Features of transition metals which make them good catalysts

HETEROGENOUS CATALYSTS
Availability of a partially filled 3d subshell which allows for the ready exchange of electrons to and from reactant molecules, thus facilitating the formation of weak bonds with the reactant molecules

HOMOGENOUS CATALYSTS:
Ability to exist in different oxidation states, and relative ease with which they can be converted from one oxidation state to another

Explain how the presence of double bonds affects membrane integrity at low temperatures.

1. Presence of C=C double bonds in fatty acid phospholipid hydrocarbon tails causes kinks, thus preventing close packing of phospholipids. [1] [what do C=C double bonds do to the structure of the cell membrane?]
2. This lowers the temperature at which the membrane becomes less fluid. [1]
3. Hence, membranes with more double bonds / unsaturated hydrocarbon tails are more fluid / tend to maintain membrane integrity at low temperatures / vice versa. [1]

Describe a non-viral gene delivery system which can be used to deliver the functional [something] allele to stem cells.

1. Liposome-mediated gene transfer
2. Plasmid containing normal functional allele is inserted into the aqueous core of an artificial phospholipid bilayer sphere
3. The liposome fuses with the stem cell's plasma membrane, releasing the plasmid containing the normal allele into the cell's cytoplasm.

How does an enhancer sequence work?

When activators bind to enhancers, spacer DNA bends, allowing the activator to directly interact with RNA polymerase/general transcription factors at the promoter.

Controlling strength of promoter in prokaryotes to regulate transcription

Strength of promoter is determined by how similar the -10 and -35 sequences are to the consensus sequences which are:

-10: 5' - TATAAT - 3'

-35: 5' - TTGACA - 3'

Stronger promoters have higher frequency of transcription.

In what way does the alpha helix (of some protein) and RNA differ?

 Helical structures in RNA is a result of it folding back on itself. The helical structures in the protein is a result of the regular coiling of the alpha helix;

 The helical structures in RNA are due to complementary base pairing between different segments of the same strand. The helical structures in protein are due to presence of hydrogen bonds within a single segment of polypeptide.

 The sections in RNA are made up of a double helix. The sections in protein are made of a single helix.

Why is [disease] suitable for treatment using gene therapy?

1. caused by a single gene
2. caused by recessive allele
3. ease of access to affected area
4. no invasive surgery needed

Describe how a specific gene mutation leads to cystic fibrosis.

A deletion of 3 base pairs occurs on the CFTR gene on chromosome 7, leading to a deletion of the codon coding for phenylalanine at position 508. The loss of phenylalanine disrupts the ATP binding site of the CFTR protein, which prevents binding of ATP and opening of the Cl^- channel, disrupting the diffusion of Cl^- out of the cell.

Warning signs for a pseudo-first order reaction

• Excess of reactant - since concentration of reactant does not change significantly, so can treat as a first-order reaction
• Solvent is a reactant
• Use of catalyst

How does temperature/pH affect enzyme activity?

Temperature: As temperature increases from _ºC to _ºC, rate of reaction/relative activity increases from __ to __.  (quote values!)

pH: – __, optimum pH at ___ at 100% activity. Any deviation in pH will result in decrease in the enzyme activity.

Size of organelles - from bio MCQ TYS

In order of size, largest to smallest
1. Nuclei
2. Chloroplasts
3. Mitochondria
4. Lysosomes
5. Ribosomes (0.02μm)/ER

Explain the role of telomeres.

1) Ensure genes are not lost/eroded due to end replication problem, preventing loss of vital genetic information

2) Protect and stabilise the terminal ends of chromosomes - prevent chromosomes from fusing with other chromosomes and prevent DNA repair machinery from recognising 3' overhangs as DNA breaks, preventing apoptosis.

3) Allow their own extension - attachment point for telomerase (germ cells, embryonic stem cells, cancer cells)

Golgi apparatus

I DO NOT OWN THESE IMAGES. Clicking on the images will take you to the page where they come from.

Explain the principles of RFLP.

1. Due to the polymorphic nature of DNA
2. genomic DNA from different individuals produce fragments of different lengths when digested by restriction enzymes,
3. resulting in a unique banding pattern among individuals

Suggest the advantages of using mitochondrial DNA. (To construct a phylogenetic tree)

There is no recombination in mitochondrial DNA from parent to offspring, hence changes in DNA sequence is solely due to the accumulation of mutations over time, so it can reliably be linked to the molecular clock.

Mitochondrial DNA has a faster mutation rate compared to nuclear DNA, hence it is useful for comparing individuals within a species/closely related species, as it requires discernible differences between DNA of organisms being compared.

