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
phi and psi angles are influenced by …
steric interference of R
groups
fill in the blank:
Atoms of the peptide bond are ____ and tend to form __________
polar; H-bonds
what are 3 requirements of secondary structures?
- H-bond requirements of the polar peptide bond
- minimizes steric strain
(limited movement of bonds due to rotation) - positioning of side chains to minimize interference
if a person has acidemia (increased [H+] in blood), what is the appropriate treatment?
hyperventilating
what does the bicarbonate system maintain?
blood pH
what is Le Chatelier’s principle?
if a dynamic equilibrium is disturbed (change of conditions), then the position of equilibrium will shift to counteract the change to reestablish an equilibrium
is the tyrosine R- group:
a.hydrophobic
b.hydrophilic
c. amphiphilic
C. amphiphilic
what compounds have hydrophobic R-groups (shown in class)?
phenylalanine and tryptophan
Enantiomers:
a. are only associated with amino acids
b. can be specific types of diastereomers
c. are never mirror images of each other
d. can exist for molecules with more than one chiral carbon
d. can exist for molecules with more than one chiral carbon
what are asymmetric carbons called?
chiral center
if a molecule has n number of chiral carbons, how many stereoisomers will it have?
2^n
can enantiomers exist for molecules that have more than one chiral carbon?
yes
One turn of the helix = ____ A along
the axis
(____ amino acid residues)
5.4; 3.6
what type of contact do atoms in the core of the helix have?
Van der Waals
Do AA side chains point inward or outward from the helix in secondary structures?
outward
what two compounds (shown in class) are least likely to form a alpha helix?
Proline and glycine
why is proline least likely to form an alpha helix?
-No rotation around C-N bond
-Results in destabilizing kink
why is glycine least likely to form an alpha helix?
Too much
conformational flexibility
what are the two ways beta sheets can form?
parallel and antiparallel
what types of bonds are formed between neighboring strands in beta sheets?
H-bonds
in parallel beta sheets, strands run in ____ direction
same
in antiparallel beta sheets, strands run in ____ direction
opposite
what is the average number of strans per beta sheet?
6
what are two small compounds (shown in class) that are common in beta sheets?
glycine and alanine
what kind of linkage links antiparallel beta sheets?
beta-turns
what kind of linkage links parallel beta sheets?
beta loops
what two compounds (shown in class) are common to have beta-turns?
proline and glycine
the hydrophobic core houses what kind of amino acids?
hydrophobic
the hydrophobic core allows polar residues to participate in what kind of bonding?
H-bonding
the hydrophobic core allows charged residues to participate in what kind of bonding?
ionic-bonding
what are the three examples of folding possibilities shown in class?
beta-alpha-beta
beta-hairpin
alpha-alpha
a hydrophilic surface has what two things?
- charged amino acids
-polar residues
what is the part of a peptide chain that is independently stable or can undergo
movement as a single entity with respect to the entire protein called?
domain
will domains retain their individual structure if separated?
yes
what are polypeptide subunits associated with each other to form a multisubunit protein called?
oligomers
a homo-oligomer has ____ subunits
identical
a hetero-oligomer has ____ subunits
different
Associations between the different subunits are ____
noncovalent
What factors drive and stabilize the folding of proteins?
Proteins fold into the conformation that is the most thermodynamically stable - lowest Gibbs free energy
label:
- denatured
- native
what effect drives protein folding?
the hydrophobic effect
what will nonpolar groups do to minimize their contact with water?
aggregate to displace water molecules surrounding the protein
what are 3 weak noncovalent interactions that stabilize protein structures?
Van der Waals forces
hydrogen bonds
ionic interactions
what is a covalent interactions that stabilize protein structures?
disulfide bonds
describe the hydrophobic collapse into molten globule
Spontaneous collapse of the polypeptide into a
compact state (molten globule)
what are 4 things that drive protein folding?
- Hydrophobic Effect (lowest Gibbs free energy)
- Ionic Bonds (Salt Bridges) - Charged Amino Acids
- Hydrogen Bonds*
- Disulfide Bonds * *Stabilizing (After Folding)
protein folding in vivo often requires what?
chaperones
name the 1, 3 letter code and property of R groups for: glycine
Gly G; nonpolar r group
name the 1, 3 letter code and property of R groups for: alanine
Ala A; nonpolar r group
name the 1, 3 letter code and property of R groups for: proline
Pro P ; nonpolar r group
name the 1, 3 letter code and property of R groups for: valine
Val V; nonpolar r group
name the 1, 3 letter code and property of R groups for: leucine
Leu L; nonpolar r group
name the 1, 3 letter code and property of R groups for: isoleucine
Ile I ; nonpolar r group
name the 1, 3 letter code and property of R groups for: methionine
Met M ; nonpolar r group
name the 1, 3 letter code and property of R groups for: phenylalanine
Phe F; aromatic r group
name the 1, 3 letter code and property of R groups for: tryosine
Tyr Y ; aromatic r group
name the 1, 3 letter code and property of R groups for: tryptophan
Trp W ; aromatic r group
name the 1, 3 letter code and property of R groups for: serine
Ser S; uncharged polar r group
name the 1, 3 letter code and property of R groups for:threonine
Thr T ; uncharged polar r group
name the 1, 3 letter code and property of R groups for: glutamine
Gln Q ; uncharged polar r group
name the 1, 3 letter code and property of R groups for: asparagine
Asn N ; uncharged polar r group
name the 1, 3 letter code and property of R groups for: cysteine
Cys C ; uncharged polar r group
name the 1, 3 letter code and property of R groups for: lysine
Lys K ; positively charged r group
name the 1, 3 letter code and property of R groups for: histidine
His H; positively charged r group
name the 1, 3 letter code and property of R groups for: arginine
Arg R ; positively charged r group
name the 1, 3 letter code and property of R groups for: aspartate
Asp D; negatively charged r group
name the 1, 3 letter code and property of R groups for: glutamate
Glu E; negatively charged r group
name the compound:
glycine
name the compound:
alanine
name the compound:
proline
name the compound:
valine
name the compound:
leucine
name the compound:
isoleucine
name the compound:
methionine
name the compound:
serine
name the compound:
threonine
name the compound:
cysteine
name the compound:
asparagine
name the compound:
glutamine
name the compound:
lysine
name the compound:
arginine
name the compound:
histidine
name the compound:
aspartate
name the compound:
glutamate
name the compound:
phenylalanine
name the compound:
tyrosine
name the compound:
tryptophan
