Semester 1 AP BIOLOGY REVIEW

1. Semester 1AP BIOLOGY REVIEW This is helpful for you to review semester 1. There is a power point handout that goes with this. Additionally, the following contains helpful resources: Your AP Packet (which you got last semester) An AP Review Book (so important!!) Remember your AP Mock is double weighted quiz on a square root curve. Highest grade between the two Mock tests counts.

2. Chemistry of Life • The main atoms of life: • hydrogen, carbon, nitrogen, and oxygen • What’s so great about carbon? • Makes four bonds! • H + O2 makes water. Water is essential because: • cohesion, adhesion, capillary action • high heat capacity (it can store a lot of heat!) • Remember: hydrogen bonds gives water it’s ability for almost everything. Hydrogen bonds is one water sticking to another water. • Water is created by a polar covalent bond

4. Bonds • Covalent – valence electrons are shared • Nonpolar – equal (O-O, H-H) • Polar – unequal; electronegativity (O-H) • Ionic – electrons not shared; electronegativity (NaCl) • Hydrogen – relatively weak; between hydrogen and oxygen/nitrogen of another molecule. • Van der Waals interactions – very weak; asymmetrical distribution of electrons

5. More Chemistry of Life • pH on a scale from 1-14 • Where is it acidic? Basic (alkaline)? • What is a buffer? • Carbonic Acid(H2CO3/Bicarbonate?) Functional Groups • Amino: -NH2 • Carboxyl: -COOH • Carbonyl: -C=O (aldehyde or ketone?) • Hydroxyl: -OH • Sulfhydrl: -SH • Phosphate: PO3 • Methyl: -CH3

6. H2O HO H HO H HO H Dehydration Synthesis Requires ENZYMES!!!!

7. Major Organic Molecules • Carbohydrates • (monosaccharide - glucose, fructose) • (disaccharide - sucrose…held by glycosidic bond) • (polysaccharides - storage like starch or structure like cellulose) • Ratio of 1:2:1 (CH2O) • Remember carbs are a great source of energy! • Glycosidic Linkages!

8. Major Organic Molecules • 2. Proteins (amino acids linked together by PEPTIDE bonds) • Primary- just the order • Secondary- influenced by H+ bonds • Tertiary- influenced by R groups • Quaternary- influenced by subunits of proteins binding together

9. Protein structure R groups hydrophobic interactions disulfide bridges (H & ionic bonds) Van der Waals 3° multiple polypeptides hydrophobic interactions 1° amino acid sequence peptide bonds 4° 2° determinedby DNA R groups H bonds

10. Major Organic Molecules Lipids • Consist of carbon, hydrogen, and oxygen but not the 1:2:1 ratio of carbs. • They have glycerol + fatty acids. • Lots of H+ = saturated. • Ester Linkages! Examples: fats, oils, phospholipids, and STEROIDS

11. Major Organic Molecules • Nucleic Acids • This includes DNA, RNA, and actually ATP. • Remember that DNA is double stranded and more stable than RNA. • Remember ATP is an energy molecule involved in energy requiring/making steps. It’s energy can easily be transferred to do cellular work.

13. Comparing Pro vs. Eu ONLY BACTERIA ARE PROKARYOTES!! Prokaryote: • no nucleus, no organelles, cell wall, ribosomes REVIEW ORGANELLE FUNCTIONS IN YOUR REVIEW BOOK! Plant Eukaryote: • square, has nucleus + organelles, ribosomes, large central vacuole, cell wall, chloroplasts, cell plate during mitosis Animal Eukaryote: • round, has nucleus + organelles, ribosomes, NO cell wall, many small vacuoles, lysosomes, centrioles, cleaveage furrow during mitosis

14. Junction, Junction…what’s your function?  Desmosome: holds adjacent animal cells together (like rivets) Gap Junction: in animal cells, allows communication between cytoplasm of adjacent cells Tight Junction: tight connection between membranes of animal cells Plasmodesmata: only in plant cells, it’s basically a gap junction in plant cells

15. Cellular Respiration

16. Let’s Vote! If you have these to pick from A) NAD+ B) NADP+ C) Oxygen D) FADH2 E) Cytochrome… could you name their functions?

