P PROTEIN SYNTHESIS S S AND MUT TATIONS S STRUCTUR RED QUEST TIONS

Q Question 1 AQA/JUN07/MAK A KEUB/Q1 The table sho ows some mRNA m base sequences and the am mino acid seq quences tha at would be produced fr rom them

(a a)

Comp plete the tab ble above to show the sequence of amino acids produced from the fin nal mRNA base sequence. s [1 1] Thr-His-Thr-His-Thr Use th he informatio on in the tab ble to give (i) one e sequence of DNA bases that code es for the am mino acid ser, [1] TCA (ii) on ne anticodon for the amin no acid ser. [1] UCA

(b b)

c) (c

The genetic code is described d as non-ove erlapping an nd degenerate. Explain the eviden nce from the e table that this code is (i) non-overlap n ping [2] no base of a given codon c contrib butes to part t of the code e of the next t codon / aft ter one codon ha as been read, the immediate 3 base es will be rea ad as the ne ext codon / A base from one e codon cannot be used for adjacen t codon For a specific s poly ypeptide co ontaining 1 type of a a.a, overlapping will produce a polypept tide made up u of more than t 1 a.a e.g. CAA C CAA CAA pr roduces gln-gln-gln, if genetic code c is over rlapping, mR RNA base s equence willl be CAA A ACA AAC pro oducing a polypept tide with diffe erent a.a/ an ny valid exam mples degenerat te [2] One ami ino acid can be encoded d by more th han one codo on ACC and d ACA both code for thre eonine (Thr) )

(ii)

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Tu utorial: PROTEIN N SYNTHESIS AND A GENE MUT TATIONS

Question 2 AQA/JUN03/PD/Q1 Fig. 2.1 shows a stage in protein synthesis. (a) (i) Name this stage. Translation (ii) What is molecule Q? Proline [1] [1]

(b) Give the base sequence on the anticodon of molecule Z. [1] CAU

(c)

Describe what will happen next to (i) molecule Y; [2] (ii) Anticodon GGG binds to CCC codon at the A-site of ribosomes through complementary base-pairing via hydrogen bonds

molecule Q. [3] Joins to (carboxyl-end of) growing polypeptide Via peptide bond formation between P and Q cataysed by peptidyltransferase

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Tutorial: PROTEIN SYNTHESIS AND GENE MUTATIONS

Question 3 Modified N06 P2Q06 Fig. 3.1 is an electron micrograph of a secretory cell from the hypothalamus of the brain. The cell synthesizes and releases ADH (vasopressin). ADH is a peptide made up of nine amino acids.

Fig. 3.1 (a) Label the structures A, B and C. [3] A: cell membrane B: mitochondrion (reject mitochondria) C: rough endoplasmic reticulum

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Tutorial: PROTEIN SYNTHESIS AND GENE MUTATIONS

(b)

Explain the role of the following structures in the synthesis of ADH. [4] Mitochondria [max 2m] Involved in aerobic respiration to release energy (reject produce energy) via production of ATP ATP used to activate amino acids required for translation/ form polypeptide of ADH

Accept: form peptide bonds between amino acids to form polypeptide of ADH Accept: ATP are monomers in the synthesis of mRNA of ADH/ tRNA / rRNA required for the translation of ADH Nuclear envelope [max 1m] Regulation/control of movement of ribonucleoside triphosphates/ gene regulatory proteins, RNA polymerase/ any valid examples required for transcription of ADH into nucleus via nuclear pores

OR Regulation/ control of movement of ADH mRNA/ ribosomal subunits / any valid examples out of nucleus via nuclear pores

Examiners comments: Marks were lost because there was poor reference to nuclear pore Nucleolus [max 2m] Site of transcription of rRNA genes to form rRNA. rRNA then assembles with ribosomal proteins imported from the cytoplasm to form ribosomal subunits required for translation of ADH mRNA

