Starter Write three practical uses of PCR on a show me board. Describe the purpose of PCR to your partner.

Task Using your learning outcomes for key areas 1.1 and 1.2, evaluate your knowledge. You can use any method you like (ticks & crosses, smiley and sad faces, colour codes).

Control of Gene Expression Key Area 1.3 Control of Gene Expression

KA1.3 (a) Protein Synthesis Outcomes Covered KA1.3 (a) Protein Synthesis

Learning Outcomes Describe the basic structure of an RNA nucleotide State the differences between DNA and RNA Name the three types of RNA and state their functions Name each stage of protein synthesis and their location Describe stage one of protein synthesis Identify complementary base pairs between DNA and RNA Name the enzyme used in stage one

RNA – Ribonucleic Acid RNA is made up of a single strand of nucleotides. Each nucleotide consists of a phosphate group, a ribose sugar and a base. phosphate base There are four bases: Adenine Uracil Guanine Cytosine ribose sugar

Comparison of DNA and RNA Type of sugar deoxyribose ribose Bases adenine, cytosine, guanine and thymine adenine, cytosine, guanine and uracil Number strands two one Location only in nucleus moves from nucleus to cytoplasm

THINK PAIR SHARE What type of RNA do you already know about and what’s its function?

Three Types of RNA mRNA (messenger) – copies the code from the DNA molecule and carries it to the ribosomes. tRNA (transfer) – found in the cytoplasm where it binds to specific amino acids and transports them to the ribosome. rRNA (ribosomal) – forms a complex with protein molecules to make the ribosome.

Show me board task On your board, write down as much as you know about protein synthesis.

Protein Synthesis Protein synthesis has two stages: Transcription Translation

transcribe – to make a copy Transcription transcribe – to make a copy The first stage of protein synthesis takes place in the nucleus. RNA polymerase unwinds the DNA strand. Hydrogen bonds are broken and the bases are exposed. RNA polymerase

Transcription Free mRNA nucleotides in the nucleus form complementary base pairs with the coding strand of the DNA. Weak hydrogen bonds form between bases. Coding strand DNA base RNA base Adenine Uracil Thymine Guanine Cytosine RNA polymerase Non - coding strand

A triplet of bases on mRNA is called a codon. Transcription Strong chemical bonds form between the phosphate of one nucleotide and the ribose of the next nucleotide, building the mRNA strand. RNA polymerase can only add nucleotides to the 3’ end of the growing mRNA molecule. The weak hydrogen bonds that were holding the DNA and mRNA strands together break, allowing the mRNA primary transcript to leave the nucleus and enter the cytoplasm. A triplet of bases on mRNA is called a codon.

transcription animation Hydrogen bonds reform between the two DNA strands and the DNA molecule rewinds to form a double helix. transcription animation

You should now be able to . . . Describe the basic structure of an RNA nucleotide State the differences between DNA and RNA Name the three types of RNA and state their functions Name each stage of protein synthesis and their location Describe stage one of protein synthesis Identify complementary base pairs between DNA and RNA Name the enzyme used in stage one

Starter/Task DNA and RNA molecules are found in the cells of both eukaryotes and prokaryotes. DNA molecules are double-stranded whereas RNA molecules are single-stranded. (i)Give two other structural differences between DNA and RNA. (ii) Describe the function of RNA polymerase in the synthesis of a primary transcript.

Learning Outcomes 8. Describe the process of RNA splicing to form a mature transcript 9. Describe stage two of protein synthesis 10. State the function of start and stop codons 11. Identify complementary base pairs between mRNA and tRNA

RNA Splicing There are long stretches of DNA that do not play a part in the coding to make proteins. Non-coding regions are called introns. The introns are removed in a process called RNA splicing. The exons are coding regions and are joined (spliced) together to form mature transcript.

