3.Gene Expression

CfE Higher Human Biology

Unit 1 Human Cells

Knowledge from Nat 5 Biology

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• What is a gene?

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• Give three examples of proteins and their function

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• What are the sub-units of proteins?

• a) Which cell structure makes proteins?

b) Name the molecule that carries a copy of DNA out

of the nucleus and to this structure?

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• Why is the shape of the protein molecule important?

Higher Human Course Specifications

Higher Human Course Specifications

Higher Human Course Specifications

Success Criteria:

• Describe what gene expression is
• Name the three types of RNA
• Compare and contrast the structure of RNA with DNA
• Describe the structure and function of mRNA
• State what a codon is
• Describe the structure and function of tRNA
• State what an anticodon is
• State which two types of molecules make up a ribosome

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Learning Intention:

To learn about the process of gene expression

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• All about making proteins!
• The human body requires over 100 000 proteins.
• These are synthesised inside cells during a complex process involving DNA and RNA (the nucleic acids), and ribosomes.

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What is gene expression?

• Proteins are composed of amino acids joined together in a specific sequence.

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• This is determined by the sequence of DNA bases in the nucleus of our cells.

What is gene expression?

• Gene expression is how the DNA instructions are transferred into the cytoplasm using RNA, and how a protein is actually constructed on the ribosomes. 

https://www.yourgenome.org/video/from-dna-to-protein (2mins)

Not all DNA codes for protein.

Only a fraction of the genes in a cell are expressed.

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As little as 1% of the DNA in humans codes for proteins (approx. 21,000 protein coding genes)

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A large proportion of the other 99% involved in the control of gene expression

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Gene expression is the process by which specific genes are activated to produce a required protein.

An overview of gene expression

This involves transcribing the genetic code from DNA into RNA, and then translating it from RNA into a protein

What do you already know about protein synthesis?

(a) Ribonucleic acid (RNA)

Transcription and translation of a gene involves ribonucleic acid or RNA

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Can you identify what's different from DNA?

Ribonucleic acid (RNA)

Ribonucleic Acid (RNA) is a single stranded nucleic acid that is produced from a template of DNA.

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It building blocks are nucleotides just like DNA, but as it is single stranded it doesn’t form the famous double helix.

RNA nucleotides� (the building blocks of RNA)

Each nucleotide contains a phosphate group, a sugar (ribose) and one of four bases:

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• Adenine (A)
• Uracil (U)
• Guanine (G)
• Cytosine (C).

Copy and complete the table to summarise the differences between DNA and RNA

Double / two

Single / one

Adenine

Thymine

Guanine

Cytosine

Adenine

Uracil

Guanine

Cytosine

Deoxyribose

Ribose

Nucleus

Nucleus and cytoplasm

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3 forms of RNA for 3 different jobs!

Produced from a DNA template. Carries a copy of the DNA code from the nucleus to ribosomes

Carries a specific amino acid to the ribosome for attachment to peptide chain during protein synthesis

Forms part of the ribosomes along with other structural proteins

mRNA and codons

• mRNA bases are arranged in triplets of bases called codons

• Each codon is the code for a specific amino acid (amino acids are the building blocks of protein)

There are 20 different amino acids BUT there are 64 different codons.

What can you say about the relationship between the number of codons and amino acids?

You will not be expected to learn every codon but you will need to know how to interpret the codons using a code sheet

Quick Quiz �Using a genetic codon decoder

Using you copy of the genetic code sheet answer the following questions. When you are finished compare your results with your work partner.

Questions

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1. The mRNA codon CCC codes for which amino acid?

A. Proline (Pro)

2. The mRNA codon UGU codes for which amino acid?

A. Cysteine (Cys)

3. Which amino acid(s) has only one codon?

A. tryptophan (Trp) and methionine (Met)

4. There are four codons which code for something

other than amino acids. Can you find them? What do

they code for?