Examiners comments: Many incorrectly thought that the nucleolus made the mRNA for ADH. ESSAY QUESTIONS 1. Outline the main events of transcription. [7] J97 gene that codes for enzyme/protein is on one of the DNA strands template strand RNA polymerase binds to promoter region Unzips DNA by breaking hydrogen bonds between bases to expose the DNA template strand for synthesis of mRNA RNA polymerase adds free ribonucleoside triphosphate (ATP, UTP, CTP and GTP) Order of bases added is through complementary base pairing (A to U and T to A and C to G) to via hydrogen bond formation with template strand ribonucleotides are joined together by phosphodiester bonds elongates in a 5 to 3 direction with respect to the growing mRNA chain transcription stops after RNA polymerase reads the termination signal (in prokaryotes) / polyadenlyation signal (in eukaryotes)

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Tutorial: PROTEIN SYNTHESIS AND GENE MUTATIONS

ADDITIONAL PRACTICE Question 1 Nov96 The figure below is a section through the rough endoplasmic reticulum representing the synthesis of proteins.

A B

C
(a) Name structures A to C. [3] A: mRNA; B: Large subunit of ribosome; C: polypeptide; (b) Describe and explain the role in protein synthesis of (i) structure A [3] messenger molecule, carrying genetic code/ information copied from DNA each codon / triplet of bases on mRNA encodes an amino acid serves as template: sequence/order of codons on mRNA determines the sequence/order of amino acids in a polypeptide (ii) structure B [3] Sites of translation to synthesis proteins Holds tRNA and mRNA in close proximity for translation to occur Contains peptidyltransferase which catalyse peptide bond formation between amino acids

Question 2 AQA/JUN06/GG/Q3 (a) (i) What is the role of RNA polymerase in transcription? [1] (i) join/attach RNA nucleotides / ribonucleotides via phosphodiester bonds;

Name the organelle involved in translation. [1] ribosome

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Tutorial: PROTEIN SYNTHESIS AND GENE MUTATIONS

b) Figure 1 shows s some e molecules involved in protein p synth hesis. (b

C Complete Fig gure 1 to sho ow (i) the ba ases on the DNA strand from which the mRNA w was transcrib bed; CGTTA ACCAA; [2] (ii) the ba ases forming g the anticod dons of the tR RNA molecu ules. CGU UAC CAA; Figure 2 show ws the effect ts of two diff ferent mutati ions of the D DNA on the b base sequen nce of the mRNA. The table sho ows the mRN NA codons for f three ami ino acids.

(c c) Name the e type of mut tation repres sented by mutation 1. [1 1] Base subs stitution;

(d d) Use the in nformation in n the table to o (i) identif fy amino acid X in Figure e 1; alanine;
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Tu utorial: PROTEIN N SYNTHESIS AND A GENE MUT TATIONS

(ii) explain how each of mutation 1 and 2 may affect the polypeptide for which this section of DNA is part of the code. [4] mutation 1 no change (to sequence of amino acids) silent mutation: GCU and GCA both encodes alanine because of the degeneracy of the genetic code mutation 2 folding/shape/tertiary structure/position of bonds may change (reject peptide bonds) Missense mutation: valine replaced by alanine Question 3 Nov04 Figs. 3.1 and 3.2 are diagrams showing transcription and translation.

(a)

Identify the structures A to D. [4] A DNA, B ribonucleoside triphosphates (accept RNA nucleotides), C mRNA, D polypeptide chain, E RNA polymerase, F ribosome State where in the cell transcription and translation occur. [2]

(b)

nucleus ribosomes

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Tutorial: PROTEIN SYNTHESIS AND GENE MUTATIONS

(c)

List three additional ways in which the process of transcription differs from translation.[3] Refer to page 23 of Protein synthesis lecture notes Features Monomers used Bonds between monomers Transcription Ribonucleoside triphosphates / RNA nucleotides / ribonucelotides Phosphodiester bonds Translation Amino acids

Peptide bonds

Enzyme involved in forming bonds between monomers Template Direction of elongation

RNA polymerase

Peptidyltransferase

DNA used as template Reading of template is in the 3 to 5 direction Ribonucleotides added to free 3end growing mRNA chain

mRNA used as template

Reading of template is in the 5 to 3 direction Amino acids added to carboxyl end growing polypeptide chain chain

Extend of replication/ transcription Products

Only a certain region (gene) of the DNA molecule is transcribed in a single process. RNA

The whole mRNA molecule is translated in a single process.