Task Collect two different coloured highlighters or two different coloured sheets of paper to help you form your next note

RNA Splicing After the primary transcript has been produced, the introns must be cut out. The exons join together to produce a mature mRNA strand. 5’ 3’ 3’ 5’ 5’ 3’

RNA Splicing RNA splicing

Producing Different RNA Transcripts Depending on which RNA segments are treated as exons and introns different segments can be spliced together to produce different mRNA transcripts.

Translation The second stage of protein synthesis takes place in the ribosome. Translation is the synthesis of protein as a polypeptide chain under the direction of mRNA. The process requires energy, in the form of ATP.

transfer RNA (tRNA) Found in the cytoplasm. Composed of a single strand of nucleotides. Hydrogen bonds between it’s nucleotides cause the tRNA to fold back on itself creating a 3D structure.

transfer RNA (tRNA) Each molecule of tRNA has only one particular triplet of bases exposed. This triplet is called an anticodon. Each anticodon is complementary to an mRNA codon. Each tRNA molecule carries a specific amino acid at its attachment site.

tRNA

Translation There are many different types of tRNA in one cell. Each tRNA picks up it’s specific amino acid at it’s site of attachment and carries it to the ribosome. The amino acid is added to the growing end of the polypeptide chain.

Ribosome Ribosomes contain ribosomal RNA (rRNA) and enzymes essential for protein synthesis. The function of a ribosome is to bring tRNA molecules in contacts with mRNA. Ribosomes have one binding site for mRNA and three binding sites for tRNA.

Ribosomes tRNA binding site P holds the tRNA carrying the growing polypeptide chain. Site A holds the tRNA carrying the next amino acid to be joined to the growing chain by a peptide bond. Site E discharges a tRNA from the ribosome once its amino acid has becomes part of the polypeptide chain.

translation animation

Translation A molecule of tRNA carrying its specific amino acid (methionine) becomes attached at site P by hydrogen bonds. The mRNA codon at site A then forms hydrogen bonds with its complementary anticodon. Before translation can begin, a ribosome must bind to the 5’ end of the mRNA template. This allows the mRNA’s start codon (AUG) to be in position at binding site P.

Translation When the first two amino acid molecules are adjacent, they become joined by a peptide bond to make a polypeptide chain.

Translation As the ribosome moves along one codon, the tRNA that was at site P moves to site E and is discharged from the ribosome to be reused. The process continues to be repeated allowing the mRNA to be translated into a complete polypeptide chain.

Translation Eventually, a stop codon on the mRNA is reached. Site A on the ribosome becomes occupied by a release factor which frees the polypeptide from the ribosome.

Polyribosome A single molecule of mRNA is used to make many copies of the polypeptide. This multiple translation is achieved by several ribosomes becoming attached at the same time. This string of ribosomes on the same mRNA molecule is called a polyribosome.

You should now be able to. . . 8. Describe the process of RNA splicing to form a mature transcript 9. Describe stage two of protein synthesis 10. State the function of start and stop codons 11. Identify complementary base pairs between mRNA and tRNA

Starter/Task

KA 1.3 (b) Expression of Proteins Outcomes Covered KA 1.3 (b) Expression of Proteins

Learning Outcomes State at which two points the mechanism of changing a protein can occur Describe the process of alternative RNA splicing Name the two types of post-translational modification Name the component of a glycoprotein and state its function Name the components of a regulatory protein and state how it is activated

One gene, many proteins... Until very recently, it was thought that each gene could produce only one protein The human genome contains between 20,000 and 25,000 genes However, there are in excess of 1 million proteins.

Altering proteins The mechanism to produce different protein can occur at two points: After transcription After translation

After transcription Modification after transcription is ‘Alternative RNA splicing’. mRNA can be edited by assembling a different sequence of introns and exons for translation. Many mature transcripts of mRNA can be derived from the same sequence of DNA.

Alternative RNA splicing

Alternative RNA splicing Arranging exons in different patterns enables cells to make different proteins from a single gene.

