module 2

Question 1

chracterisitcs of the genetic code

Answer 1

Degenerate: many codons can code for the same amino acid
Stop codons terminate protein synthesis
Start codon also codes for methionine

Question 2

outline the steps of transcription

Answer 2

1. Initiation:
   Sigma factors on RNA polymerase binds onto the promoter sequence located upstream of the initiation site
   RNA begins to unwind the double helix
2. Elongation
   -Sigma factor releases
   Moving along in a 5’ to 3’ direction, RNA polymerase synthesises a new strand using complementary free floating nucleotides whilst unwinding it
3. Termination
   At the termination site, RNA polymerase and the mRNA strand are released

Question 3

Outline steps of translation

Answer 3

Translation step 1: Initiation
Recognition site on mRNA binds to small subunit
methionine -charged tRNA binds to AUG start codon
Large subunit joins initiation complex

Translation step 2: elongation
Codon recognition: anitcodon of incoming tRNA binds to codon at A site
Peptide bond formation:
Elongation: free tRNA moves to E site and is then released as the ribosomes shifts by one codon
Repeats

Translation step 3: termination
Release factor binds to complex when stop condon enters A site
Causes the release of polypeptide from the tRNA in the P site
Remain components separate (mRNA and ribosomial subunits)

Question 4

Pre-translation

Answer 4

Pre-mRNA matures to mRNA in the nucleus, involving 5’-capping, poly-A tail, intron splicing
mRNA migrates to cytoplasm for translation to polypeptide
Signal sequences determine where protein is targeted (cytoplasm, rough endoplasmic reticulum, organelles)

Question 5

Different types if energy in biological systems

Answer 5

1. Electrical – separation of charges
   Electrical gradients across cell membranes help drive the movement of ions
2. Chemical – stored in chemical bonds
   Energy stored in covalent bonds released during hydrolysis of organic molecules
3. Light – electromagnetic radiation stored as photons
   Light energy is captured by pigments in the eye or in plant photosynthesis
4. Mechanical – energy of motion
   Mechanical energy is produced in muscle movements
5. Heat – transfer due to temperature difference
   Heat can be released in biochemical reactions and alter body temperature

Question 6

Metabolism

Answer 6

sum total of all the chemical reactions occurring in a biological system at a given time
Metabolic reactions involve energy changes.

Question 7

What is free energy and how does it relate to exergonic and endogonic reactions

Answer 7

Gibb’s Free Energy (G) = amount of energy available to do work

∆Greaction = Gproducts – Greactants
∆G < 0 — free energy is released in the reaction = exergonic
∆G > 0 — free energy is required for the reaction = endergonic

Question 8

describe catabolic and anabolic reaction

Answer 8

Catabolic reactions break down larger, more complex molecules into smaller ones and often release energy
Anabolic reactions link smaller molecules to form larger, more complex molecules and require an input of energy.

Question 9

Activation energy

Answer 9

Catalysts: increase rate of chemical reactions
Active site and substrate reaction
Reduce activation energy
Easier path
Does not change free energy
Affect orientation of substrate , physical strain/conformational changes

Question 10

How does ATP store energy

Answer 10

Potential chemical energy stored in the bonds between phosphate groups
Negative charge of phosphate group would repel each other
separation (hydrolysis) is spontaneous reactions, releasing free energy and adp (exergonic)
phosporalation of ADP forms ATP (endergonic)

