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Molecular Biology of the Gene > Iain McEwan > Flashcards

Iain McEwan Flashcards

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1
Q

Amino acids can be L or D isomers. In protein, all amino acids are which kind of isomer?

A

L isomers

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2
Q

The alpha carbon can be described as what?

A

tetrahedral

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3
Q

What are the different kinds of amino acid?

A
  • Acidic
  • Basic
  • Hydrophobic
  • Hydrophillic
  • Aromatic
  • Those with unique features
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4
Q

Briefly describe acidic amino acids.

A
  • e.g. ASPARTIC ACID and GLUTAMIC ACID
  • They are acidic as they have an extra carboxyl group
  • Negatively charged
  • Depending on their microenvironment, they can be in protonated or non-pronated form
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5
Q

Briefly describe basic amino acids

A
  • Basic because they have an extra amine group
  • High positive charges make these amino acids highly hydrophillic with lots of hydrogen-bonding sites
  • Positively charged
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6
Q

Briefly describe uncharged polar amino acids

A
  • Uncharged because the carboxyl and amino groups cancel each other out
  • Polar because the side chain is polar
  • Usually hydrophillic
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7
Q

Briefly describe uncharged non-polar amino acids

A
  • Non-polar because the R group has no polarity
  • GLYCINE is the simplest amino acid
  • ALANINE is the 2nd simplest
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8
Q

Briefly describe aromatic amino acids

A
  • Non-polar
  • HYDROPHOBIC interactions
  • Account for characteristic absorbance of proteins at 280nm
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9
Q

Name 3 amino acids with special functions.

What are their special functions?

A

Methionine; initiates chains of amino acids

Proline; causes kinks in amino acid chains

Cysteinel links amino acid chains together

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10
Q

Why don’t we use water alone as a solution in experiments?

A
  • Salts are needed to keep biological material in solution and native - Acid may be produced or consumed during reactions; water will not prevent bit changed in pH.
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11
Q

Briefly describe buffering

A

the anion picks up H+ to yield undissociated acid

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12
Q

Why is acetate (acetic acid) a buffer?

A

It can dissociate reversibly: CH3COOH CH3COO-H+

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13
Q

The pKa is defines…

A

the pH range over which that particular weak acid buffers (the weak acid is at an equilibrium)

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14
Q

What is the calculation of buffer components?

A

pH = pKa + log [A-]/[HA]

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15
Q

What is a tripeptide

A

the character if the R group dictates the proteins character

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16
Q

What is a dipeptide?

A

2-residue protein

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17
Q

Briefly describe primary protein structure

A

the planar peptide bond connects amino acid residues, each with a tetrahedral alpha-carbon

18
Q

What are the three types of secondary structure

A

alpha-helix; beta-sheet; beta-turn

19
Q

What element is the hydrogen acceptor usually?

A

oxygen or nitrogen

20
Q

Quaternary structure occurs in some ______ proteins.

A

multimeric

21
Q

Which structure level dictates the final structure?

A

primary

22
Q

What are the two broad classes of protein?

A

Globular & Fibrous

23
Q

Give examples of globular proteins

A
  • insulin; myoglobin; haemoglobin; immunoglobins & Gene regulatory proteins
24
Q

What is the function of myoglobin?

A

to bind oxygen (in muscle) used for mitochondrial oxidation

25
Q

How many alpha-helices does myoglobin have?

A

8

26
Q

What is the name of the organic ring structure within the haem group?

A

protoporphyrin

27
Q

Allosteric proteins have a what?

A

an additional binding site

28
Q

Inhibitors shift the binding curve in which direction?

A

to the right

29
Q

Briefly describe haemoglobins allosteric transition

A

Rapid and reversible transition between taut and relaxed states. T state is stabilised by inhibitors & R state is stabilised by oxygen

30
Q

Which immunoglobin is abundant in plasma?

A

IgG

31
Q

R groups point in which direction?

A

outwards

32
Q

What are the common features in DNA-binding proteins?

A
  • Helix-turn-helix motif & Zinc finger motif
33
Q

What is a motif?

A

a simple combination of a few secondary structure elements

34
Q

Give an example of a Helix-turn-helix motif

A

the lac-repressor of E.coli

35
Q

Briefly describe the structure of the leucine zipper

A

an alpha-helix with a series of hydrophonic amino acids concentrated on one side (amphipathic)

36
Q

Where do fibrous proteins get their structural strength

A
  • unusual amino acid composition; - post-translational modifications; - three-dimensional structures
37
Q

Give examples of fibrous proteins

A
  • alpha-keratin; - collagen; - elastin
38
Q

In alpha-keratin, what is the term used for a pair of helices interwound?

A

protofibril

39
Q

3 protofibrils together make a what?

A

microfibril

40
Q

Several microfibrils together make a what?

A

macrofibril

41
Q

3 collagen helices make a righthanded super-helix called what?

A

tropocollagen

42
Q

What is the hydropathy index?

A

energy required to shift amino acid from a hydrophobic solvent to water

Molecular Biology of the Gene (3 decks)

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