Amino acid and protein structure Flashcards
Importance of Proteins (2)
- They make up important substances in the body
* enzymes, hormones, receptors, antibodies, extracellular matrix
What are amino acids?
basic structure?
what can happen in different mediums?
All amino acids have a basic structure • central carbon • amine and carboxylic group on either sides • variable R group on top (L amino acid) • hydrogen at bottom
They may appear differently in different mediums (acidic, basic and neutral)
Amino acids at different pH
how do amino acids exist in neutral pH? what is this called? describe what happens
what happens if pH is lower?
what happens if pH is higher?
Each amino acid can exist in a number of different forms, depending on the pH of the environment. Amino acids tend to exist as “zwitterions” at an intermediate pH/ neutral (isoelectric point). When an amino acid is a zwitterion, the carboxyl group is deprotonated and negatively charged, while the amine group is protonated and positively charged.
If the pH is lower (3/4), then the carboxyl group gets protonated as well as the amine group being already protonated, this gives the amino acid a positive charge.
If the pH is increased, (above 9/10), then the amine group will get deprotonated (and no longer be ionised) and the carboxyl group will remain deprotonated. So the overall charge will be negative.
Formation of a peptide bond
between what? what kind of bond?
what constitutes this bond/what is removed?
A peptide bond can form between two amino acids
to form a dipeptide
• one O- is eliminated from one amino acid
• 2H+ are eliminated from the second amino acid
forming a CONH bond (called a peptide bond)
The 4 levels of protein structure
how are aa joined in primary structure?
what do higher orders of structures rely on?
what happens to proteins when exposed to high/low pH and heat?
specific when heated?
how can it reverse?
why may 3d structure of proteins be similar for 2 porteins with different aa sequence?
what is primary structure?
Amino acids are joined by strong covalent bonds in
the primary structure
Higher orders of structure are mostly dependent on weak bonds (ionic, hydrogen, and hydrophobic) but may be stabilized by covalent bonds
Proteins may denature on exposure to high/low pH and heat
• riboendonuclease when heated will denature
• by exposure to certain buffers will renature
• this proves that primary structure determines shape of the protein
3D structure of proteins may be similar for 2 proteins with different amino acid sequences as they may form similar bonds
• Primary protein structure is sequence of a chain of amino acids
Secondary Structure
when does this occur?
what 2 structures can it form?
describe beta pleated sheet, example?
another version of this?
alpha helix? r or l handed? clock or anti clockwise? bonds how many residues away? where do side chains protrude from? how can the sides differ? what do the helices form? example found where?
occurs when a sequence of amino acids are linked by H bonds
• forms beta pleated sheets
anti-parallel beta pleated sheets
one polypeptide chain goes from left to right, loops around (hydrogen bonds form)
more regular, stronger eg silk
parallel beta pleated sheets -> chains bond in the same direction
• forms alpha helices
right handed
travel in clockwise direction
stabilized by H bonds between the amide H of one amino acid and the carbonyl group of another
bonds are made 4 residues away
side chains protrude from side of the helix
sometimes one side may have hydrophilic residues and the other hydrophobic residues
in other cases some sides may have positive residues and the other negative residues
The alpha helices can form coiled coils, which are very strong, these are found in myosin for example and very strong in structure.
Tertiary structure
when does this occur?
what takes place?
what can reinforce the structure?
- occurs when certain attractions are present between alpha helices and pleated sheets
- helices and sheets are folded up into more densely packed globular structures
- formation of these structures depends on weak chemical (non covalent) interactions between side chains
- structure may be reinforced by covalent disulfide bonds between cysteine residues
Quaternary structure
what is this?
- is a protein consisting of more than one amino acid chain
* same bonds used in tertiary structure may be used in the quaternary structure to hold the sub units together
tertairy vs quaternary
myoglobin vs haemoglobin
what is myoglobin?
how is it simialr to haemoglobin? despite what?
what does this give them?
what does the haemoglobin do differently?
Example of a protein in tertiary structure is myoglobin (found in muscle), whereas a protein in quaternary structure is haemoglobin.
The myoglobin consists of multiple alpha helices which bond to a haem group, it can be seen that the helices (tertiary structure) on the myoglobin are very similar to the tertiary structures of the alpha/beta chains in haemoglobin, despite having very different primary sequences. This gives them different binding affinities (myglobin has a higher affinity). The haemoglobin chains can also undergo a conformational change to give them a higher/lower affinity depending on if in the lungs or muscle respectively.
Haemoglobin vs foetal haemoglobin -> how can they work differently?
Foetal haemoglobin also has a different affinity due to having a different primary structure, despite having a fairly similar tertiary structure.
The different Side Chain Interactions and bonding
what is ionic bonds?
what is H bonds?
what is van der waals forces?
what is disulfide bonds?
• Ionic bonds
between negatively charged side chains and positively charged side chains
- negatively charged side chains: Asp, Glu
- positively charged side chains: Arg, His, Lys
• Hydrogen bonds
H attached to F, O2, N is slightly negative
O2 has lone pair of electrons
there is a force between O2 and H which is the bond
• Van der Waals forces
dipole interactions when atoms get too close together
important in amino acids with hydrophobic side chains eg Ala, Ile, Leu, Phe, Pro, Trp, Val
• Disulfide bonds/bridges
sulfhydryl side chain of cysteine gets oxidised
sulfur and sulfur bond to form a bridge
may cross link a single polypeptide chain (tertiary) or two separate molecules (quaternary)
Different proteins vary in shape and size.
Protein structure may be determined in varous ways (2)
principally X-ray crystallography and nuclear magnetic resonance (nmr) spectroscopy).
Protein arrangement in aquoeus environment
in water, what shape? how?
two different arrangements?
Water soluble proteins are often globular in shape,
the hydrophilic amino acid side chains are on the outside, the core of the protein will contain the hydrophobic residues.
• May assemble into filaments (e.g. actin) or tubes (e.g. tubulin).
Protein arrangement in membrane proteins
how is the arrangment different?
This organization is reversed in membrane proteins:
- Membrane spanning regions have externally located hydrophobic residues that interact withthe membrane lipids.
- They may have hydrophilic central channels
Fibrous protein arrangement
what is collagen? what can it assemble into?
2 other examples of fibrous proteins?
Other proteins may be fibrous in shape:
- Collagen has a triple helix (NOT an alpha helix).
- Collagen molecules may assemble into long fibres or sheets.
- Other examples of fibrous proteins are myosin and keratin.
