1. amino acids, peptides, and proteins Flashcards
What are amino acids?
building blocks of proteins
What is the general structure of an amino acid?
acidic carboxyl group
amino group
hydrogen
R group
What part of an amino acids changes depending on the aa?
R group
What is the central molecule in an amino acid structure?
alpha carbon
What are the two stereoisomers in amino acids?
L and D - glyceraldehyde
Which form do amino acids appear in proteins?
L amino acids
What type of names do amino acids have?
three letter code and a one letter code
What amino acid is Gly?
glycine
What amino acid is Ala?
alanine
What amino acid is Pro?
Proline
What amino acid is Val?
Valine
What amino acid is Leu?
leucine
What amino acid is Ile?
isoleucine
What amino acid is Met?
methionine
What amino acid is Phe?
phenylalanine
What amino acid is Tyr?
tyrosine
What amino acid is Trp?
Tryptophan
What amino acid is Ser?
serine
What amino acid is Thr?
threonine
What amino acid is Cys?
cysteine
What amino acid is Asn?
Asparagine
What amino acid is Gln?
glutamine
What amino acid is Asp?
Aspartate
What amino acid is Glu?
gluatamate
What amino acid is Lys?
lysine
What amino acid is His?
histidine
What amino acid is Arg?
Arginine
What amino acid is E?
glutamate
What amino acid is D?
aspartate
What amino acid is R?
arginine
What amino acid is H?
histidine
What amino acid is K?
lysine
What amino acid is Q?
glutamine
What amino acid is N?
asparagine
What amino acid is C?
cysteine
What amino acid is T?
threonine
What amino acid is S?
serine
What amino acid is W?
tryptophan
What amino acid is Y?
tyrosine
What amino acid is F
phenylalanine
What amino acid is M?
methionine
What amino acid is I?
isoleucine
What amino acid is L
leucine
What amino acid is V
valine
What amino acid is P?
proline
What amino acid is A
alanine
What amino acid is G?
glycine
What are the five different groups of amino acids?
nonpolar, aromatic, polar, positively charged, negatively charged
What are the 7 nonpolar acids?
glycine
alanine
proline
valine
leucine
isoleucine
methionine
What is the simplest amino acid?
glycine
What is the unique characteristic about nonpolar amino acids?
all but one have aliphatic R groups
What is unique about methionine?
has Sulfur in is R group
What is unique about
A,V,L, and I amino acids in the nonpolar group?
exhibit the hydrophobic effect
What is unique about proline?
cyclic structure
What are the three aromatic R-groups?
phenylalanine, tyrosine, tryptophan
What characteristic is unique about the aromatic R groups?
all have cyclic structure
What is unique about tyrosine?
the OH group can form hydrogen bonds
Are the aromatic R groups nonpolar or polar and why?
nonpolar because of their rings
What do the side chains in the aromatic R groups do?
absorb UV light
What are the five polar R groups?
serine, threonine, cysteine, asparagine, glutamine
What can the side chains of the polar R groups do?
form hydrogen bonds
What is unique about cysteine?
SH groups form disulfide bonds with themselves through oxidation
What property do disulfide residues have?
strongly hydrophobic
What is unique about asparagine and glutamine?
amides of aspartate and glutamate
What are the two negatively charged R groups?
aspartate and glutamate
What part of aspartate and glutamate gives it the negative charge?
COO-
What are the three positively charged R groups?
lysine, arginine, histidine
Which amino acid group has the longest chains?
positively charged
What is unique about lysine?
second primary amino acid
What is unique about arginine?
has a positively charged guanidinium group
What is unique about histidine?
aromatic imidazole group
What are all amino acids able to do?
ionize
What does a negative hydropathy index mean?
higher the interaction with water
What two portions of an amino acids contain ionizable protons?
carboxylic acid group
amino group
What is the pKa of the carboxylic acid group?
low pH
What is the pKa of the amino group?
high pH
At high pH, how do amino acids exist?
cation form
At low pH, how do amino acids exist?
anion form
What is the zwitterion form?
middle pKa, molecule contains a positive and negative charge
Why is the pKa value for each amino acid different?
other areas of the amino acid can influence it
According to the titrations of amino acids, what other roles can they play?
buffers
What is the isoelectric point?
pH where the net electric charge is zero
In the zwitterionic form, what can the aa act as?
an acid or base
What is the isoelectric point formula for amino acids without ionizable side chains?
(pK1 + pK2)/2
When pH = pI, what is the charge?
zero
When pH > pI, what is the charge?
negative
When pH < pI, what is the charge?
positive
What are the four characteristics of aa with ionizable side chains?
have a pKa value
buffers
influence the pI
can be titrated
What is unique about the titration curves of ionizable side chain amino achids?
there are 3 ionization steps
How do you calculate the pI when the side chain is ionizable?
identify the net zero charge, and take the average of the pKr and pK2
What is the pKr?
pKa value that defines the acid strength of a zwitterion
What is the pK2?
pKa that defines the base strength of the zwitterion
What is a peptide?
multiple amino acids joined together
How do amino acids form peptides?
polymerization
What are the three characteristics of peptide bonds?
covalent
formed through condensation
broken through hydrolysis
in the formation or breakage of peptide bonds, what is either used or given off?
H2O
What end do you start with when naming and numbering peptides
amino terminus (N-terminal)
What is a polypeptide?
many amino acids
What is a protein?
thousands of amino acids
What are the three ionizable groups in peptides?
N-terminus
C-terminus
some R groups
What are the four functions of peptides
hormones
neuropeptides
antibiotics
protection
What are three common hormones and pheromones
insulin
oxytocin
sex-peptide
What is an example of a neuropeptide?
substance P - pain mediator
What is polymyxin and bacitracin examples of
antibiotics
What is a conjugated protein?
covalently bound to a nonprotein entity
What types of things can bind to polypeptides?
cofactors
coenzymes
prosthetic groups
What are cofactors?
functional non-amino acid component
What are coenzymes?
organic cofactors
What is the function of uncommon amino acids
found in specific tissues and play special roles
How are uncommon amino acids generated?
proton motive force
What is a modification that can alter protein function?
phosphorylation
What amino acid can’t be phosphorylated?
cysteine
