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Biochemistry - Victor > Steele Proteins 1 > Flashcards

Steele Proteins 1 Flashcards

0
Q

What is the transcriptome?

A

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

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1
Q

How many genes in your genome encode proteins?

A

22,333

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2
Q

What is the proteome?

A

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

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3
Q

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

A

Protein: 1-10 nm. Cell 1micron.

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4
Q

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

A

10^-3 seconds, 10^-6 seconds

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5
Q

What is primary structure?

A

amino acid sequence of the protein

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6
Q

What is secondary structure of proteins?

A

Substructures formed by hydrogen bonds between amino acids.

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7
Q

What is tertiary structure?

A

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

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8
Q

What is quaternary structure?

A

Structure formed by association of multiple subunit polypeptides.

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9
Q

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

A

True.

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10
Q

Which amino acids are at neutral pH?

A

Glycine, alanine

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11
Q

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

A

Valine, Leucine, Isoleucine, Methionine

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12
Q

Which amino acids contain aromatic side chains?

A

Phenylalanine, tyrosine, tryptophan.

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13
Q

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

A

Lysine, Arginine, Histidine

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14
Q

Which amino acid can form disulfide bridges?

A

Cysteine.

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15
Q

Which amino acids have polar side chains?

A

Asparagine, glutamine.

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16
Q

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

A

Serine, threonine.

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17
Q

Which amino acid has cyclic structure?

A

Proline.

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18
Q

Which amino acids have carboxylic acid in their side chain?

A

Aspartate, glutamate.

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19
Q

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

A

Amino, Carboxyl

20
Q

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

A

Resonance.

21
Q

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

A

True.

22
Q

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

A

True. Very rarely is it left handed helix.

23
Q

Amino acids of relatively short length are called _____.

A

Peptides.

24
Q

What are 3 examples of protein secondary structure?

A

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

25
Q

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

A

False. Dependent on H bonds of the peptide backbones.

26
Q

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

A

F. R groups are on the exterior.

27
Q

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

A
  1. Between the CO group of one and the NH group of another.
28
Q

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

A

Noncovalent.

29
Q

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

A

T.

30
Q

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

A

True.

31
Q

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

A

2.

32
Q

A beta turn allows a protein to ________ direction.

A

Reverse.

33
Q

Name 4 properties of Beta turns.

A
  1. on surfaces of proteins
  2. often sites of glycosylation
  3. important sites of immunological recognition
  4. somewhat predictable from the amino acid sequence.
34
Q

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

A

Absence. (eg lysine, glutamic acid)

35
Q

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

A

True.

36
Q

What are PI stack interactions?

A

Interactions between aromatic side chains, can contribute to stability.

37
Q

Is tertiary structure entirely dictated by primary structure?

A

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.

38
Q

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

A

Chaperone

39
Q

What are two examples of protein misfolding disease?

A
  1. Transmissible spongiform encephalopathies
    - Creuzfeldt jakob disease, mad cow, scrapie
  2. Alzheimer’s
40
Q

What are prions?

A

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.

41
Q

What is a protein domain?

A

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
42
Q

What are protein motifs?

A

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

43
Q

Are covalent protein crosslinks more common extracellular or intracellular?

A

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

44
Q

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

A

It’s both. evil flashcard.

45
Q

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

A

X ray crystallography.

46
Q

Describe the general process for NMR.

A

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

47
Q

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

A

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

48
Q

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

A

True.

Biochemistry - Victor (17 decks)

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