Brief history of life on Earth

Transcription

1 Brief history of life on Earth 4.6 Billion Years ago: Earth forms 3.6 Billion Years ago : First life on the planet (Prokaryotes = Bacteria) 2.8 Billion Years ago : First eukaryotic life (also microbial algae/protozoa) 0.4 Billion Years ago: First animals and plants (Fossil evidence indicates that modern humans originated in Africa about 200,000 years ago) Fossilized stromatolite * Stromatolites - layered rock-like structures formed in shallow water by the trapping/binding/cementation of sedimentary grains by microbes; Represent the most ancient records of life on Earth. 1

2 Two types of Cellular Organization Eukaryotic cells DNA surrounded by a membrane/envelope =>cell nucleus Prokaryotic cells DNA not surrounded by an envelope Prokaryotic Structure Relatively simple structure: DNA, ribosomes, cell membrane, cell wall, plus a few other parts (not shown) 2

3 Eukaryotic Structure By comparison, euks are much more complex, containing specialized organelles to perform particular functions Prokaryotes and eukaryotes: universal vs. distinct structures Universal: Both have DNA, ribosomes (to make proteins), and cell membranes EUK Eukaryotes have energy organelles (mitochondria / chloroplasts), an endomembrane system (ER/GOLGI) to package and sort materials, cytoskeleton (fibers that move materials around and help with cell division), and a nuclear membrane PROK 3

4 How did we get from prok to euk??? Lynn Margulis Endosymbiotic theory Euks came from proks ingesting other proks, but instead of digesting them they began to use them as organelles Evidence shows that mitochondria and chloroplasts have bacterial origins TAXONOMY Biology attempts to catalog organisms 1. Aristotle: described 500 plants and animals 2. Linnaeus: described 1000 s of plants and animals, devised the binomial system (Genus/Species), part of the hierarchal system of nomenclature 3. Whittaker: 5 Kingdom system (Animals/Plants/Fungi/Protista/Bacteria) 4. Woese: 3 Domain System 4

5 Nomenclature gives scientific names to organisms Linnaeus Binomial system: everything has two names based on genus and species (e.g. homo sapiens) His groupings were based upon shared physical characteristics. Quoted as saying GOD CREATES, LINNAEUS NAMES Whittaker s Five Kingdom System 1. Animals 2. Plants 3. Fungi 4. Protists (algae/protozoa/ + lower fungi ) 5. Monera (prokaryotes) Note that 4 out of 5 are eukaryotic organisms, only 1/5 prokaryotic 5

6 The three-domain system places the Monera in separate lineages Classification is based on differences in ribosomal RNA (and/or the DNA genes that encode these RNAs) Carl Woese Recall that all life forms have ribosomes, so by comparing how similar the ribosomes are to each other we can see how closely they are related to one another Comparison of rrna genes from diverse organisms Note that certain regions of the sequences vary from each other, so that the more similar they are, the more closely related are the organisms (more differences = more distant relationship) 6

7 Relationship between diverse organisms based on sequences of rrna genes Organisms A and B have only 2 differences between them, whereas both A+B have 6 differences from C: thus it is inferred that A+B should be closer together on a family tree than either should be to organism C (note that X is the universal ancestor of all three other organisms) Three Domain System THE THREE DOMAINS ARE: EUBACTERIA, ARCHAE, and EURKARYA (thus 2/3 PROKS and 1/3 EUKS) 7

8 COMPARISON Eubacteria OF Eubacteria Archae Eukaryotes THIS HIGHLIGHTS THE DIFFERENCES BETWEEN THE 3 DOMAINS Source: S. Finkel, 2002 Eubacterial vs. Archaeal cytoplasmic membranes ARCHAE cell membrane is much stronger with more molecules and tighter bonding than EUBACTERIA -- this helps them to survive extreme environments 8

9 Bacteria: Shapes and Arrangements Bacilli Cylinder shape Can be singles or form chains Examples: E. coli, Shigella, Salmonella, Anthrax, etc. 9

10 Cocci CUBE OF 8 = Sarcina Examples: Staph infections, Strep throat bacteria, etc. Spirals and other shapes Spirilla are thick and rigid, with a single flagellum at each end; Spirochetes are thin and flexable, with an internal flagella called an axial filament that rotates beneath the cell wall (moves like a cork screw ) 10

11 Bacteria: Structure From the outside to the inside of the cell Bacterial flagella Provide motility Rotate (clockwise/countercwise) Embedded in cell wall, extend out from there (exception: spirochetes) Allow bacteria to move toward nutrients, or away from repellants (e.g. antibiotics, white blood cells) this is called chemotaxis 11

