Biology

1. Biology For Computer Engineers Part 2: The Cell

2. Acknowledgements • Cover image, courtesy of Wellcome Images, Creative Commons license • All other images, courtesy of Wikipedia.

3. Nucleotides • PO43- • (CH2) • Nucleotide Organic molecule Consists of Base Ring structure with Nitrogen, Carbon, Oxygen, Hydrogen Sugar Phosphate (PO43-) Acidic character • Ribose

4. Nucleic Acids • Nucleic Acids are polymers of nucleotides Different nucleotides link together Phosphate at 5` of one nucleotide links to 3` Carbon of another nucleotide Called Phosphodiester bridge • Common nucleic acids • RNA • Ribonucleic acid • Sugar is ribose • DNA • Deoxyribonucleic acid • Sugar is deoxyribose

5. Nucleic Acids • Common bases Adenine (A), Thymine (T), Guanine (G), Cytosine (C), Uracil (U) DNA has only A, T, G and C as bases • Bases can form hydrogen bonds with other bases A<->T, A<->U, G<->C bonds are stabler Called base-pairing Leads to secondary and tertiary structures in nucleic acids DNA double helix, RNA folding One strand can construct its complementary strand from a soup of nucleotides Complement of the complement will be a replica of the same strand

6. Nucleic Acids • A sequence of 3 bases attracts a specific amino acid AGC->Serine, AGA->Arginine etc. Such a sequence is called a codon Sequence of codons can assemble multiple amino acids into proteins This is how protein structure is coded in nucleic acid These proteins are manufactured during biosynthesis

7. Nucleic Acids • DNA has a double helix structure and is more stable Usually forms very long chains Acts as long-term storage of genetic information • RNA is shorter, single/double stranded, less stable, more reactive RNA with genetic code created from DNA through base-pairing RNA synthesis Takes part in actual protein synthesis as protein structure code carrier and catalyzing agent

8. Water and Biomolecules • Hydrophobes repels water molecules not electrically polarized does not form hydrogen bonds with water molecules H bonds between water molecules not disturbed hence does not dissolve in water typically a large hydrocarbon group CH3(CH2)n, n>4

9. Water and Biomolecules • Hydrophiles attracts water molecules electrically polarized so forms H bonds with water molecules examples charged groups polar, uncharged groups • Amphiphiles compounds with hydrophilic and hydrophobic properties also called amphipathic has hydrophobic and hydrophilic structural areas might partially dissolve in water and non-polar solvents Carboxylate RCOO- Sulfate RSO4- Sulfonate RSO3- Phosphate PO43- Amine RNH3+ Alkyl HR Hydroxyl ROH Carboxyl RCOOH

10. Phospholipids • Amphiphilic • Polar heads hydrophilic • non-polar fatty acid tails hydrophobic • Phospholipids Forms special structures in water lipids arrange in water such that polar heads face water non-polar tails face each other Bilayer sheet polar exterior, oily core permeable to small hydrophobic molecules non-permeable to ionic and polar molecules Liposome, Micelle

11. What is Life? • Any system that has certain characteristics Self-organizing State machine with multiple stable states Action processes to handle external and internal events Feedback and control systems for process control Self-producing A new instance created by one or more existing instances Adaptive State machine modifies itself to adjust to new environments over time Adjustments passed on to newer instances Metabolizing Operation and reproduction of the system requires energy Energy required by the system is acquired from the environment

12. Evolution of Life • Prehistoric earth was a chemical potpourri No chemical equilibrium Large supply of energy • Basic organic molecules were produced Can be reproduced in lab • These chain together to form polymers proteins, polynucleotides (DNA/RNA) Happens spontaneously if there is enough energy

13. Evolution of Life • Polynucleotides can act as templates to create complementary polynucleotides 2 complements produce the original Called Autocatalysis Special RNA molecules can catalyze replication of other nucleotides Origin of reproduction