Question 11

Redox reactions and role of electron carriers in the cell

Answer 11

more reduced = more free energy

Question 12

photosynthesis

Answer 12

Co2 + H2O —> O2 + C5H12O6

Question 13

Steps of the light reaction stage

Answer 13

1. Light energy in the form of photons is absorbed chlorophyll molecules in photosystem 2 causing it to go into an excited state
2. Energy is passed to chlorophyll molecules in the reaction centre which then donates the electron to a primary electron acceptor
3. Having lost an electron, chlorophyll molecules receive electrons from the dissociation of hydrogen ions and oxygen of water
4. Excited electrons pass through a series of proteins in the membrane (Plastoquinone, cytochrome, plastocyanin) which causes it to gradually lose energy as it is being used to pump hydrogen ions across the membrane into the stroma/thylakoid lumen which creates a proton gradient
5. Electrons move to photosystem 1 and passes to chlorophyll inside reaction centre
6. Photons from light excite electrons allowing it to transfer to the electron acceptor, forming high energy electron
7. Electrons pass through NADP reductase and in the process reduced NADP+ to NADPH
8. Accumulation of hydrogen protons in the thylakoid lumen forms a proton gradient which allows ATP synthase to generate ATP from ADP

Question 14

Carbon fixation - light independent

Question 15

Microbiomes

Answer 15

The different microorganisms in an organism
example

Question 16

What is the holobiont concept

Answer 16

Holobiont: symbiotic ecological unit usually between a host and microbiota
outlines how our symbiotic relationship is impacted by the environment

Question 17

importance of a fibre-rich diet

Answer 17

microbiome in the colon converts fibre into short fatty acid chains via microbial fermentaion
Mucus layer of colon is eroded causing barrier dysfunction as they cannot form a proper structural arrangement with the host’s gut
Results in breaking down the interface of the colon causing disease.

Question 18

List the 4 different chemical signals and their affect

Answer 18

1. Autocrine signals affect the cells that made them - bind to receptors that made them
2. Juxtacrine signal affect only adjacent cells - binds to adjacent cells
   3, Paracrine signals affect nearby cells
3. Circircalitng signals: (horomones) are transported by the circulatory systems and bind to receptors in distant cells

Question 19

Requirements to respond to a signal

Answer 19

A cell must have a specific receptor to detect signal
A signal transduction pathway is the sequence of event that lead to the response
Responses may involve enzymes and transcription factors that are either activated or inactivated to have the desired response

Question 20

Process of a signal transduction pathway

Answer 20

1. Signal arrives at a target cell
2. The signal molecule binds to a receptor protein in the cell surface or inside the cytoplasm
3. Signal binding initiates the conformational change of the receptor and exposes the active site
4. Activated receptor activates a signal transduction pathway which induced cellular changes

Question 21

2 types of receptors based on its location

Answer 21

Intracellular receptors:
inside the cell interacting with physical or chemical signals
Usually respond to non polar signals as it can diffuse directly across the lipid bilayer of the cell membrane to encounter its receptor in the cytoplasm or nucleus
Membrane receptors:
large or polar ligand bind to cell membrane receptors
Respond to polar signals flowing outside the cells and cannot diffuse through the cell membrane and is embedded in the membrane

Question 22

3 types of receptors based on their mechanisms

Answer 22

Ion channel receptors: allows ions to enter or leave the cell
Acetylcholine binds to 2 of the 5 AChR subunits causing the channel to chage shape and open
Channel is lined with negatively charged amino acids, allowing Na+ to flow intot he cell
NA+ buildup in cells initiates events that lead to muscle contraction

Protein kinase receptors: phosphorylate themselves
Insulin binds to a subunits of the insulin receptor
Conformation change in the b subunit occurs, transmitting a signal to the cytoplasm that the insulin is present
Signal activates the receptor’s protein kinase domain in the cytoplasm
Phosphorylates insulin-response substrates, triggering a cascade of chemical response inside the cell

G protein-coupled receptors: work via an intermediary
Hormone binding to receptor activates the G protein - GTP replaces GDP
Activated g protein subunit activates effector protein that causes changes in cell function

Question 23

What can a cell do in response to a signal

Answer 23

Open an ion channel
Change enzyme activity
Differential gene expression

Question 24

How do adjacent cells in animal and plant cells communicate

Answer 24

Plant cells
Through plasmodesmata
Plasmodesmata: reasonably large membrane lined channel through which molecules can pass

Animals cells
Gap junctions form a narrow channel through which ions can pass