Images: synapses/synaptic cleft

The pre-synaptic cell is the one with all the secretory vesicles.

Describe the role of mitosis in maintaining genetic stability.

1. Produces two nuclei/cells with same number of chromosomes as parent cell
2. thus daughter cells are genetically identical to parents
3. DNA replicated via semi-conservative replication during interphase to give exact copies
4. Each strand of parental DNA acts as template for the exact replication to form the new daughter strand
5. through complementary base pairing
6. In prophase, chromatin condenses to form chromosome which exists as 2 identical chromatids joined by single centromere
7. During metaphase, sister chromatids are attached to microtubulues from either pole
8. During anaphase, centromere divides and microtubules shorten
9. which ensures sister chromatids are separated to opposite pole during anaphase
10. ensuring equal distribution of chromosomes to daughter nuclei
11. In asexual reproduction, mitosis produces genetically identical daughter cells
12. which are clones

During anaphase, centromere divides, it doesn't split
DNA is replicated, not duplicated

Images: nucleus

It's important to get used to how organelles look in micrographs.

Nucleus (which is euchromatin and which is heterochromatin?)

Role of NAD in oxidative phosphorylation

1. Organic molecules are oxidised during glycolysis, link reaction and Krebs cycle, producing high energy electrons and protons. 
2. NAD serves as a mobile proton and electron carrier, carrying these electrons and protons to the electron transport chain on cristae of mitochondria.  
3. High energy electrons in NADH reduce electron acceptors of ETC; NAD is re-oxidised. 
4. Electrons passing down the ETC is coupled to production of ATP. Protons liberated in the oxidation of NADH establish the proton motive force. Reoxidation of NADH allows regeneration of coenzyme NAD⁺ so they can pick up more electrons and protons from Krebs cycle etc. so that these reactions can continue.
5. 1 reduced NAD to 3 ATP through oxidative phosphorylation.

Describe the structure of a beta-pleated sheet of a spider silk protein.

Hydrogen bonds form between the C=O group of a peptide in one strand and the N-H group of another peptide in the adjacent strand. R-groups project above and below the beta-pleated sheet.

Outline the procedure of a titration experiment to determine the concentration of ammonia in the organic layer.

NB: Given 0.010 mol dm^-3 hydrochloric acid, methyl orange indicator and lab apparatus commonly used for titration.

1. Fill up a burette with 50.00cm³ of 0.010mol/dm³ HCl
2. Using a dry pipette, transfer 10.0 cm³ of the organic layer into a 250cm³ conical flask.
3. Using a measuring cylinder, add 20 cm³ of deionised water into the conical flask, then add 2-3 drops of methyl orange. 
4. Titrate the resulting mixture against 0.010mol/dm³ HCl until the colour of methyl orange changes from yellow to orange.
5. Repeat the titration until 2 consistent readings are obtained.

Equilibrium constant

Equilibrium constant of salt MX:


For homogenous equation A + B --> C + D (i.e. all in the same state):

Formatted in LaTeX using the CodeCogs editor.

What do you understand by the term 'Dynamic equilibrium'?

Dynamic equilibrium refers to a reversible reaction in which the rate of the forward reaction equals the rate of the backward reaction and there is no net change in the concentration of ions.

Principles of evolution

1. Natural populations have great reproductive potential
2. But numbers remain about constant as many offspring fail to survive
3. Due to environmental factors, competition for resources, predators, other selection pressures, that impose a limit on their number and organisms struggle to survive
4. Individuals within a population show variation for natural selection to act on
5. Variants with a selective advantage/which are best adapted to their environment are more likely to survive and reproduce
6. Producing viable fertile offspring which pass on their favourite traits, thus favourable genotypes accumulate over time, leading to increased allele frequencies of favourable alleles
7. Over many generations, evolutionary changes by natural selection and may form new species if reproductive isolation occurs which is necessary for speciation
8. Include examples which may include: Darwin's finches, giraffes and how they got their long necks, peppered moths

Note: don't neglect points 1-4! 

Reproductive isolation is key to explaining speciation

Suggest why the cytochrome b gene is used to measure changes in DNA sequences in closely related species.

