BIOL111 Cellular Biology and Biochemistry Past Paper PDF

BIOL/BCHM111 – Cellular Biology and Biochemistry Who am I? Grant Pearce Room 418, Biology building, ext 45722 [email protected] Please feel free to stop by if you have any questions Come and talk to me about… Rubisco – Structure and Function CO2 Calvin cycle RuBP O2 Photorespiration Bund...

BIOL/BCHM111 – Cellular Biology and Biochemistry Who am I? Grant Pearce Room 418, Biology building, ext 45722 [email protected] Please feel free to stop by if you have any questions Come and talk to me about… Rubisco – Structure and Function CO2 Calvin cycle RuBP O2 Photorespiration Bundela R., Keown J.R., Watkin S.A., & Pearce F.G. (2019) Structure of hyperthermostable dimeric Archeal Rubisco from Hyperthermus butylicus. Acta Cryst D75: 536-544 An Impossible RuBurger? “for a year, our prototype burgers used Rubisco, and it worked functionally better than any other protein, making a juicy burger” Pat Brown, Founder of Impossible Foods (New Yorker Magazine 2019) Plant protein vs animal protein Health & Wellness Animal Welfare Environmental concerns Limitations of plant proteins Soy Inferior taste of plant based meat alternatives is a barrier for ~60% of meat eaters Colmar Brunton poll 2019 Pea Why not the most abundant protein? he at o R ub is c W Ba rle y 1.2 Pe a pe a C hi ck So y Eg g M ilk Po rk Digestable Indispensable Amino Acid Score (DIAAS) Nutritional qualities Plant Animal 1 0.8 0.6 0.4 0.2 0 Functional properties Example of Rubisco powder prepared in the lab Solubility Soy R1 R2 Gel formation R3 Water Soy R1 R2 Foamability R3 Sounds great! Why aren’t we eating it? Dairy Leaf Soy Pea X X X Nutrition Functionality Protein content Shelf life 3.1 g/100g < 1 week 3.0 g / 100g < 1 week 18.4 g / 100g > 6 months 24.2 g / 100g > 6 months The purification process Extraction De-greening Green juice Leaf biomass Pulp Fractionation & Concentration Brown juice Green pellet White protein Challenge 1 – low protein yield Rubisco makes up ~3% of leaf dry mass (Onoda et al 2017) The moisture content is ~80% (Yeoh & Wee 1994) Rubisco ~0.6% of fresh weight Extraction Leaf biomass Green juice Pulp Challenge 2 – removal of chlorophyll 0 De-greening Heat treatment Green juice 2 4 8 16 32 min % of Initial Brown juice Green pellet Incubation Time (min) Challenge 3 – Production of high quality protein Fractionation & Concentration Brown juice White protein Current commercial efforts $USD28M $USD21.5M €5.5M Course outline Lectures 1-12 Dr Grant Pearce General Introduction to the course and overview of cell biology and biochemistry. Structure and function of biomolecules Lectures 13 – 24 Ass Prof Ashley Garrill Functional Systems: metabolism, energetics and membrane transport. Lectures 25 – 36 Dr Vanessa Morris Functional systems: cellular organisation, motility, communication and reproduction Labs Labs are held in the West 463 Biology Lab We have 3 labs this term and 4 labs next term You must bring a lab coat and safety glasses. Most people have been allocated into lab streams. Please see me if there are any problems. Attendance at laboratories is expected! Assessment Mid-term test 1 (15%) In person test, Monday 22 April, 7-8 pm Covers my lecture material (lectures 1-12) Online lecture tests (24%) Weekly online, open book tests, short multiple-choice questions Final exam (30%) 2 Hours (date to be confirmed) Covers Ashley's & Vanessa’s material Labs (31%) There will be 7 weeks of labs, with assessment including online tests and grading of lab manual Grading regulations in Biological Sciences CAREFULLY READ THE INSTRUCTIONS IN THE COURSE HANDOUT We expect you attend all class activities and submit all items of assessment To pass, you need at least 50% overall AND at least 40% for the in-course work AND at least 40% for the course exam/test. Average Lab Mark 2023 82.8% 2022 74.3% 2021 72.5% 2020 77.5% 2019 79.1% 2018 76.3% Tests 56.7% 57.8% 55.2% 64.0% 55.7% 51.0% Total 64.8% 63.0% 60.6% 68.0% 62.7% 58.5% Pass rate 78.8% 79.9% 75.8% 87.6% 76.9% 73.9% A grade - very high-quality answers B grade - good answers, could add a bit more detail C grade - know most of the basic material, some areas lacking D/E grade - did not know the material to a sufficient level Learn www.learn.canterbury.ac.nz The Learn website contains material such as lecture summaries, relevant articles to read, past test papers and more. Powerpoint projections and audio recordings will be available from EchoCenter Marks will be posted on gradebook so that we can keep track of your progress Textbook We are using an online open access textbook for this course that is freely available You are expected to be familiar with material from Chapters 1-6 and 14-15 A note on notes My lecture slides a not a complete set