A. start and stop codons

5. What does the mRNA codon AUG code for?

A. start codon and methionine (Met)

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Codon quiz

Transfer RNA (tRNA)

Each tRNA molecule carries a SPECIFIC amino acid

tRNA is a single strand that folds into its specific shape through the bonds between complementary base pairs.

Three bases called the anticodon are exposed and compatibly base pair with codons on the mRNA strand

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Ribosomes are formed from proteins and ribosomal RNA (rRNA)

rRNA and ribosomes

Ribosomes �- the site of protein synthesis

Ribosomes are found in the cytoplasm, either free floating or attached to the rough endoplasmic reticulum

• Ribosomes floating freely are used to synthesise proteins for use within the cell

• Those attached to the endoplasmic reticulum synthesise proteins for export or as part of the cell membrane.

Summarise the 3 types of RNA

RNA

More genetic codes activity

Translate the following DNA sequences into mRNA and tRNA

(b) The stages of gene expression (from DNA to protein)

Learning Intention:

Learn about RNA polymerase, transcription and RNA splicing

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Success Criteria:

• Describe the role of RNA polymerase
• Describe the process of synthesising a primary transcript of mRNA
• Describe the process of RNA splicing
• Describe the difference between introns and exons
• Identify where the processes of transcription and RNA splicing occurs in the cell

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Gene expression �Introductory / Revision videos

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• Crash Course Biology Transcription and Translation (14mins)

https://www.youtube.com/watch?v=itsb2SqR-R0

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• Amoeba sisters (9mins)

https://www.youtube.com/watch?v=oefAI2x2CQM

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• Transcription and Translation: From DNA to Protein (6mins)

https://www.youtube.com/watch?v=bKIpDtJdK8Q

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The stages of gene expression

The process of turning the information on DNA into a protein consists of these stages:

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• Transcription
• RNA splicing
• Translation

Transcription

Transcription is the production of a primary mRNA transcript from a DNA template

If a cell wants to make a protein, e.g. insulin, then the section of the chromosome with the insulin gene* needs to unwind to expose the bases.

*The insulin gene (INS gene) is located on chromosome 11 between base pairs 2,159,779 to 2,161,209

RNA polymerase

RNA polymerase moves along DNA unwinding the double helix and breaking the hydrogen bonds between the bases.

RNA polymerase synthesises a mRNA molecule.

The process of transcription

http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.swf

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• RNA polymerase adds free RNA nucleotides to their complementary base pairs on the DNA.

• The RNA nucleotides are held in place by hydrogen bonding while strong covalent bonds form between the phosphate of one nucleotide and the ribose sugar of the adjacent nucleotide.

• When transcription is complete the RNA polymerase enzyme is released.

DNA template strand

mRNA newly synthesised strand

RNA polymerase

Complete the diagram by adding the mRNA strand for this DNA base sequence

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Summary of transcription

RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence 

Nucleotides (NTP stands for Nucleoside triphosphates which are monomers of RNA and DNA) 

Real-time transcription

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RNA polymerase moves along the DNA and synthesises a primary transcript of mRNA from RNA nucleotides by complementary base pairing

Certain sections will then be removed to make a mature transcript

Primary and mature transcripts of mRNA

Gene on chromosome

(DNA)

Primary transcript

(mRNA)

Mature transcript

(mRNA)

RNA Splicing

The primary transcript of RNA is composed of introns and exons.

• Introns are non-coding regions of genes.

The non-coding introns of the primary transcript of mRNA are removed during RNA splicing.

• Exons are coding regions of genes (to produce a protein).

• In RNA splicing the primary transcript is cut at boundary points between the introns and exons.

• The non-coding introns are removed and the coding exons are joined together.

• The mature mRNA then leaves the nucleus, enters the cytoplasm and goes to a ribosome for the next stage: translation into a protein molecule.

RNA splicing animation

RNA splicing – summary diagram

Mature mRNA transcript

RNA splicing activity

Primary transcript

Mature mRNA

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Translation

• The code on mature mRNA is translated into a chain of amino acids creating a polypeptide.
• This occurs at the ribosomes.

