Unit 1 - Biological Molecules

AQA GCE A-Level Biology - Unit 1 - Biological Molecules

[3.1.1] What is a condensation reaction?

A condensation reaction joins two molecules together by removing a water molecule.

[3.1.1] What is a hydrolysis reaction?

A hydrolysis reaction breaks up a molecule into its respective monomers via the addition of water.

[3.1.1] What is a monomer?

A molecule that can be bonded to other identical molecules to form a polymer.

[3.1.1] What is a polymer?

A large molecule that is made up of many monomers.

[3.1.1] What are some examples of monomers?

Monosaccharides, Amino Acids, Nucleotides.

[3.1.2] What are the main monosaccharides?

Glucose, Fructose and Galactose.

[3.1.2] What are the two isomers of Glucose?

- Alpha Glucose

- Beta Glucose

[3.1.2] What does the condensation of monosaccharides produce?

- The condensation reaction between two monosaccharides forms a DISACCHARIDE.

- The condensation reaction between many monosaccharides forms a POLYSACCHARIDE.

[3.1.2] What type of bond holds together disaccharides?

Glycosidic Bonds.

[3.1.2] What is MALTOSE?

A disaccharide formed by the condensation reaction between two ALPHA GLUCOSE molecules.

[3.1.2] What is SUCROSE?

A disaccharide formed by the condensation reaction between an ALPHA GLUCOSE molecule and a FRUCTOSE molecule.

[3.1.2] What is LACTOSE?

A disaccharide formed by the condensation reaction between a BETA GLUCOSE molecule and a GALACTOSE molecule.

[3.1.2] What is STARCH?

A polysaccharide formed by the condensation reaction of many ALPHA GLUCOSE molecules, which are joined together to form a helix (makes it compact).

- Made of AMYLOSE (Insoluble, doesn't affect water potential).
- Made of AMYLOPECTIN (branched which allows for faster enzyme action).

Starch is the main energy storage molecule within plants, therefore it has lots of glucose storage space and is unable to diffuse out of cells.

[3.1.2] What is GLYCOGEN?

A polysaccharide formed by the condensation reaction of many ALPHA GLUCOSE molecules, which are joined together to form a helix (makes it compact). It is MORE BRANCHED than starch.

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Glycogen contains many 1-6 glycosidic bonds and is less dense, but more soluble than starch.

It is highly branched which allows it to be easily hydrolysed into glucose for use in aerobic respiration.

[3.1.2] What is CELLULOSE?

A polysaccharide formed by the condensation of many BETA GLUCOSE molecules joined in unbranched chains. It is the main structural component of plant cell walls.

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Hydrogen bonds ensure that the microfibrils are strong and stable, providing strength and rigidity to the cell wall. This prevents bursting when the cell is turgid.

[3.1.3] What is a lipid?

Molecules that are made up of GLYCEROL and FATTY ACIDS.

There are two types of lipid: TRIGLYCERIDES and PHOSPHOLIPIDS.

[3.1.3] What is a TRIGLYCERIDE?

Triglycerides are formed by the condensation reaction between a GLYCEROL molecule and three molecules of FATTY ACID.

[3.1.3] What is the bond that forms within lipids?

Ester Bonds.

[3.1.3] What are the functions of triglycerides?

- Buoyancy
- Water Proofing
- Energy Storage
- Insulation
- Water Storage
- Protection

[3.1.3] How does the structure of a triglyceride relate to its function?

- INSOLUBLE - they are good storage molecules.
- Possesses a large amount of energy per molecule.
- They heat very slowly, so good insulators.
- Maintains healthy hair and skin (water-repellent layer).

[3.1.3] What is a SATURATED fatty acid?

Fatty acids that do not contain double carbon-carbon (C=C) bonds.

[3.1.3] What is an UNSATURATED fatty acid?

Fatty acids that contain one or more double carbon-carbon (C=C) bonds.

[3.1.3] What is a PHOSPHOLIPID?

Lipids which have replaced a fatty acid chain with a phosphate group.

[3.1.3] How is the structure of a phospholipid related to its function?

- They are polar so they are able to form a PHOSPHOLIPID BILAYER in aqueous environments.
- HYDROPHILIC HEADS which keep cell membrane together.
- Able to form GLYCOLIPIDS by combining with carbohydrates at the cell membrane. Important in CELL RECOGNITION.

[3.1.3] Describe the components of a phospholipid in terms of hydrophobic and hydrophilic.

