Longer answer questions (4-6)

Made for May 2025 exam

Step-by-step transcription

1. DNA helicase breaks hydrogen bonds between complementary base pairs, unwinding the double helix and exposing the bases

2. One chain of the DNA acts as a template

3. Free mRNA nucleotides in the nucleoplasm align opposite exposed complementary DNA bases with hydrogen bonding

4. The enzyme RNA polymerase binds at the start codon and moves in the 5’ to 3’ direction, forming phosphodiester bonds between adjacent RNA nucleotides to form an mRNA copy

5. Temporary hydrogen bonds between the mRNA bases and the DNA break, and the mRNA can move out of the nucleus through a nuclear pore

Step-by-step translation

1. .Once the modified mRNA has left the nucleus through a nuclear pore, it attaches to a ribosome in the cytoplasm

2. The ribosome attaches at the start codon

3. The tRNA molecule with the complementary anticodon to the start codon aligns opposite the mRNA, held in place by the ribosome

4. The ribosome will move along the mRNA molecule to enable another complementary tRNA to attach to the next codon on the mRNA

5. The two amino acids that have been delivered by the tRNA molecule are joined by a peptide bond.

6. This continues until the ribosome reaches the stop codon at the end of the mRNA molecule. The stop codon does not code for an amino acid and therefore the ribosome detaches and translation ends

What process occurs between transcription and translation?

Following transcription, pre-mRNA has to be modified to become mRNA that is ready to leave the nucleus and be translated.

The introns are spliced out, leaving behind mRNA that is just the exons, the coding regions.

Overview of meiosis I and meiosis II

• Homologous chromosomes pair up, whereby crossing over at the chiasma may take place. By the end of the first division, the homologous pairs will have separated, with one chromosomes from each pair going into one of the daughter cells

• the arrangement of these pairs is random, meaning that the first division into the daughter cells is also random (independent segregation)

• in the second division, the chromatids separate

What occurs in prophase I

- DNA condenses and becomes visible

- Crossing over may occur at the chiasma

- Nucleolus and nuclear membrane break down

- Two sister chromatids joined at centromere

- Arranged in homologous pairs called bivalents

What occurs in metaphase I

- The bivalents line up along the equator of the spindle

What occurs in anaphase I

- Homologous pairs chromosomes are separated as microtubules pull whole chromosomes to end of spindle

- Centromeres do not divide

What occurs in telophase I

- Chromosomes reach poles of spindle

- Nucleoli form and spindle fibres break down

- Homologous chromosomes

What occurs in cytokinesis (meiosis)

• division of the cytoplasm

• this occurs after both meiosis I and meiosis II

• four haploid cells are formed

Process of crossing over

• In meiosis 1, homologous pairs come together to form bivalents and line up opposite each other at the equator

• Non-sister chromatids wrap around each other at points called chiasmata.

• This puts tension on the chromatids, and they can break up at the chiasmata so that sections of chromosomes may swap over between non-sister chromatids

• This results in different combinations of alleles on the gene, producing offspring that are not genetically the same as their parents.

Describe the process that produce variation within meiosis

• Crossing over occurs when homologous chromosomes form bivalents, and wrap around each other at points called chiasmata. The chromosomes break and sections swap between non-sister chromatids (prophase I)

• Random fertilisation

• Independent segregation/assortment is where the allocation of chromosomes into each daughter cell is random once aligned at the equator of the cell (metaphase

What are the two mechanisms in meiosis which introduce variation, and which stage do they occur in?

• independent segregation of homologous chromosomes

• crossing over between homologous chromosomes

Both occur in meiosis I

What is nondisjunction?

When the chromosomes or chromatids do not split equally during anaphase. Therefore, the resulting gamete will not have the correct number of chromosomes

Breakage of chromosomes in meiosis can result in..

