Biology I G/T

1. Biology I G/T What you should know by the end of the course! Review for the Final/HSA

2. Question #1: Examine the following group of water molecules and answer the questions. a. What kind of bond is labeled A? b. What kind of bond is labeled B? c. Which bond(s) is/are weak and constantly break and reform. A → B → • Covalent • Hydrogen • Hydrogen

3. Question #2: Why is hydrogen bonding between water molecules important for life on earth? Include the following in your answer. • Use at least two properties of water. • Explain why the hydrogen bonding is necessary to give water these properties. • Explain why the property is necessary to life on earth. Answers on next two slides

4. Property Cohesive (sticks to self) & Adhesive (sticks to other things) due to H-bonding Unique Density Property Ice (solid form) is less dense than water (liquid) due to H-bonds forming as molecules slow down - keeping molecules more spread out) Why necessary to life on earth? 1a.Water can be transported against gravity in plants – allows plants to be the base of the foodweb 1b.Causes surface tension and provides for aquatic ecosystems 2. Ice floats allowing oceans and lakes to freeze from the top down allowing living things to live underneath Possible Answers

5. 3.Almost Universal Solvent (dissolves all polar and ionic cmpds.) due to water surrounding molecules and pulling them apart – partially neg. O is attracted to pos. and partially pos. H is attracted to neg. 4. High Specific Heat (can absorb or lose a lot of heat before temperature changes) – as heat is added, energy is used to break H bonds before molecules can move faster (temp. increase) 5. High Heat of Vaporization (takes longer to evaporate) since must break H bonds before can move fast enough to evap.) 3a. Allows salts, proteins, to be dissolved in cells, blood, sap 3b. Allows blood and sap to carry oxygen, nutrients, messengers 3b. Allows biological fluids to act as buffers 4. Maintains moderate temp. on Earth Helps maintain body temperature 5a. Cools body since molecules with highest energy (temp.) leave 5b. Cools aquatic ecosystems Possible Answers

6. Question #3: pH A. If the pH of a biological solution was changed from 7 to 5, does that mean there are more or less H+ in the solution and how many times more or less? Is it more acidic or basic? B. Why is the maintenance of pH in biological systems important? C. What maintains the correct pH and why? • A. 100 x more H+ (each pH unit is 10X) more acidic • If the pH changes from normal, proteins denature (unfold) into their primary structure and do not function therefore no enzymes would function and no chemical reactions could happen • Buffers – salt solutions made of positive and negative ion pairs that can bind up any excess H+ or OH-

7. Question #4: Basic Chemistry • What determines the reactivity of an atom (if it will chemically react with another atom and what will it bond with?) • What does polar mean? • List three biologically relevant bonds from strongest to weakest. Define each. • The # of electrons in the outer most energy level • A covalently bonded molecule in which some of the atoms are larger and pull on the electrons harder so that they are closer to the bigger atom. This causes part of the molecule to be partially positive and some partially negative – the larger atom has the electrons closer so it is the partially negative one. • Covalent (sharing electrons), ionic (transfer of electrons creating oppositely charged ions), hydrogen (weak attraction between two polar molecules)

8. Question 5: Recognition of Organic Monomers. • For the next four slides: • List the name of the monomer as it appears on the screen. • State what macromolecule category the monomer goes with. • State a major function of the macromolecule. • Explain how the structure matches the function. • Monosaccharide • Carbohydrates • Short term energy • Many C-H bonds storing energy gathered from the sun in photosynthesis and easy to release the energy due to it being polar and water soluble which makes it easy to transport to the mitochondria of every cell where there is an abundance of enzymes to break it down

9. A. List the name of the monomer as it appears on the screen. B. State what macromolecule category the monomer goes with. C. State a major function of the macromolecule. D. Explain how the structure matches the function. • Amino acid • Protein • Structure (Fibrous proteins), Globular Proteins - Enzymes, Messengers and Receptors, Protein Channels, Antibodies, Carriers, etc. • Fibrous – multiple polypeptides wound around each other – twisted rope stucture makes it very strong • Globular – specific shape like enzymes fitting active site to substrate to catalyze specific chemical reactions.