The hydrophilic head of the phospholipid interacts with water whereas the hydrophobic fatty acid tails repel water.

[3.1.4.1] What is the structure of an AMINO ACID?

[3.1.4.1] How are DIPEPTIDES formed?

A dipeptide is formed by the condensation reaction of two amino acids.

[3.1.4.1] What is the bond that forms between amino acids?

Peptide Bonds.

[3.1.4.1] What is a POLYPEPTIDE?

Polypeptides (i.e. proteins) are formed by the condensation reaction of many amino acids.

[3.1.4.1] What is the PRIMARY STRUCTURE of a protein?

The linear sequence of amino acids that make up a polypeptide chain.

[3.1.4.1] What is the SECONDARY STRUCTURE of a protein?

- An ALPHA HELIX forms because hydrogen bonds form between every fourth peptide bond.
-The BETA-PLEATED SHEET forms when the protein folds so that two parts of the polypeptide chain are parallel to each other, enabling hydrogen bonds to form between the parallel peptide bonds.

These hydrogen bonds can be broken by high temperatures and extreme pH.

[3.1.4.1] What is the TERTIARY STRUCTURE of a protein?

The overall 3D structure of a protein, formed when the secondary structure folds over on itself

Held together by: HYDROGEN BONDS, IONIC BONDS, DISULPHIDE BRIDGES* and HYDROPHOBIC INTERACTIONS BETWEEN NON-POLAR AREAS.

*Disulphide bridges form between R groups (usually between two cysteines).

[3.1.4.1] What is the QUATERNARY STRUCTURE of a protein?

Two or more polypeptide chains combine to form a whole protein molecule.

[3.1.4.1] What is a GLOBULAR protein?

Tightly folded polypeptide chains in the shape of a sphere.

- Soluble in water.
- Lose solubility and become inactive when denatured.

Examples: ENZYMES, HORMONES, HAEMOGLOBIN, MYOGLOBIN.

[3.1.4.1] What is a FIBROUS protein?

Fibrous proteins form long, rope-like fibres.

- Insoluble in water.
- High tensile strength (which is lost when the protein denatures).

Examples: COLLAGEN, SILK, KERATIN.

[3.1.4.2] What is an ENZYME?

A biological catalyst which speeds up reactions (by LOWERING THE ACTIVATION ENERGY) without being used up.

They are proteins with a specific tertiary structure.

What is the INDUCED FIT HYPOTHESIS?

The active site of the enzyme changes shape to fit the substrate inside. They are complimentary shapes but not identical.

[3.1.4.2] How do enzymes catalyse reactions?

For a reaction to occur, the reacting substances must collide. The energy barrier required for this to happen is known as the ACTIVATION ENERGY,

One way of overcoming this barrier is heating the reaction. This increases the kinetic energy of the molecules which therefore increases the number of successful collisions.

[3.1.4.2] How does TEMPERATURE affect the rate of enzyme action?

- Higher Temperature = More Kinetic Energy
--> Therefore more successful collisions between the enzymes and substrates = more enzyme-substrate complexes = more product.

- After the optimum temperature, the rate of reaction decreases.

- High Temperatures break the hydrogen, ionic and disulphide bonds within the tertiary structure, altering the shape of the active site. This means it is no longer complimentary to the substrate so ES complexes cannot form.

[3.1.4.2] How does pH affect the rate of enzyme action?

- SLIGHT FLUCTUATIONS FROM OPTIMUM PH:
--> Alterations in the charge of the active site, meaning the substrate cannot bind as effectively and therefore there is a decreased rate of reaction as less product is formed.

- OPTIMUM PH:
--> Maximum activity as the R groups have correct charges and the tertiary structure is correct.

- EXTREME PH:

--> The enzyme DENATURES. The hydrogen and ionic bonds break, changing the shape of the tertiary structure. The active site is no longer complimentary to the substrate.

[3.1.4.2] How do we calculate pH?

pH = -log[H+]

[3.1.4.2] How does SUBSTRATE CONCENTRATION affect the rate of enzyme action?

Increasing substrate concentration increases the rate of reaction. (More substrates = more chance of collision)

[3.1.4.2] How does increasing ENZYME CONCENTRATION affect the rate of enzyme action?

[3.1.4.2] What are COMPETITIVE INHIBITORS and how do they affect the rate of enzyme action?

Competitive Inhibitors are a similar shape to the substrate - they temporarily bind to the active site in order to prevent the substrates from binding, therefore reducing the rate of reaction.

