Module 1 - Bio1007 - Key things to remember

Hydrophobic

Doesnt mix well with water

Hydrophilic

Mixes well with water

What are the key things making up nucelotides?

Phosphate group (negatively charged)

Pentose sugar (ribose in RNA, deoxyribose in DNA)

Nucleobase (purines and pyrimidines)

How do nucleotides attach to each other?

Phosphodiester bonds (covalent ester bonds)

Which one is hydrophobic and the other hydrophilic for bases and backbones?

Backbones are hydrophilic

Bases are hydrophobic

What are the key features of amino acids?

Carboxyl group

alpha-carbon

R-group

Amino group

What distinguishes each amino acid?

The R-group: non-polar (hydrophobic), polar (hydrophilic), charged (dependent on pH)

Which one is more stable DNA or RNA and why?

The backbone is more stable in DNA. In RNA, the extra -OH group can make it more reactive and therefore less stable as its more prone to hydrolysis.

What are the key structural differences for DNA and RNA?

DNA exist as a double helix and exists as B-DNA, making it run antiparallel (5' -> 3', 3' -> 5'). The base pairing also helps it hold strongly together. A-T, G-C bonds. More long lived

RNA exists more often as single strands. A-U, G-C bonds. Has shorter-term roles for mRNA, tRNA, and rRNA.

Define Genome, Transcriptome and Proteome

Genome: entire genetic information

- Contains chromosomes which are respirotories for gen info

- Variations can occur between organism groups (prokaryotes and eukaryotes), within species (animals vs plants, etc), between species (men and women) and within an organism i.e. RBC's as they do not have a genome.

Transcriptome: All RNA types

- mRNA -> instruction template created during transcription

- rRNA -> components of ribosomes used in translation

- tRNA -> adaptor molecules in protein synthesis

- RNA content depends on the cell type and conditions making it dynamic

Proteome: All proteins in a cell

- Highly dynamic -> dependent on cellular needs

- Can differ between cell types and within the cells themselves

What are teh differences between prokaryotes and eukaryotes in terms of genome size, storage site and shape/return.

Prokaryotes are circular, meaning that they can return to the start in replication. Unlike eukaryotes, which are linear, meaning they cannot return to the start. Eukaryotes have their storage in the nucleus and have a larger genome, compared to prokaryotes which are smaller and store in the cytoplasm.

When reading a strand of DNA/RNA how many are in a codon, which direction do you read in and what reading frame is correct?

- There are three in a codon, need to read in the 5' to 3' direction.

- Reading frame is correct if it has a start codon in it (AUG), continues with sense codons (no premature stop codons) and ends with a stop codon signalling termination.

What is a semi-conservative model of DNA replication?

Eacg new DNA model contains one parental and one newly synthesised strand.

What does DNA helicase do?

Separates the base pairs, unzipping the DNA

What does topoisomerase do

stops the DNA from supercoiling by breaking and rejoining it

What do SSB proteins do

Help stabilise separated DNA strands, whilst keeping them

What does primase do

Makes RNA primer, idenifying the start point of DNA synthesis

What does DNA polymerase III do?

Synthesises DNA strads

What does DNA polymerase I do?

Fills in gaps

What does DNA ligase do?

Binds the fragments together

How many origins do prokaryotes versus eukaryotes have?

Prokaryotes will only have one origin of replication. Whereas, eukaryotes will have multiple.

What signals the polymerase where to synthesise the new DNA strands?

The DNA primase adds OH groups for a nucleotide to attach.

What helps with simultaneous/bi-directional replication in DNA? Describe the process.

Leading and lagging strands.

Leading strands -> continuous replication from 5' -> 3'

Lagging strands -> discontinuous replication, stops when it runs into a primer. This creates Okazaki fragments which create bits of mRNA on the strands.

How is termination of replication indicated?

The joining of 2 strands to form 2 daughter strands..

What is the importance of DNA replication

For growth, repair and reproduction. DNA replicates to ensure that each DNA gets a complete copy of the genome during cell division.

Which way is the template being copied, compared its original direction?

The new strand is synthesised in 5' -> 3', the template being 3' -> 5'.

What is the importance/function of RNA transcription

RNA transcription provides temporary, disposable copies that help protect the genome. It is a selective process, only making proteins that the cell requires at a given time.

What is the primer for RNA transcription?

There is no primer needed.

Describe the initiation of RNA transcription

Starts at the promoter region, which indicates where transcription starts, usually at A/T bonds. Transcription factors then recognise the promoter, bind and recruit RNA polymerase.

Describe the elongation of RNA transcription

RNA polymerase synthesises an RNA strand. It also adds ribonucleotides complementary to the template strand. The transcription bubble created in the initiation phase closes as this goes, as opening it will wound the cell.

Describe the termination of RNA transcription and its two different methods.

Termination is where RNA polymerase stops transcription and releases newly synthesised RNA molecule from the DNA template

Rho-dependent -> rho protein binds to the rut site on RNA, pushing polymerase off the template, and releasing RNA transcript.