• Inversion: a portion of a chromosome can break, and re-join into the original chromosome but after inverting itself, resulting in a change in sequence

• Deletion: an entire region of chromosome is accidentally deleted

• Duplication: regions in a chromosome can be become duplicated

• Translocation: a portion of one chromosome accidentally switches places with a separate, non-homologous chromosome

4 comparisons between eukaryotic and prokaryotic DNA?

• Eukaryotic DNA is linear and prokaryotic DNA is circular

• Eukaryotic DNA is associated with histone proteins and prokaryotic DNA is not associated with histone proteins

• Eukaryotic DNA has introns and prokaryotic DNA does not

• Eukaryotic DNA is longer and prokaryotic DNA is shorter

3 features of the genetic code (and what do they mean)

1. Non-overlapping (means that each triplet is only read once, and there are no overlapping bases - ensures the code is read correctly and correct sequence of AA produced)

2. Degenerate (there are multiple codons for the same amino acid - reduces impact of mutations to ensure code read correctly)

3. Universal (almost every organism uses the same genetic code, and each triplet always codes for the same AA - allows genetic information to be transferred between species)

What does courtship behaviour help to achieve?

• Recognize members of their own species

• Identify a mate that is capable of breeding (opposite sex, mature and fertile)

• Form a pair bond

• Synchronise mating (mating must occur when there is the maximum chance of gametes meeting)

• Become able to breed (bring a member of the opposite sex into a 'physiological state' that allows breeding to occur)

Explain how the production of lactate is advantageous to an insect?

• lactate lowers water potential inside muscle cells

• draws in water from ends of tracheoles down water potential gradient by osmosis

• volume in tracheoles increases, decreasing pressure

• air/oxygen moves down the pressure gradient

Explain why an insect does abdominal pumping whilst flying

• it increases pressure in the tracheoles

• therefore carbon dioxide diffuses down pressure gradient out of tracheoles

Adaptations in fish for efficient gas exchange (with reasons)

• many gill filaments, and many lamellae on each filament = surface area is increased, which increases the rate of diffusion of gases between blood and water

• Gaps between lamellae = water can flow between adjacent lamellae so surface area for gas exchange increased

• constant circulation of blood = blood in capillaries next to lamellae that are saturated with oxygen is transported away from lamellae, so that the concentration gradient of oxygen is always maintained

• countercurrent exchange system = blood and water flow in opposite directions so that a concentration gradient of oxygen is maintained along the entire length of the gill (means equilibrium is not reached and blood always encounters water with a higher oxygen concentration

How is the opening and closing of the stomata regulated in response to changes in light intensity?

1. light intensity increases

2. light activates K+ pumps, which actively transport K+ ions from the epidermal cells into the guard cells (using ATP produced from photosynthesis)

3. an increased concentration of K+ in the guard cell lowers the water potential of the guard cell

4. water moves into the guard cell by osmosis, down the water potential gradient

5. this causes the guard cells to curve and become turgid, and the stomata opens - due to the fact that the inner wall is much more elastic than the outer wall

What happens to the intercostal muscles in inspiration?

• external intercostal muscles contract

• internal intercostal muscles relax

• this pulls the ribcage up and out

What happens to the volume and pressure of the lung/thoracic cavity in inspiration?

• lung volume/thoracic cavity increases

• this decreases air pressure in the lungs

• air moves down a pressure gradient from a higher pressure in the air outside to the lungs

Adaptations of the alveoli

• many alveoli in each lung = large surface area for gas exchange

• Alveoli epithelium cells are one cell thick and capillary endothelium is one cell thick = minimises diffusion distance

• Each alveolus is surrounded by a network of capillaries = The constant blood flow removes exchanged gases and therefore maintains a concentration gradient

Lipid absorption (stage 1, before entering ileum)

• The liver produces bile salts (stored in the gall bladder)

• This emulsifies larger lipid globules into smaller lipid droplets to increase the surface area, which increases the rate of digestion by lipase

• Lipase is produced by the pancreas and released into the ileum gut lumen. Lipase hydrolyses the ester bond found in triglycerides to form two free fatty acids and a monoglyceride