Polypeptide

Highlighted are the more significant points of comparisons

(d)

Briefly describe how the structure of F differs from the structure of E. [2]

Features Consists of Has binding sites for Active site formed by

RNA polymerase (E) Protein 1 single molecule DNA folding of polypeptide chain

Ribosome (F) Protein, rRNA 2 subunits mRNA, tRNA Folding of rRNA

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Tutorial: PROTEIN SYNTHESIS AND GENE MUTATIONS

C CHALLENGING QUESTION Q Question 1 NJC08 N Prelims The diagram below (Fig. 3.1) shows the t process of transcript tion of DNA to form RNA A at a particular point in n time

Fig. 3.1 (a a) Describe the events that will occu ur after the point p in time shown in Fig g. 3.1 until the completio on of transcription. [3] E ELONGATION RNA poly ymerase continues to mo ove along the DNA addin ng RNA nuc cleotides an nd catalyzing g the formation of phospho odiester bonds betwee en adjacent R RNA nucleot tides e of RNA strand / synthesizing RN NA in a 5-3 direction. to the 3 end th DNA template a compleme entary base e pairing wit Order of nucleotides added is via (max 2) ON TERMINATIO RNA poly ymerase reac ches a polyadenylation n signal seq quence; ymerase, tran nscription co omplex and RNA dissoc ciate from the e DNA. RNA poly These subseq quent diagra ams b and c in Fig. 3.2 and a Fig. 3.3 show what happens wh hen an artific cially sy ynthesized oligonucleoti o ide binds to the DNA. Th his is a meth hod to silenc ce the expres ssion of the gene.

(b b) (i) Fig.3.2 above (Diag gram b) shows the artific cially synthe esized oligon nucleotide bi inding to the maj jor groove of o the DNA, thus t forming g a triple helix (triplex) in that particular region where it binds. Explain n why, accor rding to Fig. 3.2, the RNA A polymeras se cannot biind to the DN NA at all. [2] Triple helix is no longer comp plementary/ too t large to f fit / of a diffe erent shape as compared to double e helix canno ot fit to active e site of RNA A polymeras se

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Tu utorial: PROTEIN N SYNTHESIS AND A GENE MUT TATIONS

Diagram c above shows the scenario whereby the artificially synthesized oligonucleotide binds to the coding region of the DNA. (ii) With reference to Fig. 3.2 and Fig. 3.3, account for the difference between the outcomes of Diagram b and c. [3] Difference in outcome In b, transcription does not occur at all/no RNA formed while in c, transcription can occur but is terminated early / RNA formed to be incomplete or truncated Reasons In diagram c, Oligonucleotide does not bind to promoter / control region thus transcription complex and RNA polymerase can bind to promoter to start transcription But oligonucleotide disrupts the binding of RNA polymerase as it moves down / oligonucleotide causes RNA polymerase to dissociate from DNA; (c) Despite the differences between the outcomes of Diagram b and c, both eventually silence the expression of the gene. Thus briefly explain what it means to silence the expression of the gene. [1] To prevent production of the protein by preventing production of mRNA/ transcription or causing the protein produced to be nonfunctional.

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Tutorial: PROTEIN SYNTHESIS AND GENE MUTATIONS

AN NDERSON JUNIOR C COLLEGE H2 BIO OLOGY 96 648 JC 1 NSWERS NAME: AN CL LASS:

Evaluation n: PROTEIN N SYNTHE ESIS AND GENE G MUT TATIONS Q1 Q2 Q3 TOTAL L MARKS 25
Question 1 J98P3Q3 Before the anticodon a of f a transfer RNA R molecu ule interact w with a codon n on messen nger RNA, a specific amino acid must be att tached to th he 3' end of f the transfe er RNA mole ecules. This s is carried o out by a specific enz zyme, which is able to re ecognise a tr ransfer RNA A molecule that can be linked to the specific amino acid. Fig. 1.1 below shows a molecule of f transfer RN NA and its co orresponding enzyme.

