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BIOC192 2024 > Lecture 5 > Flashcards

Lecture 5 Flashcards

1
Q

What is an amino acid residue?

A

When 2 or more amino acids are joined to form peptides, the elements of water are removed and what remains is referred to as the amino acid residue

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2
Q

What end are the amino acid residues in a polypeptide chain numbered from?

A

amino terminus

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3
Q

What are the properties of proteins?

A

Globular, 3-dimensional (except primary) , comprised of primarily alpha-helix, beta-structures and turns

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4
Q

What are the levels of protein structure?

A

Primary, Secondary, Tertiary, Quaternary

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5
Q

What is a primary protein?

A

An amino acid sequence of a protein

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6
Q

What is a secondary protein?

A

A local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues

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7
Q

What is a tertiary protein?

A

The 3D structure of a complete protein chain

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8
Q

What is a quaternary protein?

A

An interchain packing and structure for a protein that contains multiple protein chains

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9
Q

Around what size is a quaternary protein?

A

~60Å (50-100)

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10
Q

What type of bonds are between the main chain and side chain elements?

A

Flexible covalent bonds

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11
Q

What are the three main chain atoms?

A

N, alpha C and C

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12
Q

What is phi?

A

N - C(alpha) bond angle

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13
Q

What is psi?

A

C(alpha) - C bond angle

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14
Q

What do the angles of phi and psi range from?

A

0 to +/- 180 degrees

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15
Q

What is omega?

A

C - N bond angle (Peptide bond)

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16
Q

Phi

A

Φ

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17
Q

Psi

A

Ψ

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18
Q

Omega

A

ω

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19
Q

What angle is omega

A

Either 0 or 180 degrees

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20
Q

What is the alpha carbon

A

The carbon adjacent to a ketone or aldehyde

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21
Q

When is a polypeptide angle of rotation 180 degrees?

A

When it is planar

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22
Q

What is the phi-psi limitation?

A

The Vander Waal radii surrounding them causes steric hinderance

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23
Q

What does Phi rotation cause

A

O-O collision

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24
Q

Whats does Psi rotation cause?

A

NH - NH collision

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25
Q

Why is the interference pattern different for glycine?

A

Because the side chain of glycine is an independent hydrogen, therefore there is less steric hinderance

26
Q

What is the peptide bond character?

A

40% double bond character, leading to the planar shape

27
Q

What is the peptide bond shape?

A

Planar

28
Q

Why is the peptide bond planar?

A

To maximize pi bonding overlap, a sp2 system

29
Q

What is the rotational barrier (kJ/mol) of the peptide bond

A

~80kJ / mol

30
Q

What is the dipole in the peptide bond?

A

Partial negative charge on the O of the Carbon and partial positive charge on the Nitrogen

31
Q

What is the predominant isomer of the peptide bond?

A

Trans

32
Q

When the peptide bond is trans, what is the omega angle?

A

~180 degrees

33
Q

When the peptide bond is cis, what is the omega angle?

A

0 degrees

34
Q

When is the peptide bond cis?

A

In ~10% of bonds that precede proline

35
Q

What are the overall properties of the peptide bond?

A

Planar, trans and a dipole

36
Q

What are the two types of protein secondary structure?

A

alpha-helix and beta-strands

37
Q

What is the spiral direction of the alpha-helix?

A

Right handed

38
Q

Describe the hydrogen bonds in the alpha helix

A

Lie between the amide H (+) and the carboxyl O (-) of side chains and at a distance of ~2.0Å

39
Q

What is the energy of the hydrogen bonds in the alpha helix? And why?

A

3-7 kcal/mol or 12-28kJ/mol
For stabilisation of alpha helix structure

40
Q

Describe the turn / residue nature of the alpha helix

A

3.6 residues per turn; 5.4Å rise per turn at a distance of 1.5Å per residue

41
Q

Describe the dipole of the alpha helix

A

Positive N-terminus and negative C-terminus creating a force pointing towards the N

42
Q

What is the separation degree between amino acid side chains in the alpha helix?

A

100 degrees

43
Q

Describe a beta-strand

A

Two parallel or antiparallel adjacent beta strands

44
Q

What is the difference between a beta strand and sheet?

A

A beta-sheet is composed of many (2-10) strands

45
Q

What is the average number of amino acids per beta-strand?

A

~6 amino acids

46
Q

What is a parallel beta strand and what is the nature of the hydrogen bonds?

A

Where the strands run in the same direction and the h-bonds are v-shaped

47
Q

What is an antiparallel beta strand and what is the nature of the hydrogen bonds?

A

Where the two strands run in opposite directions and the H-bonds are linear

48
Q

What is the direction of the twist in the beta sheet?

A

Right-handed and pleated

49
Q

What is a turn?

A

A short, hairpin like structure of Phi-Psi bonds

50
Q

How many residues are there per turn?

A

~3 or 4

51
Q

What type of amino acid is in the turns?

A

Highly Gly and Pro content

52
Q

Why are turns needed?

A

To form globular proteins

53
Q

How much of the protein residue is in turns

A

Around 30%

54
Q

What are the two kinds of turn?

A

Type one and type two

55
Q

What is a type one turn?

A

Side chain is pointing upwards around the turn

56
Q

What is a type two turn?

A

Side chain is pointing down and into the turn

57
Q

Why are protein structures challenging to display?

A

There are lots of atoms with detailed internal cavities and complicated shapes

58
Q

How are alpha-helices displayed?

A

As spirals or cylinders

59
Q

How are beta-strands displayed?

A

As arrows, pointing from N to C

60
Q

What are the advantages of the shorthand protein structure?

A

Can easily visualise the main chain path, identify elements of the secondary structure, appreciation of proteins as 3D objects, allows comparison

BIOC192 2024 (25 decks)

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