Chapter 5 Flashcards
What is a ligand?
Any molecule that interacts with the binding site of of a protein. Does not covalently bind, so it is reversible! (ligand can come back out)
What is a substrate?
Something that an enzyme acts on
Where do disulfide bonds form and why? How do they affect protein structure?
Disulfide (covalent) bonds are formed between the sulfur atoms of two cysteine residues. These bonds play a crucial role in stabilizing the tertiary and quaternary structures of proteins.
What is meant by “reversible binding” of a ligand to a protein?
Ligands can be reused after detaching from the protein once the desired reaction occurs.
What aspect of thermodynamics drives protein folding?
ENTROPY: Because the water is more ordered when the protein is unfolded, it would be favourable to fold the protein because after folding then the water molecules can move more freely –> higher entropy –>negative ΔG –> spontaneous folding.
What is a prion and what does it do?
An unusual and infectious agent composed primarily of protein material. Unlike viruses, bacteria, or fungi, prions do not contain genetic material like DNA or RNA. PRIONS CAUSE PROTEINS TO MISFOLD into an abnormal three-dimensional structure, causing major problems in a short amount of time.
Compare and contrast chaperone proteins and chaperonins. What do they do?
Chaperones: proteins that assist the conformational folding or unfolding of large proteins or macromolecular protein complexes.
Chaperonins: a type of chaperone protein
What is a the difference between Nonspecific Interaction and Specific Protein Binding?
Nonspecific Interactions: Unspecific, weaker forces. Electrostatic interactions (between charges), hydrogen bonds,
and hydrophobic interactions play a role
(higher Kd, lower affinity)
* EX: Water with anything
Specific Protein Binding: between protein and specific target molecule or ligand. Tight Hydrogen bonds result in DNA bending. Many DNA binding proteins interact in the major groove! (lower Kd, higher affinity)
EX: antibodies with antigens
What is an operon?
A group of genes that are arranged together in a specific order on a DNA strand. These genes work together to carry out a particular function in a cell. What makes an operon special is that these genes are all controlled as a single unit and are turned on or off together.
What are promoter and operator sequences?
Promoter Sequence:
Starting point for reading the genes. It’s a signal that tells the cell’s machinery to begin making a copy of the genes.
Operator Sequence:
A region near the genes that can be turned on or off. Regulatory proteins can attach to the operator and control whether the genes are actively being read or not.
What is a repressor?
A regulatory protein that binds to an operator sequence and prevents the transcription of specific genes near that sequence.
What is the charge of DNA?
Negative (phosphate backbone is negative in solution)
What is the Dissociation Constant (Kd)? What does it tell us?
Where half the available ligand binding sites are occupied (think of a graph)
Kd tells us the strength of the binding that will occur
What does a high or low Kd value tell us?
- Higher Kd means lower affinity
- Smaller (higher negative exponent) number for Kd
means tighter binding. - SUPER HIGH AFFINITY INTERACTIONS (really tiny Kds) MAY BE CONSIDERED IRREVERSIBLE
What are two factors that play a role in binding affinity?
- Chemical Complementarity
- Specificity
Why do some proteins have high affinities for their ligands while others do not?
Chemical complementarity (compatibility) with different shapes, sizes and chemical properties plays a huge role in binding affinities, as well as the rate at which proteins are able to associate with specific ligands.
Compare and contrast the major and minor groove in DNA. How, where, and why do proteins usually bind DNA?
The major groove occurs where the backbones are far apart, the minor groove occurs where they are close together.
How: certain proteins bind to specific sequences
Where: in either of the grooves
Why: to regulate, replicate and repair genes
How does the Lac repressor regulate the lac operon?
The Lac repressor binds to two operators to shut down transcription via a loop by preventing RNA Polymerase to bind to the promoter.
Why does DNA polymerase need magnesium ions?
Magnesium acts as a “cofactor” for DNA polymerase
What are cofactors?
Provide examples.
INORGANIC compounds (such as non-protein chemical compounds or metallic ions) that are required for an enzyme’s role as a catalyst (3RD PARTY)
ex: magnesium is needed at the active site to neutralize the negative charges in DNA. (DNA is negative, cofactors bear a positive charge)
What are coenzymes. Provide examples.
SUBSET OF COFACTORS
ORGANIC compounds required by many enzymes for catalytic activity (3RD PARTY)
ex: Acetyl-Coa and vitamins
How does the enzyme structure catalyze reactions?
Enzymes have specific complementary structures to their substrate. This allows them to “strain” the substrate moving them into the transition state, which provides the catalytic properties as they lower the activation energy.
What is a retrovirus?
A type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell
- USING REVERSE TRANSCRIPTASE the family includes a number of significant pathogens, typically causing tumors or affecting the function of the immune system, e.g. HIV.
What are inhibitors?
Chemical or biological molecules that regulate chemical reactions by slowing down or blocking them from occurring.