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You Tube: Translation 3 minutes 30

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Learning Intention:

To learn about tRNA and the process of translation

Success Criteria:

• Explain the function of start and stop codons
• Explain the process by which a polypeptide is formed at the ribosome
• State the bonds between the amino acids in a polypeptide chain
• Identify where the process of translation occurs in the cell

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Start and Stop Codons

Start codons determine where translation of a gene begins and

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Stop codons determine where translation of that gene ends.

Stages of Translation

1. Mature mRNA attaches to a ribosome. The mRNA base sequence is arranged in groups of three bases called codons each which code for a SPECIFIC amino acid

2. The tRNA molecule’s anticodon compatibly matches with the mRNA codon creating the ordered sequence of amino acids. The tRNA molecule carries a specific amino acid.

U A C

Codon 5

Codon 4

A U G C C U A C G A G G G C U A C G C G U A U U

Codon 1

Codon 2

Codon3

Codon 6

Codon 7

Codon 8

G G A

3. Once the tRNA has delivered its specific amino acid to the growing polypeptide, it leaves the ribosome.

Real time Translation-RNA-to-protein

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Polypeptides and peptide bonds

• At the ribosome mRNA is translated into a polypeptide.

• A polypeptide is a long chain of amino acids

• The amino acids join each other by peptide bonds.

• All protein are polypeptides.

Quick Questions

• If there is an adenine in the DNA molecule, what is the complementary base pair found on the primary mRNA transcript?
• What is a group of 3 bases called in
• mRNA
• tRNA

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3. Name the enzyme that catalyses stage 1 of this process

Uracil

codon

anti codon

RNA polymerase

• State the term used to describe the coding regions of a primary mRNA transcript
• Explain why the primary mRNA transcript is so much shorter than chromosomal DNA

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• Explain why the mature mRNA transcript is shorter than the primary mRNA transcript

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Exons

Only one gene is transcribed to form mRNA - the primary mRNA only codes for one protein

Introns (non coding regions of genes) are removed in RNA splicing. This means the mature mRNA transcript only contains exons (coding regions of genes)

• The sequence of bases in DNA strand is shown below
• CGA TTA ACT GTC AAC

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The sequence of bases in the mature mRNA transcript, formed from the section of the DNA strand, is shown below.

GCUAUAAGUUG

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• Using this mature mRNA transcript, state the order of bases in the intron present in the primary mRNA transcript

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AUGC

GCU AAU UGA CAG UUG

GCU A__ U_A _AG UUG

Introns

What is an anticodon for:

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• Serine
• Asparagine
• Methionine

Describe the structure of RNA and the process of transcription (9)

Step 1: Transcription

This occurs in the nucleus of a cell.

DNA acts as a template for the synthesis of a primary mRNA transcript.

RNA splicing removes introns to produce mature mRNA

The mature mRNA will carry the code to the ribosomes

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Step 2: Translation

This occurs at the ribosomes within the cytoplasm of the cell.

The mRNA codons are read and translated into a chain of amino

acids called a (poly)peptide chain.

This is the simplest protein structure and is known as the

primary protein structure

Summary

From DNA to Protein 2 minutes 40

Protein Structure

Learning Intentions:

To learn about polypeptides

Success Criteria:

• Describe what a polypeptide is by naming their building blocks and the bonds between these.
• Name the types of bonds that hold polypeptides in their 3D shape
• State what determines the function of a protein
• State what determines an organism's phenotype, and what else affects this.

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Assembly and modification of �proteins after synthesis

1. Primary structure

Amino acids are linked by peptide bonds to form polypeptides.

2. Secondary and tertiary structure

Polypeptide chains fold to form the three-dimensional shape of a protein, held together by hydrogen bonds and other interactions between individual amino acids.

*Note – knowledge of primary, secondary, tertiary and quaternary structure not required for Higher Biology, but must be able to describe how proteins are built as described in the previous two slides

Building up proteins*

Proteins have a large variety of shapes which determines their function

Functions include:

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• Enzymes

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• Hormones

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• Antibodies

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• Structural proteins

Protein functions

True or False?�If false, what change would make the statement true?

