A 2 step process: descent with modification - Variability (via mutations). - Ordering that variability by natural selection.

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Ethelbert Palmer
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1 LECTURE 1: T see bilgy in an evlutinary cntext and review the three generalisatins f bilgy. T understand hw far back we have extended the fssil recrd since the days f Darwin. FIRST GENERALISATION OF BIOLOGY EVOLUTION THROUGH NATURAL SELECTION - Charles Darwin. - A great unifying thery in bilgy with this thery we can accunt fr diversity and similarities in plant and animal species. EVOLUTION - The Earth has a lng histry billin years. Life began abut 4 billin years ag. - All rganisms arse in the curse f this histry frm earlier, mre primitive frms. - As a cnsequence f this thery all rganisms are related r share a cmmn ancestr. A 2 step prcess: descent with mdificatin - Variability (via mutatins). - Ordering that variability by natural selectin. SECOND GENERALISATION OF BIOLOGY UNITY OF BIOLOGICAL PROCESSES - Because all rganisms share a cmmn ancestr, there is a unity f bilgical prcesses. - All rganisms have DNA. - All rganisms als have the machinery t carry ut the instructins frm the DNA prteins. - All rganisms share certain bichemical reactins. THIRD GENERALISATION OF BIOLOGY ALL ORGANISMS CONSIST OF CELLS - Cell = a bag, a clsed dmain where the chemical reactins required fr life are carried ut. - Cells have prbably succeeded because f the membrane separating the living prtplast and the harsh envirnment. Cell Thery - All living rganisms are cmpsed f cells. - All cells cme frm pre-existing cells. - The cell is the smallest rganizatinal unit. DARWIN S DILEMMA - Where did the first cells cme frm? - Hw did eukarytic cells evlve frm prkarytic cells? - Cambrian explsin the emergence f eukarytes greatly accelerated the pace f evlutinary change.

2 Nte: reprductin, changeable inheritance, metablic activity and cntainment (i.e. being surrunded by a membrane) define life. LECTURE 2: T understand the differences between prkarytic and eukarytic cells. T understand the structure, diversity and functin f archaea and bacteria and hw they differ. The imprtance f cyanbacteria. PROKARYOTIC VS EUKARYOTIC CELLS Prkarytes were the first cellular lifefrms t emerge. - Evlved in the ceans. - Earliest bacteria (predecessrs f cyanbacteria) were capable f anxygenic phtsynthesis. Evlving chlrphyll allwed prkarytes t capture inrganic CO 2 and turn it int rganic C, releasing O 2. THE GREAT OXYGENATION. Earth: inhspitable hspitable. Feature f Cells Prkaryte: Bacteria Prkaryte: Archaea Eukaryte Size Micrscpic µm Micrscpic (but can be macrscpic) Micrscpic µm Chrmsme structure Circular Circular with histnes Linear with histnes Chrmsme number Single Single Multiple and variable Cell divisin Binary fissin Binary fissin Mitsis/meisis Internal cmpartmentalisatin Never Never Always, endmembrane system Flagella External, flagellin acts as a mtr External, flagellin acts as a mtr Internal, 9+2 arrangement f micrtubules Cytskeletn Rudimentary cytskeletn in sme Rudimentary cytskeletn in sme Micrfilaments (actin and intermediate), micrtubules Cell wall Peptidglycan N peptidglycan Smetimes cellulse, smetimes chitin, smetimes absent Uni r multicellular Unicellular Unicellular Smetimes multicellular Auttrphism Chemsynthetic = can xidise inrganic cmpunds and harvest energy Smetimes chemsynthetic, smetimes phtsynthetic Smetimes chemsynthetic (think extremphiles) Nitrgen fixing Smetimes Smetimes Never STRUCTURE OF PROKARYOTES - All prkarytes are surrunded by a semi-rigid cell wall. - Cell membrane phsphlipid, semi-permeable. - Cytsl liquid interir. - Ribsmes translate prtein. - Tgether the ribsmes and cytsl are the cytplasm. - DNA flws freely and is a single, circular strand. Smetimes phtsynthetic

- Outer capsule cmpsed f plysaccharides. Imprtant fr recgnitin f ther cells and disease resistance. - Pili allw prkarytes t lineup and transfer DNA back and frth between different cells.

- Allws prkarytes t divide every 20 mins. ARCHAEA VS BACTERIA - Mrphlgically similar can t tell them apart under a micrscpe. - Hwever vastly different DNA.

3 - Outer capsule cmpsed f plysaccharides. Imprtant fr recgnitin f ther cells and disease resistance. - Pili allw prkarytes t lineup and transfer DNA back and frth between different cells. - Flagellum mvement. Cmpsed f a single prtein called flagella. Extra-cellular. - Rtary mtr turns the flagellum and prpels the cell. BINARY FISSION - Much simpler prcess than mitsis/meisis. - Allws prkarytes t divide every 20 mins. ARCHAEA VS BACTERIA - Mrphlgically similar can t tell them apart under a micrscpe. - Hwever vastly different DNA. - The tw central bilgical prcesses in archaea, genetic transcriptin and translatin, are mre similar t thse f eukarytes than bacteria. - Archaea lack a peptidglycan wall (a distinct feature f bacteria). - There are n knwn archaean pathgens. WHY STUDY PROKARYOTES? - Cause many diseases.

