARS-CoV-2 RNA from patient samples to confirm infection.

salivary amylase

Breakdown dietary carbohydrate for digestion (plaque formation by binding to bacterial surfaces and enamel providing simple sugars to bacteria)

lysozyme, lactoferrin, lactoperoxidase system, histatins

What are antimicrobial and protective salivary enzymes

matrix metalloproteinases (MMPs)

A family of zinc-containing enzymes that act in the extracellular space to digest various extracellular proteins and proteoglycans

tissue inhibitors of metalloproteinases (TIMPs)

Natural inhibitors to MMPs, balance is needed for homeostasis