12 Structure of bacterial flagella Basal body = motor embedded in the cell wall and membrane; Rotates, which then drives the external filament Bacterial motion mediated by flagella If the flagella rotate counterclockwise, the bacterium moves in a straight path ( run ) if they rotate clockwise, the bacterium will tend to stay in place ( tumble ) 12

13 Chemotaxis For example: If bacteria encounter food, the organisms stay around the same area (see A above). However, if food is sensed somewhere nearby, they ll move toward it (see B ). Movement of Shigella within and between cells Note that these organisms invade intestinal cells and then move from one cell to another, causing water loss = extreme diarrhea 13

14 TYPES OF FLAGELLA Monotrichous: one flagellum at one end Amphitrichous: flagella at both ends Lophotrichous: two or more flagella clustered at one end only Peritrichous: many flagella all around the cell Pili Protein fibers Help bacteria to attach to surfaces (e.g. urethra in Urinary tract infections) Special pili (conjugation pili) are used for bacteria intercourse where they move DNA between cells Enhance ability to cause disease 14

15 Binding of pili to host cells Note that the tips of pili contain proteins that dock down and lock on to receptor molecules on host cell surfaces Glycocalyx Sticky, sugary layer around cells Not all bacteria have it, but the ones that do are more dangerous! Attachment is easier (sticky) Retain water, so they don t dry out Repel the white blood cells of the immune system as WBCs are keyed to look for foreign proteins so these sugars help hide the cell 15

16 Two types: Cell wall 1. Gram-positive: thick layer of peptidoglycan (surrounds cells and protects them); also contains teichoic acid; Retains the primary (purple) gram stain in spite of gram alcohol (destaining) treatment. 2. Gram negative: thin layer of peptidoglycan, lose the gram stain when gram alcohol (destainer) is applied. ** Gram(-) also have an extra membrane outside the cell wall called LPS (lipopolysaccharide) layer contains endotoxin, an internal poison that makes these cells dangerous (re: septic shock) Structure of Gram-positive cell envelope Note the thick peptidoglycan and the Teichoic acid that binds together the cell wall components 16

17 Structure of gram-negative cell envelope Note the thin peptidoglycan sandwiched between two membranes, as well as the lack of teichoic acid This part contains endotoxin Cell envelope of Gram-Positive vs. Gram-Negative Bacteria Hint: Make sure you can compare and contrast these two for an exam! 17

18 Structure of E. coli peptidoglycan Synthesis of peptidoglycan 18

19 b-lactam antibiotics Prevent new cell walls from being formed so bacs burst apart (below)! Cell membrane Permeability barrier (cellular materials separate from environment); imports specific nutrients, exports waste, site of ATP production in bacs Chemical composition: 40% phospholipids 60% embedded proteins Both move (Fluid mosaic model) Action of disinfectants/drugs: -- Alcohols dissolve this layer; -- Some Anti-biotics (like polymyxin) poke holes in it (->leakage) 19

20 Cytoplasm Is the center of biochemical activity Structures within the cytosol --Ribosomes --Inclusion bodies: store nutrients (Phosphate/Sulfur/Glycogen) --DNA: two forms A. Chromosome(s) B. Plasmids = molecules of DNA separate from chromosome that can carry genes for toxins or antibiotic resistance Spores Are designed for dormancy Spore formation: when nutrients are limited Chemical composition: chromosome + small amount of cytoplasm surrounded by thick layers of peptidoglycan Resistance: little water so heat resistant; Dipicolinic Acid stabilizes the DNA Can survive alcohol, boiling water, etc for many years Many Pathogenic bacteria form spores including Anthrax, Botulism, and Tetanus bacteria 20

21 Bacterial Spore Formation When nutrients are available, the spore will germinate back to a normal cell again Bacterial Growth and Nutrition ph Nutrients + Oxygen Temperature 21

22 Temperature Environmental Oxygen Requirements -- can support or hinder growth 1. Aerobic need high oxygen concentration to grow 2. Anaerobic need very low or no oxygen to grow 3. Facultative can grow with or without oxygen 4. Capnophilic require high concentration of CO2 to grow 22

23 ph -- a measure of the H+ ion concentration Most bacteria prefer neutral ph (re: human pathogens 7.35) Neutrophiles live best between ph 5.5. and 8.5 Acidophiles grow best below ph 5.5, Basophiles prefer above ph affects the protein structure of cells Nutrients -- needed to produce energy -- needed for biosynthesis of cellular components Main nutrients: C / O / N / H / P / S Others needed: K / Na / Mg / Cl / Fe -- also trace metals needed 23

