proteins Flashcards
what is the importance of proteins
- Vital for cellular functions
- Shape is crucial to function
- Polymer macromolecules
- Tens of thousands exist
- Specific three dimensional structure
- Specific function
polypepetides
sequence of amino acids joined by peptide bonds
amino acids
• 20 amino acids used
• Possess carboxyl and amino groups
• Chiral (L form)
amino acids can be chiral
amino acid ionisation
amino acid has low pH when H+ added.
amino acid is a zwitterionic form when H+ is lost coo-.
pH increases when H+ is lost from nh3
- Physical and chemical properties of the amino acid is determined by the R group
- R group can be:
hydrophobic amino acids; Nonpolar (9) hydrophilic amino acids: • Polar (6) • Acidic (2) • Basic (3)
what amino acids have nonpolar R groups
glycine, alanine, valine, leucine, isoleucine(lle), methionine, phenylalanine, tryptophan, proline
what amino acids have polar R groups
serine,threonine,cysteine
which amino acid makes disulphide bridge
cyteine (S-H) to oxidised make S-S + 2H+ , 2e-. this makes cystine
what amino acids have polar R groups?
Tyrosine, Asparagine(Asn), Glutamine(Gln)
name the two amino acid which have an acidic R gruop
Aspartic acid
Glutamic acid
name the 3 amino acid which have an basic R gruop
Lysine
Arginine
Histidine
how is a peptide bond formed?
OH group is removed along with a H from NH2 group from another amino acid. this creates a covalent bond between C-NH . water is produced as byproduct.
what is the backbone of the amino acid?
the backbone is the amno acid chain which are linked by peptide bonds.
the R groups are considered as side chain.
what is the directionality of protein?
from left to right . amino terminal at the left hand side and carboxyl terminal on the right hand side.
why is peptide bonds rigid and planer ?
the lewis structure shows double bond on either the oxygen and carbon or between carbon and nitrogen. thus the true structure has bond resonance which causes peptide bond to be rigid and planer
which form of isomer is present the most in peptides?
Rotation at C usually limited by steric clashes between R groups, so the trans form is the most common
When does the cis form occur?
cis occurs in peptide bonds when they come after a proline residue
state the levels of protein structure
- Primary Structure
- Sequence
- Secondary Structure
- α helices
- Beta sheets
- Loops/random coils
- Tertiary Structure
- Attractions/folding
- Quaternary Structure
- Assembly
what is the primary structure
- Sequence of amino acids: N to C terminus
* Genetically determined for each protein
what is the importance of primary structure?
- Dictates final protein structure because sequential arrangement of R groups will influence subsequent 2°, 3° and 4° structures
- Protein structure dictates function
name an example of a disease that arises due to mutation of primary structure ?
- Genetic mutation can lead to 1° structure changes that can alter structure and function
- Sickle cell anaemia caused by a single mutation
can two 3D structures of protein have different sequence of amino acid ?
3D structure is more strongly preserved by evolution than sequence
• Human and and sea hare myoglobin have the same 3D structure but sequence is only 19% identical
what amino acid is replaced in sickle cell anaemia?
Glu to Val
what are the two types of secondary structure
• Parts of polypeptide chains take on regular patterns of hydrogen bonding resulting in:
- α-helices
- Beta-pleated sheets
The above patterns are connected by short turns and longer loops/random coils
describe the alpha helix structure
- Coiled like a spring
- Efficient hydrogen bonding
- Often amphipathic
- Numerous in membrane-spanning pore-forming proteins
- 3.6 amino acids per turn
- Usually right-handed
- Flexible and elastic
describe the The Beta-sheet structure .
- Flat sheets
- Pleated
- Short runs of 5-10 AAs
- Parallel, anti-parallel or mixed
- Sheets held together by hydrogen bonding
- Strong and resilient
- Multiple sheets often connected by short loops known as hairpin loops or turns
describe parallel and anti-parallel.
parallel has two or more peptides parallel to each other bond via hydrogen bonding
in anti-parallel: the peptide is alternating and bonds are formed (hydrogen bonding )
describe Loops (random coils)
- Connect 2° structure elements
- Usually located on the surface
- Not connected by hydrogen bonds
- Rich in polar and charged residues
- Length varies from 2 to more than 20 AAs
- Far less well conserved than other 2° structure elements
- Differences between structurally similar proteins occur almost exclusively in loops
where is random coils found ?
Frequently form part of enzyme active sites