Fig g. 1.1 (a) Explain what is mea ant by the fol llowing terms: (i) codo on [1] sequence s of f 3 bases/ tri iplet of base es found on m mRNA whic ch encodes for an amino acid (ii) antic codon [1] sequences s of o 3 bases/ triplet of bas ses found o on tRNA whiich undergo oes complem mentary base pairin ng with codon on mRNA

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Tutorial: PROTE EIN SYNTHESIS S AND GENE MU UTATIONS

(b) (i) Explain how the enzyme sho own in the Fig. F 1.1 is sp pecific. [3] enzyme has s active site es which are compleme entary in sh hape to the specific amino acid a and its s correspond ding anti-co odon on tRN NA Enzyme holds only 1 type of amino acid and on ne of its specific set of tR RNA in place e for the formation of f covalent bo ond between n them A nu umber of can ndidates inco orrectly refe erred to the a anticodons o on the tRNA A binding the e codons on th he enzyme e the minimu um number of these enz zymes in a c cell [1] (ii) State 20 me candidate es confuse this with the t 64 poss ns and mad de reference e to 64 sible codon Som enzymes d. [4] (c) Outline how RNA is synthesized RNA A polymeras se binds to promoter p on n template D DNA strand Adds s free RNA nucleotides n s / ribonucle eoside triph hosphates Via complemen c ntary base pairing p with template mRN NA elongates in 5 to 3 direction / RNA R

[T Total: 10] Question 2 Nov 11 Fig. 2.1 sho ows a prokar ryotic ribosom me during protein synthe esis.

Fig. 2.1

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Tutorial: PROTE EIN SYNTHESIS S AND GENE MU UTATIONS

(a)

Identify A-D. [4] A: Large ribosomal subunit (reject ribosome) B: Polypeptide chain (reject amino acid) C: tRNA D: mRNA State the role of rRNA in protein synthesis [3] rRNA together with the proteins, forms small & large ribosomal subunit. Within the ribosome, rRNA are able to bind mRNA and tRNA to hold them in proximity for translation to occur Has enzymatic function- peptidyl transferase, to catalyse peptide bonds formation between amino acids. [Total: 7]

(b)

Question 2 J94P2Q1 An inherited disease in humans, which results in muscle paralysis, is caused by a dominant mutant allele of the gene coding for a sodium ion channel protein found in the cell surface membrane of skeletal muscle. Sequencing of DNA from normal and affected individuals has shown that the mutation is due to a single base substitution. This results in the amino acid methionine being replaced by valine in the segment of the protein that forms the channel. The figure shows the base sequence analysis of the relevant part of the DNA from an affected individual.

(a) From the sequence in the figure, identify (i) the base that is missing in the abnormal sequence adenine (reject: adenosine) [1] (ii) the base that has been put in its place: guanine (reject: guanosine) [1]

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(b) Explain why changing a single base in the gene coding for a protein may have a major effect on the properties of a protein. [4] Missense mutation: change / different amino acid encoded R-group of new amino acid different charge/polarity Affected amino acid is found in essential region of protein (give 1 example: holds polypeptide in its shape / forms active site/ binding site ) affects R group interactions change folding of polypeptide change tertiary structure/ 3D conformation of protein

Weaker candidates referred to a codon coding for a protein! Some referred to bases being in the actual protein formed! (c) Suggest why single base substitution do not always have such a major effect on protein structure. [2] redundancy in genetic code / degenerate genetic code/ more than one codon for each amino acid / 20 amino acids and 64 possible codons hence a single base do not change the codon no change in amino acid changed amino acid occurs in in non-essential region of protein give 1 example: : not involved in holding polypeptide in its shape / does not form active site/ does not form binding site amino acid change to amino acid with similar R group property similar polarity/ charge folding of polypeptide is not affected

[Total: 8]

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