NUCELEOTIDES + NUCLEIC ACIDS

NUCLEIC ACIDS DNA + RNA

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What does DNA stand for?

Deoxyribo Nucleic Acid

what does RNA stand for?

Ribo Nucleic Acid

What are DNA and RNA? (2)

- macromolecules

- polymers

what are the monomers of DNA + RNA called?

nucleotides

what are nucleotides made up of? (3)

- phosphate group

- pentose sugar (5 carbon)

- nitrogenous base

what type of reaction joins together the 3 parts a nucleotide is made up of?

condensation reactions

condensation reactions join the 3 parts of a nucleotide together to form what?

a mononucleotide

what elements do all nucleotides contain?

C, H, O, N, P

Drawing of a mono nucleotide

State + explain the differences between DNA + RNA? (2)

1. PENTOSE SUGAR

- deoxyribose (ribose sugar w/ 1 less O atom in DNA

- ribose in RNA

2. ORGANIC BASES

- there are 4 diff bases found in DNA:

> Adenine (A) > Cytosine (C)

> Guanine (G) > Thymine (T)

- there are 4 diff bases found in RNA:

> Adenine (A) > Cytosine (C)

> Guanine (G) > Uracil (U)

which organic bases are purines?

A + G

what is a purine?

double ring structures (1 ring has 6 sides and the other has 5 sides)

Which organic bases are pyramidines?

C,T,U

What is a pyramidine?

single ring structure ( 6 sides)

in what order do the organic bases pair up? Why?

- A and T always pair up ( 1 purine, 1 pyrimidine)

- G and C always pair up (1 purine, 1 pyrimidine)

What do the special types of nucleotide have added to them?

special types of nucleotide have extra phosphate groups added to them

What is phosphorylation?

adding a phosphate group onto a molecule (the molecule becomes phosphorylated)

what are 2 examples of phosphorylated molecules?

ADP + ATP

What are ADP + ATP

nucleotides that have has one/two extra phosphate groups added to them

what are ADP + ATP made up of? (3)

- pentose sugar (ribose)

- nitrogenous base (adenine)

- phosphate groups (also called inorganic phosphates Pi)

what are ADP + ATP used in cells for?

to store + transport energy

MAKING + USING ATP

where do plant + animal cells release energy from?

glucose (respiration)

how do cells get energy for chemical reactions when cells can't get energy directly from glucose?

in respiration, the energy released from glucose is used to make ATP, then molecules of ATP provide energy for chemical reactions in the cell.

How is ATP formed?

- ATP is synthesised from ADP + inorganic phosphate (Pi- phosphate group P+O)

- ADP is phosphorylated to form ATP + a phosphate bond is formed

where is energy stored in ATP?

phosphate bonds

what happens to ATP when energy is needed by a cell

- ATP is broken down into ADP + inorganic phosphate (Pi)

- energy is released from phosphate bond + used by cell

what are nucleotides joined together by?

nucleotides are joined together by condensation reactions b/n the phosphate group of one nucleotide and the sugar group of a diff nucleotide forming a polynucleotide

what is the sugar-phosphate backbone?

chain of sugars & phosphates

What is a phosphodiester bond?

bond that holds nucleotides together in a polynucleotide chain

what is making a phosphodiester bond an example of?

condensation reaction

what is breaking a phosphodiester bond an example of?

hydrolysis reaction

how many polynucleotide chains does one molecule of DNA consist of?

2

what are the 2 polynucleotide chains in DNA linked by ?

hydrogen bonds between the bases

what are the complementary base pairing rules?

- A and T are linked by 2 hydrogen bonds

- C and G are linked by 3 hydrogen bonds

- a purine always pairs with a pyrimidine

In DNA the 2 polynucleotide chains are twisted around each other to form a ... what structure?

stable double helix

which direction do the 2 polynucleotide strands in DNA run in? what do we call this?

opposite directions - they are antiparallel

How was the structure of DNA discovered in 1953?

- Rosalind Franklin & Maurice Wilkins (both worked in London)

- X-ray photography worked out shape & size of DNA

- James Watson & Francis Crick (worked in Cambridge) used data from many studies, including the work of Franklin & Wilkins

- built a 3D model of DNA showing its double helix structure

*what was the evidence used to work out structure of DNA?