17. Photosynthesis • Light dependent reactions make ATP, NADPH, and O2. • They occur in the thylakoids. • P680 - photosystem II, makes ATP + NADPH • P700 - photosystem I, makes ATP only… • if this is the only one that goes it’s called CYCLIC

18. Photosynthesis Light independent reaction (Calvin cycle) uses the ATP and NADPH + CO2 to make glucose. Remember rubisco (RuBP) fixes CO2 in the Calvin…unless it’s a C4 plant. Then it’s PEP. Photorespiration: BAD thing, it’s the fact that rubisco fixes O2 and CO2

19. C4 Pathway

20. light energy  CO2 + H2O + C6H12O6 + O2 sunlight Putting it all together H2O Plants make both: • energy • ATP & NADPH • sugars CO2 ADP NADP SugarBuilding Reactions Energy Building Reactions NADPH ATP sugars O2

21. Let’s Review DNA Replication!

22. Transcription Transcription is the process whereby a sequence of DNA is copied into a complementary sequence of mRNA.

23. During transcription, DNA is unwound and separated by an enzyme called RNA polymerase. RNA polymerase starts making the copy of RNA at specific sites in the DNA known as promoters. There are similar places in the DNA that also tell the RNA polymerase to stop. RNA polymerase uses one of the strands to copy the genetic information into a strand of RNA.

24. Some parts of the original DNA strand contained sequences of nucleotides called introns that are not involved in coding for proteins. These must be taken out of the newly made RNA strand. The remaining nucleotides that are involved in coding for proteins are called exons. Now it is ready to go as a mRNA molecule!

25. DNA is “read” by RNA and copied into a complementary strand. That strand tells the cell which amino acids to make. A string of amino acids is known as a protein. Different orders of amino acids make different proteins. mRNA

26. mRNA's instructions are called the genetic code. The genetic code is read three letters at a time, so each “word” is three bases long. Remember that the bases of RNA are A, U, C, and G; the “word” is written from these four letters. The mRNA “word” that is three bases long is called a codon. A codon is three consecutive nucleotides long and specifies a single amino acid.

27. TRANSLATION The order of amino acids is determined by the order of nucleotide bases in an mRNA molecule. The process of reading these nucleotides into a polypeptide chain (a protein made of amino acids) is called translation.

28. Steps in Translation 1. RNA is transcribed from DNA and released into the cytoplasm 2. mRNA attaches to a ribosome. 3. Each codon is “read” and an amino acid is brought INTO the ribosome by tRNA. a. The first amino acid to be read is called the “start” codon because it starts the process of translation. i. AUG: methionine b. Each amino acid has its own specific tRNA “carrier.” c. One end of each tRNA has a specific amino acid and the other end has three unpaired bases. These bases are called the anticodon, and are complementary to three bases on mRNA.

29. Translation Steps Cont. 4. The amino acid is strung together to make a protein inside the ribosome by forming a peptide bond between each amino acid and by being removed from the tRNA molecule. 5. This process continues until the ribosome reaches a stop codon on the mRNA molecule. This signals the process of translation to stop and a complete protein is now formed. a. There are three stop codons: UAA, UAG, and UGA

30. DONE!! Now, a protein (chain of amino acids) has been made by using transcription and translation.

31. Translation Animation! http://www.biostudio.com/demo_freeman_protein_synthesis.htm

32. Questions to Think About… Answer these with either transcription or translation… Which one should happen in the nucleus (if a eukaryote)? (think about this!) Which one makes mRNA? Which one directly makes protein? Which one occurs first? Which one requires RNA polymerase?