DNA to protein role play

• DNA polymerase promotes the extension of nucleotides of the newly synthesising mRNA molecule.
• RNA is single stranded and is composed of nucleotides containing a ribose sugar, phosphate and four bases
• Once the introns have been removed from the mRNA it changes from the mature transcript to the primary transcript
• The order of the exons is unchanged during splicing.
• Each triplet of bases on the mRNA molecule is called an anti-codon and codes for a specific amino acid.
• Strong covalent bonds join adjacent nucleotides during mRNA synthesis.
• Transcription occurs on the ribosomes within the cytoplasm of a cell.
• A ribosome is made from protein
• AUG is a stop codon during translation.

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Describe protein synthesis under the following headings:

(i) Transcription of DNA

(ii) Translation of mRNA

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10 marks

(i) Transcription of DNA

1 DNA unzips/hydrogen bonds break/DNA strands separate.

2 RNA nucleotides pair with DNA bases.

3 Guanine pairs with cytosine, uracil pairs with adenine. (not base letters)

4 Sugar phosphate bonds form/sugar phosphate backbone forms.

5 This requires ATP/enzymes/RNA polymerase

6 Introns/non-coding regions are removed from mRNA/the primary transcript

(ii) Translation of mRNA

7 mRNA attaches/moves to the ribosome.

8 tRNA carries amino acid to mRNA /ribosome.

9 Each tRNA molecule is attached to a specific amino acid.

10 tRNA/mRNA has a anticodon/codon of three bases.

11 Anticodon binds to / aligns with codon.

12 Order of codons/bases determines the order of amino acids.

13 Peptide bonds form between amino acids.

14 Ribosome moves along the mRNA strand.

• (Translation/process) begins at a start codon/ends at a stop codon.

Learning Intention:

To learn how different proteins can be expressed from one gene

Success Criteria:

• Explain how different proteins can be synthesised from one gene
• Describe how different mature transcripts are made from the same primary transcript

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One Gene, Many Proteins

From earlier…

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The body has around 21000 genes

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BUT

produces 100,000 proteins.

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How is this possible??

Alternative RNA Splicing

The same gene can produce many different proteins through the process of alternative RNA splicing.

Different mature mRNA transcripts are produced from the primary transcript depending on which exons are retained.

So from the same primary mRNA transcript you can get many different proteins.

The phenotype is physical appearance and characteristics expressed by an individual

What determines the phenotype?

The phenotype is determined by:

• environment - environmental factors such as diet, climate, illness and stress influence the phenotype

• the proteins produced as a result of gene expression.

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The Influence of �Environmental Factors

The colour of our hair, shape of our features and some of the instinctive ways we behave are influenced by our genes (genotypes)

BUT..... Our weight, even our height and our skills and qualities are influenced by the environment, our experiences and the people around us.

Research Activity: Protein Function

You will have come across many proteins before and covered some of the many roles they undertake in living organisms.

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Choose ONE of the proteins listed below to research and complete its identity card, which will be used to create a classroom display.

keratin

tubulin

insulin

porin

pepsin

catalase

amylase

haemoglobin

antibody

myosin

actin

elastin

phosphorylase

oxytocin

cytochromes

collagen

helicase

integrin

polymerase

kinase

Overall structure of the protein: _____________________________________

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Where is the protein produced?:

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_____________________________________

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Protein function: _____________________________________

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_____________________________________

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_____________________________________

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_____________________________________

Protein identify card template

Key Vocabulary

Nucleotide

Single stranded

Phosphate

Ribose sugar

Uracil

mRNA

tRNA

rRNA

Amino acids

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Introns

Exons

Coding

Non-coding

Transcription

RNA splicing

RNA polymerase

Complementary

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Polypeptide

Translation

Codon

Anti-codon

Ribosome

Start codon

Stop codon

Phenotype

Related activity – Electrophoresis (p31)

• Electrophoresis is a very important technique in biochemistry and molecular biology. What is electrophoresis?

