Topic 2

Question 1

Name some important functions of proteins.

Answer 1

Catalyze biochemical reactions, transport molecules, transmit signals, offer motility/mobility to cells, & provide structural support.

Question 2

How are polypetides made?

Answer 2

Condensation reactions between monomer and other monomer or chain.

Question 3

What type of bond is a peptide bond?

Answer 3

Covalent

Question 4

How are polypeptides broken down?

Answer 4

Hydrolysis/Hydration reaction

Question 5

What are the side chains of every amino acid?

Answer 5

Basic amino group and acidic carboxyl group

Question 6

How many natural amino acids are there?

Answer 6

20

Question 7

What is the alpha carbon?

Answer 7

Carbon that is attached to the 3 R groups.

Question 8

Where is peptide bond formed?

Answer 8

Between C of carboxyl and N of amino from other amino acid.

Question 9

What are the free ends of a polypeptide?

Answer 9

N-terminal which is free end and C-terminal which is free end. N-terminus=beginning of protein strand. C-terminus gets continually extended.

Question 10

What are the two acidic amino acids?

Answer 10

Glutamic acid (Glutamate) & Aspartic Acid (Aspartate)

Question 11

What are the 3 basic amino acids?

Answer 11

Lysine, Histidine, & Arginine

Question 12

What are the polar amino acids with hydroxyl groups?

Answer 12

Serine, Threonine, Tyrosine-These 3 can be phosphorylated

Question 13

What is the polar amino acid with a sulfhydryl group?

Answer 13

Cysteine

Question 14

What two polar amino acids have a 2nd amide side chain?

Answer 14

Asparagine and glutamine

Question 15

What is the significance of the 3 polar amino acids with hydroxyl groups?

Answer 15

They have the ability to be phosphorylated which is extremely important for regulation.

Question 16

What is important about the cysteine amino acid?

Answer 16

It can form disulfide bonds-hydrophilic

Question 17

What are the 9 non-polar amino acids?

Answer 17

Glycine, alanine, valine, leucine, isoleucine, tryptophan, phenylalanine, proline, and methionine-These are all hydrocarbons.

Question 18

What is significant about the protein’s 3D structure?

Answer 18

Its 3D structure determines its function. Chemical properties are often predictable if their amino acid sequences are known.

Question 19

Review the amino acid structures.

Answer 19

Need to recognize which amino acid if given the structure.

Question 20

What non-covalent bonds for ultimate 3D protein conformations?

Answer 20

H-bonds, van der waals, ionic interactions (charged amino acids), & hydrophobic interactions (deep inside protein).

Question 21

Do most proteins have tertiary or quaternary structures?

Answer 21

Tertiary

Question 22

How do proteins get a quaternary structure?

Answer 22

Have more than one polypeptide chains interacting. Ex.) Hb

Question 23

What bonds form the primary protein structure?

Answer 23

Peptide bonds

Question 24

What bonds form the secondary protein structure?

Answer 24

Alpha-helix and Beta sheets-H-bonds only (R-groups not involved yet). Only determined by backbone of protein structure.

Question 25

What bonds form the tertiary structure?

Answer 25

R-groups are now involved-2 polypeptide chains-Van der waals, hydrophobic interactions, ionic bonds, & disulfide bonds.
Ex.) Myoglobin

Question 26

What causes a protein to take on a quaternary structure?

Answer 26

2 or more polypeptide chains interacting

Question 27

Describe Cytochrome C.

Answer 27

Has a heme binding site in the middle, inside is usually very hydrophobic, and the outside very hydrophilic. Ha s a binding site in the center.

Question 28

How does protein 3D structure affect protein function?

Answer 28

They can only successfully interact with substrates that have a structure that matches theirs. Can only recognize certain molecules.

Question 29

What are the two ways protein structure is determined?

Answer 29

X-ray diffraction and NMR.

Question 30

What are the parameters for X-ray diffraction?

Answer 30

Protein must be crystallized, but size does not matter.

Question 31

What are the parameters for NMR?

Answer 31

Proteins don’t have to be crystallized, but the protein must <150 a.a.

Question 32

Describe X-ray diffraction.

Answer 32

Apply x-ray to protein that has been crystalized. Pattern of diffraction is recorded and analyzed to determine the 3D structure.

Question 33

Is protein folding an ATP-dependent pathway?

Answer 33

Yes

Question 34

Describe the protein folding pathway of insulin.

