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Biology For Computer Engineers Part 2: The Cell
Cover image, courtesy of  Wellcome Images ,  Creative Commons license All other images, courtesy of Wikipedia. Acknowledgements
Nucleotide Organic molecule Consists of Base Ring structure with Nitrogen, Carbon, Oxygen, Hydrogen Sugar Phosphate (PO4 3- ) Acidic character Nucleotides (CH 2 ) Ribose PO 4 3-
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 Nucleic Acids Common nucleic acids RNA Ribonucleic acid Sugar is ribose DNA Deoxyribonucleic acid Sugar is deoxyribose
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 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 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 Nucleic Acids
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  Water and Biomolecules
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  RSO 4-  Sulfonate  RSO 3 -  Phosphate  PO 4 3- Amine  RNH 3 +   Alkyl  HR  Hydroxyl  ROH  Carboxyl  RCOOH
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  Phospholipids
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 What is 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 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 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 Evolution 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 Types of Life
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 Cell
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 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 Cell Functions
A fluid medium enclosed by a wall/membrane Internal parts perform various life functions Prokaryotic Cell Structure
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  Prokaryotic Cell: Cell Capsule
Cell Wall  provides rigidity and structure  polysaccharide complexes  holds cell from bursting  cell's inside pressure is higher than outside   Prokaryotic Cell Wall/Membrane Plasma Membrane  phospholipid bilayer  partially permeable membrane  like a layer of oil   has transport mechanisms for various signals and nutrients  Cell Membrane
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 Prokaryotic Cell: Cytoplasm
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 Prokaryotic Ribosomes/Nucleoid
Eukaryotic Cell: Plant Cell
Eukaryotic Cell: Animal Cell
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 Eukaryotic Cell: Membrane/Cytoplasm
Eukaryotic Cell: Mitochondrion
multiple per cell  divide and grow depending on cell's energy needs  enclosed by two membranes  each membrane is a phospholipid bilayer  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 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  Eukaryotic Cell: Mitochondrion
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  Eukaryotic Cell: Golgi Apparatus
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  Eukaryotic Cell: Endoplasmic Reticulum
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  Eukaryotic Cell: Nucleus
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 Eukaryotic Cell: Chromosomes
Chromosome Packing
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  Eukaryotic Cell: Lysosomes
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  Eukaryotic Cell: Plant cell parts
Chloroplast  organelle that contains chlorophyll  photosynthesis happens here  CO 2  + H 2 O + Light => Sugars + O 2 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 O 2  absorbed from atmosphere, CO 2  released More O2 released during photosynthesis than what is used for aerobic respiration Eukaryotic Cell: Plant cell parts
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 Cell Division
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
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
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)
We see how cells co-operate and evolve into… An Organism In Part 3…
ubiquitous   .  biology www.ubio.in

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Biology for Computer Engineers, Part 2: The Cell

  • 1. Biology For Computer Engineers Part 2: The Cell
  • 2. Cover image, courtesy of Wellcome Images , Creative Commons license All other images, courtesy of Wikipedia. Acknowledgements
  • 3. Nucleotide Organic molecule Consists of Base Ring structure with Nitrogen, Carbon, Oxygen, Hydrogen Sugar Phosphate (PO4 3- ) Acidic character Nucleotides (CH 2 ) Ribose PO 4 3-
  • 4. 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 Nucleic Acids Common nucleic acids RNA Ribonucleic acid Sugar is ribose DNA Deoxyribonucleic acid Sugar is deoxyribose
  • 5. 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 Nucleic Acids
  • 6. 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 Nucleic Acids
  • 7. 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 Nucleic Acids
  • 8. 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 Water and Biomolecules
  • 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 RSO 4- Sulfonate RSO 3 - Phosphate PO 4 3- Amine RNH 3 + Alkyl HR Hydroxyl ROH Carboxyl RCOOH
  • 10. 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 Phospholipids
  • 11. 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 What is Life?
  • 12. 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 Evolution of Life
  • 13. 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 Evolution of Life
  • 14. 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 Evolution of Life
  • 15. 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 Types of Life
  • 16. 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 Cell
  • 17. 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 Cell Functions
  • 18. 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 Cell Functions
  • 19. A fluid medium enclosed by a wall/membrane Internal parts perform various life functions Prokaryotic Cell Structure
  • 20. 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 Prokaryotic Cell: Cell Capsule
  • 21. Cell Wall provides rigidity and structure polysaccharide complexes holds cell from bursting cell's inside pressure is higher than outside Prokaryotic Cell Wall/Membrane Plasma Membrane phospholipid bilayer partially permeable membrane like a layer of oil has transport mechanisms for various signals and nutrients Cell Membrane
  • 22. 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 Prokaryotic Cell: Cytoplasm
  • 23. 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 Prokaryotic Ribosomes/Nucleoid
  • 26. 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 Eukaryotic Cell: Membrane/Cytoplasm
  • 28. multiple per cell divide and grow depending on cell's energy needs enclosed by two membranes each membrane is a phospholipid bilayer 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 Eukaryotic Cell: Mitochondrion
  • 29. 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 Eukaryotic Cell: Mitochondrion
  • 30. 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 Eukaryotic Cell: Golgi Apparatus
  • 31. 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 Eukaryotic Cell: Endoplasmic Reticulum
  • 33. 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 Eukaryotic Cell: Nucleus
  • 34. 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 Eukaryotic Cell: Chromosomes
  • 36. 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 Eukaryotic Cell: Lysosomes
  • 37. 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 Eukaryotic Cell: Plant cell parts
  • 38. Chloroplast organelle that contains chlorophyll photosynthesis happens here CO 2 + H 2 O + Light => Sugars + O 2 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 O 2 absorbed from atmosphere, CO 2 released More O2 released during photosynthesis than what is used for aerobic respiration Eukaryotic Cell: Plant cell parts
  • 39. 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 Cell Division
  • 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. We see how cells co-operate and evolve into… An Organism In Part 3…
  • 44. ubiquitous . biology www.ubio.in