• Monoglycerides and free fatty acids remain associated with bile salts to make structures called micelles

• The micelles are more soluble in water. The material in the ileum lumen is constantly moving and the function of the micelles is to carry the monoglyceride and free fatty acids close to the microvilli of the ileum epithelial cells

Lipid absorption (stage 2, ileum epithelial)

• The micelles break down right next to the epithelial cells and the monoglyceride and free fatty acids are released. They are non-polar and lipid soluble so they can enter the cells via simple diffusion

• Once inside the epithelial cells, monoglycerides and fatty acids are transported to the smooth endoplasmic reticulum, where they are recombined to form triglycerides

• In the golgi apparatus, lipoprotein and cholesterol are added to the triglycerides to form chylomicrons. These are special particles adapted for the transport of lipids

Lipid absorption (stage 3, leaving cell)

• Chylomicrons move out of the epithelial cells by exocytosis (in vesicles) and enter lacteals found at the centre of each villus

• Eventually chylomicrons pass from the lymphatic vessels into the circulatory system

• The enzyme lipase is found in the endothelial cells of blood capillaries and hydrolyses the ester bonds found in the triglycerides of chylomicrons. The products then diffuse into cells

Stages of phagocytosis

1. phagocytes are attracted to pathogens by chemicals, and the phagocyte towards towards these cells along a concentration gradient

2. Receptors on the cell surface membrane of the phagocyte bind to the antigens on the pathogen

3. the phagocyte changes shape to move around and engulf the pathogen

4. the pathogen is trapped within a phagosome vesicle, and lysosomes fuse with this phagosome - releasing the hydrolytic enzyme lysozyme that will hydrolyse the pathogen

5. the products of this digestion are absorbed into the cytoplasm

Cell mediated response

1. Once a pathogen has been engulfed and hydrolysed by a phagocyte, the antigens are displayed on the surface of the phagocyte

2. Helper T cells have receptors that can bind complementarily to the antigens on the phagocyte/APC

3. This activates the helper T cells to divide by mitosis and undergo clonal expansion

4. Cloned helper T cells can differentiate into 4 types of cell
   - memory T-cells
   - activate cytotoxic T cells
   - active B-cells
   - stimulate more phagocytosis

Humoral response

1. Surface antigens on pathogen are taken up by specific B-cells

2. The complementary helper T cell uses its receptors to bind to the displayed antigens on the B cell

3. This activates the B cells to undergo mitosis in clonal expansion

4. these clones differentiate into either plasma cells or memory B cells

5. plasma cells produce antibodies, and antigens bind to antibodies to create an antigen-antibody complex. This clumps them together to make it easier for phagocytes to locate/destroy pathogens

6. Memory B cells will divide rapidly into plasma cells when reinfected with the same pathogen to make large numbers of the antibody quickly

Lifecycle of HIV

1. gp120 attachment proteins embedded in the lipid envelope of the HIV bind to the antigen binding site on CD4 receptors on the helper T cell. They bind because the tertiary structure of the antigen binding site on the CD4 receptor is complementary to the tertiary structure of the HIV attachment protein

2. Binding causes the lipid envelope of the HIV to fuse with the cell surface membrane of the helper T cell

3. The HIV capsid releases RNA, reverse transcriptase and integrase into the helper T cell

4. The enzyme reverse transcriptase creates a HIV DNA copy of the RNA, and this travels to the nucleus of the helper T cell

5. Integrase inserts the viral DNA into the DNA of the host cell

6. an mRNA copy of this HIV DNA is made through transcription

7. the HIV mRNA diffuses out of the nucleus through a nuclear pore, and binds to a ribosome which can translate it into HIV proteins

8. HIV particles are assembled using HIV genetic material and HIV proteins

9. The HIV particle buds off of the host cell, using part of the cell surface membrane to make its lipid envelope

Interphase key ideas (mitosis)