Rho-independent -> G/C rich area, which forms hairpin structures that cause the detachment of RNA

When does translation occur?

Occurs after transcription as mRNA that has been created is read by ribosomes to synthesise a polypeptide chain using amino acids in a specific order, as otherwise it would have an altered structure/function.

What are the different RNA tools involved in translation, and their roles?

- mRNA -> template for protein synthesis, including the specific order.

- tRNA -> matches codons to the correct amino acids. Interacts with enzymes to bind ot amino acids

- rRNA -> combines with proteins to form ribosomes. Catalyses peptide bonds.

What are the steps of translation, as well as the sites?

A site -> where new tRNA enters

P site -> peptide bond forms (aligns with start codon)

E site -> exit site for the empty tRNA.

Ribsomes move from A -> P -> E.

Initiation: small/large subunits of ribosome are at the binding site, assisted by initiation factors. The AUG codon starts the process.

Elongation: newly charged tRNA enters A site where codon and anticodon ensure accuracy in matching. Peptidyl transferase forms peptide bond, ribsome shifts along mRNA to read it.

Termination: occurs when the stop codon is hit and the release factor binds. Causes the ribosome to release the polypeptide, disassembling the subunits.

What is a primary structure protein?

Means that it is linked by peptide bonds

What is a seconary structure protein?

Folding of the polypeptide chain. Also is stablised by C=O and N-H groups.

- alpha-helix: helical shape w/ R groups stuck out, stabilised by H bonds

- beta-helix: formed between segments as parallel/antiparallel sheets.

What is a tertiary structure?

Overall 3D shape of a polypedtide stabilised by interactions between side chains (R groups)

What is a quarternary structure?

Not in every protein but is the assembling of individual polypeptides into a large cluster.

What is denaturation, is it possible to recover from and to what structures does it occur?

Denaturation is the loss of structure of proteins, making them biologically inactive. Physical/chemical dconditions can affect structure.

Although typically irreversible, haemoglobin can renature into native state.

Denaturation does not affect primary structures, but does do so for above/more mature structures.

Is a proteins 3D structure related to its function, why or why not?

Its specific shape determines which molecules can bind to it, as well as how it interacts with the molecule.

Define kinetic and potential energy, along with any of their subtypes

Kinetic energy = energy from motion

- Thermal energy = related to heat

Potential energy = energy matter possesses due to location or structure.

- Chem energy = stored in molecules, released during chemical reactions.

Why do cells need energy?

To perform essential functions like growth, movement, repair and reproduction. ATP is typically stored and transferred, as it provides energy.

Describe difference between exergonic and endergonic reactions. Briefly outline equilibrium

Exergonic = favourable & spontaneous where ∆G is < 0. Reactants > products. Reactions are releasing energy.

Endergonic = unfavourable and non-spontaneous reactions where ∆G is > 0. Reactions need energy. Reactants < products.

What is entropy? And what does it do?

Entropy is the measure of disorder caused by the continual loss of energy from the system during transformations. Entropy of the universe is always increasing.

What is thermodynamics and kinetics?

Thermodynamics -> determines whether or not a reaction is energetically favourable.

Kinetics -> determines how fast a reaction reaches equilibrium. Activation energy refers to the initial energy for starting a reaction, and thus, a lower activation energy means that a reaction can proceed at a faster rate.

Describe enzymes, their effects etc. I.e. on bio function, reaction rates, and final concentrations of substrates and products of a reaction.

Enzymes are biological catalysts that quicken the reactions in cells by decreasing the activation rates.

They also lower the transition state energy, increasing the rate of both forward/reverse reactions equally by making it easier for reactants to reach the transition state.

Enzymes do not change the final equilibrium concentrations of products

Describe the different ways that enzymes bind

Lock and key model -> substrate molecule fits directly into the active site.

Induced fit model -> enzyme is a bit more dynamic and flexible. The substrate may undergo a shape change to help the reaction

Selection model -> Enzyme exists in multiple forms in equilibrium. Only 1 binds to substrate; binding to A shifts the equilibrium to allow more binding. the substrate; binding to A shifts the

What roles do enzymes and enzymatic pathways play for living organisms?

Many different enzymes are involved in many pathways. Alt pathways can compensate when others are lacking. They help to dictate all things that are going on in the body. They provide a bit of redundancy, and sometimes alternate pathways can compensate when others are lacking. Redundancies can help combat the effects of mutations.

Enzymes are compartmentalised so that they are within particular places.

Describe energy coupling and ATP's role

Energy coupling means using energy from an exergonic process to drive an endergonic reaction. ATP mediates most energy coupling in cells. Catabolism (via enzymes) helps to provide ATP.

Cellular respiration is a key exergonic process. Exergonic release from breakdown of carbohydrates, fats and proteins.

How do enzymes act in experiments?

Enzymes can work under specific conditions: temp, pH, and ion balance.

Under certain conditions, doubling enzymes doubles the rate of reactions.