2.1.2i Nucleic Acids Flashcards
What are nucleotides
Monomers which are the building blocks of DNA (store genetic info) & RNA (used to make proteins from the instructions in DNA)
How many different nucleotides are there
5
What is the basic common structure of all 5 different nucleotides
- a pentose sugar (sugar w 5 carbon atoms) joined to a phosphate group & a nitrogenous base
see page 34
What are the 5 different nucleotides
- Guanine
- Thymine (DNA only) or Uracil (RNA only)
- Adenine
- Cytosine
What are the 2 groups of nitrogenous bases
Purines & Pyrimidines
What bases are part of the Purine group
- Adenine
- Guanine
What bases are part of the Pyrimidine group
pyrimidine:
- thymine
- uracil
- cytosine
Ring structure of purine bases
Double ring structure of C and N
Ring structure of pyrimidine bases
Single ring structure of C and N
See slide 3 for structure of all 5 different nucleotides
What does DNA stand for
Deoxyribonucleic acid
What does RNA stand for
Ribonucleic acid
What are DNA & RNA an eg of
DNA & RNA are both types of nucleic acids
Similarities between DNA & RNA
- Both are types of nucleic acids
- Both are long chain polymers made up of many units called nucleotides joined tg by phosphodiester bonds in a condensation reaction
- They are attached between the sugar of one nucleotide & the phosphate of the next nucleotide. The bond that forms between the 2 nucleotides is a phosphodiester bond
Difference between DNA & RNA
- DNA is a double stranded molecule, whilst RNA is a single stranded molecule
- Have diff types of pentose sugar: DNA has deoxyribose, RNA has ribose
- Composition of nitrogenous bases: DNA has (A, G, C, T) whilst RNA has (A, G, C, U)
- DNA has hydrogen bonding, RNA does not
- Base pairing: DNA has complementary base pairing, RNA has no base pairing
Structure of a nucleotide
see slide 5
(pentose sugar attached to phosphate group and nitrogenous base)
Structure of DNA nucleotides
- Pentose sugar in DNA nucleotide is called deoxyribose
- Each DNA nucleotide has the same sugar & a phosphate group, but the base can vary (A,T,C or G)
see slide 6, pg34
Structure of RNA molecules
- Pentose sugar in RNA nucleotides is a ribose sugar
- Like DNA, RNA also has a phosphate group & one of four different bases (A,U,C or G)
- An RNA molecule is made up of a single polynucleotide chain
see slide 6,pg34
Type of pentose sugar in DNA
Deoxyribose
Type of pentose sugar in RNA
Ribose
Base composition of DNA
(A, C, G, T)
- Adenine (A)
- Guanine (G)
- Cytosine (C)
- Thymine (T)
Base composition of RNA
(A, C, G, U)
- Adenine (A)
- Guanine (G)
- Cytosine (C)
- Uracil (U)
see slide 8 to see physical difference between DNA & RNA side by side
Joining of nucleotides
Nucleotides are monomers. They need to bond to other nucleotides to form polynucleotides (eg. mRNA)
How do nucleotides join together
- The nucleotides bond between the phosphate group of one nucleotide & the sugar of another nucleotide. This is via a condensation reaction & the formation of a phosphodiester bond (consisting of the phosphate group & 2 ester bonds)
- The chain of sugars & phosphates is known as the sugar-phosphate backbone
- Polynucleotides can be broken down into nucleotides again by breaking the phosphodiester bonds (using hydrolysis reaction)
(see slide 9-11 for diagram)
How are 2 polynucleotide chains of DNA held together
2 polynucleotide chains of DNA are held tg via hydrogen bonding between complementary nitrogenous bases.
- Adenine (A) can only pair with Thymine (T) via TWO hydrogen bonds
- Guanine (G) can only pair with Cytosine (C) via THREE hydrogen bonds
(see slide 12 for dia)
What does it mean by the 2 strands of DNA being called antiparallel in the joining of base pairs
In order for the bases to be facing each other & thus able to pair, the strands must be running in opposite directions.
- The two strands of DNA are described as being antiparallel
(see slide 13 for dia)
Structure + Function of DNA
- Sugar phosphate back bone –> DNA is strong & stable
- Many hydrogen bonds –> Provides strength & stability
- Hydrogen bonds are weak –> Strands can be separated during DNA replication
- Double stranded –> Bases are protected & replication can be semi-conservative
- Long polymer –> Can store lots of genetic info
- Double helix –> compact
- Bases are in sequence (specific order) –> Info can be stored (base sequence code for amino acid/protein)
EXAM Q: A sample of DNA was tested & 17% of the total bases present were found to be Adenine.
Calculate the percentages of each of the other 3 bases present in this sample.
Adenine always base Paris w Thymine, so same amount of Thymine (17%).