• chromosomes are not clearly visible

• DNA replication occurs in this phase

The phases of interphase (mitosis)

• G1: first phase of growth
  Additional organelles synthesised, high metabolic activity
  Protein synthesis
  Cell increases in size

• S: DNA synthesis
  Chromosomes are replicated

• G2: second phase of growth
  More new organelles synthesised
  Cell double-checks replicated chromosomes are free of error and makes any repairs necessary to the DNA

Prophase (mitosis)

• chromatin condenses into chromosomes

• centrioles begin to move towards poles and form spindle fibres

Metaphase

Chromosomes aligned at the equator, attached to the spindle fibres at the centromere

Anaphase

• sister chromatids pulled apart to opposite poles of the cell by spindle fibres attached at the centromere

Telophase

• new membranes form around daughter nuclei

Lifecycle of a bacteriophage

1. The attachment proteins on the bacteriophage bind to the binding site of receptors on the bacteria because they have complementary tertiary structures

2. Viral DNA is injected into the bacteria

3. The viral DNA is replicated using the host cell’s enzymes

4. New viral proteins are made suing viral DNA and the host cell’s ribosomes (viral DNA is transcribed and translated)

5. Mature viruses are assembled within the cell using the viral DNA and proteins

6. The cell is forced to lyse and bacteriophages are released into the environment

In co-transport, where is the concentration of sodium ions lowest?

• sodium ion concentration is lower inside the ileum epithelial cell

In co-transport where is the concentration of glucose lowest?

lowest inside the ileum lumen (therefore glucose moves against the concentration gradient into the ileum epithelial cell)

How is the concentration gradient of sodium ions between the ileum lumen and ileum epithelial cell maintained?

• The Na+/K+ pump uses ATP to transport sodium ions via active transport out of the ileum epithelial cell and into the bloodstream

• this maintains lower concentration of sodium ions inside epithelial cell

• therefore facilitated diffusion occurs down the concentration gradient (from lumen to epithelial cell)

Starch key facts

• Formed through the condensation of alpha glucose

• 1,4 and 1,6 glycosidic bonds

• longer and less branched that glycogen

• the storage polysaccharide in plants (in granules in the chloroplasts)

• (includes amylose and amylopectin)

Why is starch(or glycogen) a suitable storage molecule (and reasonings)

• insoluble = doesn’t affect water potential or osmosis in cell

• large = cannot diffuse out of cell

• compact = maximises energy storage as a lot can be stored in a smaller area

• branched = larger SA for enzymes to hydrolyse into glucose

Glycogen key points

• formed through the condensation of alpha glucose

• 1,4 and 1,6 glycosidic bonds

• alpha chains tend to be shorter than starch and have more branches (enzymes can act simultaneously)

• main energy storage molecule in animals

Structure of cellulose

• unbranched straight chain

• 1,4, glycosidic bonds

• beta glucose monomer

• every alternate beta glucose must be inverted to form the glycosidic bond

What makes cellulose strong?

• many hydrogen bonds/cross-linkages between parallel chains of microfibrils

• allows cellulose in cell walls to stay strong - helps remain turgid and withstand osmotic pressure

What is the primary structure of a protein?

• The order/sequence of amino acids. This is determined by the DNA sequence

• peptide bonds (covalent)

• between adjacent amine and carboxyl groups

• condensation reaction

What is the secondary structure of a protein?

• The shape that the polypeptide chain forms as a result of hydrogen bonding (based on the amino acid sequence)
  - hydrogen bonds can cause the protein to coil into an alpha-helix or a beta pleated sheet

• hydrogen bonds

• between adjacent amine and carboxyl groups (amine group is NH+ and carboxyl is COOH- so they attract to form a hydrogen bond)

What is the tertiary structure of a protein?