14. Evolution of Life • RNA molecules can synthesize proteins Origin of Growth Proteins are very versatile Can act as catalysts, chemically diverse Can participate in a variety of chemical reactions Facilitates metabolism, regulation • Lipids can form bi-layer membranes Can form compartments enclosed by membranes Origin of cells • Cell evolution Lipid membrane enclosures containing nucleic acids and proteins

15. Types of Life • Cells Single entity that exhibits all characteristics of life Cells live co-operatively in colonies Symbiosis • Organisms co-operating cells with same source code form symbiotic relationships cells with the same ‘source code’ (DNA) behave in different ways depending on how they are created become tissue cells, liver cells, brain cells etc. cell specialization an entire system of co-operative cells together exhibit characteristics of life an animal/plant is like a colony of bacteria

16. Cell • Cell is the basic unit of life • Types of cell Prokaryotic no nucleus bacteria, archea Eukaryotic with a cell nucleus All cells that are part of a multi-cellular organism Plants, Animals, Fungii

17. Cell Functions • A cell exhibits all characteristics of life • Cells organize themselves multiple stable states feedback loops • Cells produce cells cells divide to form new cells • Cells adapt cells adjust to new environments over time behavior changes over generations cells with behavior favorable to their environment tend to survive natural selection mutations in source code (DNA) enable adaptive behavior

18. Cell Functions • cells generate energy and use it to grow metabolism energy generated from nutrients obtained from cell's environment catabolism generated energy used for various purposes anabolism for growth to build proteins and nucleic acids, called biosynthesis for motion for active transport pump substances in/out of cell for signal amplification to amplify small external events for better handling

19. Prokaryotic Cell Structure • A fluid medium enclosed by a wall/membrane • Internal parts perform various life functions

20. Prokaryotic Cell: Cell Capsule • poly-saccharide or poly-peptide wall mucous-like • not easily washed off • protects against external agents • helps to stick to surfaces • secreted during cell growth

21. Prokaryotic Cell Wall/Membrane • Plasma Membrane phospholipidbilayer partially permeable membrane like a layer of oil has transport mechanisms for various signals and nutrients • Cell Wall provides rigidity and structure polysaccharide complexes holds cell from bursting cell's inside pressure is higher than outside • Cell Membrane

22. Prokaryotic Cell: Cytoplasm • Cytoplasm space inside the cell the fluid part is called cytosol semi-transparent, gelatinous also includes elements suspended in it contains water, dissolved ions, small molecules, large water-soluble molecules catabolism happens here Creation of energy from nutrients that come into the cell Nutrients pass across cell membrane

23. Prokaryotic Ribosomes/Nucleoid • Ribosomes small granules that float around in cytoplasm RNA-multi-protein complex multiple subunits runs programs from DNA to create proteins called protein synthesis uses energy • Nucleoid mainly DNA loop storage of programs (source code) for the cell

24. Eukaryotic Cell: Plant Cell

25. Eukaryotic Cell: Animal Cell

26. Eukaryotic Cell: Membrane/Cytoplasm • Plasma Membrane lipid bilayer membrane selectively permeable not rigid, can take variety of shapes allows animal cells to change shape delimits cell boundary in animal cells • Cytoplasm similar to prokaryotic cytoplasm differences only a part of cell energy is produced in eukaryotic cytoplasm rest in mitochondria

27. Eukaryotic Cell: Mitochondrion

28. Eukaryotic Cell: Mitochondrion • multiple per cell divide and grow depending on cell's energy needs • enclosed by two membranes each membrane is a phospholipidbilayer • cellular power plants generates most of ATP produced in cell some ATP is produced in cytoplasm too • has its own DNA synthesizes its own proteins and RNA • might be remnant of a symbiotic bacteria which became part of the cell

29. Eukaryotic Cell: Mitochondrion • Parts Inner membrane has ATP synthase on its inner surface folded for increased surface area for higher ATP production folds called cristae Matrix ATP is produced here contains enzymes several copies of mitochondrial DNA special ribosomes

