Lecture 4 - Protein Structure Flashcards Preview

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Flashcards in Lecture 4 - Protein Structure Deck (26)
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1
Q

What is a Protein?

What determines the Structure of a Protein?

A

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

2
Q

What determines how a protein functions?

A

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

3
Q

what is the process to produce a protein?

A

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

4
Q

Give facts about amino acids and consequently proteins.

Draw these now if you can.

A

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.

5
Q

Define Pka

A

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

6
Q

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

A

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

7
Q

What is the primary structure of a protein?

Give info.

A

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

8
Q

what does the amino acid sequence determine?

A

the way in which the polypeptide chain folds

the physical characteristics of that protein

9
Q

Define the Isoelectric point of a protein

A

The pH of a protein where there is no overall charge

10
Q

what is the pI of basic and acidic proteins roughly?

A

Basic proteins - have a pI greater than 7

Acidic proteins - have a pI less than 7

11
Q

How does PI relate to PH

A

if the PH is less than pI the protein is protonated

if PH is greater than pI the protein is deprotonated

12
Q

what is a conjugated protein?

A

a protein that includes covalently linked components

such a hemogoblin which has an iron group

13
Q

what determines the function of a protein?

A

sequence of amino acids determines structure

structure determines function

14
Q

Explain secondary structure

A

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.

15
Q

What is the tertiary structure of a protein?

A

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

16
Q

what is collage, give details.

A

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

17
Q

explain what a globular protein is and what you know

what are motifs and domains?

A

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

18
Q

How are water soluble proteins arranged?

A
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
19
Q

what is the Quaternary structure, give an example,

A

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

20
Q

where are covalent disulphide bonds used?

A

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

21
Q

What are the force involved in maintaining protein structure?

A

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

22
Q

what is protein denaturation?

A

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

23
Q

How do proteins fold?

A

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

24
Q

what is the consequence of protein misfolding?

A

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

25
Q

what does the pKa tell you about the amino acid?

A

the smaller the pka value the more acidic the amino acid

26
Q

what is the PI of basic and acidic proteins?

A

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