Biology - Chapter 2: Nucleic Acids

What is a nucleotide made up of?

Pentose sugar, phosphate group and a nitrogen-containing base

5 bases

Adenine, Thymine, Cytosine, Guanine and Uracil

What bond forms between each mononucleotide and how?

Phosphodiester bond in a condensation reaction between the deoxyribose sugar and the phosphate group

What are the complimentary base pairings?

A-T/U
C-G

DNA vs RNA

Both:
- Made up of nucleotides
- Have bases (A, C and G), phosphate groups and pentose sugars
- Have phosphodiester bonds between each nucleotide, which form through condensation reactions

DNA:
- Longer
- 2 strands in a double helix structure
- Thymine as a base
- Deoxyribose sugar

RNA:
- Shorter
- Single strand
- Uracil as a base
- Ribose sugar

What bond holds the two strands of DNA (the backbone) together (between the bases)?

Hydrogen bonds

Describe the structure of DNA (5)

- Polymer made of nucleotides
- Each nucleotide has a phosphate group, deoxyribose sugar and base
- Double helix structure, each strand is antiparallel to each other and are held together by hydrogen bonds
- Phosphodiester bonds between the nucleotides
- Hydrogen bonds between A-T and C-G (complementary base pairs)

Why is DNA a stable molecule? (2)

- Sugar-phosphate backbone protects more chemically reactive bases
- Hydrogen bonds link organic base pairs, forming bridges between each phosphodiester upright - many hydrogen bonds provide strength

3 functions of RNA

1. mRNA
2. tRNA
3. Make up ribosomes

4 requirements for semi-conservative replication

1. 4 types of nucleotide must be present
2. Both strands of a DNA molecule must act as a template
3. Enzyme DNA polymerase
4. Source of chemical energy to drive the process

5 steps of semi-conservative replication

1. In parental DNA, DNA helicase breaks hydrogen bonds between the base pairs, causing the DNA helix to unwind into two separate strands
2. Each DNA strand acts as a template - free nucleotides in the nucleolus are attracted to their complimentary base pairs (AT, CG) on each strand template
3. The adjacent nucleotides are joined together in a condensation reaction to form phosphodiester bonds by DNA polymerase
4. Hydrogen bonds reform between nucleotides
5. Each DNA molecule contains one parental (original) strand and one new strand - semi-conservative model of DNA replication

Why did scientists doubt that DNA carried the genetic code?

It was relatively simple chemically as it had too few components

What is the conservative model of DNA replication?

The original DNA molecule remained intact - a separate daughter DNA copy was built up from new molecules. One molecule would be completely new; the other, completely original.

Who are the scientists that tested the model of DNA replication and how did they do it?

- Meselson and Stahl
- Grew bacteria in medium with 14N then spun in centrifuge - least dense
- Grew next gen of bacteria in medium with 15N then spun in centrifuge - DNA strands had 14N and 15N, slightly more dense than only 14N
- Grew next gen of bacteria in medium with 15N again - some strands only had 15N, some strands had both, most dense
- Therefore, strands from original DNA molecules are retained during replication

From a table of proportions of each base in DNA, how does it prove viruses have single-stranded DNA?

Amounts of complimentary bases are different therefore no base pairing - single stranded

2 types of bases

Purines: larger, 2-ring structure (adenine and guanine - u in guanine)
Pyrimidine: smaller, single-ring structure (cytosine and thymine/uracil - y in cytosine and thymine)

What does ATP stand for?

Adenosine Triphosphate

Structure of ATP

Adenine (base), Ribose sugar (pentose sugar), 3 phosphate groups - nucleotide

How does ATP release energy?

- Phosphate groups unstable, have low activation energy
- Terminal phosphate group removed, releasing a lot of energy

Type of reaction where ATP is broken down into ADP

Hydrolysis reaction

Hydrolysis reaction of ATP

ATP + H2O -> ADP + Pi (+ energy)

Pi?

Inorganic phosphate

What enzyme catalyses the hydrolysis of ATP?

ATP Hydrolase / ATPase

Condensation reaction of ADP

ADP + Pi (+ energy) -> ATP + H2O

What enzyme catalyses the condensation reaction of ADP?

ATP Synthase

In what reactions is ATP resynthesised?

Respiration and Photosynthesis

ADP

Adenosine Diphosphate

Why is is ATP a suitable energy source for cells / better as an immediate energy store rather than a long-term energy store? (4)

1. Relatively small amount of energy released by hydrolysis

2. Hydrolysis of ATP is a single reaction that releases energy instantaneously

3. ATP is not lost from cells

4. Can be rapidly resynthesised

Where is ATP made?

In mitochondria

5 uses of ATP

TO PROVIDE ENERGY FOR:
1. Metabolic processes (e.g. energy is used to make bigger units from smaller ones)
2. Movement (energy used for muscle contraction)
3. Active transport (energy used to change shape of carrier proteins in plasma membrane)
4. Secretion (used to form lysosomes to secrete cell products)
ALSO USED IN:
5. Activation of molecules (inorganic phosphate can phosphorylate other compounds, making them more reactive by lowering their activation energy in enzyme-catalysed reactions)

1 use of inorganic phosphate from hydrolysis of ATP

Inorganic phosphate can be used to phosphorylate other compounds, making them more reactive by lowering their activation energy in enzyme-catalysed reactions

Why is water a dipolar molecule?