After translation Modifications after translation are ‘Post- translational modifications’ Two types of post-translational modification that may be required for protein function are Cleavage Molecular addition

1. Cleavage A single polypeptide chain may need to be cleaved (cut) by enzymes to become active.

Cleavage in insulin Insulin becomes active when a central portion is cleaved. This leaves 2 chains joined by sulphur bridges.

2. Molecular addition Protein structure can be changed by adding carbohydrate or phosphate. Altering structure will change its function, adding to the diversity of proteins produced from a single gene.

Adding carbohydrate Adding carbohydrates to a protein produces glycoprotein Glycoproteins normally function as signalling, membrane and recognition molecules

Adding phosphate Adding phosphate to a protein usually forms a regulatory protein These will be inactive until phosphorylated (phosphate added)

You should now be able to . . . State at which two points the mechanism of changing a protein can occur Describe the process of alternative RNA splicing Name the two types of post-translational modification Name the component of a glycoprotein and state its function Name the components of a regulatory protein and state how it is activated

Starter From your knowledge of N5: Describe simply how proteins are produced.

KA 1.3 (c) Gene Expression and Protein Structure Outcomes Covered KA 1.3 (c) Gene Expression and Protein Structure

Learning Outcomes Define the terms ‘genotype’ and ‘phenotype’ Describe how environmental factors can affect an organisms phenotype Define the term ‘gene expression’ Name the chemical elements found in proteins Name the type of bond that links amino acids together Name the chain formed when amino acids link together State the consequences to the structure of this chain when hydrogen bonds form between the amino acids Describe the effect of further linkages (tertiary structure) on the protein Describe the quaternary structure of a protein Names the four categories of proteins and describe their function

Genotype The genotype of an organism is determined by the sequence of DNA bases in its genes The genetic code Some species have a genetic code that is quite similar to another species

Phenotype The phenotype of an organism is its physical and chemical appearance This depends on the proteins that are synthesised in that cell Protein synthesis depends on gene expression

Phenotype Production of phenotype/protein can be affected by environmental factors acting inside or outside of the cell.

Gene expression The nucleus of every cell in an organism contains the same genetic information Genes are switched ‘on’ or ‘off’ in cells to make a specific protein. This is expression. No-one wants a hairy eyeball.....

Proteins Proteins are composed of carbon, hydrogen, oxygen and nitrogen. Sometimes they contain sulphur

Proteins Proteins are made up of subunits Amino acids There are 20 different types of amino acid Proteins vary in sequence of amino acids and length

Polypeptides (primary structure) Amino acids in a specific order become linked by peptide bonds They form polypeptide chains

Hydrogen bonding (secondary structure) Hydrogen bonds can form between the amino acids on a polypeptide chain The chain becomes folded or coiled Folded (β sheet) Coiled (α helix)

Further Linkages (tertiary structure) Hydrogen bonding brings different parts of the polypeptide chain into contact Cross connections between amino acids occur Bridges(bonds) between sulphur atoms Charged bonds (+/- interactions) More hydrogen bonding

Further Linkages (tertiary structure) These cause the specific 3-dimensional shape that gives each protein its function

Quaternary structure Non-protein elements are added E.g. Iron in haemoglobin protein

Classes of proteins Proteins can be categorised by their function Enzymes Structural proteins Hormones Antibodies The function is dependent on the structure

Enzymes Enzymes increase the rate of chemical reactions needed to sustain life The folding of the protein exposes an active site. The active site is complementary to a specific substrate.

Structural protein Structural proteins play a vital role in the structure of every cell E.g. Membrane protein

Hormones Hormones have a regulatory role in growth and metabolism. They act as chemical messengers that travel in the blood. E.g. Insulin in regulation of blood glucose Q. How would the action of insulin impact the availability of ATP in the body?

Antibodies Antibodies are produced by white blood cells to defend against foreign antigen