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BIO1007notes - Lecture notes All Lectures

From Molecules to Ecosystems (University of Sydney)

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Friday, 18 August 2017

BIO1007 Lecture 2 Information in cells: • Explore the properties of information and how these features apply to the molecular basis of genetic information.

- Information is the opposite of entropy— where entropy is about disorder, information is about order

- information is working against entropy **NOTE: transcription is all RNA, not just mRNA— FOR EXAM***

- DNA is ‘hard drive’ or ‘long term memory’ - mRNA is the ‘short term memory’ ** HIV is retrovirus- treatment attacks reverse transcriptase as humans do not have it naturally

- where reverse transcription is possible (RNA to DNA), proteins cannot be reversed • Summarise the flow of genetic information from DNA to RNA to protein in terms of the central dogma.

- DNA in almost every cell in the body contains the same information (excepting RBC, WBC, sex cells)

- every cell needs a few proteins in large numbers, and many at a low number •

Describe the general features of information biopolymers.

- polymers produced by living organisms, contain monomeric units that are covalently bonded to form larger structures

Lecture 3 Information in biopolymers: • Identify the main chemical components of nucleic acids and the interactions involved in base pairing between nucleic acid strands. Describe how these interactions can be promoted or disrupted in experimental situations. They are composed of monomers, which are nucleotides made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a simple ribose, the polymer is RNA (ribonucleic acid); if the sugar is derived from ribose as deoxyribose, the polymer is DNA (deoxyribonucleic acid).

- purines (adenine and guanine) always bond with pyrimidines (thymine and cytosine) 1 Distributing prohibited | Downloaded by Sidra Akbar ([email protected])

Friday, 18 August 2017

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• Distinguish DNA from RNA, given a structure, and explain how these differences relate to their different roles. DNA

RNA

Double stranded Double Helix Deoxyribose rugar Stores and transmits genetic information Adenine- Thymine Found only in nucleus Base is a heterocyclic ring, either purine or pyrimidine Uracil is methylated at position 5 forming thymine

single stranded Single Helix Ribose sugar RNA acts as template for making proteins Adenine- Uracil Found everywhere in the cell Negative charge- ionic character hydrophilic 5’ phosphate is the start of the polymer, 3’ hydroxyl is the end of the polymer Monomers are held together by phosphodiester bond, and when it breaks a lot of energy is released RNA breaks down in sodium hydroxide (NAOH)

• Identify the major features of proteins: peptide bond, amino and carboxyl terminals, side chains, alpha carbon. Lecture 4 information in biopolymers 2 • Predict some chemical properties of amino acid side chains (solubility hydrophobic/hydrophilic, polarity, charge), given their structure.

• Describe the main weak forces which maintain the protein fold and give an example of each.

- Hydrogen Bonding— results from the small dipole (uneven electron distribution) that exists in certain side chains and in the peptide bond. The peptide bond: The amine N of the peptide bond is an H bond donor while the carbonyl O (from another peptide bond) acts as an acceptor). The interaction is largely sequence dependent

- Electrostatic or ionic interaction — Side chains with a positive charge (His, Arg, Lys) can interact with those side chains with a negative charge (Asp, Glu) if they are close enough. The strength of the interaction is also dependent on the local environment. The presence of high concentrations of salts, particularly on the protein surface tend to weaken or dampen down the strength of this force.

- Van der Waal’s interactions — Occurs when a charged or polar groups comes in close proximity with a non-polar group. The charged group will induce a small dipole not he 2 Distributing prohibited | Downloaded by Sidra Akbar ([email protected])

Friday, 18 August 2017 non polar group. A transient dimple can be induced just from fluctuations in the electron distribution in neighbouring atoms. While these interaction are quite weak singly, they make a major contribution in a macromolecule like a protein where many of these interactions occur.

- Hydrophobic interaction— No polar side chains will tend to cluster together rather than mix with polar solvents, which is entropic effect- polar solvent molecules (usually water) have more options when the non- polar groups are clustered than when they’re scattered throughout the polar solvent. In order to minimise loss of entropy the nonpolar groups cluster together and bury themselves in the core of a water soluble protein • Explain how 3D protein structure is related to function using the example of the alpha helix in DNA binding proteins.