Answer 34

Protein folding is not random like once believed. It is actually an highly ordered/ controlled process that requires other proteins help and ATP.
Ex.) Insulin folding process- Has a signal peptide sequence that helps the protein to the ER and is present at the n-terminal of newly synthesized proteins. It is recognized by signal recognition particles to be brought to ER. Signal recognition particle is cut by signal peptidase in the ER. Other sequences are cut to process insulin. C-terminal, another sequence is cut off. There are 6 cysteine residues in insulin that can form 3 disulfide bonds that allow for hormone function. The 4th and 5th cysteine always form 1st disulfide bond. The 1st and 6th cysteine then for the 2nd disulfide bond. Then the 2nd and 3rd will form the last disulfide bond. This always happens in this order and between these specific cysteine residues. This discovery showed that it is not random, but highly ordered. Does consume energy and require chaperone proteins to help fold it.

Question 35

Describe the discovery of heat shock proteins.

Answer 35

E.Coli cells were put into the incubator at what he thought was 37 degrees celsius to crow them. The temperature was changed to a much higher temperature (maybe 50 degree celsius). Researcher came back next day and saw the temperature was too high and that the E.Coli did not grow well, but there were still some colonies that survived in the abnormally high temperature. He extracted the proteins from the cell colonies and grew a new set of E.Coli cells in the 37 degree temp. and extracted proteins from that. He had heat treated colonies and control colonies. The proteins expressed were different. There are 2 major proteins expressed in heat treated protein that aren’t expressed in the control. He cloned the colonies, and made mutations. The mutated E.Coli could not survive abnormally high temperatures. This led to the discovery of the two chaperone proteins, initially termed heat shock proteins, GroEL and GroES.

Question 36

Describe the diagram of how they work.

Answer 36

When the environmental condition is higher than ideal temperature, the newly synthesized proteins, can be deposited inside the GroEL and then covered by GroES that makes unique internal environment. This environment can allow the proteins to fold and form normal structures. ATP is also present since it is an ATP-dependent pathway. . The protein is released when it is done folding. These chaperone proteins are present in all eukaryotes and essentially have the same function. (Heat, stress, extreme conditions, etc.)

Question 37

Name the 3 major ways proteins can be denatured.

Answer 37

Heat, UV, 6-10M Urea

Question 38

Describe heat denaturation

Answer 38

Completely destroys protein 3D structure and breaks peptide bonds and no way to renature the proteins.

Question 39

Describe UV light denaturation.

Answer 39

Completely denatures proteins and damages DNA.

Question 40

Describe Urea denaturation.

Answer 40

6-10M Urea ideal to study protein folding and renaturation because it can destroy the 3D structure (non-covalent bonds), but doesn’t break the peptide bonds. It can then be renatured.

Question 41

Describe the process of of degradation of mis-folded proteins.

Answer 41

Ubiquitin-mediated protein degradation. Ubiquitin recognizes and tags mis-folded proteins to form a mis-folded protein-ubiquitin complex. It leads the mis-folded protein to a proteasome where proteases can destroy the protein. Ubiquitin will not enter proteasome, but the protein will be dropped of and digested. Ubiquitin is recycled as are amino acid residues.

Question 42

Describe the proteasome structure.

Answer 42

Contains 2 caps on both ends, 2 alpha subunits close to the caps, and then two beta subunits on the inside.

Question 43

Describe Alzheimers, a disease caused by mis-folded proteins.

Answer 43

Ubiquitin sometimes does not recognize mis-folded proteins. There are plaques in the brain that form tangles within the nerve cells that damages them. Tau protein can be highly phosphorylated (has many Tyr, Ser, &/or Thr). When it is highly phosphorylated, it will absorb a lot of water which changes its 3D structure. This can not be recognized by ubiquitin. The tangles/twists may possibly be caused by the tau protein.

Question 44

What is Creutzfeld-Jakob Disease (Mad Cow Disease)?

Answer 44

Caused by eating undercooked meat contaminated by CNS tissue from a cow that had the disease. Damages brain cells causing spongiform encephalopathy, which are sponge like lesions in the brain tissue that cause a deterioration of brain function. Marked by rapid decrease in brain function, dementia, and death.

Question 45

What are the mis-folded proteins called in the Mad Cow Disease? Describe it.

Answer 45

Prion-No mutation in the gene, rather it is a rogue/mis-folded protein. No DNA, RNA, or nucleic acid difference. This busted the assumption that infections were all caused by nucleic acids or bacteria.

Question 46

Describe the previous assumptions of pathogens before prions.

Answer 46

Infection–> Bacteria, Sickness–> Virus, Fungi, parasites, etc.