PH1123 - question time

Question 1

what is a peptide ?

Answer 1

A small protein containing 50 or less amino acid residues

Question 2

Briefly describe the nomenclature of peptides.

Answer 2

Peptides should be named, using three letter or single letter amino acid abbreviations starting
from the N-terminal residue and listing sequentially to the C-terminal. Abbreviations separated by
dashes.

Question 3

Describe the process of protection - activation - coupling - deprotection for the synthesis of peptides.

Answer 3

Therefore the sequence required is to:
protect the amino group in the N-terminal amino acid and the carboxyl group in the C-terminal amino acid
couple the two amino acids by forming the new amide bond
deprotect the termini of the new peptide (as and if required)
By repeating the process, polypeptides can be grown one amino acid residue at a time, or by building pieces and then joining those together.

Question 4

Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp

a) Name the N-terminal amino acid.
b) Name the C-terminal amino acid.
c) State the side chain property of each amino acid in the peptide.

Answer 4

. a. Lysine

b. Aspartic acid
c. Lys – basic; Ala, Val, Leu and Ile – hydrophobic; Ser – polar; Asp –Acidic.

Question 5

Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp

How you would expect this peptide to fold in an aqueous solution?

Answer 5

Briefly, in an aqueous environment, hydrophobic residues e.g. Ala, Val etc
would be folded away from water into the interior of the protein.
Hydrophilic residues, e.g. Ser, would face the solvent. Charged side chains
would form an interaction where possible, e.g. as shown.

Question 6

Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp

Would you predict this peptide to be water soluble? Briefly explain your answer.

Answer 6

No correct answer, marks awarded for a sensible answer.
E.g, Will have some water solubility,
although mostly non-polar amino acids there are three polar aa’s, two of which form a salt. OR –
will not be soluble in water as 7 non-polar aa’s versus 3 polar.

Question 7

Describe the structure of a globular protein.

Answer 7

. Compact (tightly folded), roughly spherical, structurally complex, comprised of many elements
of secondary structure, e.g. alpha helix, beta sheet, often clearly defined active site / cleft, internal
bonding to maintain structure, e.g. disulfide bridges etc etc.

Question 8

Give an example of a globular protein.

Answer 8

Any enzyme, 100’s of examples, e.g. trypsin etc etc

Question 9

Describe the general properties of a globular protein.

Answer 9

Hydrophobic interior, hydrophilic exterior, water soluble, often function as catalysts etc etc.

Question 10

Describe how the three dimensional structure of a globular protein is maintained.

Answer 10

Discuss, give examples and expand upon – ionic interactions, hydrogen bonding, hydrophobic
interactions, covalent crosslinks etc etc.

Question 11

is the alpha helix a double helix ?

Answer 11

The alpha helix is a single peptide backbone coiled around itself and stabilised by
intra-strand H-bonds. [By contrast, DNA is an example of a double helix – two chains stabilised by
inter-strand H-bonds]

Question 12

The peptide bond usually adopts a trans conformation(true or false)

Answer 12

c. TRUE. Cis-amide bonds force unfavourable steric interactions between aa side chains and are not
commonly found in proteins

Question 13

Which are more stable ? beta sheets or anti parallel beta sheets ?

Answer 13

Anti-parallel beta sheets are more stable – the network of inter-strand H-bonds are better
aligned and more stable in the anti-parallel type.

Question 14

define Native conformation

Answer 14

Proteins do not exist as a linear conformation of amino acids (the primary sequence) they fold
very specifically into a specific conformation called the native conformations. This is generally the
biologically active form of the protein

Question 15

Describe the alpha helix of a protein

Answer 15

. Alpha helix important form of secondary protein structure. Single polypeptide strand coiled in a
tight helix excluding water from the centre. + + Describe properties and H-bonding network etc.
Some proteins composed exclusively of a-helix, usually as coils of coils, e.g. keratin, collagen. Also
common in membrane spanning receptors

Question 16

what is a non essential amino acid ?

