1. CHAPTER 3 Cells: The Living Units

2. CELL THEORY Cell is basic unit of life. Cell is basic unit of life. Activity of the organism is dependent on the individual and collective activities of its cells. Activity of the organism is dependent on the individual and collective activities of its cells. All cells come from pre-existing cells. All cells come from pre-existing cells. Principle of Complementarity=biochemical processes are dictated by subcellular structures. Principle of Complementarity=biochemical processes are dictated by subcellular structures.

3. CELL DIVERSITY

4. TYPICAL ANIMAL CELL

5. PLASMA MEMBRANE Basically similar in all membranes Basically similar in all membranes Fluid mosaic model Fluid mosaic model Mixed composition Mixed composition Lipids not fixed in place, can move Lipids not fixed in place, can move

6. PLASMA MEMBRANE

8. PROTEIN FUNCTIONS

9. SPECIALIZATIONS OF THE PLASMA MEMBRANE

10. CELL MEMBRANE TRANSPORT PASSIVE PROCESSES PASSIVE PROCESSES Simple Diffusion Simple Diffusion Facilitated Diffusion Facilitated Diffusion Osmosis Osmosis Filtration Filtration ACTIVE PROCESSES ACTIVE PROCESSES Active Transport Active Transport Vesicular Transport Vesicular Transport

11. SIMPLE DIFFUSION

12. FACILITATED DIFFUSION

13. OSMOSIS

14. EFFECTS OF TONICITY

15. ACTIVE TRANSPORT

16. EXOCYTOSIS

17. ENDOCYTOSIS

18. CYTOPLASMIC ORGANELLES

19. CYTOPLASM

20. NUCLEUS

21. Endoplasmic Reticulum (ER) Endoplasmic Reticulum (ER) Rough Rough Ribosomes attach Ribosomes attach Protein synthesis Protein synthesis Smooth Smooth No ribosomes No ribosomes Lipid synthesis Lipid synthesis Carbohydrates Carbohydrates

22. Ribosomes Ribosomes Synthesize proteins Synthesize proteins

23. Golgi Bodies Golgi Bodies Package and process proteins & lipids Package and process proteins & lipids Vesicles—sacs containing enzymes Vesicles—sacs containing enzymes Lysosomes—intracellular digestion Lysosomes—intracellular digestion Peroxisomes—break down fatty acids & proteins Peroxisomes—break down fatty acids & proteins

25. Mitochondria Mitochondria Forms ATP (energy) Forms ATP (energy) Requires oxygen Requires oxygen H+ stored in outer compartment, controlled flow into inner (cristae) H+ stored in outer compartment, controlled flow into inner (cristae) Similar to bacteria: have their own DNA & ribosomes Similar to bacteria: have their own DNA & ribosomes

26. Centrioles—produce microfilaments during cell division. Centrioles—produce microfilaments during cell division.

27. Cytoskeleton Cytoskeleton Protein filaments between nucleus & plasma membrane Protein filaments between nucleus & plasma membrane Microtubules—keep organelles & cell structures in place or move them Microtubules—keep organelles & cell structures in place or move them Can fall apart in controlled ways (amoebas) Can fall apart in controlled ways (amoebas) Some poisons can affect Some poisons can affect

28. Microfilaments Microfilaments Thin filaments Thin filaments Help in cell division (contracts midsection) Help in cell division (contracts midsection) Anchor membrane proteins Anchor membrane proteins Muscle contraction Muscle contraction

29. Flagella—long outer structures for movement Flagella—long outer structures for movement Usually only a few Usually only a few Cilia—short outer structures for movement Cilia—short outer structures for movement Usually many Usually many Pseudopod Pseudopod “False foot” “False foot”

30. LIFE CYCLE OF A CELL

31. INTERPHASE G1 G1 Most of life for many cells Most of life for many cells Normal functions Normal functions Length varies depending on cell type Length varies depending on cell type S New strands of DNA created from existing strands New strands of DNA created from existing strands Chromosome doubles into connected sister chromatids Chromosome doubles into connected sister chromatids Duration is same for all cells in a species Duration is same for all cells in a species G2 G2 Microtubules and others made for cell division Microtubules and others made for cell division

32. S=DNA REPLICATION Helicase DNA Polymerase Ligase Semi-Conservative Replication

33. DNA replication--steps Step 1—helicase attaches to DNA Step 1—helicase attaches to DNA Step 2—helicase “unzips” hydrogen bonds between base pairs Step 2—helicase “unzips” hydrogen bonds between base pairs This causes double helix to “unwind” This causes double helix to “unwind”

34. DNA replication--steps Step 3—DNA polymerase forms new, complementary strand of DNA from free nucleotides Step 3—DNA polymerase forms new, complementary strand of DNA from free nucleotides Moves along entire length of DNA Moves along entire length of DNA

35. DNA Replication--Steps Step 3b—DNA ligase binds short stretches of new DNA on “lagging” strand Step 3b—DNA ligase binds short stretches of new DNA on “lagging” strand Okazaki fragments— short sequences of DNA on lagging strand Okazaki fragments— short sequences of DNA on lagging strand

36. DNA Replication--steps Step 4—helicase separates from DNA Step 4—helicase separates from DNA Two new strands now formed Two new strands now formed Sister chromatids!!! Sister chromatids!!!

