Steele Proteins 1

Question 0

What is the transcriptome?

Answer 0

The complete set of RNAs transcribed from a genome of a cell.

Question 1

How many genes in your genome encode proteins?

Answer 1

22,333

Question 2

What is the proteome?

Answer 2

The complete set of proteins encoded by the genome of a cell.

Question 3

How big is a protein? How big is a cell?

Answer 3

Protein: 1-10 nm. Cell 1micron.

Question 4

How much time does it take for an enzymatic reaction? For conformational change to occur in a protein?

Answer 4

10^-3 seconds, 10^-6 seconds

Question 5

What is primary structure?

Answer 5

amino acid sequence of the protein

Question 6

What is secondary structure of proteins?

Answer 6

Substructures formed by hydrogen bonds between amino acids.

Question 7

What is tertiary structure?

Answer 7

The 3d structure of a protein, contributed by primary structure, secondary structure, and other stuff (disulfide bonds, loops).

Question 8

What is quaternary structure?

Answer 8

Structure formed by association of multiple subunit polypeptides.

Question 9

T or F. All amino acids are in the “L” isomeric form.

Answer 9

True.

Question 10

Which amino acids are at neutral pH?

Answer 10

Glycine, alanine

Question 11

Which amino acids which have bulky, aliphatic (non-aromatic),
hydrophobic side chains (the “greasy amino acids.”)

Answer 11

Valine, Leucine, Isoleucine, Methionine

Question 12

Which amino acids contain aromatic side chains?

Answer 12

Phenylalanine, tyrosine, tryptophan.

Question 13

Which amino acids have side chains that could be basic, or positively charged?

Answer 13

Lysine, Arginine, Histidine

Question 14

Which amino acid can form disulfide bridges?

Answer 14

Cysteine.

Question 15

Which amino acids have polar side chains?

Answer 15

Asparagine, glutamine.

Question 16

Which amino acids have side chains ending in a hydroxyl group?

Answer 16

Serine, threonine.

Question 17

Which amino acid has cyclic structure?

Answer 17

Proline.

Question 18

Which amino acids have carboxylic acid in their side chain?

Answer 18

Aspartate, glutamate.

Question 19

A peptide bond is a covalent bond between the _______ group of one amino acid with the ______ group of another amino acid.

Answer 19

Amino, Carboxyl

Question 20

The peptide bond has planar character because of ________ across the peptide bond.

Answer 20

Resonance.

Question 21

T or F. The bonds on either side of the peptide bond can rotate relatively freely.

Answer 21

True.

Question 22

T or F. Amino acids are commonly organized in a right handed helix. (phi and psi angles).

Answer 22

True. Very rarely is it left handed helix.

Question 23

Amino acids of relatively short length are called _____.

Answer 23

Peptides.

Question 24

What are 3 examples of protein secondary structure?

Answer 24

Helix (alpha common), Beta sheets (parallel, antiparallel), Beta turns

Question 25

T or F. Alpha helix of protein secondary structure are dependent on the H bonds of the R groups.

Answer 25

False. Dependent on H bonds of the peptide backbones.

Question 26

T or F. The R groups of the amino acids of an alpha helix protein are situated on the interior of the helix.

Answer 26

F. R groups are on the exterior.

Question 27

How many residues apart are the amino acids that form the bonds of an alpha helix protein?

Answer 27

4. Between the CO group of one and the NH group of another.

Question 28

In a coiled coil protein like keratin, are the two alpha helical polypeptide chains are held together by covalent or noncovalent interactions?

Answer 28

Noncovalent.

Question 29

T or F. The part of a transmembrane protein that traverses the membrane is usually alpha helical.

Answer 29

T.

Question 30

T or F. Protein beta sheets can be arranged in parallel, antiparallel, and sometimes both.

Answer 30

True.

Question 31

A minimum of _____ amino acids is required for a protein beta turn.

Answer 31

2.

Question 32

A beta turn allows a protein to ________ direction.

Answer 32

Reverse.

Question 33

Name 4 properties of Beta turns.

Answer 33

1. on surfaces of proteins 2. often sites of glycosylation 3. important sites of immunological recognition 4. somewhat predictable from the amino acid sequence.

Question 34

Charge pairs (electrostatic bonds) of tertiary structure are strong only in the _______ of water.

Answer 34

Absence. (eg lysine, glutamic acid)

Question 35

T or F. There is generally one energy minimum in regards to protein folding.

Answer 35

True.

Question 36

What are PI stack interactions?

Answer 36

Interactions between aromatic side chains, can contribute to stability.

Question 37

Is tertiary structure entirely dictated by primary structure?

Answer 37

An experiment applied beta mercaptoethanol (disulfide bridges) and urea (hydrogen bonds) to an enzyme. When BME/urea was removed, enzyme structure was restored. However, this does not work for all proteins, and protein folding is sometimes faulty.

Question 38

__________ proteins help protein folding but do not direct the process.

Answer 38

Chaperone

Question 39

What are two examples of protein misfolding disease?

Answer 39

1. Transmissible spongiform encephalopathies - Creuzfeldt jakob disease, mad cow, scrapie 2. Alzheimer's

Question 40

What are prions?

Answer 40

The prion precursor (a normal cell) changes structure, becoming a template for other normal precursors to become prions as well. Prions aggregate into amyloids, disrupting cellular function and causing disease.

Question 41

What is a protein domain?

Answer 41

A unit of a protein 3D structure that: 1. folds autonomously 2. is formed by secondary structural elements connected by loops 3. has its own hydrophobic core 4. has independent structural or functional properties

Question 42

What are protein motifs?

Answer 42

Functional/structural units within domains. (eg DFG motif that coordinates the magnesiums that bind to the phosphates of ATP)

Question 43

Are covalent protein crosslinks more common extracellular or intracellular?

Answer 43

Extracellular. The reducing environment inside the cell prevents SH bonds. Covalent bonds help with the harsher conditions outside the cell.

Question 44

Are the disulfide bonds in Bovine insulin is intrapeptide or interpeptide?

Answer 44

It's both. evil flashcard.

Question 45

3D structures of proteins and protein complexes are usually determined using what method?

Answer 45

X ray crystallography.

Question 46

Describe the general process for NMR.

Answer 46

Apply magnetic field to protein, aligning the spin states of the nuclei. Nuclei relax to original state, emit radiation which reveals structure.

Question 47

What is an advantage and disadvantage of using NMR for determining protein structure.

Answer 47

Advantages: can determine protein structure in solution, does not require crystals. Disadvantages: only good to about 100K MW

Question 48

T or F. Like tertiary structure, quaternary structure is primarily stabilized by weak interactions.

Answer 48

True.