a List four amino acids in each case which you think have
i
non-polar
side chains
Glycine (Gly), Alanine (
I chose these ones because they are hydrocarbons. They don’t have any polar hydroxyl
groups. I don’t really know about the
polarity of nitrogen and sulphur bonds though L.
ii
polar
side chains
Serine (Ser), Threonine (Thr), Tyrosine (Tyr), Aspartic Acid
(Asp)
These ones all have OH groups so that must make them polar.
iii
ionisable
groups on their side chain.
All carboxylic acids are ionisable (to H+). So Aspartic acid (Asp) and Glutamic Acid
(Glu) must be ionisable. I don’t know if
Proline (Pro) contains a carboxylic acid, because it only says –COOH. Might be one. I can’t think of a reason for any others to
be ionisable but I don’t know very much about the other groups. Maybe –NH is, which
would make Arginine (Arg) ionisable.
b Look at the structures of leucine and isoleucine. Explain why isoleucine is so named.
Isoleucine is a structural isomer of leucine. Much like 2,2,4-trimethylpentane
is called iso-octane because it is an isomer of octane, isoleucine must be so
named because it is an isomer of leucine.
c List one amino acid in each case in which the R group contains
i
a
primary alcohol group Serine (Ser)
ii
a
secondary alcohol group Threonine (Thr)
iii
a
phenol group Tyrosine (Tyr)
iv
a
carboxylic acid group Glutamic acid (Glu)
· Amino acids combine to form a protein
· The carboxylic acid group on one amino acid joins the amino group on the next amino acid
· Since and H and an OH are lost in the joining, water is formed
· This process is called condensation
· The –CONH- (secondary amide) group linking the amino acid residues in the protein formed is called a peptide link
· Two amino acids joined by a peptide link are called a dipeptide
This reaction
is the condensation of two amino acids into a dipeptide
This dipeptide is called
a Draw the structure of the dipeptide Ala Gly.
b In the tripeptide Ser Gly
i
NH2
group? Ser (Serine)
ii
COOH
group?
· Amino acids have a three-dimensional structure
· All except glycine, that’s 19 amino acids, can exist as either of two isomeric forms
· These isomers are known a D or L optical isomers
· D stands for dextro- since it turns a plane of polarised light to the right
· L stands for levo- since it turns a plane of polarised light to the left
· Two optical isomers which are the mirror images of each other are called enantiomers, meaning opposite molecules in Greek.
· Chemical Ideas 3.6 is about optical isomerism. 3.3 is about shapes of molecules and 3.5 is about geometric isomerism.
a In the formation of RNA, what type of reaction is responsible for
the linking of
i
the
ribose and phosphate? condensation
ii
the
ribose and base? condensation
b The skeletal formula of ribose is shown in the illustration of
RNA. Draw a full structural formula for
ribose.
Table 2 shows that
for some amino acids only the first two
bases of the RNA codon are important.
The identity of the third base does not matter. Make a list of these amino acids.
Amino acids
followed by ticks are those for which every codon begins with the same two
bases.
1) Alanine (GCx) ü
2) Arginine (CGx)
3) Glycine (GGx) ü
4) Leucine (CUx)
5) Proline (CCx) ü
6) Serine (UCx)
7) Threonine (ACx) ü
8) Valine (GUx) ü
For other amino
acids, it is important that all three
bases are correct. Make a list of these
amino acids.
1) Arginine (AGA, AGG)
2) Asparagine (AAU, AAC)
3) Aspartic acid (GAU, GAC)
4) Cysteine (UGU, UGC)
5) Glutamine (CAA, CAG)
6) Glutamine (GAA, GAG)
7) Histidine (CAU, CAC)
8) Isoleucine (AUU, AUC, AUA)
9) Leucine (UUA, UUG)
10) Lysine (AAA, AAG)
11) Methionine (AUG)
12) Phenylalanine (UUU, UUC)
13) Serine (AGU, AGC)
14) Typtophan (UGG)
15) Tyrosine (UAU, UAC)
a Use the codons from Table 2 to predict the peptides obtained if RNA molecules with the following patterns
of bases were used:
i
AAAAAA...
ii
CGCGCGCGC...
iii
UACCUAACU
Tyr Leu Thr
b Predict the anti-codons for these amino acids
i
Trp Base pairs: U-A and C-G
Codon = UGG →
Anti-codon = ACC
ii
Asp. Codons = GAU, GAC →
Anti-codons = CUA, CUG