WJEC AS Biology Unit 1.5 - Nucleic acids and their function

Nucleotides

Monomer of nucleic acid comprising a Penrose sugar, a nitrogenous base and a phosphate group

Structure of nucleotides (description)

• Three components, combined by condensation reactions;

  • A phosphate group; which has the same structure in all nucleotides

  • A pentose sugar; in RNA = ribose and in DNA = deoxyribose

  • An organic, nitrogenous base

Structure of nucleotides (diagram)

DNA nucleotides

• Phosphate group

• Deoxyribose pentose sugar

• Nitrogenous base (A, C, G, T)

RNA nucleotides

• Phosphate group

• Ribose pentose sugar

• Nitrogenous base (A, C, G, U)

ATP nucleotides

• 3 Phosphate groups

• Ribose pentose sugar

• Adenine nitrogenous base

ATP as an energy carrier

• Known as the universal energy currency as it is a common energy source/energy carrying molecule used in all cells in all living organism

ATP synthesis

• Formed when ADP (adenosine diphosphate) is combined with a third phosphate group (Pi; inorganic phosphate)

• Endergonic reaction as it requires energy to be taken in

• The energy is then trapped in bonds between the phosphate groups

• ADP is phosphorylated to ATP, which means it gains an inorganic phosphate group

• ADP + Pi + Energy —> ATP + Water

• Condensation reaction

• Catalysed by enzyme

Hydrolysis of ATP

• energy is released

• ATP is hydrolysed to ADP and Pi

• Exertions reaction as it releases energy

• 30.6 kilojoules of energy is released per mole of ATP

Energy required to combine ADP and inorganic phosphate to form ATP and water

• comes from exerting reactions, e.g. cell respiration

ATP as the “universal energy currency”

• common energy source used in all biochemical reactiosn in all living organisms

Phosphorylation

The addition of a phosphate group

Advantages of ATP as a supplier of energy/energy carrier molecule

• Hydrolysis of ATP to ADP and Pi = single reaction that releases energy immediately. Breakdown of glucose requires many intermediates and takes longer for energy to be released

• One enzyme needed to release energy from ATP (ATP Synthase). Many needed to release energy from glucose glucose

• More manageable amount of energy released

• Easily regenerated from ADP and Pi

• Provides common source of energy for all chemical reactions —> increasing efficiency + control in the cell

• Small molecule —> can easily diffuse throughout the cytoplasm

Uses of ATP

• Metabolic processes

• Active transport

• Movement

• Nerve transmission

• Secretion

• Cell division

DNA

• DNA is made from one strand of nucleotides linked by hydrogen bonds between the bases to another strand that runs antiparallel to the first.

• composed of 2 polynucleotide strands wound around each other —> double helix structure

• Pentose sugar in nucleotides = deoxyribose

• Four organic bases = 2 purines; adenine and guanine + 2 pyrimidines; cytosine and thymine

• Sugar phosphate back bone formed by deoxyribose sugar and phosphate groups

• Complementary base pairing; A+T and C+G

• Hydrogen bonds join the bases, forming complementary pairs + maintaining the shape of the double helix

• Adenine + Thymine joined by 2 Hydrogen bonds

• Cytosine + Guanine joined by 3 hydrogen bonds

Antiparallel strands in DNA

• The 2 polynucleotide strands antiparallel

• The nucelotides in 1 strand are arranged in the opposite direction from those in the complementary strend

• parallel but facing in opposite directions

• Run in opposite directions; one from the 5’ prime end to the 3’ prime end, the other from the 3’ prime end to the 5’ prime end

Pyrimidine base

• Bases made up of a single six-sided ring

• Class or nitrogenous bases including Cytosine and Thymine in DNA and Cytosine and Uracil in RNA

Purine bases

• Bases made up of one six-sided ring and one five-sided ring

• Class of nitrogenous bases including adenine and guanine in both DNA and RNA

Bond between nucleotides in the backbone

Phosphodiester bonds

Bonds between bases in DNA

Hydrogen bonds;

• 2 between A and T

• 3 between C and G

RNA

• single stranded polynucleotide

• Contains the pentose sugar ribose

• Contains the nitrogenous bases Adenine + Guanine (purines) and Cytosine and Uracil (pyrimidines)

• Three types;

