Which part gives the amino acids it’s distinct structure
The R group
What is Glycene’s distinct structure group
Hydrogen is it's R group
What is a carbon with four different substitutions
asymmetrical and optically active
L amino acids are ----------- incorporated
ribosomally
D amino acids are made by
enzymatically made and it's sometimes ribosomally made
D amino acids have evidence that they arose by past------
transcriptional isomerazation
In what environment is the amino acid completely protanated and what are the charges?
very low pH, the carboxylic acid and amino group have positive charges
What is the state of the amino acid at the Physiological pH and what is the Physiological pH?
The carboxylic acid will ionize by the amino acid has the hydrogen on it. and the physiological ph is a ph of 6.5
How will you be able to pull the hydrogen off the amino group? What will the charge?
by raising the alkalinity and you will have a negative species
What is a double charge and when do you normally see them?
zwitter ion, and you normally see them in physiological pHs
What cause discourages ionization?
surrounded by hydrophobic groups
what bond encourages ionization and which bond discourages it?
Ionic bonds encourage ionization, and hydrogen bonds discourage ionization
What is the PK3?
the ionization constant of the R group
Examples of Hydrophobicity
Oil and grease
true/false R groups only have hydrophobic properties
False. R groups can have both properties of hydrophobic and hydrophilic
Globular proteins are viewed as --------- because
creme filled chocolates because they have a hydrophilic outside layer and a hydrophobic center.
What interacts with water and is responsible for the water solubility of proteins?
hydrophilic amino acids
what bonds does the hydrophilic amino acids tend to have?
ionic and hydrogen
acidic amino acids have additional ------- and where are they attached?
carboxylic acids and they are attached to the alpha carboxylic acid not the Carbon
the core part of the acidic amino acid is the------
alpha carboxylic acid
the--------is blocked so the---------stands out
alpha carboxylic acid, R group
Aspartic acid has what attached to it?
one methylated group
Glutamic acid has what attached to it?
2 methylated groups
At what pH are Aspartic and glutamic acid ionized?
physiological pH
What are lysosymes able to do?
they cleave carbohydrates due to the environment
the amide on aspartic acid makes it------
asparagine
the amide on glutamic acid makes it-----
glutamine
what two acidic amino acids can be amidated?
Glutamic acid and Aspartic acid
T/F amides are negatively charged
False, they have no charge
to be hydrophobic it must be------
uncharged
to be hydrophilic it must be -------
charged
what is electron greedy on the amino acid?
the carbonyl's oxygen. the electrons are presumably shared betwwn a carbon and oxygen but they spend more the oxygen. this way giving the O a neg. charge and the C a positive charge
why is the carbonyl group able to interact with water?
Because it is polar due to the slight charges on the carbon and oxygen.
what can attach to asparagine? And where are they attached?
carbohydrates, and the sugars attach to the Nitrogen sometimes known as N-linked sugars
what are glycoproteins?
Proteins that have sugars attached
Glutamines are involved in -------
cross-linking, they are 1 or 2 covalent links that can occur n proteins.
How many amino acids can have carbohydrates attached?
Three: asparagine being one
Lysine has an extra--------group
amino group
Lysine can cross-link with what?
glutamine
What bond forms between the peptide chain of glutamine and the peptide chain of lysine?
isopeptide
what is the enzyme that removes the amide to form the isopeptide bond between glutamine and lysine?
Transaminase
when we couple amino acids together (glutamine & lysine) we see that the alpha carboxylic acid will form -------. In addition, amino groups form------- with-------.
will form the same type of modified amides
schiff bases
aldehydes
what is in the active site of amylases that are involved with a number of aldehydes?
lysine
What modifications can lysine undergo?
acetalation
methylation
what group does arginine have attached by a carbon chain?
guanidinium group
what is not involved with schiff bases?
Arginine
Why is Histadine considered basic?
Because it has a aninozole group that is protanated with a positive charge.
What is the PK3 of histadine?
6.5 (physiological pH)
the Pka is the PH when ----
when 50% of the groups are ionized
what would you have to drop the pH down to to protanate half the aminozoles on the histadine?
6.5 (histadine is not charged at 6.5)
Proteins that are sensitive to pH have a critical -------- environment.
histadine
what is the critical function of histadine?
It acts as a pH sensor.
T/F aminozole can resonate
True
What holds iron in place in hemoglobin?
Histadines
what drives the folding process of proteins?
Hydrophobic amino acids trying to get away from water comes together and forms the core
what stabilizes the folding of proteins?
Van der waal bonds between the hydrophobic amino acids
Hydrophobic amino acids are also important in ------
membrane proteins
what are the membrane proteins made of?
hydrophobic alpha helix
How can you find where the alpha helixes are in the membrane?
By a hydropathy plot
the membrane proteins can also form -----------
Hydrophobic pockets
what does the negative numbers mean on the hydropathy plot?
hydrophilic molecules
what does the positive value mean in the hydropathy plot?
Hydrophobic molecule
what are examples of molecules that are carried in the hydrophobic pockets?
steroids
fatty acids
cholesterol
hydrophobic amino acids
what amino acid forms the basis for all the other amino acids? Also known as the smallest.
glycene
Glycene is the only amino acid that is not---------because------
optically active because you have two identical substitutions on it
what is just a teeny bit hydrophobic?
alanine
Alanine is usually found at----------
at the interface between the lipid and the hydrophilic cytosol
Valine, Leucine, Isoleucine and Methonine are all very-----
hydrophobic
what amino acid deals with packing? what bond is used?
Methionine, van der waals
what are aromatic hydrophobic amino acids?
tyrosine
phenylalanine
typtophan
what is involved in signaling growth factors and signaling mitogenesis?
Phosphorylated Tyrosine
where does the amino acid have to be to be phosphorylated?
exposed to the surface
tyrosine and tryptophan are usually found------
in binding pockets
what happens if the proteins use a ionic bond to bind a ligand?
The ionic bond attracts water and you will have a sphere of hydration that blocks the access of the ligand to the binding site.
what is the unique characteristics of tyrosine and typtophan?
they are hydrophobic enough to dispel the sphere of hydration but they still hydrogen bond with the ligand.
what two amino acids have hydroxyl R groups?
Serine and threonine
Serine and threonine can be ----------- and they are very involved in ----------
phosphorylated
enzyme regulation
which amino acids can attach sugars to their oxygen?