39. Animations! Brief Replication Overview Brief Replication Overview Brief Replication Overview Brief Replication Overview Brief DNA Replication Brief DNA Replication Brief DNA Replication Brief DNA Replication Detailed DNA Replication Detailed DNA Replication Detailed DNA Replication Detailed DNA Replication

40. STAGES OF MITOSIS

42. MITOSIS Animation! Animation! Basic w/ narration Basic w/ narration Basic w/ narration Basic w/ narration Cell POV, no narration Cell POV, no narration Cell POV, no narration Cell POV, no narration

43. PROTEIN SYNTHESIS: From DNA to RNA to Protein

44. RNA Compared to DNA

45. TYPES OF RNA Ribosomal RNA (rRNA) Ribosomal RNA (rRNA) Messenger RNA (mRNA) Messenger RNA (mRNA) Transfer RNA (tRNA) Transfer RNA (tRNA)

46. Summary RNA Polymerase unravels part of the DNA strand RNA Polymerase unravels part of the DNA strand The polymerase creates a template based on a section of DNA. This is the mRNA. The polymerase creates a template based on a section of DNA. This is the mRNA. mRNA leaves the nucleus mRNA leaves the nucleus mRNA binds to ribosome mRNA binds to ribosome tRNA carries an amino acid (AA), matches to a section of the mRNA in the ribosome tRNA carries an amino acid (AA), matches to a section of the mRNA in the ribosome Another tRNA carries the next AA, the two AAs bond Another tRNA carries the next AA, the two AAs bond tRNA leaves tRNA leaves Subsequent AAs continue to bond, forming a peptide chain Subsequent AAs continue to bond, forming a peptide chain At the end of the sequence, the peptide breaks off into the cytoplasm, the ribosome releases the mRNA, and the mRNA breaks apart to be recycled. At the end of the sequence, the peptide breaks off into the cytoplasm, the ribosome releases the mRNA, and the mRNA breaks apart to be recycled.

48. Transcription “The process by which an mRNA template, carrying the sequence of the protein, is produced for the translation step from the genome.” “The process by which an mRNA template, carrying the sequence of the protein, is produced for the translation step from the genome.” Copying something to be read by someone else in another place. Copying something to be read by someone else in another place. In this case…copying the gene to be used as an instruction manual to make protein in another part of the cell. In this case…copying the gene to be used as an instruction manual to make protein in another part of the cell.

49. TRANSCRIPTION

50. Step by Step! Initiation Initiation RNA polymerase binds to a specific part of the DNA strand. This is the gene. RNA polymerase binds to a specific part of the DNA strand. This is the gene. Polymerase unravels this part of the strand, separating the base pairs. Polymerase unravels this part of the strand, separating the base pairs.

51. Elongation Elongation Polymerase begins to slide along the DNA Polymerase begins to slide along the DNA Ribonucleotides match to opposite base, then bond Ribonucleotides match to opposite base, then bond This creates a chain, which is the mRNA This creates a chain, which is the mRNA

52. Termination Termination Introns (unwanted parts) are “cut out” and removed Introns (unwanted parts) are “cut out” and removed Exons (coding parts) are fused together Exons (coding parts) are fused together A “cap” is put on the end of the mRNA for protection A “cap” is put on the end of the mRNA for protection