of notes – they are a framework to build on If you sit passively through a lecture you will not remember things very well Taking notes helps you understand and retain lecture content A linear chain of amino acid residues is called a polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds between adjacent amino acid residues. A linear chain of amino acid residues is called a polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds between adjacent amino acid residues. A note on notes 121 Students were shown the star facts in Arial font (control group) while 154 students were shown identical facts in Monotype Corsiva font. 35 Minutes later they were given a short multiple choice test. The white dwarf star Amethyst is in the constellation Cassiopeia. It is half the mass of the sun, but we have not yet found any planets orbiting it. The white dwarf star Amethyst is in the constellation Cassiopeia. It is half the mass of the sun, but we have not yet found any planets orbiting it. 100 90 80 % Score in test 70 60 Arial 50 Monotype% 40 30 20 10 0 https://www.tandfonline.com/doi/full/10.1080/00220671.2012.736430 A B C D Overall Dyslexic WANT TO BE PAID FOR YOUR NOTES? Student Accessibility Service is looking to buy high quality lecture notes from students enrolled at UC. These notes will be used by students who experience difficulties taking notes for themselves for disabilityrelated reasons, and SAS will pay $10 per hour and $20 for 2 - 3 hours lecture. STEP ONE: Email [email protected] as soon as possible with two samples of lecture notes you’ve taken. STEP TWO: Complete the application form that we will email back to you. STEP THREE: Keep an eye on your UC email. If we like what we see and you’re selected, we’ll be in touch! For most arts courses the notes need to be taken in MS Word. However, notes in science courses where formulas and math symbols are used can be handwritten and scanned. Student Accessibility Service | University of Canterbury Icons: Vectee zy.com Outline of my lectures Topic 1: Introduction to the philosophy of science Topic 2: A recap of biochemistry and biomolecules Topic 3: Life needs energy Topic 4: Life is ordered Topic 5: Life requires the expression and transmission of genetic information TOPIC 1: The Philosophy of Science What is biology? (and life?) Biologists look at things on a wide spatial and time scale There is a correlation between structure and function Why should you learn more about Biology? Should you believe what you read on the internet? Required reading – chapter 1 Aims for Lecture 1: Have a good idea about the logistics of the course Know how this course (and biology) fits into the grand scheme of things Be familiar with some of the common themes of biology: We need energy for life's processes Life requires information Living systems interact and exchange matter and energy with the environment Living systems have hierarchical organisation At all levels in life there is a correlation between structure and function Start to think about the scientific method Required reading: Chapter 1 Biologists study things in different spatial and time scales Biology is the study of life and living systems But what is life? Biology needs energy to create order First law of thermodynamics: Energy can be transferred or transformed, but not created or destroyed. Second law of thermodynamics: Every energy transfer or transformation increases the disorder of the universe. Most biological systems are made of the same things Most biological systems are made of the same things Structure is important to function (at all levels) Structure is important to function (at all levels) Life requires transfer and transformation of information DNA molecule Gene 2 Gene 1 Gene 3 DNA template strand TRANSCRIPTION mRNA Codon TRANSLATION Protein Amino acid Life requires transfer and transformation of information Life requires transfer and transformation of information https://esr-cri.shinyapps.io/wastewater/#region=Canterbury&log_or_linear=linear&period=twelveMonthsButton Life requires transfer and transformation of information BA.2.86 L455S JN.1 THE NATURE OF SCIENCE Science seeks to develop an accurate description through observation and experimentation Discovery based science often describes nature while hypothesis based science often explains nature Reductionism breaks larger systems down into their component parts Research can be applied or basic Weaving Indigenous knowledge alongside science Indigenous knowledge over covers much longer time scales Indigenous groups often transmit knowledge within stories or myths to ensure longevity https://thespinoff.co.nz/atea/14-11-2022/busting-the-myths-about-matauranga-maori Discovery vs Hypothesis Science Discovery (inductive) reasoning describes nature