- 1951, American chemist, Erwin Chargoff analysed DNA

- he used chromatography to separate 4 bases from diff species

- measured amounts of each base

- providing evidence that bases pair up in DNA

*Erwin Chargoff measurements of each base

Organism %ofA %ofC %ofT %ofG

Yeast 32 18 32 18

TB bacterium 16 34 16 34

Locust 29 21 29 21

Human 31 19 31 19

DNA EXTRACTION PRACTICAL

What is the equipment needed for the DNA extraction practical?

- 1 kiwi

- knife/scalpel to peel + chop kiwi

- pestle & mortar

- cutting board

- 250ml beaker x2

- 250ml beaker containing cold water (leave in fridge overnight)

- pinch of salt

- stirring rod

- tea strainer

- 50ml washing up liquid in 100ml beaker

- 10ml syringe

- 2x test tubes + test tube rack

- stop watch

- bottle of ice-cold ethanol

- wire loop/wooden stick to collect DNA clumps

What is the method for the DNA extraction practical?

1. Peel & chop one kiwi using a knife/scalpel

2. mash up kiwi thoroughly using pestle & mortar

3. place mashed kiwi in a 250ml beaker

4. add similar vol of cold water to beaker & pinch of salt

5. mix thoroughly using plastic stirring rod

6. strain mixture using mesh strainer & collect liquid in clean beaker

7. add 10ml of washing up liquid & swirl to mix (don't produce foam)

8. let mixture settle for 10mins

9. pour mixture into test tubes to make each 1/3 full

10. tilt tube to 45° & slowly pour ice-cold ethanol into tube so it forms a layer on top of mixture - about same volume as mixture

11. salted DNA does not dissolve in ethanol & will form white clumps where water & ethanol layers meet (DNA forms precipitate)

12. use wooden stick/wire loop to collect DNA. Dip stick into tube & touch white layer. Twirl rood & DNA should spool onto rod

How does the DNA extraction practical method work? (5)

- pestle & mortar break down cell walls

- detergent breaks down cell membranes

- salt prevents hydrogen bonds forming b/n water molecules & DNA

- protease enzymes (naturally present in kiwi) breaks down histone proteins

- ethanol causes DNA to precipitate out of solution

why do cells divide?

cells divide so that an organism can grow or repair damaged tissues (by replacing old cells)

what are the 3 things a cell must do before dividing?

- make new organelles & tissues

- copy DNA

- DNA checked for mutations

What occurs in stage one of semi-conservative DNA replication?

- double helix unwinds & unzips so that the 2 polynucleotide strands separate

- hydrogen bonds are broken that hold complementary bases together

- unzipping is carried out by DNA helicase

- each separated strand is referred to as a template strand (both strands can be copied)

What occurs in stage two of semi-conservative DNA replication?

- free DNA nucleotides will then pair w/ their complementary bases that are exposed on the template strands

- hydrogen bonds form b/n complementary bases

What occurs in stage three of semi-conservative DNA replication?

- new nucleotides are joined by phosphodiester bonds

- enzyme DNA phosphodiester bonds

- enzyme DNA polymerase catalyses formation of these bonds (moving in a 3' to 5' direction on template strand)

- DNA replication produces 2 new molecules

- each molecule contains 1 old strand and 1 new strand ( this is called semi-conservative replication)

What kind of molecule is DNA?

DNA is an antiparallel molecule

what can the template strand that is unzipped from the 3' end do?

the template strand that is unzipped from the 3' end can be continuously replicated (as new nucleotides are added in a 5' to 3' direction)

the template strand that is unzipped from the 3' end can be ...... (as new nucleotides are added in a ...... direction)

1. continuously replicated

2. 5' to 3' direction

what do template strand make?

leading strand

what does DNA polymerase have to wait for before working back along the strand?

DNA polymerase has to wait until a section of strand has unzipped and then work back along the strand

what direction are new nucleotides joined in?

5' to 3' direction

what are the sections DNA is produced in?

Okazaki fragments

what happens to the Okazaki fragments?

they are joined together

how are Okazaki fragments joined together?

