Week 2 Flashcards
What makes up an amino acid?
alpha carbon
amino group
carboxyl group
R group
What kind of bond is formed between two amino acids? How?
covalent peptide bond
condensation reaction between OH on carboxyl and H from amino group of 2 amino acids
How often is H bonding repeated? Between which atoms?
3.6 aa/turn
carbonyl O and amide H 4 aa’s later
overall protein structure
primary (sequence) –> secondary (local folding) –> tertiary (long-range folding) –> quaternary (multimeric organization) –> multiprotein complexes
primary
amino acid sequence
Amino group, Hydrogen, and carboxyl all attached to alpha carbon
What does the R group determine?
acid/base, uncharged polar, nonpolar
OVERALL CHARACTERISTICS
type of aa
What determines the amino acid used?
3 RNA letter sequence
What trend does the amino acid chart unintentionally adhere to and why?
grouped somewhat by polarity because helps cells withstand some mutations / major mutation
if only one letter is messed up and changes the amino acid used, it will still have similar properties as the intended amino acid
What bond can 2 cysteine amino acids form?
disulphide bonds
What amino acid forms disulphide bonds?
cysteine
R group = H2C-SH —> S-S
How are disulphide bonds between 2 cysteine amino acids formed?
in OXIDATION conditions, 2 S’s form a covalent bond
What are the 2 types of cysteine disulphide bonds?
- INTERchain: b/w 2 different proteins/polypeptides
- INTRAchain: w/i same polypeptide/protein
What is the function of disulphide bonds?
braces, stabalises protein structure
Under what conditions and where in the cell do disulphide bonds form?
cytosol - REDUCTION environment so no bonds
endoplasmic reticulum - OXIDATION environment so bonds form
What organelle aids in linking 2 amino acids? How?
RIBOSOME takes OH from carboxyl and H from amino
note: never from side R chain
What is the carbon in the peptide bond called?
carbonyl (from carboxyl carbon)
What is the nitrogen in the peptide bond called?
amide (from amino nitrogen)
Quick way to find peptide bond?
look for O=C-N
What is the backbone of a polypeptide comprised of? What is the pattern? How do you distinguish the 2 ends?
residues (peptide bonded amino acids)
N-C-C
amino end - N terminus
carboxyl end - C terminus
How do you order/number residues? What is important not to change?
Left N terminus to right C terminus (unless told otherwise)
don’t change order of individual ends or direction of residues
True or false: Amino acid side chains help to stabilize alpha-helix and beta-sheet secondary structures.
false
Compare DNA and an alpha helix (3 main things)
- side chain direction
alpha - R groups face outwards
DNA - bases faces inwards - strands
alpha - 1
DNA - 2 - ordering/ends
alpha - N and C terminus
DNA - 5’ and 3’ ends
Do side chains stabilize the helix?
no