Analysis of large volumes of data with the goal of finding patterns or correlations Examples – mutations and disease, health issues, drug screening, human genome project Hypothesis (deductive) reasoning proposes an explanation Scientists propose a tentative answer based on observations, and then make predictions, which are then tested and reviewed Examples – structure of DNA, drug design, The Scientific Method How do we make a drug? Need to make a compound that has high affinity, selectivity, stability, and bioavailability. Drugs - Digoxin ‘Dropsy’ (congestive heart failure) causes shortness of breath, leg swelling and fatigue due to the inability of the heart to pump enough blood around. In the 1780’s a physician noticed that a patient with dropsy quickly recovered after taking a herbal remedy from the foxglove (Digitalis). Currently used to treat several heart conditions. Binds to a Na+/K+ pump in the membrane of heart cells. Drugs - Taxol 1964 – it was found that an extract from Pacific Yew bark was cytotoxic. 1967 – the compound was isolated, and named Taxol 1971 – 10g of Taxol was produced from 1,200 kg of bark. 1978 – it was shown to be effective against leukemia in mice 1984 – beginning of human trials, which were shown to have a response rate of 30% of patients with ovarian cancer. 1992 – approved for general treatment 1993 – developed processes to harvest Taxol from cell cultures Drugs – Tamiflu & Zanamivir Used the structure of neuraminidase, a viral protein, in complex with an inhibitor Computational modelling was used to improve the binding of the ligand (eg a hydroxyl group near a negatively charged region was changed to an amino group) Drugs – Penicillin "When I woke up just after dawn on September 28, 1928, I certainly didn't plan to revolutionise all medicine by discovering the world's first antibiotic, or bacteria killer, but I suppose that was exactly what I did.“ Alexander Fleming Should you believe what you read on the interweb? What is the evidence? Where did the research come from? Did the study use controls, and was it big enough? Is it reviewed and repeatable? Do the results support the claims? Should you believe what you read on the interweb? https://goodhealth.co.nz/product_range/brain-power/ Should you believe what you read on the interweb? https://www.nature.com/articles/s41598-020-80045-2 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153866/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3746283/ Is it reproducible? https://doi.org/10.1007/s10648-018-9442-x How do we know if the treatment is effective? Enrolled 1,000 patients at 132 hospitals in first 15 days. Currently 47,605 participants How do we know if the treatment is effective? How do we know if the treatment is effective? How do we know if the treatment is effective? How do we know if the treatment is effective? What about new strains? DOI:https://doi.org/10.1016/S1473-3099(23)00575-3 Scientific studies may miss important interactions Reductionism an approach to understanding the nature of complex things by reducing them to the interactions of their parts, or to simpler or more fundamental things Emergence The way complex systems and patterns arise out of a multiplicity of relatively simple interactions What about new strains? https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00813-7/fulltext#sec1 BIOCHEMISTRY RECAP By the end of this section you should know the atoms, chemical bonds, and chemical groups that are important in biology We are mostly made up of C, N, O and H (with some P, S, metals and salts) Covalent bonds are very strong Weaker bonds cause molecules to stick together Molecular shape is very important for its function Temperature is the average kinetic energy of molecules Water is a good solvent because lots of biomolecules are polar Diffusion is the movement of a substance from a region of high concentration to a region of low concentration The universe hates order, and tends to create disorder Transfer of energy is not very efficient (tend to get heat as a byproduct) Required reading: Chapters 2-4 What elements are we made up of? Elements have a different number of protons and electrons Example of an atom from the element Helium (He) Orbits: electron shells or energy levels An electron normally exists in the lowest available energy shell (closest to the nucleus) Electrons fill orbitals closest to nucleus first, then those further away in order (i.e. 1n fills first, then 2n, then 3n, etc Elements have a different number of protons and electrons Hydrogen 1H Atomic number 2 He Atomic mass First shell 4.003 Helium 2He Element symbol Electron distribution diagram Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Sodium 11Na Magnesium 12Mg Aluminum 13Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Second