REVERSIBLE BY ADDING MORE SUBSTRATES.

[3.1.4.2] What is a NON-COMPETITIVE INHIBITOR and how do they affect the rate of enzyme action?

Non-Competitive Inhibitors are a different shape to the substrate. They bind to the enzyme AWAY from the active site, causing the tertiary structure to permanently change shape. This means that substrates cannot bind, causing the rate of reaction to decrease.

IT IS NOT REVERSIBLE.

[3.1.4.2] What is END-PRODUCT INHIBITION?

As the enzyme converts substrate to product, the end-product begins to bind to the original enzyme - causing a change in shape of the active site.

The end product can detach itself and be used elsewhere, allowing the active site to be reformed.

[3.1.5.1] DNA (Deoxyribonucleic Acid) is a chemical that determines characteristics. What are the abilities of DNA?

- It carries the genetic code (codes for characteristics/proteins).

- It can make exact copies of itself.

[3.1.5.1] How is DNA stored in eukaryotic cells?

The DNA molecules are LINEAR and very long - they are wound around proteins called HISTONES*, making the DNA much more compact.

*Histone Proteins also help support the DNA.

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The DNA and proteins are tightly coiled to form chromosomes, of which each being a 'thread-like' structure.

[3.1.5.1] What are the main components of DNA?

- A pentose sugar (deoxyribose)
- A phosphate group
- A nitrogenous organic base

These components combine to form a NUCLEOTIDE.

[3.1.5.1] How are dinucleotides formed?

Dinucleotides are formed via the condensation reaction between two nucleotides.

The bond holding the nucleotides together is a PHOSPHODIESTER bond.

[3.1.5.1] What are the organic bases found in nucleotides?

- PURINE BASES (Double-Ring) = Adenine and Guanine

- PYRIMIDINE BASES (Single-Ring) = Thymine and Cytosine

[3.1.5.1] What is the structure of a phosphate group?

[3.1.5.1] DNA can be described as ANTIPARALLEL. What is meant by the term 'antiparallel'?

DNA consists of polynucleotide strands running in OPPOSITE DIRECTIONS.

[3.1.5.1] What is COMPLIMENTARY BASE PAIRING?

Complimentary Base Pairing ensures that polynucleotide strands are always the same distance apart.

ADENINE pairs with THYMINE (2 hydrogen bonds)

CYTOSINE pairs with GUANINE (3 hydrogen bonds)

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The two ends of DNA (5 prime and 3 prime) are not equivalent. The 5 prime end of DNA has phosphate group while the 3 prime end has a hydroxyl group.

5 prime is complimentary to an enzyme.

DNA polymerase is the enzyme that assembles DNA strands by attaching the 5′ phosphate of the new nucleotide to the 3′ carbon of the last. So, in this way, a DNA strand is always constructed from 5′ to 3′.

[3.1.5.1] How does the structure of DNA relate to its function?

- Large Molecule
--> Stores lots of information.

- Strong Sugar-Phosphate Backbone
--> Stabilises DNA, prevents damage.

- Complimentary Base Pairing
--> DNA Replication.

- 4 Base Code Sequence
--> Codes for Amino Acids.

- Weak Hydrogen Bonds
--> Nucleotide Chains can split.

- Coiling of DNA
--> Makes it compact.

[3.1.5.1] What is the structure of RNA?

- A pentose sugar (ribose)
- A phosphate group
- A nitrogenous organic base

[3.1.5.1] What are the bases in RNA and what are they paired to?

ADENINE pairs with URACIL

CYTOSINE pairs with GUANINE

[3.1.5.1] What are the three types of RNA and their functions?

mRNA (messenger) is SINGLE STRANDED and LINEAR. It passes into the cytoplasm and attaches to ribosomes for protein synthesis.

tRNA (transfer) is SINGLE STRANDED and 'CLOVERLEAF'. It brings amino acids to the ribosomes for protein synthesis.

rRNA (ribosomal) is essential for protein synthesis.

[3.1.5.2] What are the four requirements for DNA replication?

1. The four types of FREE NUCLEOTIDE, containing the bases A, C, T and G in order to build a new strand.

2. Both strands of the parent DNA to act as a template.

3. DNA Helicase and DNA Polymerase.

4. A source of chemical energy.

[3.1.5.2] What is the SEMI-CONSERVATIVE MODEL of DNA Replication?

The replication process in which one DNA strand is conserved, whereas the other strand is newly synthesised.

