Proteins and Enzymes Flashcards
bond that occurs between two oppositely charged amino acids
salt bridge
which bond helps protect a protein from denaturation during changes in blood pH or salt concentrations?
disulfide bonds - strong bonds
what is an example of an extracellular protein that is held together by disulphide bonds?
insulin
a protein composed of two subunits
dimer
a protein composed of several subunits
oligomer
a protein composed of many subunits is called a
multimer
what are proteins that help other proteins get into their correct shape and correct cellular locations?
chaperones
how are chaperone proteins released?
ATP hydrolysis
___ are common chaperone proteins that bind and stabilize portions of proteins not yet folded
heat shock proteins
- get induced in cells during various stress conditions produced by cellular insult, environmental changes, temperature, infections, tumors etc
a ___ is any repeating structural unit within a multimeric protein
protomer
enzymes are an example of a type of ____ protein
globular
enzymes are protein ____ that speed up specific reactions and remain ______ by the reaction
protein catalysts that speed up specific reactions and remain unchanged by the reaction
the minimal amount of energy needed to make/break the bonds necessary for a reaction to occur
activation energy
Enzyme molecules contain a special cleft called the
active site
The active site forms by precise _____ structure of the protein
quaternary
Amino acids in the active site participate in substrate binding and catalysis
Binding of substrate is thought to induce a conformational change in shape of the enzyme is called
the Induced fit model
the addition or removal of a proton can make a substrate more reactive
acid-base effect
Which amino acid side chain do you think can function easily as an acid or a base?
positively or negatively charged amino acids
A nucleophilic side group in the enzyme active site forms a temporary covalent bond with the substrate
Covalent catalysis
Common nucleophilic side groups include:
- 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
molecules that aid in substrate recruitment
cofactors and coenzymes
Cofactors are typically metal cations
Mg and Zn
We have already discussed the role of Mg2+ in several glycolytic enzymes involving ATP. What was the role of magnesium?
- Magnesium helped to position the ATP in the enzyme active site
- Helped to stabilize the negative changes on the ATP
examples of coenzymes?
Typically derived from vitamins
B3: NAD+ <>NADH + H+
Can accept or donate elections in redox reactions
3 ways coenzymes and cofactors can help enzymes speed up reactions
- help position the substrate in the active site
- stabilize negative charges on the substrate or the TS to make it easier for a nucleophilic attack to occur
- can accept/donate electrons in redox reactions
what is the optimal temperature for enzymes
the temperature of the organism
Do you think a fevers are good or bad?
There are benefits to a certain point
- Enzyme activity can be increased, metabolism can be increased (to fight infection) and bacteria can no longer function
BUT temps that are too high can cause enzymes to not function = fatality
Changing the pH can change the ______ state of the enzyme and/or the substrate
protonation
What types of bonds between Enzyme and Substrate would potentially be disrupted by a change in pH?
H-bonds – for example:
- 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.
Electrostatic interactions - for example:
- Adding an H can turn COO- into COOH
- Removing an H can turn NH3+ into NH2
Main site of intracellular enzymatic degradation for a wide range of molecules. They have proteolytic enzymes that break unwanted material in the cell.
function of lysosome
enzymes can be controlled in four main ways
- genetic
- covalent modification
- allosteric regulation
- compartmentalization
Enzymes transcription can be induced or repressed
based on the needs of the cell
genetic modification
Involves altering the structure of an enzyme (or “proenzyme”) by making or breaking covalent bonds
covalent modification
Involves the addition or removal of a group to the enzyme that causes it to convert to its active or inactive form
reversible covalent modifcation
- Other common groups that can be added to or removed
enzymes include ____ and ______ groups
methyl and acetyl
The main regulated enzyme in glycogenesis is ________ by phosphorylation
deactivated
while the main enzyme in
glycogenolysis is _______ by phosphorylation.
activated
what enzyme in glycogenolysis is activated by phosphorylation
Glycogen phosphorylase kinase
and Glycogen phosphorylase
what enzyme in glycogenesis is deactivated by phosphorylation
glycogen synthase
Involves cleavage of peptide
bonds in proenzymes or zymogens. Make sure the enzyme is not used until it is in the correct location and until it is needed.
Irreversible covalent
modification
Binding to enzyme’s allosteric site changes the conformation and activity of the enzyme. Changes the binding affinity of the substrate at the active site
Allosteric modification
Increase binding of the substrate to the enzyme
Effector = activator
Decrease binding of the substrate to the enzyme
Effector = inhibitor
Separation of enzymes from opposing pathways into different cellular compartments, and selective transportation of substrates
- Compartmentalization
Creation of unique microenvironments
2.Compartmentalization