24 Bacteria: Reproduction by Binary fission A Bacterial Growth Curve 24

25 Metabolism = the sum total of all biochemical reactions taking place in a cell A. Catabolism: breaking down of chemical compounds from larger to smaller; break bonds, release energy ( exergonic reactions) B. Anabolism: synthesis of chemical compounds; requires energy to create new bonds ( endergonic reactions) Role of Enzymes in Metabolism -- catalyze reactions (speed them up) -- decrease activation energy required to start a reaction -Act via enzyme-substrate complexes: bind to substrates, either break bonds or create new bonds, then release products Sometimes require cofactors = small metals (zinc/iron) Sometimes require coenzymes = small organic molecules (Vitamins) Usually proteins but can also be RNA (aka ribozymes ) 25

26 Enzymes lower the Activation Energy of Reactions Enzymes often act in Metabolic Pathways The product of one enzymatic reaction becomes the substrate for the next reaction i.e. enzymes often work together to put together a final product 26

27 ATP = Energy Currency -- cannot be stored, must be made and used constantly (short-term) -- utilized in anabolic reactions, often created during catabolic reactions ATP ADP + Phosphate + ENERGY ATP/ADP Cycle 27

28 Metabolic Pathways are coupled to the ATP/ADP Cycle High-energy phosphate compounds and Reactions in which they play a role 28

29 Long-term Energy storage: Polysaccharides, Fats, and Proteins Polysaccs: broken down via glycolysis, krebs cycle, electron transport chains, or fermentation Fats: broken down via Beta-oxidation of fatty acids (products are put into Krebs cycle) Proteins can be broken down via Deamination, products enter the Krebs cycle Focus on.. Sugars Two types of glucose transport 29

30 Glycolysis 9 reactions Initial substrate: glucose (6 carbons) End products: ATP 2 Pyruvates (3 carbon molecule) NADH+ The Krebs cycle Sometimes, pyruvate can be processed via the Krebs cycle ~8 reactions Endproducts: ATP NADH+ / FADH 2 Carbon Dioxide 30

31 Electron Transport Chain: RESPIRATION Requires electrons and protons (carried in by reduced NAD/FAD) Occurs at cell membrane in bacteria, and at mitochondria in eukaryotic cells Can be aerobic if final electron acceptor is Oxygen (Aerobic Oxidative Phosphorylation is shown) Can be anaerobic if final electron acceptor is something other than Oxygen Making ATP 31

32 Structures of molecules involved in oxidation-reduction reactions Structures of molecules involved in oxidation-reduction reactions 32

33 Respiration Aerobic Anaerobic Anaerobic respiration examples E. coli : NO 3 - NO 2 - Desulfovibrio:. SO 4-2 H 2 S Methanogens: CO 2 CH 4 {Note that final electron acceptor is reduced} 33

34 Fermentation Can be used when respiration is not possible Produces some ATP and allows glycolysis to continue Other end products include many acids, gases, and alcohols Example acid: lactic acid Example alcohol: ethanol Example gas: CO2 Anabolic Process: Photosynthesis -- two stages of reactions -- end product: glucose 1. Energy-fixing reactions: sunlight excites electrons in chlorophyll pigment, energy is captured as ATP and NADPH 2. Carbon-fixing reactions: products of first stage are used to convert carbon dioxide to sugars (glucose) 34

35 Nutritional Classification of Microorganisms The Cycles of Elements in the Environment There s a limited amount of carbon, sulfur, phosphorus, nitrogen, etc. in the biosphere. Therefore, these elements must constantly be recycled to be used by living organisms Who are the recyclers??? Bacteria and Fungi 35

36 The Carbon cycle The Sulfur cycle 36

37 The Nitrogen cycle N 2 gas in the air Nitrogen needed as part of proteins, DNA, RNA, ATP, etc. When organisms die, bacteria and fungi rerelease N 2 gas back to the atmosphere, completing the cycle Bacteria take it from the air and convert it to ammonia, nitrites, and nitrates that can be used by plants; animals eat the plants Interaction of Rhizobium meliloti and alfalfa 37

38 Interaction of Rhizobium meliloti and alfalfa SUMMARY: In roots of leguminous (pod-bearing) plants, bacteria live in symbiosis with the plant. Plant gets fixed nitrogen from bacs, and in return feeds them sugar and gives them a house Root Nodules Leguminous Plant 38