10. A. List the name of the monomer as it appears on the screen. B. State what macromolecule category the monomer goes with. C. State a major function of the macromolecule. D. Explain how the structure matches the function. • Nucleotide • Nucleic acid • Code for proteins, replicate • Can form an inforamtional code because - 4 different nitrogen bases that can be put in any order and are held in that order by the strong covalent bonds between the sugars and phosphates in the backbone. The order determines the order of amino acids and thus protein structure. Base pairing alllows it to always match the right 3 nucleotides to the right amino acid. • It can copy itself – base pairing ensures an ability to make an exact copy after separation of the two strands. The strands separate easily due to weak hydrogen bonds between the base pairs.

11. A. List the name of the monomer as it appears on the screen. B. State what macromolecule category the monomer goes with. C. State a major function of the macromolecule. D. Explain how the structure matches the function. • Fatty acid • Lipids • Long term energy storage, insulation, padding, phospholipids for cell membranes • Most C-H bonds of any organic molecule so more compact storable energy form. Not water soluble, hard to transport and mix with enzymes so can be stored for a long time, slow to break down.

12. Question 6: Protein Folding A. What folding level of structure(s) is functional for a protein? B. Where in the cell do proteins fold if they are secreted proteins? C. Why is protein shape so critical to living things? D. Give an example of a misshapen protein, it’s effect on the organism, and what caused the protein to be the wrong shape • Tertiary or quarternary • Rough Endoplasmic Reticulum • Protein shape governs the function of the proteins and proteins run everything in the body. If enzymes are misshapen then chemical reactions can’t happen; if messengers are misshapen, the cell can’t receive signals to tell it what to do etc. • Hemoglobin – causes sickle cell anemia – red blood cells can’t carry oxygen as effectively, cellular respiration slowed, lack of energy, clogging of capillaries due to shape of blood cells – caused by a single nucleotide change in the gene that codes for the hemoglobin protein

13. Question #7: General Enzymes • Why do living things need enzymes to do chemical reactions? • Why is it good that living things need enzymes to do chemical reactions? • How do enzymes lower the activation energy? Explain at the molecular level. • Body temperature cannot be too great so there isn’t enough activation energy to get chemical reactions to go so enzymes must lower the activation energy • If reactions could happen on their own (if body temperature provided enough activation energy) then there would be no control over any reactions, they would all just happen anywhere in the body all of the time. Since enzymes are needed, specific chemical reactions will only happen when and where the enzymes are located • For breaking chemical bonds – the induced fit strains the bonds making them weaker so that it doesn’t take as much energy to get the reaction to go and body temperature will be enough for the activation energy. • For making chemical bonds – it squeezes them tightly together so that its doesn’t take as much energy to form the bond

14. A. Label the following reaction with active site, enzyme, products, substrate, enzyme/substrate complex Question #8: Enzymatic Reactions `

15. Questions #9: How do things effect the rate of enzyme reactions? • How can you speed up an enzyme catalyzed reaction? • How does temperature effect the rate of enzyme catalyzed reactions and why? • How does the enzyme and substrate concentration effect the rate of enzyme reactions and why? • How does pH effect the rate of enzyme reactions and why? • Increase temp, amount of enzymes, amt. of substrates, decrease the space they’re in • Increases the rate of reactions due to increase enzyme/substrate collisions but after the optimal temperature is reached, the activity quickly goes to zero due to denaturation of enzymes • If you increase either the enzyme or the substrate concentration there will be more enzyme substrate collisions so increase rates of reaction – however it will level off at a certain point since there is only so much enzyme if you are increasing the substrate and only so much substrate if you are increasing the enzyme • If you change the pH from the normal pH of the enzyme then it denatures and you get no activity

