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My Packs: (UWO) (BIOCHEM 2280) > (Dr. Choy) (Unit A) Topic Note 3 > Flashcards

(Dr. Choy) (Unit A) Topic Note 3 Flashcards

1
Q

What are amino acids connected to each other by?

A

Peptide bonds

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2
Q

Where is a peptide bond formed?

A

Between:
1. a-amino group of one amino acid
2. a-carboxyl group of another amino acid

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3
Q

What type of reaction forms a peptide bond?

A

Condensation reaction

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4
Q

How are peptides written conventionally?

A

Starting from the N-Terminus

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5
Q

What is the “backbone”?

A

NCC-NCC-NCC-NCC…

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6
Q

Is a peptide bond a single bond?

A

Peptide bonds actually have some characteristics of double bonds
* Due to resonance
* Makes bonds unrotateable

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7
Q

Primary Structure

A

The sequence of residues making up the protein

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8
Q

What bonds do primary structures involve?

A

Covalent bonds

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9
Q

What is the average molecular weight of a residue?

A

110 Daltons

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10
Q

Secondary Structure

A

Local folding pattern of the polypeptide backbone

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11
Q

What forces are present in secondary structure?

A

Hydrogen Bonds

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12
Q

What are the most common secondary structures?

A

a-Helices
b-Sheets

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13
Q

In an a-helix, how are the hydrogen bonds formed?

A

Each carbonyl is linked to a N-H located 4 residues further on in the sequence within the same chain

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14
Q

What are the dimensions of an alpha helix?

A
  • 3.6 residues per turn
  • 0.54 nm per turn
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15
Q

Where do side chains go in a alpha helix?

A

Project outward

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16
Q

What determines whether a sequence will fold into a specific secondary structure?

A
  1. Steric hindrance between nearby large side chains
  2. Charge repulsion between nearby similarly-charged side chains
  3. Presence of proline and glycine
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17
Q

Why will proline and glycine prevent alpha helix and beta sheet formation?

A
  • Proline: Forms ring, creates no H-bond, cannot fit into alpha helix
  • Glycine: Small, imparts flexibility and disrupt structures
18
Q

Tertiary structure

A

How regions of secondary structure fold together to form 3D arrangement of single polypeptide chain

19
Q

Tertiary structures result from interactions between what?

A
  • Side chains
  • Between side chains and polypeptide backbone (often distant)
20
Q

What forces are present in tertiary structure?

A

All 4 “weak forces”

21
Q

Do polypeptide chains contain both hydrophobic and hydrophilic residues?

A

Yes

22
Q

When are proteins most stable?

A

When hydrophobic parts are buried in the core

23
Q

What forces can contribute to tertiary structure?

A
  1. Hydrophobic effect
  2. Ionic bonds between side chains
  3. Hydrogen bonds
  4. van der Waals forces
  5. Disulfide bonds
24
Q

Where do disulfide bonds form?

A

Between cysteine residues

25
Q

What proteins have disulfide bonds? Why?

A

Only important in non-cytoplasmic proteins
* Enzymes are present in cytoplasm to remove disulfide bonds

26
Q

What is a domain of a protein?

A

An independently folded part of a protein that folds into a stable structure

27
Q

How many domains can proteins have?

A
  • One single
  • Multiple
28
Q

What kind of unit are domains?

A

Structural units and/or Functional units

29
Q

Quaternary structure

A

The number and arrangement of the individual polypeptide chains

30
Q

In a quaternary structure, what is each polypeptide known as?

A

Subunit of the protein

31
Q

What is native state?

A

A folded, biologically-active protein, generally though to be the conformation with least free energy

32
Q

How can proteins be unfolded?

A

Treatments with solvents that disrupt weak bonds

33
Q

How does high concentrations of urea or guanidine cause unfolding?

A

Disrupt hydrophobic effects and interfere with hydrogen bonding

34
Q

Besides solvents, what else can cause protein denaturing?

A

Extreme pH and Heat

35
Q

Renaturation

A

Proteins refolding and regaining activity

36
Q

Is renaturing easy for proteins? What can help?

A

No, renaturing is hard for some proteins
“Molecular chaperones” assist in protein folding

37
Q

How are chaperones thought to work?

A

Masking the exposed hydrohpobic regions to prevent aggregation during the multi-step folding process

38
Q

Lipoproteins

A

Proteins that combine tightly with lipids

39
Q

Metalloproteins

A

Proteins that combine tightly with metal ions

40
Q

Glycoproteins

A

Proteins are modified by the attachment of carbohydrates

41
Q

Why is obtaining a pure protein challenging?

A

There are thousands of proteins inside a cell as well as nucleic acids, lipids, and carbohydrates

My Packs: (UWO) (BIOCHEM 2280) (23 decks)

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