[3.1.5.2] What are the steps of semi-conservative replication?

1) The parent DNA strand is joined by hydrogen bonds.

2) DNA Helicase breaks these hydrogen bonds, separating the double helix.

3) Bases on free nucleotides line up against their complimentary base on the parent strand.

4) DNA Polymerase joins the nucleotides together, forming two new strands.

5) New sugar-phosphate backbones form, producing two identical DNA strands.

[3.1.5.2] What is the difference between the conservative and semi-conservative model of DNA replication?

[3.1.5.2] What was Meselson and Stahl's research?

Their work was based on three facts:

1. All bases contain nitrogen.

2. Nitrogen has 2 isotopes - N-14 and N-15.

3. Bacteria will incorporate nitrogen to make new DNA.

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- The E.coli was grown in a medium of nitrogen-15.

- E-coli was allowed to replicate once with a medium of nitrogen-14.

- The E.Coli was allowed to replicate twice with a medium of nitrogen-14.

[3.1.6] What is ATP?

Adenosine Triphosphate (ATP) is a nucleotide derivative. It is often known as a phosphorylated nucleotide.

The formation of ATP requires energy, which originates from sunlight.

[3.1.6] What is the reaction between ATP, ADP and Pi?

[3.1.6] What are the uses of ATP?

- Hydrolysis of ATP makes energy instantly available.

- ATP breakdown releases a small amount of energy, idea for driving reactions.

- ATP is broken down in one step.

[3.1.6] What is the role of ATP?

- Metabolic Processes, e.g. digestion

- Active Transport

- Movement, e.g. muscle contraction

- Secretion, e.g. hormone and enzyme secretion

- Activation of Other Molecules - making molecules more reactive

[3.1.7] What are the functions of water?

- Water is a METABOLITE in many metabolic reactions, including condensation and hydrolysis reactions.

- Water is a SOLVENT, important for metabolic reactions.

- Helps with TEMPERATURE CONTROL (large SPECIFIC HEAT CAPACITY and SPECIFIC LATENT HEAT OF VAPORISATION).

- Very COHESIVE which is useful for substance transport.

[3.1.7] What is the structure of water?

The shared negative hydrogen electrons are pulled towards the oxygen atom, leaving the hydrogens with a slight positive charge.

The unshared negative electrons on the oxygen atom give it a slight negative charge.

Therefore water is a polar molecule.

[3.1.7] What are the properties of water?

- IMPORTANT METABOLITE:
--> Many metabolic reactions involve condensation or hydrolysis reactions, both of which require water.

- HIGH LATENT HEAT OF VAPORISATION:
--> It takes a lot of energy to break the hydrogen bonds between the water molecules. This is useful for living organisms as they can use water loss through evaporation to cool down without losing too much water.

- BUFFERS (RESISTS) CHANGES IN TEMPERATURE:
--> The hydrogen bonds can absorb a lot of energy which means it has a high specific heat capacity. Useful for living organisms as water doesn't experience rapid temperature change.

- GOOD SOLVENT:
--> Water is polar, meaning that ions become surrounded by water and dissolve.

- COHESION:
--> Water molecules are cohesive because they are polar. This helps water to flow and has a high surface tension in contact with air.

[3.1.8] What is an INORGANIC ION?

An ion which doesn't contain carbon.

[3.1.8] What is an ION?

An atom that has LOST or GAINED ELECTRONS.

- CATIONS have LOST electrons.

- ANIONS have GAINED electrons.

[3.1.8] What are SODIUM IONS?

The symbol for a sodium ion is Na⁺.

A molecule of glucose or an amino acid can be transported across a cell membrane alongside Na⁺ (co-transport).

[3.1.8] What are IRON IONS?

The symbol for an iron ion is Fe²⁺.

Haemoglobin is made up of four polypeptide chains with an Fe²⁺ ion in the centre. The Fe²⁺ binds to oxygen and temporarily forms an Fe³⁺ ion until the oxygen is released.

[3.1.8] What are PHOSPHATE IONS?

The symbol for a phosphate ion is PO₄³⁻.

When PO₄³⁻ is attached to a molecule, it becomes a phosphate group. DNA, RNA and ATP contain them.

It is the phosphate bonds which store energy in ATP.

[3.1.8] What are HYDROGEN IONS?

The symbol for a hydrogen ion is H⁺.

pH is calculated based on the concentration of H⁺ in the environment.

MORE H⁺ = LOWER PH = MORE ACIDIC

Enzyme reactions are affected by pH.