Review:
7.3.S2 The use of molecular visualization software to analyse the structure of eukaryotic ribosomes and a
tRNA molecule.
This understanding requires a review of 2.7.U5. The
ability to draw and label ribosomal structure is important
for full understanding of the translation process.
1. Draw a diagram to outline the structure of a
ribosome. Label the following:
a. large subunit
b. small subunit
c. three tRNA binding sites (located on
the large subunit)
d. mRNA and the mRNA binding site
(located on the small subunit)
e. A growing polypeptide chain
N.B. In some texts ribosomes are shown with two binding
sites, the A (aminoacyl) site where tRNA carrying amino acid attach and the P (peptidyl) site where the growing polypeptide is located.
The third site, the E (exit) site, is not always regarded as a proper site.
2. State what molecules a ribosome consists of.
Ribosomes are made up of proteins for stability and RNA for enzymatic actions
Label the following regions on this generalised tRNA molecule, outlining the function of each.
a. Acceptor stem at the 3’ end
function: attachment to the amino
acid – Recall also that the tRNA
activation enzyme enables the
formation of this bond with the energy
from ATP which is then stored in the
bond between the amino acid and the
tRNA and later used for the formation
of peptide bonds formed by
dehydration synthesis between a.a.
b. hydrogen bonds
function: – complimentary binding via
hydrogen bonds form double stranded
regions between the two single
strands of RNA causing the tRNA to
forms its 3D structure
c. anticodon
function: associates with the
mRNA codon (via complementary
base pairing)
• The T arm associates with the ribosome (via the E, P and A binding sites)
• The D arm associates with the tRNA activating enzyme (responsible for adding the amino acid to the acceptor stem)
3. Use the RCSB Protein Bank to explore the following Jmol images:
a. The small ribosomal subunit http://www.rcsb.org/pdb/explore/jmol.do?structureId=1GIY&bionumber=1
b. The large ribosomal subunit http://www.rcsb.org/pdb/explore/jmol.do?structureId=1JGO&bionumber=1
c. A tRNA molecule http://www.rcsb.org/pdb/education_discussion/educational_resources/tRNA_jmol.jsp
Nature of Science: Developments in scientific research follow improvements in computing—the use of
computers has enabled scientists to make advances in bioinformatics applications such as locating genes
within genomes and identifying conserved sequences. (3.7)
4. Without computers analysis of the molecular structure such as ribosomal and tRNA structure would not be
possible. Bioinformatics also relies on computers to large extent.
a. Outline the field of bioinformatics and what it involves.
b. Explain why computers are a necessity for Scientists working in this field.
You can omit this question. It is from the old curriculum. Sorry I left it in
7.3.A1 tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylation.
5. Explain why there is more than one type of tRNA-
activating enzyme.
Each tRNA molecule binds with a specific amino acid in the
cytoplasm in a reaction catalysed by a tRNA-activating
enzyme
§ Each amino acid is recognised by a specific enzyme (the
enzyme may recognise multiple tRNA molecules due to
degeneracy)
6. Refering to the diagram below outline how tRNA is
activated.
The binding of an amino acid to the tRNA acceptor stem
occurs as a result of a two-step process: http://www.ib.bioninja.com.au/_Media/trna_activation_med.jpeg
§ The enzyme binds ATP to the amino acid to form an amino
acid–AMP complex linked by a high energy bond (PP released)
§ The amino acid is then coupled to tRNA and the AMP is released – the tRNA molecule is now “charged” and
ready for use
7. State the use of the energy transferred to the ‘charged’ tRNA molecule by ATP.
The function of the ATP (phosphorylation) is to create a high energy bond that is transferred to the tRNA
molecule
§ This stored energy will provide the majority of the energy required for peptide bond formation during translation
7.3.U1 Initiation of translation involves assembly of the components that carry out the process. AND 7.3.U2
Synthesis of the polypeptide involves a repeated cycle of events. AND 7.3.U3 Disassembly of the
components follows termination of translation.
These understandings require a more detailed summary of 2.7.U8. It is recommended, for clarity, that effective diagrams are used to
make the steps as clear as possible. More than one diagram maybe used per step if required.
8. Complete the table to summarise the process of translation.
I am just going to refer you to the BioNinja site for this one. Its all there to check your work
http://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/73-translation/translation-hl.html
7.3.U6 Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear
membrane.
9. State two reasons why translation can occur immediately after transcription in prokaryotes.
• There is no nucleus so both processes occur in the cytoplasm
• Prokaryotic mRNA is not processed between transcription and translation
7.3.S1 Identification of polysomes in electron micrographs of prokaryotes and eukaryotes.
10. A polysome is a structure that consists of multiple ribosomes
attached to a single mRNA translating it simultaneously to quickly
create many copies of the required polypeptide.
a. Label the eukaryote polysome to right to indicate:
• mRNA
• Ribosomes
• Polypeptide chains
b. Describe how polysomes in prokaryotes may differ in
structure from polysomes in eukaryotes.
You can omit this question too. Don’t need to know it.
http://www.nobelprize.org/educational/medicine/dn
a/a/translation/pics_em/polysome.gif
7.3.U7 The sequence and number of amino acids in the polypeptide is the primary structure.
7.3.U8 The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen
bonding.
7.3.U9 The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups.
7.3.U10 The quaternary structure exists in proteins with more than one polypeptide chain.
n.b. the next two questions are based on a review of 2.4.U5 and 2.4.U6 and the extension question posed
11. Once translated the polypeptide will naturally fold into a structure. The structure is the result of the polar
nature of water in the cytoplasm, hydrogen bonds and interactions between the R-groups.
a. The R-groups of an amino acid are classified as having one of a number of different properties. List
the properties can they possess.
• Polar
• Non-polar
• Charged (positive or negative)
• Contain sulphur
b. Complete the table to outline the four different levels of protein structure.
Notes Fibrous or Globular
Primary • The order / sequence of the amino acids of which the protein Neither (– will fold to
(polypeptide) is composed
become one of the
• Formed by covalent peptide bonds between adjacent amino
acids subsequent levels of
• Controls all subsequent levels of structure
structure)
Secondary • The secondary structure is the way a polypeptide folds in Fibrous
a repeating arrangement to form α-helices and β-pleated
sheets
• This folding is a result of hydrogen bonding between the
amine and carboxyl groups of non-adjacent amino acids
• Sequences that do not form either an alpha helix or beta-
pleated sheet will exist as a random coil
• Secondary structure provides the polypeptide chain with a
level of mechanical stability (due to the presence of
hydrogen bonds)
Tertiary • The tertiary structure is the way the polypeptide chain coils Globular
and turns to form a complex molecular shape (i.e. the 3D
shape)
• It is caused by interactions between R groups; including H-
bonds, disulfide bridges, ionic bonds and hydrophobic
interactions
• Relative amino acid positions are important (e.g. non-polar
amino acids usually avoid exposure to aqueous solutions)
• Tertiary structure may be important for the function of the
protein (e.g. specificity of active site in enzymes)
Quaternary • Multiple polypeptides or prosthetic groups may interact to Globular
form a single, larger, biologically active protein (quaternary
structure)
• A prosthetic group is an inorganic compound involved in
protein structure or function (e.g. the heme group in
haemoglobin)
• A protein containing a prosthetic group is called a
conjugated protein
• Quaternary structures may be held together by a variety of
bonds (similar to tertiary structure)
