Biochemistry Exam 3

Ch 6, 7, Ch 11, 12

What are Myofibrils

Repeating sarcomeres

What are sarcomeres

A & I bands bounded by a Z disk

What are A bands?

Thick filaments, Myosin

What are I bands?

Thin filaments, Actin

What is the (-) part of actin?

The binding site of the polymer

What is the (+) part of actin

The end that binds to the Z disk

What is tropomyosin?

Binds to thin filament blocking myosin binding site

What is Troponin:

Binds Ca2+ released from sarcoplasmic reticulum, acts a sensor

What happens to the sarcomere during a contraction

Length is reduced caused by I band and H zone reduction

What is the sliding filament model?

Thick & thin filaments slide past each other

What triggers a muscle contraction?

Ca2+ binding to troponin C

What happens when there is low Ca2+

Myosin head is blocked, unable to bind to actin

What protein is most abundant in eukaryotic cells?

Actin protein

How is an immune response activated?

Antigens

What is the structure of Immunoglobulins

4 subunits, 2 light chains & 2 heavy chains

How are immunoglobulins associated?

Disulfide bonds & non-covalent interactions

What is the 1st antibody to be secreted

IgM

What is the most common antibody?

IgG

IgA has multiple structures, what are they?

Monomer, dimer or tetramer

What antibodies fight parasites

IgE & IgD

What is a Fab fragment?

Antigen binders

What is a Fc fragment?

Stem of the IgG antibody structure

What kind of protein is Myosin

A motor protein

What is the monomeric form of Actin?

G-Actin

What is the polymerized form of G-Actin?

F-Actin

What are microfilaments?

Nonmuscle actin filaments

What is Humoral Immunity?

Antibodies produced from B lymphocytes/cell

What is cellular Immunity?

Mediated by T lymphocytes/Cells

What are the two antibody preparations?

Monoclonal & Polyclonal antibodies

How many heme groups does Myoglobin have?

One heme group

What is the porphyrin ring in myoglobin?

Fe(II) binds molecular oxygen

How does myoglobin facilitate diffusion?

Myoglobin binds to O2

What is the major role of myoglobin?

Deliver O2 to muscles

What kind of curve does myoglobin have?

Hyperbolic curve

What is the p50 of Myoglobin?

2.8 torr

The steepness of the hyperbola _____ as K ______

Increases, decreases

Hemoglobin binds what, where?

O2 in the lungs

What is Deoxyhemoglobin?

T state

What is Oxyhemoglobin?

R state

What kind of curve does Hemoglobin have?

Sigmoidal curve

What is the p50 for hemoglobin?

26 torr

Hemoglobin binds how?

Cooperatively

Myoglobin binds how?

Non-Cooperatively

What kind of protein is Hemoglobin?

Allosteric Protein

What is the symmetry model?

Oligomer can exist in R or T state

What is the sequential model?

One bound subunit influences the others

If ligand binds tightly to R than T, what happens?

The shift from T → R is favored

What causes the T state to shift to the R state?

Oxygen binding to heme iron

During the T → R transition what happens?

Fe(II) moves to the center of heme plane using His F8

If the T → R transition is tightly packed, what happens if one changes?

The other 3 are changed as well

BPG binds tightly to what state?

T state

BPG weakly binds to what state?

R state

What has a low BPG affinty?

Fetal Hemoglobin

Bohr Effect

Effect of pH and CO2 on the binding and release of O2 by hemoglobin

Geometric Complementarity

Substrate binds to surface of enzyme complementary in shape of substrate

Electronic Complementarity

The amino acid residues forming the binding site are arranged to attract substrate

Induced fit

Enzymes alter shape of substrate binding site

What are coenzymes

Organic molecule cofactors

What is a Holoenzyme

Active enzyme - cofactor complex

Apoenzyme

Inactive enzyme - cofactor complex

Greater the value of Delta G⁺  

The slower the reaction rate

How do catalyst act?

They decrease the activation energy

Covalent Catalysis

Speeds reaction through formation of catalyst-substrate covalent bond

What does a Reaction Coordinate Diagram consist of?

Free energy vs reaction coordinate

What is the highest transition state?

Rate determining step

Delta G < 0

Products are favored

Delta G > 0

Reactants are favored

General Acid Catalysis

Proton donated stabilizes & makes reaction easier

General Base Catalysis

Proton removal from base increases rate

What are metaloenzymes?

Tightly bound metal ion cofactor

How do metal ion’s participate?

Binding substrates orient them, mediate oxidation - reduction rxn and electrostatically stabilize/shield negative charges

Enzymes binding to transition state:

Lowers activation energy, increasing reaction rate

Lysozyme does what?

Cleaves glycosidic link between NAM & NAG

How many residues does lysozyme binding cleft hold?

6 residues (sugars)

What two amino acids does lysozyme cleave between?

Asp & Glu

What are the three Serine proteases?

Chymotrypsin, Trypsin and Elastase

What is the catalytic triad?

His, Ser & Asp

Where is the catalytic triad?

Located inside substrate binding site

Chymotrypsin

Prefers bulky hydrophobic residues. Cuts next to Phe

Trypsin

Prefers positively charges residue. Cuts next to Lys & Arg

Elastase

Prefers small neutral residue. Like chains with Ala, Gly & Val

Affinity Labeling

Technique in which labeled substrate analog reacts irreversibly with enzymes active site; use to identify

What are zymogens?

Large inactive precursors

What is trypsinogen?

The zymogen of trypsin

Activation of Trypsinogen

Trypsinogen → Enteropeptidase → Trypsin

Sequential reactions occur in what two ways?

Random & Ordered mechanism

Competitive Inhibition

Competes with normal substrate for binding to enzyme

What effect on Km does a Competitive enzyme have?

Increases Km

Uncompetitive Inhibition

Binds only to the [ES] complex; inactivate active site

What effect does Uncompetitive Inhibition have on Km and Vmax?

Decreases both Km & Vmax

Mixed Inhibition

Binds to both free and substrate bound enzyme. Interferes with substrate binding

What effect does Mixed Inhibition have on Km and Vmax?

Decreases Vmax, Km is decreases or increased

Protein kinases

Catalyzes attachment of phosphoryl groups to specific amino acid residue

Phosphates:

Remove phosphoryl groups from the same target protein

Transition State Analogs

Stable molecules resemble transition states

What two ways does allosteric control have on enzyme activity

Altering amount of enzyme, modifying catalytic activity through allosteric effects or covalent modification

Feedback Inhibition

Inhibits earlier step in own biosynthesis

Allosteric Control: ATP

Positive allosteric regulator stabilizes R state

Allosteric Control: CTP

Negative allosteric regulator stabilizes T state