  • mRNA; made as a complementary copy of the DNA genetic code in the nucleus during transcription. The molecule length is related to the length of the gene transcribed. It attaches to a ribosome in the cytoplasm. long, single stranded molecule. Synthesised in the nucleus + carries the generic code from DNA to ribosomes in cytoplasm

  • rRNA; found in the cytoplasm + comprises large, complex molecules. forms ribosomes

  • tRNA; carries an amino acid at the 3’ end and an anticodon arm to attach to the mRNA. small single stranded molecule. Folds so that, in places, there are base sequences —> complementary pairs

tRNA structure

• The 3’ end of the molecule has the base sequence cytosine-cytosine-adenine where the specific amino acid the molecule carries is attached

• Also carries a sequence of 3 bases = anticodon

• molecules of tRNA transport specific amino acids to the ribosomes in protein synthesis

Properties, structure and formation to function of ATP

• ATP releases energy in one hydrolysis reaction controlled by one enzyme.

• ATP releases energy in small, usable amounts.

• ATP travels easily to where it may be used for secretion, muscle contraction, nerve transmission or active transport.

How DNA is suited to its functions

• very stable molcule and ita information content passes essentially unchanged from generation to generation

• very large molcule and carries a large amount of genetic information

• the 2 strands are able to seperate, as they are held together by hydrogen bonds

• as the base pairs are on the inside of the double helix, within the deoxyribose-phosphate backbones, the genetic information is protected

Major functions of DNA

• Replication

  • DNA comprises 2 complementary strands, the base sequence of 1 strand determining the base sequence of the other. if 2 strands of a double helix are separated, 2 identical double helices can be formed, as each parent strand

• Protein synthesis

  • sequence of bases represents the information carried in DNA and determines the sequence of amino acids in proteins

Comparison of DNA and RNA

Semi-conservative replication of DNA

• Each of the strands of DNA acts as a template to make a new strand. New DNA molcules are made of an original strand linked to a new strand

• Meselson and Stahl carried out an experiment which gave evidence to the theory of semi-conservative replication of DNA.

Conservative replication

• bpth parent strands stay together and the parental double helix remains intact/is conserved and a whole new double helix is made

• direct copying of the nucleotide sequence onto a new double stranded molecule which would give one light and one heavy molecule in generation 1.

Dispersive replication

• sections of old and new DNA are found in sections all strands so all copies would be intermediate density

• where half the nucleotides are placed randomly in the DNA being replicated to make new molecules which would give successively lighter molecules and therefore a band between hybrid and light in generation 2.

Meselsohn and Stahl Experiment

• Gives evidence of the semi-conservative theory of DNA replication and disproves other theories; dispersive and conservative

  1. Grow bacteria with a heavy isotope of nitrogen. Centrifuge a sample – a heavy band is seen.

  2. Remove bacteria with heavy DNA and place into a medium with light nitrogen and allow bacteria to divide. They will synthesise DNA with the nitrogen isotope available meaning their DNA will contain 1 new (14N) and 1 old (15N) strand, making it intermediate in density when centrifuged.

  3. Allow 1 more generation to grow and the hybrid strands will now be copied in a semi conservative way creating 50% hybrid and 50% light DNA

Enzymes in DNA replication

• DNA Polymerase

• DNA Helicase

Process of DNA replication

• Replication starts at a specific sequence on the DNA molecule; the replication origin

• DNA helicase unwinds and unzips DNA, breaking the hydrogen bonds that join the complementary base pairs, forming 2 separate strands

• Bases are now exposed and unpaired

• Free nucleotides in the nucleoplasm are bound to their complementary bases on the unzipped strand.

• DNA polymerase joins the nucleotides together by condensation reactions between sugar and phosphate groups of adjacent nucleotides, forming phosphodiester bonds in the new strands of DNA being formed

• A winding enzyme winds the new strands up to form double helices

• 2 new DNA molecules are formed from 1 old molecule and 1 new molecule. The 2 new molecules are identical to the old molecule. One of the chains in each new molecule was present in the original molecule

• This process = semi-conservative replication

Name two enzymes now known to be involved in DNA replication and explain their functions

• DNA lipase; unwinds and unzips the DNA, breaking hydrogen bonds between the complementary base pairs and forming 2 separate strands

• DNA polymerase; joins the new nucleotides to each other by phosphodiester bonds via condensation reactions forming the sugar-phophate backbone. Joins free nucelotides to the ends of the new DNA strands

DNA replication fork diagram

Direction of DNA replication

5’ to 3’

The genetic code

• The genetic code is a linear, triplet, non-overlapping, degenerate, unambiguous, universal code for the production of polypeptides

The genetic code as linear

It is a linear code with no overlaps, so it can be ‘read’ without any ambiguity.

