Lecture 4 - Protein Structure

Question 1

What is a Protein?

What determines the Structure of a Protein?

Answer 1

A protein is a sequence of amino acids joined by peptide bonds.
The amino acid sequence is encoded by the gene, which is determined by its nucleotide sequence
Proteins vary greatly in size from very small to massive
100’s of residues to 1000’s of residues

Question 2

What determines how a protein functions?

Answer 2

the complex and specific 3D structure of a protein (how it will fold), is determined by its amino acid sequence
This then determines its function

Question 3

what is the process to produce a protein?

Answer 3

DNA replicates itself in cell division
The process of transcription will produce RNA
RNA will be translated by ribosomes to produce proteins

Question 4

Give facts about amino acids and consequently proteins.

Draw these now if you can.

Answer 4

Amino acids contain a amino group (NH2) which is a basic proton acceptor and a Craboxyl group which is an acidic proton donor.
Humans have 20 key amino acids which all have unique R groups that determine protein structure and function and acid-base behavior.
They join to form proteins via a condensation reaction, forming peptide bonds. these bonds give what we call amino acid residues. W
Proteins have N terminus(NH3+) and a C terminus (COO-) ends.

Question 5

Define Pka

Answer 5

The point at which equal amounts of the molecule are protonated and deprotonated.

Question 6

How do the ph and pk of a molecule relate to it in solution?

Answer 6

if the solutions PH is LESS THAN the PK value, it will be protonated
of the solutions PH is GREATER THAN the PK it will be deprotonated

Question 7

What is the primary structure of a protein?

Give info.

Answer 7

the linear amino acid sequence of the polypeptide chain.
the peptide bond is planar, this is because there is delocalisation of electrons to act like a double bond and prevent rotation.
There is rotation around bonds either side of the peptide bond, which will go on to determine the higher order structures of the protein.
The peptide bond is in a trans arrangement as opposed to cis, as cis has lots of steric hindrance, making it unfavourable.

Covalent Bonding

Question 8

what does the amino acid sequence determine?

Answer 8

the way in which the polypeptide chain folds

the physical characteristics of that protein

Question 9

Define the Isoelectric point of a protein

Answer 9

The pH of a protein where there is no overall charge

Question 10

what is the pI of basic and acidic proteins roughly?

Answer 10

Basic proteins - have a pI greater than 7

Acidic proteins - have a pI less than 7

Question 11

How does PI relate to PH

Answer 11

if the PH is less than pI the protein is protonated

if PH is greater than pI the protein is deprotonated

Question 12

what is a conjugated protein?

Answer 12

a protein that includes covalently linked components

such a hemogoblin which has an iron group

Question 13

what determines the function of a protein?

Answer 13

sequence of amino acids determines structure

structure determines function

Question 14

Explain secondary structure

Answer 14

the spatial arrangement of the polypeptide
there are two conformations alpha helixes and B sheets
a helix is stabalised by h bonds between n-h and c=o 4 units appart. it is in a coil. only some sequences are stable as helices
B sheets are the extended confirmation of stacking B strands
they can arrange anti parallel or parallel (less stable)
both anti and parallel can exist in one mixed sheet
they are stabilised by H bonds between the strands.

Question 15

What is the tertiary structure of a protein?

Answer 15

The 3 dimensional arrangement of a protein
due to the folding in the secondary structure
it is possible for amino acids very far apart in the primary structure to interact in the tertiary structure

covalent and all other forms of bonding

Question 16

what is collage, give details.

Answer 16

its a fibrous protein
they provide support and strength
they arrange in long strands or sheets
and are a single type of repeating structure
it forms a triple helical arrangement, with h bonds between chains stabilising
chains crosslink to form fibrils, which cross link to form fibres

Question 17

explain what a globular protein is and what you know

what are motifs and domains?

Answer 17

they have key roles in catalysis and blood - haemoglobin
compact in shape,
many different secondary structures will exist in a protein
motif- folding pattern containing 1 or more secondary structure
domain part of a polypeptide chain that folds into a distinct shape. it has a specific functional role ie a binding domain

Question 18

How are water soluble proteins arranged?

Answer 18

they fold so the hydrophobic side chains are buried and polar chains are on the surface
a porin (trans-membrane channel) is the opposite of this

Question 19

what is the Quaternary structure, give an example,

Answer 19

different polypeptides associating to form a multi subunit protein
ie heamoglobin, which has 2 a and 2 B subunits

covalent and all other forms of bonding

Question 20

where are covalent disulphide bonds used?

Answer 20

disulphide bonds can happen in the tertiary structure between two cys residues.
it is a redox reaction, hence reducing agents break them

Question 21

What are the force involved in maintaining protein structure?

Answer 21

1) electrostatic interactions between charged groups
2) hydrogen bonds
3) the hydrophobic effect - water displacement
4) Van Der Walls forces

Question 22

what is protein denaturation?

Answer 22

a breaking of the proteins structure, caused by temp, Ph (breaks H bonds) and detergents

Question 23

How do proteins fold?

Answer 23

all the information that is needed for protein folding is contained in the primary sequence
the folding process is ordered, each step involves localised folding, and stable confirmations are held
driven by the need to form the most stable confirmation

Question 24

what is the consequence of protein misfolding?

Answer 24

it can cause disease
a protein can misfold to form an b sheet, this one misfolded protein can cause other proteins to follow suit, forming the amyloid fibers.
amyloid fibers and insouble, when the normal protein would have been soluble. they are highly ordered b sheets that stabilise each other

Question 25

what does the pKa tell you about the amino acid?

Answer 25

the smaller the pka value the more acidic the amino acid

Question 26

what is the PI of basic and acidic proteins?

Answer 26

basic proteins PI is GREATER THAN 7, so will contain mainly basic amino acids
acidic proteins PI is LESS THAN 7 so will contain mainly acidic amino acids