Amino acids bound by condensation and the peptide bond can be broken by hydrolysis
How can we count and name peptides?
Start from amino terminus and end at the carboxyl terminus. When naming you can use the full amino acid names , three letter code or Letters
What are properties of peptides?
Is not ionized but presents partial charges , is a resonance hybrid of two canonical structures (planar) and therefore is more stable and less reactive (rigid bond).
What are the types of rotations that occur on the peptide bond?
Phi: Around the alpha carbon-amide nitrogen bond
Psi: Around the alpha carbon - carbonyl carbon bond
(substituents are usually trans) (In a fully extended peptide both phi and psi are 180)
What is a Ramachandran plot?
A plot with the distribution of the angles found in a proteins and it shows common pattern
What is the alpha helix?
a secondary structure present in alpha keratins and in many globular proteins
How to identify a left or right-handed helix?
look at one loop (one section) and if its from left-right then its right handed. IF its from right to left then left handed
What are parameters of the helix?
N = number of monomers in a full turn (3.6aa)
P = distance between two equivalent points (5.4Å)
D = How helix moves in respect to each monomers (1.5Å)
What does it mean if P is small?
If p is small then there is more space
What is the backbone structure?
All c=o and N-H of peptide bonds are involved in a hydrogen bond at 4 aa of distance. Only amino acid and carboxyl terminus are not involved in hydrogen bonds. Hydrogen bonds are parallel with the helix axis.
What are characteristics of the side chains in the alpha chain?
The R point out and are perpendicular with helical axis
Restrictions due to R will depend on: Electrostatic repulsion , volume of adjacent R , presence of proline
How does proline affect the alpha helix chain?
Acts as an alpha helix breaker because the rotation around the N-C alpha bond is impossible. Can also form cis peptide bonds (most present in Beta turns). Proline isomerase is the enzyme responsible for the reaction.
What are alpha keratins?
Filament forming protein produced by the skin
What are the characteristics of alpha keratins?
Rich in ala ,leu , arg and cys
Two right-handed alpha-helix form a left-handed coiled coil bound by disulphide bonds
Dimers align to form a protofilament also bound by disulphide bonds
What are the characteristics of the beta sheet?
Present in B keratins and in many globular proteins , pleated sheet , side chains point out from the sheet alternating in up and down direction. Held by its bonds between C=O and N-H of different strands
What are the arrangements of the B sheets?
Antiparallel: Sheets run opposite, resulting in linear H bonds (strong)
Parallel: Sheets run in same direction, resulting in bent H bonds.
What are the characteristics of B keratins?
Main component of feathers , silk
Piled together in a compact way
Ala and Gly are abundant in B keratins
What are characteristics of B turns?
Strands in B sheet change direction
A 180 turn is obtained over 4 aa
Turn is stabilized by a Hydrogen bond from a carbonyl oxygen to amide protein three residues down
Pro in position 2 and gly in position 3
What are the characteristics of collagen?
Most abundant in nature , present in bones and cornea
Sequences: triplets of glycine-x-y where x and y are frequently proline or hydroxyproline
What is the structure of alpha chains?
A left handed helix , Pro and Oh-pro are responsible for the turns , inner diameter of the helix is so small only the H or. gly fits into it
What are the parameters of the alpha chains?
N = 3 aa
P = 9.3 Å
d = 3.1 Å
What is the structure of tropocollagen?
Super helix with three strands folded in a right handed way. Bound together by H bonds between Co and NH from backbone of different chains (only gly)
What are characteristics of the collagen fiber?
Units of collagen (tropocollagen) pile up to form fiber and bound by covalent cross-links involving hydroxy-lysine
What are proteins?
Polymeric macromolecules comprising one or more polypeptide chains (>50 aa)
What are conjugated proteins?
proteins that derive part of their function from prosthetic groups. They have cofactors (Functional non-amino acid molecules) and prosthetic groups
What is a holoprotein?
Apoprotein + prosthetic group
What are the functions of proteins?
Catalysis , transport , structural and motion
What are the characteristics of globular proteins?
Quite compact , no knots in protein folding and 70% of polypeptide with some kind of secondary structure
How do secondary structures combine?
To form motifs and domains (a defined part of the protein)
What are the forces in the tertiary structure?
Tertiarys tructure is stabilized by many weak interactions. Disulfide bonds between two cysteines.
What are the hydrophobic forces in tertiary structure?
Apolar R are in the inner core of proteins and in membrane proteins also in the surface in contact with lipids.
How are structure and function related in proteins?
FUnction of proteins can be carried out by amino acids of the polypeptide chain and cofactors
What is a structure and function of myoglobin?
A monomeric oxygen binding proteins. Polypeptide chain (153aa) forms a globin domain with a prosthetic group (heme - iron)
How does globin bind to oxygen?
Heme (prosthetic group). The globin provides a chemical microenvironment and so heme can facilitate oxygen binding.
How does the structure of heme allow for oxygen binding?
Includes a histidine which stabilizes oxygen binding as well as hydrophobic amino acids which prevent Fe oxidation
How can we protect heme from CO binding?
CO binds to heme with more affinity than oxygen so the globin fraction diminishes CO affinity for heme
How can protein structure be altered?
Proteolysis or degradation (breaking peptide bonds) , modification of amino acids (phosphorylation) and changes in spatial arrangement
How can a protein be denatured?
heat or cold
Extreme Ph
Organic solvents
chaoropic agents
hydrochloride
What happens when a protein is heated?
weak forces of the protein can be altered bby moderate stress and melting the properties of protein change (Tm)