39 Bacteria: Genetics, Genomics, and Genetic Engineering -- genetics: study of hereditary information -- gene: a section of DNA that encodes an RNA molecule, some of which are used to make proteins Bacterial DNA DNA is located in two places in bacteria: 1. chromosome has the genes needed for growth, reproduction, everyday life 2. PLASMIDS, small rings of DNA with genes that confer antibiotic resistance, toxin production, etc Humans have 21,000 genes, E. coli has about 4400, it is wound like a rubber-band (super-coiled) to fit into cells 39

40 Plasmids The Central Dogma of Molecular Biology transcription translation DNA RNA Protein replication 40

41 DNA replication Start with one chromosome or plasmid, end with two Each of the two parental DNA strands is used as a template to make a new daughter DNA strand Bidirectional: goes both ways around the loop; major enzyme involved is called DNA polymerase (reads template DNA and writes new daughter DNA) Semi-conservative: half of each new chromosome or plasmid is parental, and half is new daughter material Transcription -- DNA processed into RNA molecules A. mrna: carries the genetic message to the ribosomes, codons = triplet mrna sequences that code for amino acids B. trna: adaptor molecule that carries amino acids on one side and has anti-codons on the other side that bind to codons C. rrna: forms part of the ribosome, catalyzes reactions there 41

42 Translation Processes RNA into protein All three RNA types involved Begins at start codon on mrna (AUG) Ends at Stop Codons (UAA/UAG/UGA) Anti-codon of each trna binds to codon on mrna, bringing in the appropriate amino acid to build protein chains The Genetic Code 42

43 Polyribosomes Operons and Control of Protein Synthesis 43

44 Mutations Permanent change in the DNA of an organism; can be beneficial, harmful, or neutral. Does it affect fitness = ability to survive and reproduce??? A. Spontaneous: occurs as a results of errors during replication (1 in a billion base pairs is incorrect) B. Induced: occur due to a physical or chemical agent in the environment. Induced mutations UV light binds adjacent Thymine (T) molecules together Re: skin cancer due to too much sunlight exposure T-T dimers can be repaired, but not always, can cause DNA to be unreadable in that location. 44

45 Result of Mutations Types of Point mutations Affect a single base pair in DNA Silent: don t change the amino acid, even if DNA changes; usually neutral Mis-sense: one amino acid changes; can be beneficial, harmful, or neutral Non-sense: inserts early stop codon shorter protein Insertion or Deletion: remove or add one nucleotide; frameshift as all codons after it are changed 45

46 The Ames test can identify potential mutagens -- used to test household chemicals; -- if bacteria show a mutation, don t use the product!! DNA Repair: An Example 46

47 Genetic Transfer in Bacteria -- vertical: parent to daughter cells; horizontal: between non-related cells V E R T I C A L HORIZONTAL Three Types of Horizontal Gene Transfer 1. Transformation: uptake of free DNA from the environment 2. Transduction: viruses transfer DNA between bacteria 3. Conjugation: two bacteria get together and DNA is pushed from one to the other 47

48 Natural Transformation Artificial Transformation 48

49 Griffith s Discovery of Transformation Transduction 49

50 Conjugation = Bacterial Dating Two Types of Conjugation A. B. 50

51 Horizontal gene transfers make some bacteria more dangerous to humans Discoverer of Transposons Barbara McClintock 51

52 Transposable genetic elements INVERTED REPEATS Movement of an antibiotic resistance gene 52

53 Genetic engineering Manipulation of DNA to make a product Aka Biotechnology Example: use yeast to make Cow Growth Hormone in mass quantity Result: cow s milk contained elevated levels of hormones, may be cancerous Restriction Enzymes and Recombinant DNA Restriction enzymes can cut DNA at particular locations DNA ligase pastes together separate DNAs (creates hybrid) 53

54 Construction of a Recombinant DNA Molecule Human genes can be cloned in bacteria 54

55 Applications of Genetic engineering Insert Human gene for insulin production into E. coli bacteria E. coli produces insulin chemically identical to human version 55

56 Transgenics why does it work? PCR: The Polymerase Chain Reaction = a DNA copy machine 56

57 Microbial Genomics Genomics: study of entire DNA sequences of organisms (e.g. DOG/ CHIMP / HUMAN) -- lets us compare organisms + species to see how closely related they are to each other -- lets us examine sick vs. healthy populations of humans to screen for disorders 57