Adenine & Thymine tg is 34%, so Cytosine & Guanine must be (100 - 34 = 66%).
Cytosine always base pairs w Guanine, sp equals same amount, 66/2=33.
Therefore, cytosine 33% % guanine 33%
ATP & ADP are…
…phosphorylated nucleotides
(to phosphorylate a nucleotide, you add one or more phosphate groups to it)
What is ATP energy required for
- All organisms require a constant supply of energy to maintain their cells & stay alive
- In all organisms this energy is required for:
- ANABOLIC REACTIONS (building larger molecules from smaller ones)
- MOVING SUBSTANCES across the cell membrane or moving substances within the cell
What else is ATP required for (specific to animals only)
- MUSCLE CONTRACTION: to coordinate movement at the whole-organism level
- The conduction of nerve impulses
Why is ATP known as the universal energy currency
In all known forms of life, ATP from respiration is used to transfer energy in all energy-requiring processes in cells
What does ATP stand for
Adenosine Triphosphate
Structure of ATP
- ATP is another type of nucleic acid & hence it is structurally very similar to the nucleotides that make up DNA & RNA.
- It is a phosphorylated nucleotide
- Adenosine (a nucleoside) can be combined with 1, 2 or 3 phosphate groups:
- 1 phosphate group = adenosine monophosphate (AMP)
- 2 phosphate groups = adenosine diphosphate (ADP)
- 3 phosphate groups = adenosine triphosphate (ATP)
(see slide 18 for dia)
What is the process used for purifying DNA
We can purify (isolate) DNA via the process of precipitation
What is the process of precipitation (purifying DNA)
The process of converting a chemical substance into a solid form from a solution by changing the substance into an insoluble form.
When the reaction occurs in a liquid solution, the solid formed is called the precipitate
Why might we want to isolate DNA (purification)/why is it important
Isolating DNA from cells is an essential starting point for a huge range of other investigations
What is the name of the common method used to isolate DNA
The ‘Marmur preparation’
- This method is derived from the work of Julius Marmur (1926-96), an American molecular biologist who made significance contributions to DNA research
3 basic steps of the ‘Marmur preparation’
- Breaking (lysing) the cells & disrupting the nuclear membranes to release the DNA
- Using enzymes to denature & remove the proteins (histones) associated with the DNA
- Precipitating the DNA using an organic solvent (eg. ethanol)
Good eg for purification of DNA practical
Onions are good to use for this investigation as their cells contain a relatively large amount of DNA
- Fruits that also have large amounts of DNA in their cells sa strawberries, bananas, kiwis can also be used
Equipment needed for purification of DNA practical
- ice-cold ethanol (10 cm^3)
- protease enzyme (2-3 drops)
- ice water bath
- plastic funnel
- plastic syringe
etc
What is the difference between a PURINE & PYRIMIDINE base
A purine base contains 2 carbon-nitrogen rings joined tg
A pyrimidine base only has 1 carbon-nitrogen ring. So a pyrimidine base is smaller than a purine base
(see pg34 for dia)
How are ATP & ADP phosphorylated
- ATP (adenosine triphosphate) contains the base adenine, the sugar ribose & 3 phosphate groups
- ADP (adenosine diphosphate) contains the base adenine, the sugar ribose & @ phosphate groups
What is ATP synthesised from
ATP is synthesised from ADP & inorganic phosphate using the energy from an energy-releasing reaction.
The ADP is phosphorylated to from ATP & a phosphate bond is formed
How is energy released from ATP
- Energy is stored in the phosphate bond.
- When this energy is needed by a cell, ATP is broken back down into ADP & inorganic phosphate (Pi).
- Energy is released from the phosphate bond & used by the cell
(pg35)
Method of purification of DNA (onion)
- Break up the cells in your sample (onion) in a blender
- Make up a solution of detergent (a dilute washing-up liquid will do), salt (sodium chloride) & distilled water
- Add the broken-up cells to a beaker containing the detergent solution. Incubate the beaker in water bath at 60dc for 15mins
- Once incubated, put beaker in ice bath to cool the mixture down. Then, filter the mixture. Transfer a sample of mixture to a clean boiling tube
- Add protease enzymes to the filtered mixture. These will break down some proteins in the mixture. Adding RNase enzymes will break down any RNA in mixture.
- Slowly dribble some cold ethanol down side of the tube, so it forms a layer on top of the DNA-detergent mixture
- Leave tube for a few mins, the DNA will form a white precipitate (solid), which you can remove from the tube using a glass rod
Method of purification of DNA: what is the point of the detergent, salt, water bath
- The detergent in the mixture breaks down the cell membranes.
- The salt binds to the DNA & cause it to clump tg.
- The temp of the water bath should stop enzymes in the cells from working properly & breaking down the DNA