shell Third shell The most stable configuration occurs when the outer shell is filled Different elements have different chemical properties Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) Covalent bonds are the sharing of electrons Covalent bonds are the sharing of electrons Unequal electron sharing results in polarity Electronegative atoms (O, N, F) tend to accumulate more negative charge Ionic bonds involve the transfer of electrons + - Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion (a cation) ClChloride ion (an anion) Sodium chloride (NaCl) Acids and bases pH reflects the hydrogen ion concentration An acid is a substance that increases the hydrogen ion concentration A base is a substance that decreases the hydrogen ion concentration Important chemical groups in biology Chemical Group Sulfhydryl group (—SH) Compound Name Examples Thiol Cysteine Phosphate group (—OPO32−) Organic phosphate Glycerol phosphate Methyl group (—CH3) Methylated compound 5-Methyl cytosine Important chemical groups in biology Chemical Group Hydroxyl group (—OH) Compound Name Examples Alcohol Ethanol Carbonyl group ( C＝O) Ketone Aldehyde Acetone Carboxyl group (—COOH) Carboxylic acid, or organic acid Acetic acid Amino group (—NH2) Amine Glycine Propanal Biology has lots of weak (but important!) chemical bonds Type of interaction Energy (kJ/mol) Covalent bond 300-500 Ionic interaction 12-17 Hydrogen bond 2-6 Van der Waals 3-4 Van der Waals interactions result from uneven charge distribution Hydrogen bonds occur when hydrogen is attached to an electronegative atom We refer to the hydrogen atom as the bond donor, and the electronegative atom as the acceptor Hydrogen bonding gives water unusual properties – Hydrogen bond + H Polar covalent bonds + O – H – + + – Water molecules tend to stick together Adhesion Water-conducting cells Direction of water movement Cohesion 150 µm Ice floats because hydrogen bonds are more ordered Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds break and re-form Ice floats because hydrogen bonds are more ordered https://www.science.org/doi/10.1126/science.abq2105 Water has a high melting point, boiling point, and heat of vaporisation Water Melts at 0˚C Boils at 100 ˚C Ethanol Melts at -117˚C Boils at 78 ˚C Water can hold lots of energy Specific heat of water is 4186 J/kg/K Specific heat of air is 718 J/kg/K Specific heat of steel is 450 J/kg/K Remember: Temperature represents the average kinetic energy of molecules 1 calorie is the amount of energy required to heat 1 g of water by 1˚C Water’s high heat capacity is due to hydrogen bonding Heat is absorbed when hydrogen bonds break Heat is released when hydrogen bonds form Water can absorb or release a large amount of energy with only a small change in temperature Evaporative cooling helps stabilise temperatures The small size and polarity of water make it a good solvent – + + – – – – + + + Cl– + – Cl– + – Na + – Na+ – + – – Different compounds interact differently with water Hydrophobic = water fearing Hydrophilic = water loving Even large molecules such as proteins can dissolve in water if they have ionic and polar regions on the surface Diffusion (nature hates gradients) “Diffusion is the net movement of molecules or atoms from a region of high concentration (or high chemical potential) to a region of low concentration (or low chemical potential).” (Wiki) Osmosis “Osmosis is the movement of solvent through a semi-permeable membrane into a region of higher solute concentration” (Wiki) Osmosis in cells The molecules of life All living things are made up of four classes of biomolecules: carbohydrates, lipids, nucleic acids, and proteins Macromolecules are large polymeric structures made up of many repeating units (monomers) Each cell has thousands of different molecules inside, but they are precisely organised into a living unit Synthesis and hydrolysis of polymers HO 1 2 3 H HO H H2O HO 1 2 3 4 H (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 4 H H2O HO 1 2 3 (b) Hydrolysis of a polymer H HO H Creating polymers helps create order & complexity Creating order requires energy Second law of thermodynamics: there is a tendency towards disorder (maintaining order requires energy) Creating polymers also helps manage water potential Molecular shape and function N H CH3 C - O O Non-covalent interactions stabilise the binding of macromolecules at chemically complementary interfaces Molecular shape and function Molecular shape and function Molecules with similar shapes can have similar biological effects Key Natural endorphin Carbon Hydrogen Nitrogen Sulfur Oxygen Morphine Natural endorphin Brain cell (a) Structures of endorphin and morphine Endorphin receptors (b) Binding to endorphin receptors Morphine