16. Question #9 continued • What are two ways to increase substrate concentration? • Give two ways that the body uses to control enzymes so that chemical reactions happen at a certain time. • Increase the amount of substrate, decrease the space or volume of fluid the enzymes and substrates are in • Activate enzymes when needed that are inactive, turn on genes to make the enzyme needed, have certain areas of the body at different pH levels since enzymes only work at the right pH, make more enzymes to increase the enzyme concentration, feedback inhibition – the product inhibits an earlier enzyme in the enzymatic pathway so that as more product is made, the reaction goes slower

17. Question #10: Cells in General • Why must all living things be made of cells? Give the three major reasons. • Why must cells be microscopically tiny? • What is the major part of the cell membrane made out of and why? • What is the major function of all cells? • Living things need to made out of small compartments mostly because it is necessary to keep enzyme/substrate concentrations high enough to get chemical reactions to happen in a decent amount of time – in a bigger space, chemical reactions would be too slow. • Beside the speed of chemical reactions, speed of diffusion is way too slow unless the surface area/volume ratio is high and it is only in very small compartments, otherwise it would take too long to get nutrients. 2nd – speed of transport – slow (15 cm/day) but since cells are so small it only takes about 1 sec. to cross the cell • Phospholipids – cells live in a water environment and most of cytoplasm is water and lipids are the only organic molecule that doesn’t dissolve in water. • To make proteins which then carry out all of the cells functions – contracting in muscles, sending messengers to other cells, determining what chemical reactions that cell does, receiving messages to know what to do, etc, etc.

18. Question #11 Cell Membrane Parts On the drawing below are the parts of a cell membrane. Label each numbered part. Hint: there are three different types of protein channels, a receptor protein and a marker protein beside the main structure of the membrane 2 ↓ 3 ↓ 1 ↑ 8 ↑ 7 Phospholipid ↑ 5 ↑ 6 Phosphate ↑ 4 Marker Protein

19. Question #12 Methods to get in and out of cells • What process uses proteins channels, but uses no energy because specific molecules move from high to low concentration through the channel? Give a real life example. • What process is a way to get really large things into the cell? Give a real life example • How does Oxygen pass through the membrane? • What processes used protein channels to pump things from low to high concentration? Give an example. • Facilitated diffusion (type of passive transport) This is how most things get in and out of cells like glucose in, amino acids in, Na+ in, nucleotides in • Endocytosis – for things like cholesterol, all food in a single celled organism since they don’t have a digestive system to break down food into monomers, macrophages take in whole bacteria this way • Simple diffusion – right thru the phospholipid bilayer part • Active transport – muscle cells pump out Na+, ocean fish can pump salt out of their cells

20. See Methods Illustration Below

21. Question #13: Cell Organelles • State the name and function of each organelle as it pops up – be sure to give a detailed function! Label all three things! SER – makes phospholipids, in muscles cells it stores calcium, in liver cells it detoxifies drugs and alcohol Ribosomes – makes proteins – where the tRNA matches up the mRNA codons with the right amino acids RER – where completed protein folds and is modified and then sent to Golgi Golgi Apparatus Modifies and packages proteins for export from the cell Any proteins that need to go to a particular place need localization signals to tell them where to go Mitochondria Cellular Respiration, slowly breaks down organic molecules – usually sugar – to make ATP to supply useable energy to the cell

22. Question #14 Organelle Cont. • Label #1 and #2 – • State the function of #2 • What do the microfilaments and microtubules make up? • Give two functions of the microtubules. • Digest old worn out cell parts, in protozoa digests all foods since they don’t have a digestive system, macrophages use them to digest whole bacteria #1 • Cytoskeleton • Transport things around the inside of the cell and give the cell shape and structure – the shape of the cell ultimately determines the function of the cell since it influences which genes get read #2

