Protiens & Amino Acids Flashcards
What is the primary structure of the protein?
What type of bond is present here?
- linear amino acid sequence of the polypeptide chain
- only peptide (covalent) bonds
What is the secondary structure of a protein?
What bond is present here?
- local spatial arrangement of polypeptide backbone e.g alpha helixes, beta pleated sheets
- hydrogen bonds
What is the tertiary structure of a protein?
what type of bonds are found here?
- overall 3D configuration of the protein
- different types of non-covalent e.g hydrogen bonds
What is the Quaternary structure of a protein?
what type of bonds are found here?
- more than one polypeptide chain associated
- different non-covalent bonds e.g hydrogen bonds
How is a peptide bond formed?
- linking of 2 amino acids in a hydrolysis reaction
- expulsion of water
What are some features of peptide bonds?
- planar (flat)
- rigid (cannot rotate)
- always have trans formation
- bonds either side of a peptide bond can rotate
- peptide bond C-N has partial double bond characteristics.
Define the isoelectric point.
The pH at which the protein has a net charge of 0
Features of a globular protein
- compact
- usually have several types of secondary structure
Features of a fibrous protein
- extended formation
- single type of repeating secondary structure
How do polypeptide chains fold?
Hint: hydrophilic & hydrophobic
- hydrophobic on inside
- polar, charged & hydrophilic on outside to interact w water
Can protein folding be random?
No- would take too long
Each step is ordered w localised folding & stable conformations maintained
*misfolding can lead to disease
How is the amino acid sequence created?
-the nucleotide sequence of a gene determines the amino acid sequence of a protein
What is the general structure of an amino acid
-central carbon, NH2,COOH, R-group & H
What is a zwitterion?
State of amino acid when NH2 protonated (NH3+) & COOH deprotonated (COO-)
What are amino acids classified according to?
- their R groups
- these determine the protein folding & acid base behaviour
Define the following:
aliphatic, aromatic, hydrophobic, hydrophilic, polar, non-polar, acidic, basic
Aliphatic= only C and H Aromatic= phenyl ring
What does the pKa value tell you about an amino acid?
It’s a measure of how strongly acidic an amino acid is
e.g pKa of 2.5 means the amino acid is strongly acidic
If the pH is higher than the pKa, what does this tell you in regards to protonation/ deprotonation?
- This means the acid is fairly weak
- therefore not likely to protonate -so more commonly in its deprotonated form
The protein serum albumin has an isoelectric point of 5. Would it move towards a positive or negative electrode?
(at physiological pH)
- physiological pH is 7
- at pH 5, net charge is 0
- going up in pH to 7 means it’s more basic (more OH-)
- more negative charged therefore would move to positive electrode
The protein serum albumin has an isoelectric point of 5. Would this protein move to the positive or negative electrode at a pH of 5?
- wouldn’t move
- pH = isoelectric point
- no net charge so protein cannot move
The isoelectric point of histones is very high, around 10.8
What charge will histones have under physiological conditions?
Why do you think they have this charge?
-physiological conditions= pH7
-going down in pH from 10.8 to 7 means it’s getting more acidic
-more H+ ions so histamine will have a positive charge
They have this charge as they can bind to DNA which is negatively charged
Give some features of enzymes
- catalysts
- increase rate of reaction
- DO NOT alter eqm of chemical reaction
- decrease activation energy
- can form ESC by binding to active site
Describe the active site of an enzyme
- occupies a small part of the enzyme
- formed by amino acids from different parts of the primary sequence
- it is a cleft or crevice (excludes water)
- has a complimentary shape to the substrate
- substrates can bind to enzymes via weak bonds
What does the rate of reaction depend on?
The substrate concentration
Define Km
The substrate conc required to achieve half of Vmax
-provides an idea of the strength of binding of the substrate to the enzyme
What does a low Km value suggest?
-low Km means the enzyme has a HIGH affinity for the substrate
What is the relationship between rate of reaction & enzyme concentration?
What is the effect of enzyme concentration on the Km value?
- rate of reaction is DIRECTLY PROPORTIONAL to the enzyme concentration
- e.g if enzyme concentration is doubled, rate doubles
- if enzyme concentration halves, rate is halved
2. Enzyme concentration doesn’t change Km
What is a competitive inhibitor?
What effect does it have on Km & Vmax?
- binds at active site, reduces proportion of enzyme molecules bound to the substrate (blocks active site)
- adding enough substrate will ALWAYS overcome the effect of the inhibitor, so no effect on Vmax
- Km increases as the substrate has a lower affinity for the enzyme
What is a non-competitive inhibitor?
What effect does this have on Km & Vmax?
- binds to enzyme at allosteric site, decreases concentration of functional enzyme
- enzyme no longer functional so increasing substrate conc has no effect, Vmax decreases
- Km unaffected as enzyme concentration has no effect on Km
Define the term Vmax.
The maximum rate of reaction achieved when all the enzymes are fully saturated with substrate
