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Biochemistry for Biosciences > Lecture 1-3 > Flashcards

Lecture 1-3 Flashcards

1
Q

What are two methods of looking on a nanometre scales at proteins ?

A
  1. X-ray crystallography
  2. Single particle cryyo-EM
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2
Q

Why is structure important ?

A
  1. Encodes function
  2. Medical purposes
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3
Q

What did Max von Laue discover ?

A

Cyrstals can difract an x-ray beam

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4
Q

What did W.L Bragg discover ?

A

Structure of NaCl

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5
Q

What did John Kendrew do ?

A

Solves the first protein structure called myoglobin

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6
Q

What amino acid is not chiral ?

A

Glycine

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7
Q

What is glycine ?

A

A zwitterion

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8
Q

What is a zwitterion ?

A

Has a positive and negative charge

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9
Q

How is the peptide bond formed ?

A

By the reaction of the alpha carboxyl group of one amino acid with the alpha amino group of another amino acid

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10
Q

What is a dihedral angle ?

A

Any angle which links four atoms

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11
Q

What is the secondary structure ?

A

The arrangement of the polypeptide backbone ignoring the confirmation of the individual sidechains

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12
Q

What is configuration ?

A

The position of the atoms which are non-rotatable

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13
Q

What is conformation ?

A

Relationship of four atoms or three bonds that are related by a rotatable single bond

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14
Q

What is the configuration of the peptide bond in a polypeptide?

A

Trans

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15
Q

What amino acid has the occasional cis configuration of the peptide bond ?

A

Proline

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16
Q

Whys is the tans bond preferred ?

A

To stop repulsion

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17
Q

What does the rotation of phi and psi angles allow ?

A

Polypeptides to adopt their various structures

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18
Q

What is steric hindrance ?

A

The idea that side chains can influence the type of secondary structure

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19
Q

What is a hydrogen bond ?

A

An attractive ineraction between the hydrogen atom of a fairly electronegative donor group and a pair of non-bonding electrons on an acceptor group.

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20
Q

What are hydrophobic interactions ?

A

In proteins, the association of two like hydrophobic atoms to minimes the water layer and maximise hydrogen bonding among water molecules . ENergetic gains are both enttropic and enthalpic

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21
Q

What is the driving force for globular or soluble proteins ?

A

Hydrophobic interactions

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22
Q

What is van der waals force ?

A

Attraction from close approach of two atoms/molecules due to induces dipole.

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23
Q

What is van der waals limited by ?

A

Spatial overlap of electron clouds when molecules approach too closely

24
Q

What is a electrostatic/salt bridge ?

A

Attractive force between a cation and an anion.

25
What is the energetic contribution to stability of proteins highly dependent on in a electrostatic/salt bridge ?
Environment and distance
26
What is a disulphide bond ?
Oxidation of two cyesteine residues to form a covalent "cystine" bond
27
Who predicted te existance of the alpha helix ?
Linus Pauling
28
What are p-loops ?
Have a particular sequence which must be conserved. Important for form and function
29
What is an amphipathic helix ?
Hydrophilic amino acids on one face of the helix cylinder and the hydrophobic amino acids on the other face
30
What is the helical wheel diagram based on ?
A five turn helix (18 residues )
31
How many degress are adjacent residues in the helical wheel diagram ?
100 degrees apart on the wheel and a residue occurs every 20 degrees
32
What is a polypeptide ?
A string of amino acids linked by peptide bonds
33
What is a secondary structure ?
A repeating array of backbone phi/psi angle
34
What is a motif ?
A short segment of a polypeptide containing one or several secondary structure elements. Usually refer to highly conserve amino acid sequences that perform a specific function
35
What is a domain ?
An independently folding polypeptise unit often encoded by a single exon
36
What is a protein ?
A polypeptide that folds into one or more distinct domains
37
What does a ramachandran plot describe ?
The allowed regions in the graph og phi and psi
38
What results in the regular structure in a ramacharan plot ?
Repeating values of phi and psi along the chain
39
How can you connect secondary structures ?
1. Loops 2.Turns
40
What are reverse turns ?
Connect two beta strands which are in anti-parallel
41
What are included in DNA binding motifs ?
1. Helix-turn helix 2. Zinc finger and loop 3. Leu zipper 4. B sheets and B hairpins
42
Where are zinc fingers found ?
In a variety of transcription factors
43
What are the two types of zinc fingers ?
1. Cys-His 2. Cys-Cys
44
What is the cys-his consensus sequence ?
Cys-X2-4, -Cys-X3-Phe-X5-Leu-X2-His-X3-His
45
What does a typical Cys-His gene have ?
Three or more fingers
46
Where is the Cys-His found ?
Factors for Pol II and Pol III
47
What is the Cys-Cys consensus sequence ?
Cys-X2-Cys-X13-Cys-X2-Cys
48
How many genes does a cys-cys finger have ?
Two
49
Where is a cys-cys found ?
Steroid hormone receptor superfamily members
50
What may be zinc finger genes be both involved in ?
DNA and RNA binding
51
What does TFIIIA bind ?
DNA and RNA product
52
What does eIF2B recognise ?
Translational initiation sites
53
What is the purpose of zinc fingers ?
To arrange residues such that zinc ions can be coordinated
54
What may zinc fingers form ?
Alpha helical structures that fit into the major groove of the DNA helix
55
What may multiple zinc fingers do ?
Act cooperatively to bind nucleic acids

Biochemistry for Biosciences (9 decks)

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