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7. Nucleic Acids (AHL) – 7.3 Translation

Name:

Understandings, Applications and Skills (This is what you maybe assessed on)

Statement Guidance7.3.U1 Initiation of translation involves assembly of the

components that carry out the process.Examples of start codons are not required. Names of the tRNA binding sites are expected as well as their roles.

7.3.U2 Synthesis of the polypeptide involves a repeated cycle of events.

Workbook Activity 217-218 p. 300

7.3.U3 Disassembly of the components follows termination of translation.

Examples of stop codons are not required.

7.3.U4 Free ribosomes synthesize proteins for use primarily within the cell.

7.3.U5 Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes.

7.3.U6 Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane.

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.

Workbook Activity 219 p. 302

7.3.U9 The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups.

Polar and non-polar amino acids are relevant to the bonds formed between R groups.

7.3.U10 The quaternary structure exists in proteins with more than one polypeptide chain.

Quaternary structure may involve the binding of a prosthetic group to form a conjugated protein.

7.3.A1 tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylation.

7.3.S1 Identification of polysomes in electron micrographs of prokaryotes and eukaryotes.

7.3.S2 The use of molecular visualization software to analyse the structure of eukaryotic ribosomes and a tRNA molecule.

Recommended resources:http://bioknowledgy.weebly.com/73-translation.html

Allott, Andrew. Biology: Course Companion. S.l.: Oxford UP, 2014. Print.


http://bioknowledgy.weebly.com/ (Chris Paine)

http://bioknowledgy.weebly.com/

http://bioknowledgy.weebly.com/73-translation.html

Transfer RNA (tRNA)tRNA molecules fold into a cloverleaf structure with four key regions:

The _____________________ (3’-CCA) carries an amino acid The _____________________ associates with the mRNA codon (via complementary base pairing) The _____________________ associates with the ribosome (via the E, P and A binding sites) The _____________________ associates with the tRNA activating enzyme (responsible for adding the amino acid to

the acceptor stem)Ribosomes

Ribosomes are made of protein ( _____________________ ) and ribosomal RNA ( _____________________ ) They consist of a large and small subunit: The small subunit contains an _____________________ _____________________ The large subunit contains three tRNA binding sites – _____________________ (A) site, _____________________

(P) site and _____________________ (E) site Ribosomes can be found either freely floating in the cytosol or bound to the rough ER (in eukaryotes) Ribosomes differ in size in prokaryotes and eukaryotes (prokaryotes = 70S ; eukaryotes = 80S)

7.3.A1 tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylationThe binding of an amino acid to the tRNA acceptor stem occurs as a result of a two-step process:

The enzyme ___________________ _____________________ to form an amino acid–AMP complex linked by a high energy bond (PP released)

The amino acid is then _____________________ _____________________ and the AMP is released – the tRNA molecule is now “charged” and ready for use

The function of the ATP (phosphorylation) is to _____________________ that is transferred to the tRNA moleculeThis 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.Initiation

1. mRNA binds to the small subunit of the ribosome.2. The small subunit of the ribosome moves along the

mRNA molecule in a _____________________ until it reaches a start codon (AUG)

3. A molecule of tRNA (with it’s amino acid, _____________________ ) complementary to the start codon (UAC) binds to the P site of the ribosome

4. The _____________________ of the ribosome binds to the tRNA and small subunit

Elongation5. A second tRNA (with amino acid attached) complementary to the second codon on the mRNA then binds to

the A site of the ribosome6. The amino acid carried by the tRNA in the P site is transferred to the amino acid in the A site as a

consequence of the ribosome catalyzing a new peptide bond (condensation reaction). The growing polypeptide increases in length.

7. The _____________________ one codon along the mRNA (in a 5’ – 3’ direction):• The tRNA in the P site is moved to the E site and then released• The tRNA in the A site is moved into P site

8. Another tRNA binds, complementary to the next codon on the mRNA, binds to the A site.9. Steps 6, 7, and 8 are repeated until a stop codon is reached.

Termination10. When a stop codon is reached translation is stopped:

• a _____________________ attaches to the A site• the polypeptide chain is released• the ribosome complex dissembles ready for reuse translating another mRNA molecule




In prokaryotes ribosomes _____________________ to the chromosomes whereas in eukaryotes the mRNA needs to be relocated from the nucleus to the cytoplasm (through the nuclear membrane)

In eukaryotes the _____________________ , e.g. spliced, (here labelled processing) after transcription before translation, this does not occur in prokaryotes


A polysome is a structure that consists of _____________________ _____________________

Multiple ribosomes translating mRNA simultaneously enables the cell to quickly create _____________________ of the required polypeptide

In prokaryotes the chromosome may have _____________________ attached directly to it.

