Lecture 6 Flashcards
Properties of proteins:
have definite size and shape, but can be flexible and change conformation
Fuction of proteins:
proteins transport molecules across membranes, provide structural framework to cells, function as machines for muscle contraction, immune function and blood clotting
The function of protein is dependent on:
the 3-D structure, changing the genomic sequence changes the protein sequences which can change the protein structure and in turn change the protein function
Myoglobin:
a protein which is important for oxygen binding and storage in tissues
When do proteins fold:
after translation
The building blocks of proteins:
amino acids
Composition of proteins:
- amino group
- alpha carbon
- carboxylic acid group
- side chain
- hydrogen
Ionization varies with pH:
functional groups or side chain get protonated/ deprotonated depending on the relationship between physiological pH (7) and pI
pKa of carboxylic acid:
~2.00
pKa of R group:
~10.0 pKa
Zwitterionic form:
where amino acid is half protonated and deprotonated
Nonpolar aliphatic amino acids:
- Glycine (Gly; G)
- Alanine (Ala; A)
- Valine (Val; V)
- Leucine (Leu; L)
- Isoleucine (Ile; I)
Nonpolar amino acids:
- Proline (Pro; P)
- Methionine (Met; M)
Nonpolar aromatic amino acids:
- Phenylalanine (Phe; F)
- Tyrosine (Tyr; Y)
- Tryptophan (Trp; W)
Polar amino acids
- Serine (Ser; S)
- Cysteine (Cys; C)
- Threonine (Thr; T)
- Asparagine (Asn; N)
- Glutamine (Gln; Q)
Positively charged polar amino acids:
- Histidine (His; H)
- Lysine (Lys; K)
- Arginine (Arg: R)
Negatively charged polar amino acids:
- Aspartic acid (Asp; D)
- Glutamic acid (Glu; E)
L- and D-isomers:
mirror images of each other (amino acids are commonly in the L-conformation)
L-Alanine and D-Alanine
the two models are nonsuperi mposeable mirror images
Aymmetric structures are said:
to have a chiral center, or stereo center
A chiral or stereocenter are said to have:
D-isomers and L-isomers, 2 stereoisomers
Bonds forming amino acids into a protein:
peptide bond formed between carboxylic acid group of one amino acid and amino group of the other; removal of water
How are peptide chains written:
from the amino terminal (N-terminal) to the carboxyl termina (C-terminal)
Peptide backbone geometry:
- Single bond (C-N): 1.49 A, rotatable
- Peptide bond (C-N): 1.32 A, cannot rotate
- Double bond (C=N): 1.27 A, cannot rotate
Consequences of resonance:
- planar structure of the peptide bond
- cis/trans configuration of the peptide bond
Most favored peptide bond configuration:
Trans: alpha carbons on opposite sides because there is no hindranc
Structure of peptide backbone:
- peptide bonds
- sidechains (R groups)
- the only ionizeable groups in a peptide backbone are the side chains except for terminal amino and carboxyl groups
