Lecture 4 Amino Acids and Proteins Flashcards
How many standard amino acids are there?
20
How are the 20 standard amino acids similar and different?
20 standard amino acids share a typical structure but differ in their side chains
What do peptide bonds do in a polypeptide?
Link amino acid residues
Some amino acid side chains contain…..
….ionizable groups whose pK
values may vary
What are all proteins composed of?
20 Standard amino acids
What are the common amino acids known as?
α-amino acids
Why are the common amino acids are known as α-amino acids?
They have a primary amino group (—NH2) as a substituent of the α carbon atom, the carbon next to the carboxylic acid group
At physiological
pH …..
…. the amino group is protonated and the
The carboxylic acid group is unprotonated
Describe condensation of two amino acids
Formation of a CO—NH bond
with the elimination of a
water molecule produces a
dipeptide.
What is the residue of condensation of 2 amino acids?
The residue with a free amino group is the N-terminus of the peptide, and the residue with a free carboxylate group is the C-terminus.
Amino acid side chains can be (name 3 things) ?
Nonpolar, Polar, or Charged
Name the non polar amino acids
Gly, Ala, Val, Leu,
Ile, Met, Pro, Phe, Trp
Name the uncharged polar amino acids
Ser, Thr, Asn, Gln, Tyr, Cys
Name the charged amino acids
Lys, Arg, His, Asp, Glu
Name the Aliphatic amino acids
Alanine, Valine, Leucine, Isoleucine, Proline
Name the - charged amino acids
Aspartic acid, Glutamic acid
Name the + charged amino acids
Lysine, Arginine, Histidine
Name the aromatic amino acids
Phenylalanine, Tryptophan, Tyrosine
Name the amidic amino acids
Asparagine, Glutamine,
Name the hydroxylic amino acids
Serine, Threonine
Name the sulfur containing amino acids
Cysteine, Methionine
Watch the lecture recording to make notes on Classifying Amino Acids p6
Yes, do that Nadya
What do the pK Values depend on?
The pK Values of Ionizable Groups Depend on Nearby Groups
What is the isoelectric point (pI) for the α-amino acids?
The pH at which a molecule carries no net electric charge is known as its
isoelectric point, pI.
What is the formula for calculating pl?
pI = 1/2(pKi + pKj)
What are the Ki and Kj in this calculation?
Ki and Kj are the dissociation constants of the two ionizations involving the neutral species
Calculate the isoelectric point of aspartic acid. In the neutral species, the α-carboxylate group is
deprotonated, and the α-amino group is protonated. Protonation of the α-carboxylate group or deprotonation of the
β-carboxylate group would both yield charged species. Therefore, the pK values for these groups (1.99 and 3.90)
pI = (pKi + pKj)/2
= (1.99 + 3.90)/2 = 2.9
Amino acids and many other biological compounds are…..
,,,,chiral molecules
whose configurations can be depicted by Fischer projections
The amino acids in proteins all have what configuration?
L stereochemical configuration
All the amino acids recovered from polypeptides are optically active except which one?
Glycine
What does optically active mean?
They rotate the plane
of polarized light
What can the direction and angle of rotation be measured with?
An instrument
known as a polarimeter
The central atoms in such molecules are known as….
…asymmetric or chiral centers and are said to have the property of chirality
What is the Fischer convention?
The Fischer Convention Describes the Configuration of Asymmetric Centers.
In the Fischer convention….
…..horizontal bonds extend above the plane of the paper, and vertical bonds extend below the plane of the article
Are the 20 standard amino acids the only amino acids that occur in biological
systems?
No
Nonstandard amino acid residues are often important constituents of what?
Proteins and
biologically active peptides
The non-standard amino acids are a result of what?
The specific modification of an amino acid residue after the synthesized polypeptide chain
What does amino acids modification include?
The simple addition of small chemical groups to specific amino acid side chains
Name amino acid modification processes (5)
Hydroxylation, methylation, acetylation, carboxylation, and phosphorylation
At neutral pH, the amino group of an amino acid is ______ , and its carboxylic acid group is _________
- Protonated
- Ionized
What are proteins?
Proteins are polymers of amino acids joined by peptide bonds.
When can the pK values of the ionizable groups of amino acids be altered?
When the amino acid is part of a polypeptide
Amino acids are -_____ molecules
Chiral molecules
Only what acids occur in proteins ? (mention the exception)
Only L-amino acids occur in proteins (some
bacterial peptides contain D-amino acids)
How can amino acids be modified ?
Covalently modified after they have been incorporated into a polypeptide
What is the size and composition of polypeptide chains limited by in a cell?
By the efficiency of protein synthesis and by the ability of the polypeptide to fold into a functional structure
What is a protein’s primary structure?
The amino acid sequence of its polypeptide chain, or chains if the protein consists of more than one polypeptide
Except glycine, all the amino acids recovered from polypeptides are what?
Optically active; they rotate the plane of polarized light
What can the direction and angle of rotation be measured with?
Polarimeter
The central atoms in such molecules are known as what?
Asymmetric or chiral centers and are said to have the property of chirality
What does the Fischer Convention Describe?
The Configuration of Asymmetric Centers
In Fischer Convention, the configuration of the groups around an asymmetric center is compared to what?
Glyceraldehyde, a molecule with one asymmetric center
In the Fischer conventions how are the bonds represented?
Horizontal bonds extend above the plane of the paper, and vertical bonds extend below the plane of the article
Higher levels of protein structure—secondary, tertiary, and quaternary refer to what?
To the three-dimensional shapes of folded polypeptide chains
A relatively small protein molecule may consist of a single polypeptide chain of
___ residues.
100
How many possible unique polypeptide chains of this
length are there?
100 130
20 ≈ 1.27 × 10
Forty residues appear to be near the minimum for a polypeptide chain to do what?
To fold into a discrete and stable shape that allows it to carry out a particular function
The longer the polypeptide….
….the greater the likelihood of introducing errors during transcription and translation
The solubility of a protein at low ion concentrations ______ as salt is added
increases