Answer 16

An amino acid that can be biosynthesized with the body and therefore is not essential in the diet.
E.g. Ala, Gly, Pro, Ser etc. It requires energy and raw materials to synthesize aa’s so in practice
these are obtained from diet whenever possible

Question 17

explain a cyclic peptide

Answer 17

A polypeptide joined via an amide (peptide) bond between the N and C terminal amino acids
creating a continuous cyclic peptide backbone. Have pharmaceutical use. E.g. ciclosporin, a
microbial cyclic peptide that contains non-coding biosynthesized amino acids. When non-amino
acid groups are incorporated known as a pseudo-peptide.

Question 18

Very briefly describe how enzymes function as catalysts

Answer 18

by lowering the activation energy barrier to the reaction. Achieved by precise orientation of the
substrate in the active site in a reactive conformation and provide missing functional groups or
cofactors for the reaction. Enzymes provide the reaction ‘template’.

Question 19

. Briefly describe how enzymes are named and classified. Illustrate your answer with suitable examples.

Answer 19

Two methods, trivial and systematic. Trivial – name associated with the function or substrate (or
both) is suffixed with –ase. E.g. L-dopa decarboxylase or DNA polymerase. Systematic system
(enzyme commission: EC) assigns a unique serial number comprised of 4 digits. First digit is one of
the six classes (list them) followed by two sets of sub classes and finally the unique identifier, e.g.
alcohol dehydrogenase = EC1.1.1.1.

Question 20

Many enzymes require cofactors for their biological function. Discuss this statement using alcohol dehydrogenase
and another enzyme of your choice to illustrate your answer.

Answer 20

The 20 amino acids that occur naturally in proteins have limited functional groups / chemistry in
their side chains. Co-factors, which can be metal ions or organic molecules (co-enzymes) supply
this chemistry. Alcohol dehydrogenase uses two co-factors, a zinc ion and a NAD+
coenzyme. The
zinc aligns the substrate in the active site to the –OH group. The NAD+
contains a functional group
that accepts a proton (i.e. dehydrogenation). Could also include a sketch? Another example could
be L-Dopa decarboxylase. The enzyme uses a co-enzyme (pyridoxal phosphate/vitB6) to facilitate
the removal of a carboxylic acid. The co-enzyme contains an aldehyde functional group – not found
in amino acids – to form an intermediate (imine) with the substrate etc etc

Question 21

. Briefly discuss the importance of metals in protein function. Give one example of a protein that requires a metal
atom to function.

Answer 21

Proteins containing metal ions are known as metalloproteins or metalloenzymes if they have a
catalytic function. The 20 amino acids that occur naturally in proteins have limited functional
groups / chemistry in their side chains. Co-factors, which can be metal ions or organic molecules
(co-enzymes) supply this chemistry. Metals are important in transport proteins (e.g. haemoglobin,
Fe required to bind, store then release O2, four Fe atoms held in 4 prosthetic haem groups etc etc).
Alcohol dehydrogenase and Zn etc etc.

Question 22

what do the intermediate filaments do in the cytoskeleton?

Answer 22

Provide structural support to the cell helping to resist mechanical stress

Question 23

What do the microfilaments in the cytoskeleton do ?

Answer 23

They’re involved in the movement of the entire cell from within
for example: during cell division

Question 24

What is the definition of the cytoskeleton ?

Answer 24

A network of fibrillar proteins organised into filaments and tubules which aids in cell motility and structure

Question 25

What do microtubules produce ?

Answer 25

Cilia, flagella and centrioles

Question 26

Describe dna replication

Answer 26

DNA helicase breaks the hydrogen bonds unwinding the double strand

RNA primer binds to the end of the leading strand
RNA primers are added to the lagging strand in chunks

DNA polymerase functions in the 5’ - 3’ direction generating complementary nucleotide bases

In the lagging strand Okazaki fragments are added between the primers

Exonuclease removes all RNA primers which are then replaced by complementary nucleotides

DNA ligase then joins all of the Okazaki fragments together

Question 27

describe the structure of beta sheets

Answer 27

A  sheet is a secondary protein structure in which several strands (called  strands) of the peptide backbone are hydrogen bonded to themselves.

Inter-strand hydrogen bonds between backbone carbonyl oxygen and amide nitrogens stabilize the  sheet.
In the  sheet, side chain interactions (mostly hydrophobic interactions between small groups) can provide additional stabilization.