The genetic code as a triplet code

3 bases code for one amino acid

The genetic code as non-overlapping

Each base is part of only one triplet

The genetic code as degenerate

more than one triplet can specify an amino acid

The genetic code as unambiguous

each each triplet/codon specifies only one amino acid/stop codon

The genetic code as universal

is the same in all living things, so each specific codon codes for the same amino acid in all species

The triplet code for amino acids

• 3 bases = 1 amino acid

• Amino acids are coded for by triplets of bases in the DNA.

• The DNA is transcribed to produce codons in mRNA and then translated to produce a sequence of amino acids.

Exons

• regions of the nucelotide sequence of DNA that contain the code for proteins

• remains present in the final mature mRNA, after introns have been removed

Introns

• Regions of non-coding DNA between exons

• removed by post-transcriptional modification from pre-mRNA

Eukaryotic genes

usually discontinuous genes with coding exons and non-coding introns

Prokaryotic genes

usually continuous genes, lacking non-coding sequence.

Stages of protein synthesis

1. Transcription (DNA to mRNA)

2. Translation (mRNA to polypeptide)

Process of transcription

• occurs in the nucleus

• the molecule formed is called pre-mRNA as it contains both exons and introns

  1. DNA helicase binds to DNA and unzips a section (gene) of the DNA by breaking the hydrogen bonds between complementary base pairs in the helix. This seperates the 2 polynucleotide strands by breaking the hydrogen bonds

  2. The unpaired bases on the template strand are exposed

  3. One chain acts as a tenplate for the formation of mRNA

  4. RNA polymerase links to the template (coding) strand of DNA and attaches mRNA nucleotides one at a time to their complementary base pairs, e.g. Adenine in DNA now pairs with the mRNA base Uracil, Cytosine continues to pair with Guanine.

  5. RNA polymerase joins the nucelotides via forming phosphodiester bonds between ribonucleoitdes, condensing the ribose-phosphate backbone

  6. This copying stops at a stop sequence / codon. RNA polymerase detahces. mrRNA leaves the nucleus via the nucelar pores when a stop sequence is reached

  7. The newly made premRNA then leaves the DNA.

  8. Post-transcriptional modification of the pre-mRNA takes place to remove the non-coding introns, leaving only the coding sections (exons) in the mature mRNA. This leaves the nucleus to be translated into a protein in the cytoplasm.

Post-transcriptional modification

• Post- transcriptional modification of pre-mRNA then occurs to remove the introns from the molecule to produce functional mRNA.

• removal of introns (remain inside nucleus)

• Exons are spliced together

Post-transcriptional modification in eukaryotes

• in eukaryotes, mRNA contain coding (exons) and non-coding (introns) regions

• Introns must be removed by splicing - a newly synthesised pre-mRNA is transformed into a mature mRNA - involves the removal of introns and joining of exons

Prokaryotic vs Eukaryotic Transcription

• Prokaryoties; no post-transcription modification

• Eukaryoties; the introns are removed by splicing

Process of Translation

• mRNA is a linear chain of 3 base codons. There are complementary anticodons on tRNA molecules

• The large subunits of a ribosome have 2 attachment sites for tRNA. The ribosome holds the mRNA and the tRNA (which have attached amino acids) in position for the amino acids to form peptide bonds and create a polypeptide chain. The codon on the mRNA (3 base code) therefore determines the tRNA as the tRNA which attaches must have a complementary 3 base code. E.g. mRNA CGA, tRNA GCU.

• The tRNA that matches the codon on the mRNA has a specific amino acid attached to the 3’ end of the tRNA molecule.

• Termination;

  • When the mRNA leaves the nucleus, it attaches to the small subunit binding sites of a ribosome.

  • Ribosome attaches to mRNA’s ribosome binding site and moves along to start codon

  • Two codons exposed on mRNA

  • First tRNA interacts with first codon and is attached to a specific amino acid via complemenentary base pairing

  • A second tRNA interacts with a second codon

  • The ribosome catalyses the formatio of s paptide bond between 2 amino acids, forming a dipeptide

  • The ribosome moves along the mRNA holding each tRNA in place until the amino acid attaches. In this way the mRNA (translated from a gene) carries the code for the formation of a polypeptide chain with amino acids set out in a particular order.

