Lecture 2 Flashcards
what is the operating system for nearly all biological functions?
the proteome
what are 4 things common to all amino acids?
-alpha carbon
-Carboxyl group
-Amino group
-Variable R group
The R groups in amino acids differ by what two things?
size and charge
how many standard amino acids are there?
20
what are the four types of R groups that categorize amino acids?
-nonpolar R groups
-polar R groups
-polar charged R groups
-aromatic R groups
where are nonpolar R groups located?
the intertior of proteins where they don’t interact with water
what were the 7 molecules shown in class with nonpolar R groups?
Glycine, alanine, proline, valine, leucine, isoleucine, methionine
what were the 5 compounds shown in class with uncharged polar R groups?
serine, threonine, cysteine, asparagine, glutamine
what are the 3 molecules shown in class with positively charged polar R groups?
lysine, arginine, histidine
what are the 3 molecules shown in class with negatively charged polar R groups?
aspartate, glutamate
true or false? if false, correct statement
polar charged R groups are (almost) always charged under
physiological conditions
true
true or false? if false, correct statement
polar charged R groups can be either positively or negatively charged
true
what are the 3 compounds shown in class with aromatic R groups?
phenylalanine, tyrosine, tryptophan
true or false? if false, correct statement
Certain polar-uncharged amino acids can become charged
depending on the environment
true
what compound is very versatile in catalyzing chemical reactions?
Histidine
true or false? if false, correct statement
Histidine can act only as a base
false; Histidine can act as an acid and a base
true or false? if false, correct statement
The position of an AA relative to its neighbors
DOES NOT affect stability of helix
false; The position of an AA relative to its neighbors
DOES affects stability of helix
true or false? if false, correct statement
the microenviroment of the active site does not affect the protonation state of amino acids
false; the microenviroment of the active site DOES affect the protonation state of amino acids
true or false? if false, correct statement
Proteins have diverse properties and an incredible
number of functions
true
true or false? if false, correct statement
alpha helix and beta sheets meet the requirements of a secondary structure
true
what is something that is very important for protein structure?
covalent links between polypeptide chains and subunits
what configuration are all AA residues in proteins?
L-configuration
are amino acids chiral or achiral?
chiral
all AA are chiral except for what compound? what atom is repeated?
glycine; H
every AA has at least how many ionizable groups?
2
what is a compound?
a substance formed by two or more different types of elements chemically combined in a fixed proportion
what is a molecule?
a group of two or more atoms held together by chemical bonds
define zwitterion and at what pH does it occur?
a molecule that has both a positive and negative charge, but has a net charge of zero, making it electrically neutral; occurs at neutral pH
AA with ionizable R groups will have how many ionizable groups?
3
what are two things each ionizable group will have?
- pKa
2.region of buffering capacity
what does pKa meassure?
it measures the tendency to lose s proton
how do ionizable groups act?
they act as acids with increasing pH (give up protons)
what type of environment stabilizes the protonated form?
a hydrophobic environment
what causes repulsion and can affect protonation state?
proximate amino acids of similar charged
the point at which the pH of a molecule has no net electrical charge is the …
isoelectric point
how does the buffer zone on a titration curve look? what happens in these zones?
the relatively flat section of the curve where the pH changes very little with the addition of titrant
what are comprised of a wide variety of amino acid monomers with varied charge distribution?
proteins
what are four types of proteins?
-structural
-enzymatic
-carrier
-regulatory
where are structural proteins found?
hair, skin, eyes, muscle, silk
what do carrier proteins help with?
respiration and metabolism
what do enzymatic proteins help with?
digestion, blood clotting, replication, transcription, translation
what do regulatory proteins do?
coordinate events within and between cells
protein 3D structure depends on the …
primary sequence of AAs
what happens if you change a single amino acid in the primary sequence?
small changes at the amino acids level can affect structure which can lead to sickness and disease
what is an example (shown in class) of changing a protein at the amino acid level? what is the outcome?
hemoglobin at 6 position changing from a Glu to Val can cause sickle cell anemia
what type of bonds link amino acids to make proteins?
peptide bonds
what are the 3 things to keep in mind about the polarity of peptides?
-it goes from left tor right
-free amino group is on the left - N Terminus
-Free carboxyl group is on the right – C Terminus
what property of the polypeptide depends on the R groups?
electrostatic property
what are the four levels of protein structure?
primary
secondary
tertiary
quaternary
name the protein structure:
Sequence of AAs
primary
name the protein structure:
Conformation of backbone
(main chain atoms only –no regard to side chains) (arrangement of
adjacent AAs)
-alpha helix or beta sheet-
secondary
name the protein structure:
How multiple secondary structures are arranged relative to each other in one polypeptide (arrangement of adjacent and distant AAs)
tertiary
name the protein structure:
Multiple polypeptides arranged
relative to each other to form
a protein with different subunits
quaternary
name the protein structure:
primary
name the protein structure:
secondary
name the protein structure:
tertiary
name the protein structure:
quaternary
what are peptide bond characteristics?
-Partial sharing of electrons between the carbonyl oxygen
and the amide nitrogen
-partial double bond character across the peptide bond
-no rotation around the C-N