Chapter 3: Amino Acid Flashcards
All amino acids are precursors to
other —
biomolecules
Fischer projection
In a Fischer projection, every atom is identified and the bonds to the central carbon atom are represented by horizontal and vertical lines. By convention, the horizontal
bonds are assumed to project out of the page toward the viewer, whereas the vertical bonds are assumed to project behind the page away from the viewer.
An α-amino acid contains: (5)
Aka the 20 amino acids
- a central carbon atom, called the α carbon,
- an amino group
- a carboxylic acid group
- a hydrogen atom
- a side chain, called the R group
With four different groups connected to the tetrahedral αcarbon atom, α-amino acids are —- and may exist ….
- chiral
- they may exist in one or the other of two mirror-image forms, called the L isomer and the D isomer
The L and D isomers are —– of each other
mirror images
Only —- amino acids are constituents of proteins
L
Free amino acids in solution at neutral pH exist predominantly as —-
dipolar ions (also called zwitterions)
Dipolar ions (also called zwitterions) forms:
In the dipolar form, the amino group NH3+ is protonated and the carboxyl group COO- is deprotonated.
Acids ___ hydrogen ions
donates
Explain what happens to an amino acid when its in acid
- the amino group is protonated NH3+ and the carboxyl group is not dissociated (-COOH)
As the PH of the amino acid solution is raised…
- ## As the pH is raised, the carboxylic acid is the first group to give up a proton, because its pka is near 2.
The dipolar form persists until—-
- the pH approaches 9, when the protonated amino group loses a proton. Under physiological conditions, amino acids exist in the dipolar form.
Under physiological conditions, amino acids exist in the — form at a PH of —-
- dipolar/ zwitterionic
- 7.4
Twenty kinds of side chains varying in size, shape, charge,
hydrogen-bonding capacity, hydrophobic character, and chemical reactivity are commonly found in proteins. Many of these properties are conferred by ——
- functional groups
Although there are many ways to classify amino acids, we
will assort these molecules into four groups on the basis of the general chemical characteristics of their R groups (4):
- Hydrophobic amino acids with nonpolar R groups
- Polar amino acids with neutral R groups but the charge is not evenly distributed
- Positively charged amino acids with R groups that have a positive charge at physiological PH
- Negatively charged amino acids with R groups that have a negative charge at physiological pH
hydrophobic amino acids (10)
What they are + who they consist of
- The amino acids having side chains consisting only of hydrogen and carbon
- phenylalanine, leucine, isoleucine, alanine, glycine, tryptophan, valine, methionine, and proline,
The amino acids are all chiral, with the exception of —, whose side chain is —.
- glycine
- H
Larger aliphatic side chains are found in the branched-chain amino acids (4)
- valine
- leucine
- isoleucine
- Methionine
Why is proline special (2)?
side chain+ amino group
- Proline is unique in that it is the only amino acid where the side chain is connected to the protein backbone twice (both the α-carbon and the nitrogen atom), forming a five-membered nitrogen-containing ring.
- its amino group, through which it links to the other amino acids, is a secondary amine, rather than a primary amine group (−NH2), as in the other nineteen amino acids.
The —-isomer of proline, is the only form that is involved in protein synthesis
L
The hydrophobic amino acids, particularly the larger
aliphatic and aromatic ones, tend to —-
cluster together inside the protein away from the aqueous environment of the cell.
Name the amino acids that contain hydroxyl groups (-OH) (3):
—serine, threonine, and tyrosine
The hydroxyl groups on serine, threonine, and tyrosine make them more hydrophilic (water-loving) and reactive than their respective nonpolar counterparts ——.
alanine, valine, and phenylalanine
Cysteine vs Serine (2)
struturally+ the difference causes
- Cysteine is structurally similar to serine but contains a sulfhydryl (-SH), or thiol group in place of the hydroxyl group.
- The sulfhydryl group is much more reactive than a hydroxyl group and can completely lose a proton at slightly basic pH to form the reactive thiolate group
the set of polar amino acids includes —- and —-, which contain a terminal carboxamide
asparagine and glutamine
Name all the polar amino acids (6)
- serine (Ser)
- threonine (Thr)
- cysteine (Cys)
- asparagine (Asn)
- glutamine (Gln)
- tyrosine (Tyr)
What characteristics do lysine and arginine share?
- have long side chains that terminate with groups that are positively charged at neutral pH
Histidine properties:
- contains an imidazole group, an aromatic ring that also can be positively charged
- the imidazole group of histidine is unique in that it can be uncharged or positively charged near neutral pH, depending on its local environment
Negatively Charged Amino Acids Have —- Side Chains
Acidic
Negative amino acids (2):
List em
aspartic acid and glutamicacid
—– are positively charged at neutral pH.
Lysine, arginine, and histidine
Seven of the 20 amino acids——have readily ionizable side chains. These seven amino acids are able to form
— bonds as well as to donate or accept protons to facilitate reactions
- tyrosine
- cysteine
- arginine
- lysine
- histidine
- aspartic acid
- glutamic acid
- ionic
acid–base catalysis
The ability to donate or accept protons
Essential amino acids
Amino acids that cannot be generated in the body and must be supplied by the diet
Lower the pka the more
acidic
At a pH below the pKa for each functional group on the amino acid, the functional group is —–. At a pH above the pKa for the functional group it is —–. If the pH equals the pKa, the functional group is —–.
- protonated
- deprotonated
- 50% protonated and 50% deprotonated
How do you differentiate between D and L isomer?
- Look down the H-C (alpha) bond
- Clockwise CORN = L isomer
PKa of carboxyl group
Lysine pka of positive charge
Arginine pka of positive charge
12.5
How to find Isoelectric point (pI)
Which amino acid side chains are capable of ionization
- lysine
- histidine
- arginine
- asparatate
- glutamate
- cysteine
- tyrosine
