DO MCM 03 Protein Structure and Function

What is transcription? What is Translation?

Transcription: DNA —> RNA; Translation: RNA —→ Protein

Which Amino Acid can’t be coded by the genetic code alone?

Selenocystein: Needs the genetic code and secondary structure in the mRNA

What is the zwitterion form? When does it occur?

It is when the protein’s amino group is Protonated and the Carboxyl group is Deprotonated. It occurs at physiological pH (7.4)

what is protonation/deprotonation dependent on?

pH and pKa

What happens when pH = pKa?

groups is protonated in half of the molecules and is deprotonated in the other half.

What are the hydrophobic Amino acids?

glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Phenylalanine, Tyrosine, Tryptophan, Methionine

What force is responsible for hydrophobic cores made up of hydrophobic Amino Acid?

Van der Waals Forces

What are the Polar, Uncharged Amino Acid?

Asparagine, Glutamine, Serine, Threoine, Cysteine, Selenocystein

dksl is a protein with strong antioxiant activity. Which amino acid do you expect to be in abunance?

Selenocysteine

Which group of amino acids uses hydrogen bonding interactions?

Polar, Uncharged Amino Acids

Which amino acids create disulfide bridges? How does this affect the protein?

cysteine. Increases stabilization

How is Cystine formed?

Formed via disulfide bridge between two cystEine, creating a dimmer. This is formed under oxidative conditions!

What are the charged Amino Acids? How do they interact with each other/ other charged molecules?

Aspartate, Glutamate, Arginine, Lysine, Histidine;

interact via ionic bonds

What are peptide bonds? Where are they formed?

Peptide bonds are the bonds that hold individual amino acids together. They are formed between the amino group/carboxyl group of different amino acids.

If somebody’s DNA got damaged, which level of structure is affected in proteins?

Primary Structure because the genetic code determines this

how many free amino/carboxyl groups are there in a protein?

1 each

Describe the four levels of protein structure

Primary: protein sequence
Secondary: localied substructure in proteins

Tertiary: 3d structure of protein

Quarternary structure: association between polypeptide chains

what are the four main types of secondary structures? What bond holds them together?

Alpha helixes, Beta sheets, random coils, Beta turns. H-bonds hold them together.

You noticed that a patient has aggregation of a specific protein. What secondary structure is most likely in excess?

Beta Sheets

What are the four super-secondary structures?

Helix-turn helix, Helix-loop-helix, Leucine Zipper, Zinc Finger

Bam! a source of radiation completely destroyed all super-secondary structures in a person. What genetic function would be the most impaired? Why?

Transcription. Because these super secondary structures are often used as DNA-binding zones for transcription factors.

a witch cursed you! now, every 7th amino acid is mutated. Which protein structure will be the most affected?

Leucine Zipper, because every 7th amino acid in the zipper is a leucine.

What is the purpose of Zinc Finger?

Necessary for stabilization.

What is this? Label

What is this? Label?

What is this? Label?

Which structure is IMPORTANT for protein function and why? Give examples

Tertiary Structure because these 3d structures creates pockets that is important for function! For examples, Myoglobin uses pockets to bind Oxygen and Enzymes uses these pockets as active sites.

What are protein domains? (T/F) They have similar functions

protein regions that folded independently; False, they can have different functions within the protein

what are some examples of different domains found in a protein?

a protein could have a ligand-binding domain, transmembrane domain, and a cytoplasmic domain.

a protein has a trans membrane domain. describe the amino acid/structure found in this domain.

hydrophobic Amino Acids, mainly alpha helixes

Describe the chains of Type II collagen

Homotrimer; three identical chains held together by non-covalent interactions/ covalent bonds

Describe the chains of heterotrimeric G-Proteins

Heterotrimer; 3 different protein chains (alpha, beta, gamma); held together by non-covalent interactions

Describe the chains of hemoglobin

2 alpha chains and 2 beta chains. held together by noncovalent interactions (A2B2 tetramers)

what are the advantages of having quaternary structure? Examples of each?

Increased cooperative (Hemoglobin),stability (collagen), and regulate activity of protein (heterotrimeric G proteins)

What determines how a protein folds?

Primary structure

What are chaperonins?

accessory proteins that some proteins require to fold to their native forms

Describe the difference between HSP70 and HSP60

70: bind to the growing protein and prevent it from folding too early

60: Folds the protein using ATP by using a template

What two things does protein misfolding lead to?

aggregation/precipitation —→ pathological consequence

What are the four main causes of protein misfolding

Mutation, proteolytic cleavage, oxidation, environmental conditions

List the symptoms of a1- antitrypsin deficiency as a result of mutation.

aggreagation of mutant protein in ER of liver, liver dysfunction (child)/cirrhosis (adults), lungs problems due to lower antitrypsin in circulation

what is the function of a1-antitrypsin, where produced, secreted?

protease inhibitor, produced in liver, secreted in circulation.

what are the three forms/causes of creutzfeld-jakob disease. What are the percentages of each forms?

sporadic form due to unknown cause (85%)

familail form due to mutation (5)

acquired from abnormal protein from another source (mad cow)

why does abnormal structure caused by creutzfeld-jakob increase exponentially over time?

This is because the abnormal structure could induce change in the normal type to become like the abnormal structure. Thus, it is capable of creating more of themselves.

What is creutzfeld-jakob? What could this disease lead to?

denaturation of prion proteins. These proteins will precipitate in the brain, causing fast brain degeneration/eath

How does AA amyloidosis occur? What is this associated with?

precipitation of serum amyloid A Fragments due to proteolytic cleavage; rheumatoid arthritis

How does Al amyloidosis occur? What is this associated with?

precipitation of antibody Light chain fragments (bence-jones proteins) due to proteolytic cleavage; multiple myeloma (cancer of antibody-producing plasma cells)

How does Alzheimer disease occur? What is this associated with?

AB amyloidosis. Caused by precipitation of B-amyloid protein which is the precursor for the amyloid protein. Causes Brain degeneration

Why are heinz body formed due to G6PD deficiency?

G6PD makes NADPH which protects against oxidative damage. A deficiency in this enzyme would make the Hb in RBC more prone to this damage. The result is heinz bodies

list the environmental conditions that would cause protein denaturation

Extreme pH, high temperature, exposure to organic solvents

Give an example of mutation leading to beneficial changes in protein structure.

In insulin, exchanging Pro28 and Lys29 leads to less insulin aggregation, better absorption and faster action.