• The folding of the polypeptide chain that is a result of the interactions between the R groups, forming a 3D shape

• hydrogen bonds

• ionic bonds (between charged R groups)

• disulphide bridges (covalent S-S, amino acid cystine)

• hydrophobic and hydrophilic interactions

What is the quaternary structure of a protein?

The arrangement of two or more polypeptide chains in a protein

Biochemical test for proteins

Biuret reagent
- composed of a dilute alkali and dilute copper sulphate (CuSO4)

A positive test turns purple and detects the presence of peptide bonds

Biochemical test for lipids

Add ethanol and water then shake - cloudy white emulsion indicates a positive result

Test for reducing sugars

• a reducing sugar is a sugar that can donate electrons to (or reduce) Benedict’s reagent

• all monosaccharides are reducing sugars, and the disaccharides maltose and lactose are reducing sugars also

• when Benedict’s reagent is heated with a reducing sugar, insoluble Cu2O is formed and gives a red precipitate

• as the concentration of sugar increases the colour of the precipitate changes from green - yellow - red

Test for non-reducing sugars

• also add HCl and sodium hydrogencarbonate

• the HCl will hydrolyse any glycosidic bonds present, meaning there are now electrons available to donate, and the resulting sugar becomes reducing

• sodium hydrogencarbonate is added before testing with Benedicts because it is an alkali so will neutralise the acid (benedicts does not work in acidic conditions)

5 key properties of water

1. it is a metabolite

2. it is a solvent

3. has a high heat capacity

4. high latent heat of vaporisation

5. strong cohesion between molecules/high surface tension

Metabolic properties of water

• involved in many chemical reactions e.g. condensation, hydrolysis

• Approximately 90% of plasma in the blood is water, and the cytoplasm of cells are largely composed of water also

Water as a solvent

• substances can dissolve in water because it is charged (polar)

• allows vital substances to be transported around the bod

• The slight + charge on hydrogen atoms will attract any negative ions in solutes

• The slight – charge on oxygen atoms will attract any positive ions in solutes

High specific heat capacity of water

• a lot of energy is required to raise the temperature of water

• because the heat energy is used to break the hydrogen bonds between molecules

• acts as a buffer to temperature/resists temperature change

• useful in habitats/organisms as it maintains constant temperature of water

• important so enzymes do not denature

High latent heat of vaporisation

• lot of energy is required to convert water from its liquid state to a gaseous state

• due to energy required to overcome hydrogen bonds

• provides a cooling effect - e.g. sweating in humans and transpiration in plants

Strong cohesion between water molecules

• molecules ‘stick’ together due to hydrogen bonds

• creates columns of water, which are easier to move than individual molecules

• provides surface tension to provide habitats for small insects

The two types of DNA replication and descriptions of

Conservative

• suggests that the original DNA molecule remained intact, and a separate daughter DNA copy was produced

Semi-conservative

• the original DNA molecule splits into two separate strands, and each of the new molecules has one strand of new material and one of the original

Semi-conservative DNA replication step-by-step

1. DNA helicase breaks the hydrogen bonds between the complementary base pairs between the two strands of the double helix

2. This causes the DNA to unwind and each of the separated DNA strands acts as a template.

3. Free DNA nucleotides within the nucleoplasm align opposite the exposed bases by complementary base pairing

4. DNA polymerase joins adjacent nucleotides together by phosphodiester bonds in a condensation reaction

5. DNA ligase joins the fragments of nucleotides to form the complementary strands of DNA

6. Two sets of new DNA produced, containing one strand of the parental DNA and one newly synthesised strand

Vaccination

• Small amounts of weakened or dead pathogens, or antigens, are injected into the bloodstream (or introduced via the mouth)

• Exposure to the antigens activates B-cells to go through clonal expansion and differentiation (clonal selection) 

• B-cells undergo mitosis to make large numbers of cells, and these differentiate into plasma cells or memory B-cells.  

• The plasma cells make antibodies  

• Memory B-cells can divide rapidly into plasma cells when reinfected with the same pathogen, to make large numbers of antibodies rapidly