Okazaki fragments are joined together using the enzyme DNA ligase

what is a spontaneous & random change in the sequence of bases in DNA called?

mutation

EVIDENCE FOR SEMI-CONSERVATIVE ENERGY

What was Meselson & Stahl's experiment? (6)

- they grew bacteria in a culture containing amino acids made with isotope 15N ('heavy' nitrogen)

- bacteria absorbed these amino acids & used them to make new DNA

- DNA was extracted & centrifuged (spun in a tube at high speed) in caesium chloride solution. DNA settled in the tube at a point depending on its mass

- all DNA of bacteria in starter culture contained 'heavy' DNA

- bacteria were then transferred into a different culture containing amino acids made with isotope 14N ('light' nitrogen)

- bacteria were allowed to replicate once & then DNA was analysed again

what is the genetic code?

sequences of bases found in each DNA molecule

wha is the sequences of bases?

instructions for linking amino acids together (therefore the bases are the instructions for making polypeptides)

what codes for 1 amino acid?

3 bases (a triplet) code for 1 amino acid

do all organisms use the same triplet code for the same amino acids?

yes, the genetic code is universal

what is a gene?

a short section of DNA on a chromosome

what does a gene contain the code for?

for making a polypeptide

what is a polypeptide?

a chain of amino acids linked together

a polypeptide is a chain of amino acids linked together, so what is a code?

instructions for linking amino acids together (primary structure of a protein)

what is a triplet code called?

codon

how many different bases are there in DNA?

4

if bases occur in triplets, how many different possible combinations of bases in DNA?

64 (4³)

how many amino acids are there (that need to be coded for)?

20

where is the "start" codon located?

the first codon of a gene

where is the "stop" codon located?

at the end of a gene

why is the "stop" codon located at the edge of a gene?

it doesn't code for an amino acid

what do ribosomes do?

read the code during protein synthesis

where do ribosomes star reading the code?

ribosomes always start at the start codon and then read each codon in order, base by base

what is a non-overlapping code?

each base in a DNA or mRNA sequence is only read once as part of a single triplet (codon)

what is degenerate code?

different codons can code for the same amino acid

what are the stages of protein synthesis?

stage 1: transcription

stage 2: translation

what are the 3 types of RNA involved in protein synthesis?

- mRNA (messenger RNA)

- tRNA (transfer RNA)

- rRNA (ribosomal RNA)

what is the function of mRNA (messenger RNA)

carries instructions of how to make a polypeptide from the nucleus to a ribosome

what is the function of tRNA (transfer RNA)

carries an amino acid to a ribosomes

what is the function of rRNA (ribosomal RNA)

what ribosomes are made up of

what happens to mRNA during transcription?

a mRNA molecule is built up against one DNA strand (template strand) of a gene

- the enzyme RNA polymerase catalyses the formation of mRNA

what enzyme catalyses the formation of mRNA?

RNA polymerase

what happens to mRNA during translation?

mRNA is read (translated) by ribosomes, one codon at a time

how many different types of tRNA are there?

20

what happens to tRNA during translation? what is this called

- tRNA attaches to a specific amino acid in the presence of an enzymes and ATP

- this is called amino acid activation

- tRNA contains an anticodon which is complementary to the mRNA codon

- 2 RNA's can fit into a ribosome at any one time

- a peptide bond links the 2 amino acids together

- tRNA molecules will then leave the ribosomes and are free to pick up another amino acid

how many RNA's can fit into a ribosome at any one time?

2

what links the 2 amino acids together?

a peptide bond

outline the synthesis of polypeptides

1.

- there's room for 2 mRNA codons to fit in the ribosome

- the first exposed codon is always AUG, which codes for the amino acid methionine (start codon)

- tRNA molecule with the anticodon UAC enters ribosomes & forms complementary base pairs with mRNA codon

2.

- second exposed codon is AUA

- different tRNA with anticodon UAU (codes for tyrosine) enters the ribosome & binds to second codon

3.

- condensation reaction takes place & peptide bond forms between the 2 amino acids (forming a dipeptide)

4.

- ribosome moves along mRNA reading third codon (UUU)

- different tRNA with anticodon AAA brings in different amino acid (phenylalanine)

- peptide bond forms between amino acid and dipeptide that has already been made

- first tRNA leaves ribosome and is free to pick up another amino acid from the cytoplasm

5.

- whole polypeptide chain is gradually built up

- it is released when stop codon is reached on mRNA

- there are no corresponding tRNA's for stop codons: UAA, UAG or UGA

- stop codon = no tRNA