7.3.U7 The sequence and number of amino acids in the polypeptide is the primary structure. AND 7.3.U8 The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding. AND 7.3.U9 The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups. AND 7.3.U10 The quaternary structure exists in proteins with more than one polypeptide chain.

Primary Structure The first level of structural organisation in a protein is the _____________________ _____________________ which

comprise the polypeptide chain The primary structure is formed by _____________________ _____________________ between the amine and

carboxyl groups of adjacent amino acids Primary structure _____________________ _____________________ because it determines the nature of the

interactions between R groups of different amino acids

Secondary Structure• The secondary structure is the way a polypeptide folds in a _____________________ to form α-

helices and β-pleated sheets• This folding is a result of _____________________ 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)



• In pictures, alpha helices are represented as spirals (purple ; left) and beta-pleated sheets as arrows (blue ; right)

Tertiary Structure The tertiary structure is the way the polypeptide chain coils and turns to form a _____________________ (i.e.

the 3D shape) It is caused by _____________________ _____________________ ; 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 Structure• Multiple polypeptides or prosthetic groups may interact to form a single, larger, biologically active protein

(quaternary structure)• A prosthetic group is an _____________________ 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)

7.3 U4 - Free ribosomes synthesize proteins for use primarily within the cell. AND 7.3 U5 - Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes.

All proteins produced by eukaryotic cells are initially synthesised by ribosomes _____________________ circulating within the cytosol

If the protein is targeted for _____________________ within the cytosol, the ribosome remains free and unattached If the protein is targeted for _____________________ or use in lysosomes, the ribosome becomes bound to the ER

Protein destination is determined by the presence or absence of an initial signal sequence on a nascent polypeptide chain

The presence of this signal sequence results in the recruitment of a signal recognition particle (SRP), which halts translation

The SRP-ribosome complex then docks at a receptor located on the ER membrane (forming rough ER) Translation is re-initiated and the polypeptide chain continues to grow via a transport channel into the lumen of the

ER The synthesised protein will then be transported via a vesicle to the Golgi complex (for secretion) or the lysosome Proteins targeted for membrane fixation (e.g. integral proteins) get embedded into the ER membrane The signal sequence is cleaved and the SRP recycled once the polypeptide is completely synthesised within the ER

Review:




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 subunitb. small subunitc. 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.



3. Label the following regions on this generalised tRNA molecule, outlining the function of each.

a.

function:

b. hydrogen bonds

function:

c.

function:

4. 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)

5. 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.



http://www.rcsb.org/pdb/education_discussion/educational_resources/tRNA_jmol.jsp

http://www.rcsb.org/pdb/explore/jmol.do?structureId=1JGO&bionumber=1

http://www.rcsb.org/pdb/explore/jmol.do?structureId=1GIY&bionumber=1

b. Explain why computers are a necessity for Scientists working in this field.

7.3.A1 tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylation.

6. Explain why there is more than one type of tRNA-activating enzyme.

7. Refering to the diagram below outline how tRNA is activated.

8. State the use of the energy transferred to the ‘charged’ tRNA molecule by ATP.


http://www.ib.bioninja.com.au/_Media/trna_activation_med.jpeg

http://www.ib.bioninja.com.au/_Media/trna_activation_med.jpeg


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.

9. Complete the table to summarise the process of translation.

Stage Key steps Diagrams and Notes

Initiation 1. mRNA binds to the small subunit of the ribosome.

2.

3.

4. The large subunit of the ribosome binds to the tRNA and

small subunit

The mRNA contains a series of codons (3 bases) each of which codes for an amino acid.

Elongation 5. A second tRNA (with amino acid attached)

complementary to the second codon on the mRNA then

binds to the A site of the ribosome

6.

7.

8. Another tRNA binds, complementary to the next codon on

the mRNA, binds to the A site.

9. Steps 6, 7, and 8 are repeated until a stop codon is

reached.

charged tRNA contains energy in the bond with the amino acid attached which will be used to form the peptide bond.

There are three binding sites on the large subunit of the ribosome, but only two can contain tRNA molecules at a time.

Termination 10. When a stop codon is reached translation is stopped:




10. State two reasons why translation can occur immediately after transcription in prokaryotes.


11. 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.


http://www.nobelprize.org/educational/medicine/dna/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

12. 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.

b. Complete the table to outline the four different levels of protein structure.

Notes Fibrous or Globular

Primary (polypeptide)

• The order / sequence of the amino acids of which the

protein is composed

• Formed by covalent peptide bonds between adjacent amino

acids

• Controls all subsequent levels of structure

Neither (– will fold to

become one of the

subsequent levels of

structure)

Secondary •

•

•

Tertiary •

•

•

Quaternary •

•



· web viewexamples of start codons are not required. names of the trna binding sites are expected...

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