Oxygen atom has slightly negative charge (negative dipole), each hydrogen atom has a slightly positive charge (positive dipole) - has both positive and negative poles so is dipolar

What bond is present between water molecules and why?

Hydrogen bonds - negative dipole of oxygen attracts positive dipole of hydrogen

5 main properties of water

1. Metabolite in condensation/ hydrolysis / respiration / photosynthesis
2. Good solvent - metabolic reactions can occur + can transport dissolved substances
3. High specific heat capacity - buffers changes in temperature
4. Large latent heat of vaporisation - provides a cooling effect through evaporation of sweat
5. Cohesion - supports columns of water in plants (transpiration stream) / produces surface tension, supports small organisms

Importance of water as a metabolite?

- Used to break down compounds in hydrolysis
- Produced in condensation reactions
- Chemical reactions take place in water

Importance of water as a solvent?

- Water is polar so positive dipole attracts negative ions, while negative dipole attracts positive ions
- Water molecules surround ions, so the ionic compound dissolves
- As a result, water can dissolve substances like useful ones (O2, inorganic ions), enzymes and waste products (ammonia, urea) to transport them in an organism's body

Importance of water's high SHC?

- Due to hydrogen bonding, water has to absorb a lot of energy before it increases in temperature.
- Acts as a buffer against sudden temperature changes by absorbing large amounts of heat energy before temperature increase

Importance of water's latent heat of vaporisation?

- Due to hydrogen bonding, water has to absorb a lot of energy in order for it to evaporate
- Sweating can be used to cool mammals down by using heat energy to evaporate the sweat
- Also means water is a liquid at room temperature so can be used as a transport/medium for reactions

Importance of water's cohesion?

- Water molecules attracted to one another
- Due to hydrogen bonding, water molecules can be pulled up together in a tube
- Water can be pulled up in xylem from roots to leaves (transporting dissolved ions too)

Importance of water's adhesion?

- Water molecules attracted to other molecules
- Occurs due to water's polarity
- Water can be pulled up in xylem from roots to leaves

Importance of water's surface tension?

- Due to hydrogen bonding, water molecules can stick together
- When water molecules meet air, they are pulled back into body of water rather than away from it
- Water surface can be used to support organisms and habitats

Importance of water's transparency?

- Water is colourless and transparent
- Sunlight rays can pass through water and reach plant cells so photosynthesis can occur

Importance of water's density

- Due to hydrogen bonds forming, water expands when it freezes so ice is less dense than water
- As a result, ice floats on top of water so forms an insulating layer over it

Why are non-polar molecules insoluble?

They have no poles so cannot attract the water molecules

Where do inorganic ions occur?

In the cytoplasm and body fluids of organisms

Give the formula of a:
1. Hydrogen ion
2. Iron ion
3. Sodium ion
4. Phosphate ion

1. H +
2. Fe 2+
3. Na +
4. PO4 3-

Importance of hydrogen ions?

- Controls pH - more H+ ions, lower pH (more acidic)
- Affects enzyme-controlled reactions
- Concentration of H+ ions is used to calculate pH

Importance of iron ions?

Component of haemoglobin that binds to the oxygen

Importance of sodium ions?

Used in co-transport to transport glucose and amino acids

Importance of phosphate ions?

- Store energy in ATP
- Act as phosphodiester backbone in DNA
- Allow nucleotides in DNA and RNA to form polynucleotides

Importance of having complimentary base pairs in DNA replication (2)

- Enables identical copies of DNA to be created
- Reduces copying errors (would result in mutations)

Function of DNA polymerase?

Catalyses the joining together of adjacent nucleotides by causing condensation reactions between the phosphate groups and deoxyribose sugars to form phosphodiester bonds.

Function of DNA helicase?

Breaks the hydrogen bonds between the DNA strands.

What part of the DNA strand is DNA polymerase complementary to?

3' end (works in 5' to 3' direction)

Name the two scientists who proposed models of the chemical structure of DNA and of DNA replication.

Watson and Crick

Role of DNA strand in DNA replication

Acts as a template to determine the order of bases

Role of DNA nucleotides in DNA replication

Forms complementary pairs / DNA strand

3 features of DNA important for semi-conservative model of DNA replication

1. Weak hydrogen bonds between bases, easily broken - allow DNA strands to unzip
2. Two strands - both act as templates
3. Complementary base pairing - accurate replication

Why are new nucleotides added in a 5' to 3' direction? (4)

- Enzymes have active site - specific to substrate
- Nucleotides have different shapes on 5' end compared to 3' end
- Shape of DNA polymerase is complementary to 3' end of strand so it can only bind to that end
- DNA has antiparallel strands

6 features of DNA

1. Sugar-phosphate backbone + double stranded SO provides strength and protects bases
2. Large molecule SO stores lots of information
3. Helix SO compact
4. Base sequence SO can code for amino acids/protein + information can be stored
5. Double-stranded SO replication can occur semi-conservatively and each strand can act as a template + can have complementary base-pairing for accurate replication
6. Weak hydrogen bonds SO DNA can unzip for replication / many hydrogen bonds SO strong and stable

How are iron ions able to carry out their function?

They’re charged / from part of haemoglobin, so binds with oxygen to transport it in the blood