Proteins Flashcards
What is the shape and structure of proteins determined by
The amino acid sequence
What is a repeating sequence of atoms called
A polypeptide chain
In a polypeptide chain what give the amino acid its unique properties
The side chains
What chemical properties are given by side chains
Negative
Positive
Uncharged polar
Nonpolar
What controls the folding of polypeptide chains
Weak iteractions Such as - Hydrogen bonds - requires hydrogen - Ionic bonds - requires charge - Van der Waals Forces - requires hydrophobicity
Molecular chaperones help proteins to fold
How many different amino acids are there
20
There are 20 different r groups
When proteins are denatured, what happens to their shape once the denaturing element is removed
They do not return to their original shape
Urea is an example of a solvent used to denature/ unfold proteins–> Creates a flexible polypeptide chain with no shape
Removal can cause spontaneous protein refolding or renaturation –> This tends to be in small proteins
What impact does folding have on the amino acid
This is a very particular process. Folded one by one to produce the amino acid.
This is less of a problem with very simple very small proteins
Are the two ends of a polypeptide chain same
No they are different there is an amino terminus NH2/NH3+ and a carboxyl terminus COOH / COO-
Conventionally N to C terminus direction
What are some examples of things that influence the way proteins fold
Proteins tend to fold with non polar (hydrophobic) chains buried inside to avoid contact with water.
Proteins fold with polar hydrophillic chains on the outside –> these form hydrogen bonds with water
Polar groups tend to hydrogen bond with other polar groups
Fold into a conformation of lowest energy
- Free energy is minimised
Small proteins are often
Soluble Diffusible In the blood stream Most proteins in the body are small Tend to be globular
Large proteins are often
Structural
e.g. actin and myosin
Tend to be fibrous
What do hydrogen bonds do for the protein
Stabilise the molecule in 3D
The primary structure is
The sequence of the polypeptide chain
Understanding what the amino acids are
This influences the secondary structure
Secondary
either alpha helix
- H bond every 4th amino acid
-Abundant in membrane proteins (e.g. Receptors)
- If 2 of these have non polar side chains on one side they form a coiled coil.
- Found in rod like elongated proteins
or
Beta sheet
- Parallel and antiparallel–> dependent on the directions of the proteins
Tertiary
3D Conformation
- Often fibres
Quaternary structure
Complete structure if more than 1 polypeptide chain
- Might have non proteinous structures that sit within the protein itself
What is a protein domain
Any part of a protein that can fold independently into a compact stable structure
Domains are 50-350 amino acids
These are the modular units from which larger proteins are constructed
Different domains have different functions
Proteins are so precisely built that a single amino acid change –> catastrophic loss of function
Proteins have binding sites which are
Complemetory
-they fit together depending on structure– the binding sites will decide what attaches and how many
A chain or helix can be formed if the binding site on a protein is complementary to another region on the same molecule
Disulphide bond
The only covalent bond you would see in a protein
Can’t denature these
Only happen if you have a certain amino acid in the sequence (quite rare)– Cystine
Usually present in larger proteins
These only ever form between oxidation and reduction
Cystine amino acid SH2SH
Cystine’s have sulphur and you need this present for the disulphide bridge
These happen after the protein has been built
These stabilise extracellular proteins by covalent cross links
Can tie two amino acids in the same proteins of link subunits in a multi subunit protein
Very stable
Wherever you have a cystene it is almost certain you’ll have a disulphide bridge.
Protein function: How
Proteins function by binding to other molecules
This interaction is always very specific
Ions, small molecules and macro molecules can bind
This binding involves non covalent bonds and a binding site.
Binding site
Usually cavities formed by certain amino acid arrangements
Binding sites of antibodies of antibodies are extremely versatile –> meaning they can bind to almost any other molecule
Enzymes
Are themselves proteins
Powerful and highly specific catalysts
All end in -se
Enzyme substrate complex involves multiple non-covalent bonds
Lysozyme
- Is a model enzyme
- Hydrolyses bacterial polysaccharide
- Easy to work on experimentally
- Cheap, easy and quick to purify
- Stable to work on
- Stresses substrate by bending critical bonds that participate in reaction
There are two key amino acids in the active site of the lysozyme that matter.
- Aspartic acid 52 - Stabalises positively charged transition state
- Glutamic acid 35 - accurately positioned high concentration of acidifying H+ ions
Active sites can
Bring two substrates together
Can rearrange electrons
Physically force a transition state
Kinetic rates of enzymes
- Vary considerably
- Can be measured using purified enzymes, substrates and defined conditions
- Some enzymes have more of an affinity to a substrate–> means ‘tighter’ bonds
- Concentration of enzyme - There reaches a plateau where an increase in concentration will not help as all the active sites are occupied.
How is enzyme catalytic activity regulated
- Negative inhibition
- Positive inhibition
- The product at an end point acts as an inhibitor for an enzyme further up
Allosteric inhibitors
These are enzymes that have 2 binding sites that interact
- Active Site - substrate attaches
- Regulatory site - ‘switches’ it on and off
Binding of a regulatory molecule causes a conformational change in the enzyme –> This alters the enzymes activity
Conformational change
- can alter enzyme activity
- can be driven by protein phosphorylation
What does phosphorylation do to a protein
Changes its function
Whether it turns it on or off you need to know more about the proteins
What do protein kinases do
Catalyse phosphate transfer to Ser Tye of Thr side chains