23. Question 15: Still Organelles • How can you distinguish plant cells from animal cells? • What two organelles create turgor pressure and why is turgor important? • Why is the nucleus called the control center of the cell? • Plant cells have a large central vacuole, cell wall, chloroplasts, no centrioles, and usually no lysosomes where animal cells have many small vacuoles, no cell wall. remember that plants do have mitochondria – the chloroplasts make the sugar and the mitochondria breakdown the sugar to make ATP which is the useable form of energy • Cell wall and vacuole together to create the turgor – the vacuole fills with water and presses against the cytoskeleton which presses against the cell wall Tugor is important because plants don’t have bones and muscles and this makes them stand up to help the leaves be exposed to more sunlight • The nucleus contains, protects, and organizes the DNA which codes for proteins and proteins run the cell - if the DNA gets destroyed then the cell dies, the organization of the DNA determines what genes get read which controls what proteins are mdae in the cell, also provides a small space for enzyme/substrate concentration so that transcription and replication happen efficiently

24. Questions #16: Photosynthesis • What four things are needed for photosynthesis? • In what part of photosynthesis is each used? • What are the products of photosynthesis? • Carbon dioxide and water, chlorophyll and light • Water is used in the light reactions to replace the hydrogens that leave the chlorophyll with their high energy electrons. Light is used to energize the electrons on the H in chlorophyll, chlorophyll provides the H for the sugar, carbon dioxide ( provides the carbon and oxygen part of the sugar • Sugar and oxygen (biproduct)

25. Question #17: Cellular Respiration • What is needed for aerobic cellular respiration? • Why must cellular respiration take place in all living things? • What part of cellular respiration yields the most energy? • What are the products of CR and what molecule stores the energy at the end of CR? • What is produced during fermentation in yeast? • Where does the Kreb’s cycle happen? • Sugar, oxygen • If glucose was burned more quickly too much heat would be released causing proteins to denature • Electron transport chain (32 per glucose) • Carbon dioxide, water, and ATP – ATP • Alcohol and carbon dioxide • Mitochondrial matrix

26. Question #18: DNA Structure • Where are H bonds in DNA and why is it important that they are H? • Where are the covalent bonds and why is it important that they are covalent? • What part of the nucleotide is the coding part? Why? • What are the two functions of the DNA molecule? • Why is base pairing important to DNA carrying out both of it’s functions?

27. Question #19: Protein Synthesis • What is transcription and translation and where in the cell do each take place? • What is a codon and an anti-codon? • Given the following DNA sequence, give the mRNA, tRNA, and amino acid. TACGGCATCAAA • How does the RNA polymerase know where to begin transcription? • How does the ribosome know where to begin translation? • What happens during RNA processing. • What happens to the final protein if one nucleotide is mutated – please give three possibilities and explain why each would happen?

28. Question #20: Cell Cycle • What happens during S phase of the cell cycle and why does it need to happen? • Tell the difference between chromatin and chromosomes and when during the cell cycle you would find each. • What are the phases of mitosis and in general what happens in each? • When during the cell cycle is most of the protein synthesis happening? • What enzyme copies the DNA? • What enzyme opens the replication forks? • Draw a picture showing two replication forks at an origin of replication and show the leading and lagging strands.

29. Question #21: Meiosis vs. Mitosis • Happens in somatic cells • Happens in germ cells (tricky) • Has two divisions • Has 46 chromosomes lined up down the equator of the cell • Has chromosomes lined up in pairs down the equator of the cell • Makes haploid cells • Has daughter cells that are an exact replica of the original cell • Forms an embryo from a zygote • Happens only in the ovaries and testes

30. Question #22: Meiosis • What three ways bring about genetic variation through meiosis? • How does Mendel’s Law of Segregation relate to meiosis? • How does Mendel’s Law of Independent Assortment relate to meiosis? • What form is the DNA in during meiosis? • What is the purpose of meiosis?

31. Question #23: Genetics • A man with sickle cell anemia has a daughter will sickle cell? What are the chances that he and his wife will have a second child with sickle cell?