Lecture 5 Enzymes • Describe and explain the difference between the thermodynamic and kinetic properties of a reaction

- If you cool something down you lower the effect of entropy - At equilibrium, ΔG is 0. AMOUNT OF ENERGY IN PRODUCT EQUALS AMOUNT OF ENERGY IN SUBSTRATE

- Cells are an open system- exchange matter and energy with the environment - Cell needs to have a lot of free energy- it DOES NOT WANT TO BE AT EQUILIBRIUM. People achieve equilibrium upon death. Homeostasis is a steady state but is NOT equilibrium

- Cell works hard to keep itself away from equilibrium - Thermodynamics— Negative ΔG makes a reaction thermodynamically more favourable. Large negative ΔG = the more the reaction favours product formation (favours the left)

- Kinetics vs. thermodynamics- kinetics is about the rate of reaction, and height of the curve (lowered by enzymes). A reaction can be thermodynamically favourable, but if the peak of the curve is too high, it will be very slow. Enzymes do not change the thermodynamics of a reaction.

- Enzymes obey the laws of thermodynamics. They don’t change the Keq (equilibrium constant). Enzymes do not change the energy required. They only speed up the process of reaching equilibrium.

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Friday, 18 August 2017 •

Explain briefly how enzymes act as catalysts

- Enzymes increase the rate of reaction, are not used up in a reaction, are substrate specific, can be localised in organelles, can be organised into pathways.

- Enzyme concentration doesn't change throughout a reaction - Lock and key is not entirely accurate- the active site is not exactly complementary to the substrate

- Assay is a reaction that measures something. Enzyme assay measures amount of enzyme • Describe the significance of the enzyme properties: Km, Vmax, Kcat, and how they are measured

- Vmax- maximum point that reaction rate is trying to get to. Substrate concentrate gives 1/2 Vmax. Vmax is how fast an enzyme can go.

- Km- describing shape of the curve. Higher affinity for the substrate means that there is a smaller amount of substrate required to reach Vmax. Km: Rate of dissociation/ rate of association. Lower Km = higher affinity

- Kcat- number of molecules of substrate converted to product per molecule of enzyme in one second when the enzymes is saturated with substrate (Vmax conditions) • Calculate the activity of an enzyme catalysed reaction from experimental data •

Explain how enzymes can be used experimentally

Lecture 6 • Describe the general properties of the polymerisation of information containing biopolymers. - growing chain is base paired to the template.

- as chain grows, to phosphates are released (pyrophosphate), an enzyme breaks them down to two single phosphates. Thermodynamically pulling off one product, driving the reaction in that direction

- 3’ hydroxyl— many anticancer drugs and AZT exploit the need for a 3’ OH in order to lengthen a chain. • Outline the general mechanism for copying DNA to DNA before cell division, replication. List the unique problems associated with replication and describe the strategies used by the cell to overcome these. 4 Distributing prohibited | Downloaded by Sidra Akbar ([email protected])

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- DNA is copied to DNA or RNA by polymerase enzymes. There are DNA and RNA polymerases. The Name is based on the product on the template- ie RNA polymerases may copy DNA to RNA. Reverse transcriptases make DNA from an RNA template

- DNA and RNA polymerase: - Copy new strand 5’ to 3’. Only work in one direction, require a template, form a phosphodiester bond, use nucleotide triphosphate as substrate.

- DNA polymerases need a primer to start, proofread the last nucleotide added; 3’ to 5’ exonuclease activity— exonuclease takes from the end. They use dexoynucleotide triphosphates

- RNA polymerase- don’t need a primer to start, do not proof read. Use ribonucleotide triphosphate as substrate challenges of replication

- once in a lifetime activity- is either ‘on’ or ‘off’ - occurs just before cell division - whole genome must be copied at the same time and the same place - polymerases only work in one direction- 5’ to 3’ challenges of transcription • Outline the general mechanism for copying DNA to RNA, transcription. List the unique problems associated with transcription and describe the strategies used by the cell to overcome these. - liver cells from the same individual would contain the same genome, but different transcriptome challenges of transcription