• Elongation;

  • The first tRNA leaves the ribosome

  • Thr ribosome moves along the mRNA by 3 nucleotides, exposing another codon

  • The tRNA then leaves, the ribosome moves along and the next tRNA attaches to the next codon

  • Another tRNA interacts with the newly exposed codon

  • The ribosome catalyses the formation of a peptide bond, forming a polypeptide chain of 3 amino acids

• Termination;

  • The sequence repeats until a ‘stop’ codon is reached

  • The mRNA seperates from the ribosome

  • The polypeptide sperates from the ribosome

• In this way the mRNA (translated from a gene) carries the code for the formation of a polypeptide chain with amino acids set out in a particular order.

Prokaryotic vs Eukaryotic Translation

• Prokaryotic; less post-translational modification, Chemical modification

• Eukaryotes; the start of the protein may be removed and carbohydrates added to form glyco-proteins

Stop codon

A sequence of 3 nucelotides in DNA or mRNA that signals a halt to protein synthesis in the cells

Gene

A section or sequence of DNA that codes for a polypeptide

Explain the steps in the process that produces viralm proteins from viral mRNA, using host cell machinery. [5]

• The viral mRNA is translated to produce a viral protein

• Ribosomes attaches, exposing the codons on the mRNA

• tRNA with complementary anticodons interact with exposed codons

• the tRNA are each attached to a single specific amino acid

• The ribosome forms a peptide bond betweeen the 2 amino acids

• The ribosome moves along 3 nucleotides and the process repeats

• When the ribosome reaches a stop codon, it detaches

The ‘one gene - one polypeptide’ hypothesis

each gene is transcribed and then translated into a single polypeptide

The further modification and combination of some polypeptides

• May be structurally or chemically modified = post-translational modification

• Polypeptides can be chemically modified in the Golgi Body by combination with non-proteins such as ;

  • + carbohydrates —> glycoproteins

  • + lipids —> lipoproteins

  • + phosphate —> phospho-proteins

• Structural modification; in the ER, many polypeptides are folded into secondary, tertiary or quaternary structures. occasionally the primary structure of a polypeptide is functional but it is usually folded/strtucturally modified

• Polypeptides can be combined, as exmeplifies by haemoglobin; highly-modified molecule. each polypeptide has an alpha-helix region (secondary structure), and is folded (tertiary structure). 4 polypeptides are combined (quaternary structure). the protein is modified by combination with 4 non-protein haem groups to make the functional molecule

Draw a simple labelled diagram to show the structure of a nucelotide

What are the components of ATP?

• 3 phosphate groups with high energy bonds between them

• ribose (pentose sugar)

• adenine (nitrogeous base)

What is the difference between an endergonic and exergonic reaction?

• Endergonic reaction =a reaction that requires an input of energy. e.g. ATP synthesis via condensation

• Exergonic reaction = a reaction that releases energy. e.g. ATP hydrolysis. The energy required to combine ADP and inorganic phosphate (Pi) to form ATP (and water) comes from exergonic reactions e.g. cell respiration.

How much energy is released from one mole of ATP when it is hydrolysed to ADP and Pi?

30.6kJmol^-1

What does universal energy currency mean?

common energy source used in all living organisms

List 3 advantages of using ATP to provide energy in cells

• ATP releases energy in one hydrolysis reaction controlled by one enzyme.

• ATP releases energy in small, usable amounts. ATP travels easily to where it may be used for secretion, muscle contraction, nerve transmission or active transport.

What is the sugar in DNA?

deoxyribose

Which bases are in the nucleotides of DNA?

Cytosine and Guanine, Adenine and Thymine

What is the sugar in RNA?

Ribose

What are the bases in RNA?

Cytosine and Guanine, Adenine and Uracil

How does the structure of ATP differ from that of DNA?

• ATP;

  • 3 phosphate groups bonded together by high energy bonds

  • ribose (pentose sugar)

  • adenine (nitrogenous base)

• DNA;

  • 1 phosphate group

  • deoxyribose

  • Adenine, Thymine, Cytosine or Guanine

How does the structure of ATP differ from that of RNA?

• ATP;

  • 3 phosphate groups bonded together by high energy bonds

  • Ribose

  • Adenine

• RNA:

  • 1 phosphate groups

  • Ribose

  • Adenine, Uracil, Cytosine or Gunaine

What does DNA stand for?