33. Molecular Genetics • Replication vs. Transcription vs. Translation…Think about where these are involved! • DNA polymerase • RNA polymerase • DNA ligase • Okazaki fragments • Restriction Enzyme • Reverse Transcriptase • Primer • Promoter • Helicase

34. Frequently Missed Genetic Words Epistasis (example: albinism) Pleiotrophy (example: siamese cat color and cross eyed) Polygenic Inheritance (example: skin) Complete Dominance vs. Incomplete Dominance vs. Multiple Alleles

35. Reproductive BarriersLeading to Speciation • Prezygotic Barriers • Postzygotic Barriers • Habitat Isolation • Temporal Isolation • Behavioral Isolation Mating • Mechanical Isolation • Gametic Isolation Fertilization • Reduced Hybrid viability • Reduced Hybrid fertility • Hybrid breakdown

36. 4% of a sheep population has black wool, 96% white. If black wool is recessive what % of the population is heterozygous? q2=.04 q = √.04= .2 1-q = p 1-.2= .8 So q= .2 p=.8 Substitute in 2pq 2 (.8) (.2) = .32 or 32%

37. 4% of a sheep population has black wool, 96% white. If black wool is recessive what % of the population is heterozygous? What % of the population is homozygous for white wool? Substitute in for p2 .82= .64 = 64%

38. Operons • In Prokaryotes • Region of a chromosome where a set of genes are transcribed at one time. • Allows all of the enzymes needed for a pathway to be present at once. • Two Types • Inducible are usually off but can be turned on. Like the lac operon.

40. In Prokaryotes… -DNA is circular -It is smaller that eukaryotic DNA -Less elaborately structured -And also, you should know, that it is loosely anchored by fiber that is anchored to the plasma membrane (and it’s not in a nucleus…there is no nucleus!)

41. But…in eukaryotes… -It is complex, with a large amount of protein to form chromatin -Highly extended and tangled in interphase -And then of course for mitosis it gets short, thick, “fat” and able to be seen visibly when stained

42. DNA Packing -You need to do it because there is an enormous amount of DNA -There are four levels you will be required to know. (This is similar to the primary, secondary, tertiary, and quaternary structure of a protein in a way…we’re starting out small and getting to the bigger picture) What are those four levels?

44. Lab REVIEWLab 1: Diffusion & Osmosis

45. Lab 1: Diffusion & Osmosis • Concepts • semi-permeable membrane • diffusion • osmosis • solutions • hypotonic • hypertonic • isotonic • water potential

46. Lab 1: Diffusion & Osmosis • Conclusions • water moves from high concentration of water (hypotonic=low solute) to low concentration of water (hypertonic=high solute) • solute concentration & size of molecule affect movement through semi-permeable membrane

47. Lab 1: Diffusion & Osmosis ESSAY 1992 A laboratory assistant prepared solutions of 0.8 M, 0.6 M, 0.4 M, and 0.2 M sucrose, but forgot to label them. After realizing the error, the assistant randomly labeled the flasks containing these four unknown solutions as flask A, flask B, flask C, and flask D. Design an experiment, based on the principles of diffusion and osmosis, that the assistant could use to determine which of the flasks contains each of the four unknown solutions. Include in your answer: • a description of how you would set up and perform the experiment; • the results you would expect from your experiment; and • an explanation of those results based on the principles involved. Be sure to clearly state the principles addressed in your discussion.

48. Lab 2: Enzyme Catalysis • Description • measured factors affecting enzyme activity • H2O2 H2O + O2 • measuredrate ofO2 production catalase

49. Lab 2: Enzyme Catalysis • Concepts • substrate • enzyme • enzyme structure • product • denaturation of protein • experimental design • rate of reactivity • reaction with enzyme vs. reaction without enzyme • optimum pH or temperature • test at various pH or temperature values

50. Lab 2: Enzyme Catalysis • Conclusions • enzyme reaction rate is affected by: • pH • temperature • substrate concentration • enzyme concentration calculate rate?