Proteins and Enzymes Flashcards
What is a protein?
Linear covalent polymers of amino acids which have a specific 3D structure
What is a fibrous protein?
Elongated in 1 direction
What are the roles of fibrous proteins?
Specialised for mechanical strength and support
What are globular proteins?
Compact proteins which are often water soluble
What are the roles of globular proteins?
Dynamic proteins such as enzymes or receptors.
What is an example of a part globular, part structural protein?
Myosin
What percentage of dry cell weight do proteins represent?
50%
What is the role of proteins?
to perform the functions essential for life
What is the structure of an amino acid?
Carboxyl group
Amino group
R group
H atom
What causes the folding of proteins?
The hydrophobic effect (driven by the need of internalise hydrophobic polypeptide chains) (polar chains on outside, non-polar on inside)
What is the hydrophobic effect?
globular proteins internalise the non polar hydrophobic side chains of amino acids and externalise the polar amino acids which can form hydrogen bonds with the external environment.
What is pKA?
PH value at which a weakly ionising group is 50% associated
What is the role of di-sulfide bridges?
Hold polypeptide chains in shape
What is the most hydrophobic amino acid?
Phenylalanine
What are the aromatic amino acids?
Tryptophan, Tyrosin and Phenylalanine
In what form do amino acids exist as?
Zwitter ions
What are required to form polypeptides with other amino acids?
Charged interactions between amino acids
What is the simplest amino acid?
Glycine
What are the main hydrophobic amino acids?
Valine, Leucine and Isoleucine
What is special about the cystine amino acid?
Contains a very reactive sulphydral group which can form di-sulphide bonds with other cystine residues in a spontaneous oxidation reaction
what is special about Tyrosine?
It is an aromatic amino acid which is polar due to its reactive OH group.
What is the primary structure?
linear sequence of amino acids
What is the secondary structure?
regions of regularly repeating conformations of the peptide stabilised by hydrogen bonding between the peptide groups e.g alpha helices and beta sheets
What is tertiary structure?
the 3D shape of the folded chain. Arrangement of all amino acids including R groups and any prosthetic groups (in a single polypeptide chain)
What is the quaternary structure?
the arrangement of two or more polypeptide subunits in an oligomeric protein (multi chain only)
which amino acids have ionising side chains?
Asp, Glu, His, Arg, Ly, Tyr and Cys
How do we know that ionising side chains have an effect on protein structure and function?
Use electrophoresis to separate proteins and amino acids at different PHs, because they carry different charges at different PHs
Describe the structure of a right handed alpha helix
Each C=O is hydrogen bonded with the amide hydrogen of the residue 4 places ahead
What’s an example of an alpha helix
Alpha Keratin
What’s an example of a beta pleated sheet?
virus coat proteins
Describe the tertiary structure of Mb
- contains a heme group
- globular
- folded to be very compact (with hydrophobic on inside)
- 75% of amino acids folded into a right handed alpha helix
Why is Hb an allosteric protein?
It has multiple ligand binding sites
What is the structure of Hb made up of?
Two molecules of alpha globin
Two molecules of beta globin
Tetramer organised into a pair of dimers
Largely alpha helical
What is collagen?
A major protein in vertebrae connective tissue (25-35% of total proteins in mammals)
What is collagen made up of?
- Units of the triple stranded tropocollagen molecule. The triple helix is held together by H bonds between chains.
- multiple repeats of -Gly-X-Y (where X is often proline and Y is often hydroxyproline)
- Three left handed helical chains coiled around each other in a right handed supercoi
What is an enzyme?
Usually a protein (can sometimes be RNA) that accelerates biological reactions
Why are enzymes important for life?
- Accelerates metabolic reactions
- enables regulation of metabolic reactions
- integration of metabolism
What are the biomedical applications of enzymes?
- Diagnostic reagents (e.g enzymes being released into blood after tissue damage)
- Lab reagents
- Drug metabolism
- Drugs work by inhibiting enzymes
What are isozymes?
Tissue-specific physically distant form of an enzyme
What is important about the Methionine residue?
Important at the start of translation as is coded for by the AUG. This is an essential amino acid
What is important about the Lysine residue?
+tve charge which helps packaging of DNA in the nucleus forming chromatin.
Which amino acids are the small amino acids?
Glycine (gly)
Alanine (Ala)
Which are the nucleophilic amino acids?
Serine (Ser)
Threonine (Thr)
Cystine (Cys)
Which are the aromatic amino acids?
Phenylalanine (Phe)
Tyrosine (Tyr)
Tryptophan (Trp)
Which amino acids are hydrophobic?
Valine (Val) Leucine (Leu) Isoleucine (Ile) Methionine (Met) Proline (Pro)
Which amino acids are amides?
Glutamine (Gln)
Asparagine (Asn)
Which amino acids are Acidic?
Aspartic acid (Asp) Glutamic Acid (Glu)
Which amino acids are Basic?
Histamine (His)
Lysine (Lys)
Argenine (Arg)
What is an essential amino acid?
Amino acids which cannot be made in the body and therefore must be obtained through the diet
What are the essential amino acids?
Thr
Phe, Trp
Val, Leu, Ile, Met
His, Lys
What is a non-essential amino acid?
An amino acid that can be made within the body
What are the non-essential am ino acids?
Pro Cys, Ser Gly, Ala Gln, Asn Arg Asp, Glu Tyr
What is the side chain to Cystine?
CH2 - SH
What is the side chain to Glutamic acid (glutamate)?
CH2-CH2-C=O-OH
What is the side chain to Glutamine?
CH2-CH2-C=O-NH2
What is the side chain to Glycine?
H
What is the side chain to Serine?
CH2OH
What is the side chain to Phenylalanine?
CH2-aromatic ring
What is the side chain to Tyrosine?
CH2- aromatic ring - OH
What is the side chain to Valine?
CHCH3-CH3