- small sections of genome need to be transcribed - these sections often have to be copied thousands of times - some sections are rarely copied in one cell but copied many times in another - some sections need to be copied in response to a stimulus or trigger, they are up and down regulated

- RNA polymerase needs to be able to find the start of transcription - RNA polymerase binds to region known as promoter and starts transcribing downstream from that region 5 Distributing prohibited | Downloaded by Sidra Akbar ([email protected])

Friday, 18 August 2017

- **principle of gene expression**— If RNA polymerase binds more frequently the gene will be transcribed more often and there will be more copies of the RNA sequence. If RNA sequence is a mRNA, this usually means more copies of the protein • Compare and contrast the two processes; replication with transcription, focusing on the cell contexts and the differing requirements for fidelity

Lecture 7 • Explain the unique problems associated with converting the information as a nucleic acid sequence to an amino acid sequence. Describe how these issues are overcome, with reference to the universality and redundancy of the genetic code.

- need three positions to code for all bases (We have 4 bases, and 3 positions) - 61 combinations to code for 20 amino acids - the codon sequence is coded 5’ to 3’ from the mRNA - Implications of the universal code: Need to know

- the stop codons- UAG, UGA, UAA - the start codon which also codes for methionine, AUG - One other example- e.g. Leucine which has 6 codons: CUU,CUA,CUC,CUG, UUA,UUG

- amino acid is covalently bound through carboxylic acid. notes***

- tRNA— bridges the nucleic acid world with the protein world - amino acid has to be activated and covalently attached with a set of special enzymes - peptide bond formation happens in cells - the enzyme tRNA synthase has a site for amino acids, the binding must be accurate

•Outline the unique problems associated with protein synthesis, with particular reference to the unfavourable thermodynamics of peptide bond formation and the requirement for order. Describe the strategies used by cells to overcome these problems. 6 Distributing prohibited | Downloaded by Sidra Akbar ([email protected])

Friday, 18 August 2017

- The need to somehow convert a sequence of nucleotides (with 4 different bases) to a sequence of amino acids (where there are 20)

- the need to have the correct order of amino acids— the order of amino acids determine the fold and function of the protein

- Peptide bond is very thermodynamically unfavourable - You need precise start and stop for proteins - process of translation occurs on ribosomes. Ribosomes create an environment for peptide bond formation

Lecture 8 (photosynthesis): •

Describe the major evolutionary events to maximise light capture by plants

- 2.5 billion years ago “great oxidation event”— bacteria produced free oxygen into the atmosphere. Green bacteria have chloroplasts

- endosymbiosis- mitochondria engulfed - first land plants, around 450 million years ago- o2 reacted in upper atmosphere to produce ozone (uv protection). plants started colonising the land. 400 million years ago, plants are widespread but have simple morphology. co2 concentration in the atmosphere is low (VERY BAD FOR THE PLANTS). Note** biochemistry for photosynthesis is aqueous**

- the solution was that leaves formed- large flat surfaces to capture light, with waterproof cuticles and complex breathing structures. • Describe, in overview, the conversion of radiant energy into chemical energy - photosynthetic electron transport: cytochrome (b6f) is stuck within the membrane, passes the electron onto a mobile enzyme that sits within the lumen, plastocyanin (PC), takes hydrogen from stoma to lumen.

- Electron passed onto ferredoxin, which passes it to ferredoxin NDP reductase. That electron allows NADP to be reduced to NADPH.

- this process drives ATP synthase • II

Explain the overall organisation of the light reactions in photosystems I and

- Light energy is converted into chemical energy in the form of ATP and reduced NADP in the light reactions 7 Distributing prohibited | Downloaded by Sidra Akbar ([email protected])

Friday, 18 August 2017

- ATP and reduced NADP serve as energy sources •

Define ATP and describe it’s synthesis during photosynthesis

- ATP/ADP- the cell’s energy carrier - NADPH/NADP- the cell’s reducing agent - ATP synthesis is a result of photophosphorylation, carried out by thylakoids.

