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Flashcards in Lecture 1 Deck (60)
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1

What can be used to mostly infer primary structure

The DNA sequence

2

What are the two ways of predicting the secondary structure of a protein

Can be determined from the primary structure de novo or by alignment with other proteins of known structures using a website database

3

? helices are formed by hydrogen bonding within the polypeptide chain, known as intra-chain hydrogen bonding, T or F

T

4

What can be said about the direction of hydrogen bonds in ? helices

They are vertical hydrogen bonds

5

What is the major disadvantage of X-ray crystallography

Extremely expensive (£200,000 in the lab, >£300m for professional synchrotron sources)

6

What is meant when referring to ? helices as heptad structures

7 amino acids for every two turns of the helix

7

The more ordered and symmetrical the protein specimen is that is used in cryo-EM, the easier the averaging process, T or F

T

8

Describe the structure of a ? sheet

Beta strands are connected laterally by backbone hydrogen bonds

9

What is the main function of circular dichroism

Used to induce secondary structure in proteins

10

In what plane do the hydrogen bonds between ? sheet polypeptide chains occur

Horizontal hydrogen bonds

11

Which amino acid residues form hydrogen bonds with water molecules and are exposed on the outside of the proteins

Hydrophilic polar side chains

12

Which types of amino acids residues are found in the middle of the ? strands/sheets and give examples

Aromatic residues such as tyrosine, phenylalanine, tryptophan, valine and isoleucine

13

How can CD be used to infer the stability of a protein upon heating

Less stable proteins will lose its characteristic CD spectrum upon heating

14

Describe the structure of a triple-coiled-coil protein

Another stable structure formed by ? helices. This is where 3 amphipathic helices twist around a central axis with the hydrophobic side chains of all three exposed in the centre of the structure. This creates a stable hydrophobic core

15

What are the 4 different ways of representing protein structure

Sticks, space-filling, ribbon and backbone

16

CD gives a relative % or fraction of each of the secondary structure types in any protein by its unique spectrum, T or F

T

17

What two types or arrangements of ? strands in ? sheets can be observed

Parallel and antiparallel

18

Protein databases provide a wealth of information and predictions based on sequence alignment, domain composition, post-translational modification, protein-protein interactions and structures, T or F

T

19

The position of an amino acid in the primary sequence enables you to predict the secondary structure of a protein, T or F

T

20

Duplication and multimersiation occurs often in proteins, T or F

T

21

Give some examples of diseases associated with protein misfolding

Huntington’s, cystic fibrosis (CFTR), cancer (p53) and Alzheimer’s

22

At which terminus does protein synthesis start at

Amino-terminus

23

What are the different domains of the src-tyrosine kinase

Large kinase domain, small kinase domain, SH2 and SH3

24

What is the main advantage of NMR

The process is very dynamic and can be used to determine protein structure in solution

25

How can CD be used to look at changes in protein structure

CD can be used to investigate the effects on protein structure due to changes in pH and temperature. For example, increasing pH increases helix formation whilst decreasing ? sheet formation. In addition, it can be used to visualise protein unfolding due to increasing temperatures.

26

Two which terminus of the ? sheet do the arrows seen in ribbon diagrams point to

Carboxyl (C) – terminus

27

Describe how Edman degradation can be used to obtain the primary protein structure

Using phenyl isothiocyanate (PCT) to bind to and break away the terminal amino acid in a step by step process you can determine the unique sequence by high performance liquid chromatography (HPLC). This is done based on the molecular weight of each residue

28

Define the tertiary structure of a protein

The way in which individual secondary structural elements pack together within a protein and between sub-domains of proteins

29

What is the name of the enzyme responsible for catalysing the conversion of sugar(s) into ethanol and carbon dioxide often used in wine making

Zymase

30

Describe an ? helical structure

Spiral conformation in which every backbone amino group donates a hydrogen bond to the backbone carboxyl group of the amino acid located 3-4 residues earlier in the protein sequence