1. Cytochrome b is a homologous gene meaning that it is conserved in all the species being compared 
2. was found in their common ancestor; forms the basis of comparison 
3. Yet there are sufficient differences in the DNA of cytochrome b for scientists to distinguish between closely related species 
4. It is found in the mitochondria and hence do not undergo recombination and any mutation accumulates at a regular rate in the maternal line --> can be used for molecular clock

Characteristics of stem cells

1. Are unspecialised/undifferentiated
2. Able to differentiate
3. Can undergo extensive proliferation and self-renewal

Standard electrode potential

The standard electrode potential, E^⦵, of a half-cell is the electromotive force measured at 298 K between the half-cell and the standard hydrogen electrode, in which concentration of any reacting species is 1M/gaseous species is at 1 atm.

Remember to indicate the surrounding temperature when drawing half-cells!

The standard cell potential, E^⦵_cell is the maximum potential difference between two half-cells under standard conditions.

Some definitions

What is recombinant DNA?
DNA that contains genes/sections of DNA from two species/two types of organisms.

What is a vector?
A carrier such as a virus or plasmid used to carry the gene of interest into another host/gene

Why are plant tissue cultures initially grown in sterile conditions?

1. Prevent contamination by bacteria/fungi
2. which may produce toxins which will inhibit growth of plant cells;
3. as culture medium is suitable for the growth of mirobes, may outgrow the cells of the plant and deplete nutrients from the culture

Note: idea of 'outgrowing' is stronger than merely 'competing'.

Creating a cDNA library

1. Isolate mRNA from [tissue] 
2. Use reverse transcriptase to synthesise a cDNA strand using RNA as a template
3. Use DNA polymerase to make double-stranded cDNA and amplify using PCR
4. Cut plasmid with restriction enzyme that leaves blunt ends
5. Use terminal transferase to add extra cytosine nucleotides to the blunt end of DNA strands and add guanine nucleotides to that of plasmids to form sticky ends
6. Mix plasmid with cDNA; complementary sticky ends anneal to one another by hydrogen bonding;
7. Add DNA ligase to seal nicks by forming covalent phosphodiester bonds to form recombinant plasmid

What causes a unique banding pattern in Southern blots?

1. Polymorphic nature of DNA in individuals → variations in number/sequence of restriction sites/RFLPs
2. Resulting in unique banding pattern between individuals

Could also be for  gel electrophoresis.

Standard answer for chi-square test

1. At chi-squared value of [value], p is greater than [value]. Since p is more than 0.05/p is less than 0.05 @ 5% significance level, 
2. We do not reject the null hypothesis that there is no significant difference between observed and expected ratios and any difference is due to random chance.

Note: our teacher says to only state what the difference in observed phenotype is if you absolutely sure! 

What causes genetic variation in meiosis?

• Chiasma formation and crossing over- portions of non-sister chromatids of homologous chromosomes may break and rejoin. Exchange of alleles between homologous chromosomes ⇒ new combination of alleles 
• In metaphase I – (independent assortment) orientation of homologous chrm pairs at equator is random and how one homologous pair orientates does not affect how other homologous pair orientates. Metaphase II- orientation of non-identical sister chromatids of one chromosome at equator is random. Each daughter cell will receive a random mix of maternal and paternal chromosomes. 
• Random fusion of two gametes will result in 223x223 different possible types of offspring in humans. Can also be non-disjunction of homologous chromosomes in mei I or non-disjunction of sister chromatids during mei II resulting in polyploidy.

How does Southern Blot work?

1. DNA fragments separated by size using gel electrophoresis
2. Gel slab containing DNA fragments laid under nitrocellulose membrane, set in alkaline medium to denature dsDNA into ssDNA. ssDNA is drawn upwards onto the nitrocellulose membrane and binds to the membrane.
3. Membrane incubated with probe complementary to the target sequence in the DNA fragments, which contains radioactive marker. Hybridization via complementary base pairing occurs.
4. The bands formed are then visualized using autoradiography. Radioactive regions expose the film, forming image that shows where the bands have formed complementary base pairs with the probe.

How gel electrophoresis works

1. DNA fragments are pipetted into the wells at the top of the gel furthest from the anode;
2. Dense loading buffer mixed with DNA sample to help it sink to the bottom of the well
3. Loading dyes added to allow visualization of separation process
4. Negatively charged DNA migrates out of well, toward anode when subjected to an electric field
5. Fragments migrate through an agarose gel matrix made out of a meshwork of polysaccharides, which impedes movement of longer fragments more than shorter fragments.
6. Longer fragments migrate slower compared to shorter fragments.

How mutations result in differences in [protein]

1. Single base substitution → change in one codon → different amino acid incorporated in the polypeptide chain. Protein → different conformation that can no longer bind to [protein]
2. Deletion → frameshift mutation → viable [protein] not produced, could result in premature termination due to a new STOP codon /newly synthesized mutant protein quickly targeted for breakdown