Lecture 9 (photosynthesis ll):

Most abundant protein on earth- rubisco has 8 large sub units, gene within chloroplast DNA, 8 small subunits

•Explain fixation of carbon dioxide in the Calvin cycle

1) Fixation. For every three turns of the Calvin cycle, three atoms of carbon are fixed from three molecules of carbon dioxide. In the carbon fixation stage, carbon dioxide is attached to RuBP by the enzyme rubisco. ... When three carbon dioxide molecules enter the cycle, six molecules of 3-phosphoglycerate are produced. •

Compare carboxylation and oxygenation by Rubisco

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• Describe the co-evolution of photosynthesis and the earth’s atmosphere over time

•

Predict how photosynthesis might respond to future climates

c4 plants have rings, c3 plants do not

Lecture 10 (respiration in plants):

- Laws of thermodynamics: - energy can be changed from one form to another, but not created or destroyed - in energy exchanges and conversions, the potential energy of the final state will always be less than the potential energy of the initial state

- photosynthesis and respiration cause huge cycles in global atmospheric CO2 concentrations annually

- redox reactions in photosynthesis- electrons transferred from h20 to c02. co2 is reduced •

Explain the differences between anabolism and catabolism

- anabolism- molecule synthesis..increase in atomic order, decrease in entropy, usually energy- requiring, NADPH is a product

- catabolism- breakdown of larger molecules…decrease in atomic order, increase in entropy, usually energy liberating, involves NADH

•

Describe the electron transport chain in mitochondria

- starts with h20, energises an electron to flow through - uses NADH

•

Describe, in overview, the TCA cycle and glycolysis

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Friday, 18 August 2017

- glycolysis- glucose breakdown… glucose + 2NAD+ + 2ADP + 2Pi —> 2 pyruvate + 2NADH + 2H+ + 2ATP +2H2O

- TCA cycle (Krebs or citric acid cycle): Pyruvate enters via acetyl CoA, releases co2 through breaking bonds, NAD converted to NADH, ATP is formed • Compare photosynthetic electron transport and the electron transport chain in the mitochondria

•

Predict how respiration might respond to future climates

Lecture 11 Metabolism in Animals: •Describe how cellular respiration transfers electrons! from glucose to oxygen through a range of intermediate chemicals which release their energy by breaking bonds to the electron transport chain

- Fuel oxidation— extracting electrons and hydrogens from fuels and dismantling fuel molecules (fuel being protein fat and carbohydrates)

- fuels become acetates bound to coenzyme A - co2 is the most oxidised form of carbon that there is - co2 is formed post krebs cycle - NAD and FAD are H/e- strippers and carriers. NAD becomes NADH and FAD becomes FADH2. THEY ARE IN VERY LIMITED SUPPLY WITHIN THE CELLS. Once they carry H/e-, they cannot do anymore stripping

- reaction between hydrogen and oxygen liberates lots of energy. We capture that as chemical/ potential energy. Proton gradient- a “battery”

Making ATP with the H+ gradient

- protons flow UNDER PRESSURE through the channel in the inner mitochondrial membrane

- as the protons come in, they cause another protein to rotate, which in turn interacts with the subunits of the ATP synthase, to generate ATP from ADP and phosphate

- ATP then goes to the cytoplasm to do work

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Friday, 18 August 2017 • Describe the components of cellular respiration including glycolysis, formation of Acetyl coenzyme A, citric or TCA cycle and electron transport chain and the production of ATP - Start with fuels which have H+ ripped out, fuels dismantle, carbon atoms become oxidised = make carbon dioxide. energy captured makes proton gradient.

fats cannot cross the blood brain barrier Beta oxidation:

- fatty acids trapped in cytoplasm as fatty acetyl-coA - transported into the mitochondria - h/e- ripped out by FAD and NAD - fatty acid part loses an acetate chunk, and the cycle repeats - Glucose - hydrophilic, partially oxidised, reasonably reduced, inefficient, major fuel for the brain, can be used by all tissues Glucose oxidation

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Friday, 18 August 2017 Protein

- protein is a last ditch fuel source

•Describe why the preferred energy storage in the human body is fat

- weighs less when stored than glucose

Lecture 12 Cell diversity: Phosphate has a 2- charge most of the time Fibroblasts lay down fibrin Cells have been around for 3....