30. Eukaryotic Cell: Golgi Apparatus • stacked membrane disks • processes and packages macromolecules produced in cell proteins, lipids etc. for secretion or for internal use immediate secretion store-till-signal and secrete adds carbohydrates, phosphates etc. modifications help the molecules attach to (reach) destinations where they are needed molecules come to and leave golgi through vesicles different vesicles for secretion and internal transport Vesicles are small membrane-bound sacs post-office of the cell

31. Eukaryotic Cell: Endoplasmic Reticulum • rough endoplasmic reticulum protein production done by attached ribosomes similar to prokaryotic ribosomes folding and transport of cell membrane proteins • smooth endoplasmic reticulum lipid and carbohydrate production calcium ion storage

32. Eukaryotic Cell: Nucleus

33. Eukaryotic Cell: Nucleus • enclosed in a double membrane • contains cells's DNA stored in chromosomes • small molecules and ions can freely move in and out of nucleus through nuclear pores • movement of larger molecules is controlled cannot move through pores need to be passed across the membrane through active transport • most cells have one nucleus some have none red blood cells some have many some fungii

34. Eukaryotic Cell: Chromosomes • organized structures that contain DNA DNA molecules held in a specific arrangement by protein molecules called histones DNA packed into a small space allows large DNA molecules to fit into nucleus called chromatin • multiple chromosomes might be present in a nucleus chromosomes come in pairs human cells contain 23 pairs of chromosomes

35. Chromosome Packing

36. Eukaryotic Cell: Lysosomes • only seen in animal cells • organelles that are very acidic inside PH 4.8 • contains digestive enzymes • breaks down excess or worn-out organelles, food particles, and engulfed viruses or bacteria • fuses with vesicles containing target material • used in cell suicide when lysosomes break digestive enzymes destroy cell contents

37. Eukaryotic Cell: Plant cell parts • Cell Wall made of cellulose semi-permeable, semi-rigid function same as bacterial cell wall • Central Vacuole helps manage pressure difference between inside and outside of cell acts like a water balloon helps in cell elongation surrounded by a membrane contains cell sap

38. Eukaryotic Cell: Plant cell parts • Chloroplast organelle that contains chlorophyll photosynthesis happens here CO2 + H2O + Light => Sugars + O2 The oxygen is released into atmosphere Part of sugars produced in chloroplast used for growth Some sugar is decomposed in mitochondria to produce ATP ATP => ADP transition provides energy for biosynthesis Aerobic respiration O2 absorbed from atmosphere, CO2 released More O2 released during photosynthesis than what is used for aerobic respiration

39. Cell Division • called Mitosis triggers external proteins internal proteins accumulated during some regular cellular process triggers when a critical level is reached oscillating chemical reactions protein production and degradation reactions slow build-up (during growth) fast return (after division) reactions

40. Eukaryotic Cell Division • DNA strands in chromosomes replicate • Two poles form, connected by microtubules • Chromosomes align to poles • Microtubules attach to chromosomes • Microtubules pull chromosomes replicas apart • Membrane and cytoplasm divides into two separate cells

41. Prokaryotic Cell Division • no detailed cell cycle • DNA is a double stranded loop in prokaryotes • DNA replication starts from one point and proceeds till end

42. Cell Metabolism • all metabolism uses ATP-ADP cycle for energy storage ATP (Adenosine Triphosphate)  ADP (Adenosine Diphosphate) + Energy Enzyme catalyzed cycle • variety of catabolic mechanisms to generate energy from environment aerobic and anaerobic respiration, photosynthesis alcohol fermentation (in Yeast) lactic acid fermentation (in muscle cells under strenuous activity)

43. In Part 3… We see how cells co-operate and evolve into… An Organism

44. ubiquitous. biology www.ubio.in