2. What three factors affect how a protein moves through the gel?

3. Why is it important to eliminate two factors before you can do a proper separation of the different proteins present of 4 fish species.

4. What is the standard sample for?

5. How do you know that protein g has the smallest molecular weight (kDa)?

6. Which species of fish has all of the seven proteins looked for?

Starter questions

Codons

Starter questions

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• Every cell contains the same DNA and therefore the same genes. However, depending on the role of the cell, only certain genes are ‘expressed’. What does that mean?

2. In protein synthesis, what is the difference between transcription and translation?

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3. A mRNA molecule has a 9-base sequence of UACCGCAAA which needs to be translated into a protein. Using the codon-decoder, what is the sequence of amino acids in this protein?

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Starter questions

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• Temperature questions about the PCR
• What temperature does it need to be for DNA polymerase to do its work?
• What temperature does it need to be for the primers to work?

2. What does the PCR actually do?

3. (a) What is the function of tRNA?

(b) Which molecule is longer: mRNA or tRNA?

4. For how many amino acids does a mRNA code for if it consists of 1734 nucleotides?

5. What is the difference between the primary transcripts and the mature transcripts of a mRNA molecule?

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Fill in the missing words in boxes 1-8

Starter questions

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1. What are introns?

2. How is it possible that you can get more than one protein from one gene?

3. What are the three temperatures used in the PCR and explain the importance of them.

4. What is the role of RNA polymerase?

5. Why is the shape of proteins so important?

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Starter questions

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• How can different proteins be expressed from one gene?
• What kind of bonds link amino-acids?
• What do you call a chain of amino-acids bonded together?
• Proteins fold into a 3D shape due to various bonds happening between the different amino-acids. Name one of these bonds.
• Why is the shape of proteins so important?

DNA structure

• What do you find at the 3’ and 5’ end? A deoxyribose or a phosphate?
• Why is the DNA molecule described as a ‘double-stranded antiparallel structure’?

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DNA replication

1. (a) What is the structure of a primer?

(b) What is the function of a primer?

2. What happens during the second stage of the PCR process where the temperature is reduced to 50-65°C

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Gene expression

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• What is the function of tRNA?
• What is RNA splicing?
• How can you get more than one protein from

one gene?

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4. What is gel electrophoresis?

Gene expression - quick quiz

• Name the molecule produced by transcription of DNA.

A. (primary) mRNA / messenger RNA

• Name the molecule produced by the translation of mRNA at the ribosomes.

A. protein / polypeptide

• Name the locations of (a) transcription and (b) translation in gene expression.

A. (a) nucleus (b) ribosomes in cytoplasm

• Give 2 differences in the structure of DNA and RNA.

A. DNA double-stranded, RNA single stranded

DNA has deoxyribose, RNA has ribose sugar

DNA has thymine, RNA has uracil

• Which molecule carries specific amino acids to the ribosome?

A. tRNA / transfer RNA

• Name the 2 things a ribosome is composed of.

A. rRNA / ribosomal RNA and proteins

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Splicing quick quiz

• Name the sequence of bases in eukaryotic genes which (a) do and (b) do not code for proteins.

(a) exons

(b) introns

2. Name the non-functional mRNA molecule which contains both coding and non-coding regions.

Primary transcript

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3. Name the process that involves the modification of the non-functional mRNA molecule to form the functional mRNA.

RNA splicing

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More challenging questions

• Describe the function of mRNA. (2)

carries a complementary copy of the sequence of DNA bases/copy of genetic code (1) from the nucleus to the ribosome (1)

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2. Describe the function of tRNA. (2)

transfers specific amino acids (1) to the ribosome (1)

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3. Describe the general structure of a molecule of tRNA.

amino acid attachment site (1)

triplet anticodon site (1)

single folded strand of RNA held by complementary base pairs (1)

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