Deoxyribonucleic acid

What does RNA stand for?

Ribonucleic acid

What are the 2 functions of DNA?

replication and protein synthesis

What are the 3 types of RNA?

• mRNA (Messenger RNA)

• rRNA (Ribosomal RNA)

• tRNA (Transfer RNA)

Which is longer; DNA or RNA?

• DNA as it contains all of the complete genetic information of an organism

• tRNA and rRNA are short; mRNA varies but shorter than DNA

Which bases are pyrimidines and which are purines?

• Pyrimidines; Thymine, Cytosine and Uracil

• Purines; Adenine and Guanine

Complementary bases are linked by bonds, what type of bonds are these?

• Hydrogen bonds

• 2 between C and G

• 2 between A and T/U

What does antiparallel mean?

Running parallel but facing in opposite direction

What is the shape of DNA?

Double Helix

Why does DNA replication need to occur?

When cells divide to form new daughter cells, they must receive an exact copy of the DNA. Therefore, chromosomes must be able to make exact copies of themselves.

What is the accpeted model of DNA replication?

Semi-conservative replication

What does semi-conservative replication mean?

• Each of the strands of DNA acts as a template to make a new strand. New DNA molcules are made of an original strand linked to a new strand

• Meselson and Stahl carried out an experiment which gave evidence to the theory of semi-conservative replication of DNA.

What are the main steps in DNA replication?

• Replication starts at a specific sequence on the DNA molecule; the replication origin

• DNA helicase unwinds and unzips DNA, breaking the hydrogen bonds that join the complementary base pairs, forming 2 separate strands

• Bases are now exposed and unpaired

• Free nucleotides in the nucleoplasm are bound to their complementary bases on the unzipped strand.

• DNA polymerase joins the nucleotides together by condensation reactions between sugar and phosphate groups of adjacent nucleotides, forming phosphodiester bonds in the new strands of DNA being formed

• A winding enzyme winds the new strands up to form double helices

• 2 new DNA molecules are formed from 1 old molecule and 1 new molecule. The 2 new molecules are identical to the old molecule. One of the chains in each new molecule was present in the original molecule

• This process = semi-conservative replication

What is the enzyme that catalyses DNA replication?

DNA helicase, then DNA polymerase

Which 2 scientists undertook the experiment that showed how DNA replication happens?

Meselson and Stahl

Which part of the DNA molecule was labelled in the Meselson and Stahl experiment? What were they labelled with?

Nitrogenous bases with isotopes of nitrogen

Draw the results for generation 0, 1 and 2 of the Meselson and Stahl experiment, labelling the lines on the tubes

How do the results of the Meselson and Stahl experiment show that conservative and dispersive replication do not occur?

• Meselsohn and Stahl’s experiment disproves alternative theories.

• Conservative replication – direct copying of the nucleotide sequence onto a new double stranded molecule which would give one light and one heavy molecule in generation 1.

• Dispersive replication – where half the nucleotides are placed randomly in the DNA being replicated to make new molecules which would give successively lighter molecules and therefore a band between hybrid and light in generation 2

What does DNA polymerase do?

• joins the new nucleotides to each other by phosphodiester bonds via condensation reactions forming the sugar-phophate backbone. Joins free nucelotides to the ends of the new DNA strands

What does the base sequence in DNA code for?

The order of amino acids in a protein

How many bases code for each amino acid?

3

What is the process by which the code is copied from DNA to mRNA?

Transcription in the nucleus

What is the relationship between DNA and mRNA?

mRNA is transcribed from DNA

Which enzyme controls transcription?

DNA helicase, then DNA polymerase

What is an exon and what is an intron?

• Exon; regions of the nucelotide sequence of DNA that contain the code for proteins. remains present in the final mature mRNA, after introns have been removed

• Intron; Regions of non-coding DNA between exons. removed by post-transcriptional modification from pre-mRNA

What is meant by post-transcriptional modification?

• Post- transcriptional modification of pre-mRNA then occurs to remove the introns from the molecule to produce functional mRNA.

• removal of introns (remain inside nucleus)

• Exons are spliced together

Where are proteins synthesised?

Ribosomes in cytoplasm and RER

How does mRNA leave the nucleus?

Via the nuclear pore

State 2 structural differences between DNA and RNA

• DNA has a deoxyribose sugar. RNA has a ribose sugar

• DNA is a double-stranded double helix. RNA is single stranded