- Decmpsers and recyclers critical in remving dead rganic matter, recycling carbn, nitrgen, sulfur, degrading txic chemicals etc. - Agents in industrial and agricultural prcesses. E.g. bacteria fermenting fd.

4 - Decmpsers and recyclers critical in remving dead rganic matter, recycling carbn, nitrgen, sulfur, degrading txic chemicals etc. - Agents in industrial and agricultural prcesses. E.g. bacteria fermenting fd. - Nitrgen fixatin i.e. can bring nitrgen int rganic material. - GM bacteria prduce pharmaceuticals human insulin, human grwth hrmne etc. CYANOBACTERIA - Majr primary prducers. - Cntain chlrphyll A and generate mlecular xygen during phtsynthesis (similar t plants and algae nt ther bacteria). - Respnsible fr the earth s atmsphere becming xygen-rich. - Strmatlites which frmed frm the activities f cyanbacteria are the ldest fssil evidence f life n earth. LECTURE 3: T understand the cmplex structure and differentiatin f eukarytic cells and the pssible rigin f mitchndria and chlrplasts thrugh the prcesses f endsymbisis. FEATURES OF THE EUKARYOTIC NUCLEUS - Duble membrane nuclear envelpe. Inner and uter which are jined at nuclear pres (annular pres). Outer membrane is cntinuus with ER. Nuclear pres regulate the passage f prteins and RNA int and ut f the nucleus.

- Nuclelus sub-regin cntaining ribsme genes. Nucleus can cntain ne r several. Darkly staining regins. Cntain high cncentratins f RNA, prtein and DNA.

Lng DNA mlecules wind arund clusters f histne mlecules (simple prteins) t frm nuclesmes (=1 histne grup with DNA wrapped arund).

5 - Nuclelus sub-regin cntaining ribsme genes. Nucleus can cntain ne r several. Darkly staining regins. Cntain high cncentratins f RNA, prtein and DNA. Site f synthesis f ribsmal RNA (rrna) and assembly f ribsmal subunits fr exprt t the cytplasm fr prtein synthesis. - DNA. Lng DNA mlecules wind arund clusters f histne mlecules (simple prteins) t frm nuclesmes (=1 histne grup with DNA wrapped arund). This arrangement allws DNA t twist int a helix, frming a chrmatin strand. (DNA has a negative charge because f phsphate backbne and histnes have a psitive charge allws assciatin between them). Eukarytes have multiple chrmsmes (vs prkarytes which have a single, circular mlecule). - Mitchndria pwerhuse f the cell. Cells may cntain ne r several. AEROBIC RESPIRATION generate ATP. Duble membrane. Outer membrane smth, permeable. Inner membrane arranged int flds (cristae) t increase SA, highly impermeable. Matrix space (inside inner membrane) cntains mitchndrial ribsmes and cpies f mitchndrial DNA. Enzyme cmplexes are respnsible fr ATP synthesis. - Chlrplasts energy catchers f plants. Cells may cntain ne r many. PHOTOSYNTHESIS cntain chlrphyll, a light-absrbing pigment. Duble membrane. Outer. Inner frms flattened disc-like sacs, thylakids, which lie n tp f each ther frming stacks, grana. Large SA f internal membranes increases ability t capture light (chlrphyll is assembled n thylakid membranes).

6 ORIGINS OF COMPLEX ORGANELLES Mitchndria believed t be derived frm purple bacteria. Chlrplasts believed t be derived frm cyanbacteria. PRIMARY ENDOSYMBIOSIS - Endsymbisis = an rganism living inside anther (fr the benefit f them bth). - Mitchndrial evlutin is thught t have preceded the evlutin f chlrplasts. - A eukarytic hst engulfed a purple bacterium (prkaryte) in a fd vacule = phagcytsis. - The purple bacteria didn t get digested (perhaps because f a mutatin in the cell wall). - The purple bacterium lst its autnmy and became an rganelle. - Evlutin f the chlrplast invlved primary endsymbisis. - Chlrplast evlved frm cyanbacteria. SECONDARY ENDOSYMBIOSIS - When eukarytes stle their chlrplast frm anther eukaryte rather than engulf a prkaryte. - Prtistan pirates. - The number f membranes arund the chlrplast indicates whether primary r secndary endsymbisis. 2 membranes = primary. 3 r 4 membranes = secndary.

EVIDENCE FOR THE ENDOSYMBIOTIC THEORY Mitchndria and chlrplasts: - Are mrphlgically similar t bacteria. I.e. they lk like prkarytes. - Are surrunded by an uter membrane similar t a cell membrane.

7 EVIDENCE FOR THE ENDOSYMBIOTIC THEORY Mitchndria and chlrplasts: - Are mrphlgically similar t bacteria. I.e. they lk like prkarytes. - Are surrunded by an uter membrane similar t a cell membrane. - Are semi-autnmus. They retain their wn genme (DNA, RNA). - Als retain their wn ribsmes. - Similar metablism t existing prkarytes. - Sme chlrplasts still have the bacterial peptidglycan wall between the inner and uter membranes.

BIOLOGY SUMMARIES. All living things share biochemical reactions eg. DNA and proteins

BIOLOGY SUMMARIES. All living things share biochemical reactions eg. DNA and proteins BIOLOGY SUMMARIES LECTURE 1-Intrductin t Bilgy Evlutin There are 3 life creating theries- Panspermia-ET rigins/infectin f spres frm anther planet/star Special creatin by divine frces Evlutin-tells us Earth