53. RNA PROCESSING

54. The bases in the introns are recycled. There are several hypothesis about the origin of introns. It has been suggested that some may have a function in the cell, before or after excision. The RNA comes off the DNA template which reforms a double-stranded DNA molecule The introns are removed. A typical human gene has 6 introns, but there may be hundreds; a few have none. A typical human intron is around 1 kb but it can be hundreds of kb. On average, introns are 10-20 times larger than exons. The exons are joined together, in sequence. The removal of introns and the joining of the exons occur concurrently and the process is known as “splicing”. It actually occurs while the RNA is still being synthesized. A poly A tail is added. The tail is usually around 150 Adenine bases; a few bases at the end of the RNA molecule are “trimmed”, before poly-adenylation. The tail is also required for the initiation of translation and stability. Capping, splicing and poly-adenylation are known as “RNA processing”. A cap is added to the RNA: The cap is necessary for the RNA to bind to the ribosome for translation to begin, and probably aids stability. “Capping” actually occurs immediately after RNA synthesis begins. Using the DNA template strand, RNA polymerase manufactures an RNA molecule (pre-mRNA) using the complementary base pair rules. In RNA, Uracil is complementary to Adenine in DNA. The DNA strand that acts as the template strand varies from gene to gene. In the region of the gene, the DNA unwinds and the 2 strands come apart. RNA polymerase, an enzyme, is the key molecule for the manufacture of RNA from DNA A gene: a sequence of double-stranded DNA. On average, a human gene is about 14kb (14,000 base pairs) but the size is highly variable. The dystrophin gene, encoding a muscle protein, has 2.4Mb (2.4 million base pairs). Typically, there is 75kb between human genes. Note the complementary base pair rules; A-T and G-C Transcription: making RNA from a DNA template. While an average human mRNA molecule has about 2,600 bases, the size is highly variable. Transcription C G C A U A A G C G A C U A G U C A C C C G C U A A GC C G C A U A A G C G A C U A G G C U U C A C C C G C U A A A A A A A A G A U U A U G C G C A U A U G C G A C U A G C U U C A C C C G C U A A G A U A U G C G A C U A G G A C C C G C U A A G C G C A U A U G C G C A U A A G C G A C U A G G C U U C A C C C G C U A A G A U C G A C U A G G A C C C G C U A A GU C A C C C G C U A A G C G C A T A A G C G A C T A G G C T T C A C C C G C T A A G A T C G A C U A G G A C C C G C U A A GU C A C C C G C U A A GC G C A U A U GC G C A U A A G C G A C U A G G C U U C A C C C G C U A A G A U DNA G C G T A T T C G C T G A T C C G A A G T G G G C G A T T C T A C G C A U A A G C G A C U A G G C U U C A C C C G C U A A G A UA U A U G C G A C U A G G A C C C G C U A A GC U U C A C C C G C U A A G A A A A A A mRNA C G C A T A A G C G A C T A G G C T T C A C C C G C T A A G A T G C G T A T T C G C T G A T C C G A A G T G G G C G A T T C T A C G C A T A T G C G A C T A G G C T T C A C C C G C T A A G A T G C G T A T T C G C T G A T C C G A A G T G G G C G A T T C T A

55. Translation “Protein translation involves the transfer of information from the mRNA into a peptide, composed of amino acids. This process is mediated by the ribosome, with the adaptation of the RNA sequence into amino acids mediated by transfer RNA.” “Protein translation involves the transfer of information from the mRNA into a peptide, composed of amino acids. This process is mediated by the ribosome, with the adaptation of the RNA sequence into amino acids mediated by transfer RNA.” Taking something in a language you can’t use, and making it into a language that you can use. Taking something in a language you can’t use, and making it into a language that you can use. In this case…taking the “language” of the DNA & mRNA, which the cell can’t directly use, and converting it into the “language” of proteins, which the cell can use. In this case…taking the “language” of the DNA & mRNA, which the cell can’t directly use, and converting it into the “language” of proteins, which the cell can use.

56. Step by Step! (Again) Ribosomes (two subunits) are in cytoplasm Ribosomes (two subunits) are in cytoplasm tRNA attaches to amino acids in cytoplasm tRNA attaches to amino acids in cytoplasm Ribosome binds to the beginning of the mRNA chain Ribosome binds to the beginning of the mRNA chain

57. Initiation Initiation Starts with a 3-base section of the template, a “codon”, specifically the “start codon” Starts with a 3-base section of the template, a “codon”, specifically the “start codon” tRNA with matching “anticodon” attaches tRNA with matching “anticodon” attaches Another tRNA matches to the next codon Another tRNA matches to the next codon Amino acids bond Amino acids bond

58. Elongation Elongation Ribosome moves down the mRNA one codon at a time Ribosome moves down the mRNA one codon at a time tRNA continues to match codon to anticodon, bringing more AAs tRNA continues to match codon to anticodon, bringing more AAs AAs bond, forming a lengthening chain AAs bond, forming a lengthening chain

59. G A UC C GU A C met G C U arg A A G phe U G G thr G C G arg C A U val U G C thr gly leu Stop C G C A U A U G C G A C U A G G C U U C A C C C G C U A A G mRNA Start Translation Polypeptide

60. Bring it all together…. Transcription Transcription Initiation Initiation Elongation Elongation Termination Termination Translation Translation Initiation Initiation Elongation Elongation Termination Termination

61. GENETIC CODE

62. SUMMARY OF PROTEIN SYNTHESIS