Properties of proteins Flashcards
What can cause a protein to denature? (4)
1.) Strong acids or bases, or reducing agents: Add or remove hydrogens
2.) Organic solvents, detergents: Disrupt hydrophobic, polar and charged interactions
3.) Salts: Disrupt polar and charged interactions
4.) Heavy metal ions
What 2 groups can a heavy metal bind with to denature it by changing its shape?
1.) negatively charged groups
2.) sulfhydryl (SH)
Enzymes are an example of what type of protein?
Globular
Enzymes speed up a reaction by lowering the ___________ of the reaction with out changing the ____________ nor ___________.
activation energy/standard free energy/equilibrium
________ is the minimal amount of energy needed to make/break the bonds necessary for a reaction to occur.
Activation energy
True or false.
Activation energy is sometimes defined as the amount of energy needed to reach the transition state.
True
The _____________ is the highest energy configuration formed when changing from reactants to products.
transition state
The transition state is (transient/constant) and (isolated/not isolated).
transient/not isolated
The activation energy is (increased/lowered) in the catalyzed reaction.
The overall standard free energy of the equation is (lowered, increased, not changed)
lowered/not changed
The active site is formed by precise (primary/secondary/tertiary/quaternary) structure of a protein
quaternary
Do amino acids in the active site participate in substrate binding and catalysis?
Yes
Once inside the active site, the substrate binds the enzyme forming an __________________ complex.
enzyme-substrate (ES)
In the __________ model, binding of substrate is thought to induce a conformational change in shape of the enzyme.
induced fit model
What are the mechanisms of an enzyme, once it has bound to the active site?
1.) electrostatic interactions to form between S and E
2.) ensures correct positioning of catalytic groups in the enzyme
In what 2 ways do catalytic groups speed up reactions?
1.) acid-base catalysis
2.) covalent catalysis
In _____________ mechanism, the addition or removal of a proton can make a substrate more reactive.
Acid-base catabolism
(The side chains of certain amino acids can add or remove H+’s by acting as general acids or bases)
Acid- base effects:
When there are no catalysis, the reaction is slow, it is fast with either acid catalysis or base catalysis, with BOTH acid and base catalyses, it is (the fastest/the slowest).
fastest
In ________________ enzyme mechanism, a nucleophilic side group in the enzyme active site forms a temporary covalent bond with the substrate
covalent catalysis
What are 2 common nucleophilic side groups of AA?
Asp and Glu (R- COO-)
Ser (R-OH) and Cys (R-SH)
Serine and Cystein are only weakly nucleophilic, but their nucleophilicity is enhanced by the presence of other amino acids that can remove the H*
Cofactors are typically _____ cations.
metal (mg2+, Zn2+)
What is magnesium’s role in several glycolytic enzymes involving ATP?
helps position the ATP in the enzyme active site
helps to stabilize the negative changes on the ATP
What are coenzymes typically derived from?
vitamins
In what 3 ways can cofactors and coenzymes speed up reactions?
1.) Can help position the substrate in the active site of the enzyme
2.) Can stabilize negative charges on the substrate or the TS to make it easier for a nucleophilic attack to occur
3.) Can accept/donate electrons in redox reactions
The optimal temperature for an enzyme is usually (higher than, lesser than, equal to) the organism.
Equal to
Changing the pH (can/cannot) change the protonation state of the enzyme and/or the substrate
Can
What types of bonds between E and S would potentially be disrupted by a change in pH? (2)
1.) H-bonds
If an H is removed, no H-bond can be formed
If an H is added, an H-bond might form that is not usually formed.
2.) Electrostatic interactions
Adding an H can turn COO- into COOH
Removing an H can turn NH3+ into NH2
What is the function of a lysosome?
Main site of intracellular enzymatic degradation for a wide range of molecules
What 4 main ways can enzymatic activity be controlled?
- Genetic
- Covalent modification
- Allosteric regulation
- Compartmentalization
True or false.
Enzymes transcription can be induced OR repressed based on the needs of a cell.
True
Which type of enzyme regulation, Involves altering the structure of an enzyme (or “proenzyme”) by making or breaking bonds
Covalent modification. (making or breaking covalent bonds)
The main regulated enzyme in glycogenesis is (activated/ de-activated) by phosphorylation while the main enzyme in glycogenolysis is (activated/deactivated) by phosphorylation.
deactivated/ activated
Phosphorylation is catalyzed initially by the same enzyme____________.
protein kinase A (PKA)
Which type of enzyme regulation involves cleavage of peptide bonds in proenzymes or zymogens and
ensures the enzyme is not used until it is in the correct location and until it is needed
covalent modification
Phosphofructokinase-1 is (inhibited/activated) allosterically by high levels of ATP
inhibited
Phosphofructokinase-1 in (activated/inhibited) allosterically by high levels of AMP
activated
Compartmentalization of enzymes via membrane-bound organelles allows for regulation by: (2)
- Separation of enzymes from opposing pathways into different cellular compartments, and selective transportation of substrates
- Creation of unique microenvironments (ex. pH levels)
