Bio 111 Janech Exam 2

What type of an organism is a yeast?

A yeast is a single celled fungi, used to make beer/wine and the CO2 rises bread in alcohol fermentation.

What is one big difference between making ATP in cellular respiration, and making it in photosynthesis?

ATP is made from sunlight into glucose in PS, and glucose to ATP in CR.

What happens in the citric acid cycle? How many times does this happen per glucose? Why is it a cycle? Where does it take place? What is the starting material that is regenerated?

Acetyl CoA bond with oxaloacetate to make Citrate, next 7 steps decompose citrate to oxaloacetate, making process a cycle. 2 times per one glucose, in the matrix of mitochondria. Regenerated; oxaloacetate

What is the final electron acceptor in aerobic cellular respiration? What is it reduced into that we find in the equation for cellular respir.? What happens to H+ during this process, and why do we care?

Aerobic- Oxygen is final e- acceptor. Reduced into H2O. H+ follow the e-, to form water.

What happens to all of the carbons in glucose? Where do they end up? At which stages? What about all of the energy?

All 6C's released as CO2, most energy still stored in NADH and FADH2.

Why is an electron transport chain important? What does it do? Why?

An ETC is a series of proteins that move e-, responsible for oxidation, they pass e- from 1 molecules to another in the chain, releasing energy from the redox reactions, which is used to move protons across the inner membrane of mitochondria.

What is an enzyme and how does it work? What is special about most enzyme names? Make sure that you know all of the parts involved and how it works. What does it do to the activation energy? How might temperature and pH affect an enzyme? What is "induced fit"?

An enzyme is a protein that functions as a catalysis, or speeds up chemical reactions. They have reactant molecules called substrates in active sites (cavities). End in -ase. Enzymes lower activation energy (which increases the rate of the reaction). Temp affects the folding and movement of an enzyme, pH affects carboxyl and amino groups and also active sites ability to participate in reactions that involve the transfer of protons or electrons. An induced fit is a model proposing that an enzymes active site is constantly changing shape until interactions with a substrate.

Why do we say that glycolysis is evolutionarily significant?

Because is does not require oxygen, occurs in cytosol (does not require organelles), and occurs in nearly all organisms.

What is the basic, general formula for cellular respiration (products and reactants)? What is being oxidized and what is being reduced? What do each of those terms mean?

C6H12O6+ 6O2 —> 6CO2+ 6H2O+ energy (heat) glucose oxidized to 6CO2; oxygen reduced to water

Why do carbohydrates have such high free energy? What type of a reaction is photosynthesis? What does this mean?

Carbohydrates have high free energy because they store energy in photosynthesis. Photosynthesis is an endergonic reaction. This means that it starts with lower energy reactants and ends up with higher energy products and it needs energy to happen.

What are the 4 stages of cellular respiration and what is happening during each? Where do they take place? CAN YOUR DRAW AND DESCRIBE THEM FROM MEMORY?

Cellular Respiration: 1. Glycolysis; 6C glucose broken into 2 pyruvate molecules (3C), ATP produced from ADP + Pi, NAD+ reduced to NADH. In cytoplasm of euk and prok. 2. Pyruvate Processing; pyruvate processed to release one CO2 molecule, remaining 2 C's used to form acetyl CoA. Oxidation of pyruvate results in more NAD+ reduced to NADH. Matrix of mitochondria (prok). 3. Citric Acid Cycle; Acetyl CoA oxidized to 2CO2, more ATP and NADH produced, FAD reduced to FADH2. Matrix of mitochondria (prok). 4. ET and Oxidative Phosphorylation; e- from NADH and FADH2 move through electron transport chain. Energy creates proton gradient across membrane used to make lots of ATP and makes H2O. Inner membrane of mitochondria or plasma membrane of prok.

Think big picture, as well as details, for both respiration and photosynthesis - what is being oxidized or reduced at different steps? What does this mean?

Cellular Respiration: 1. Glycolysis; NAD+ reduced to NADH 2. Pyruvate Processing; oxidation of pyruvate results in NAD+ reduced to NADH 3. Citric Acid Cycle; CoA oxidized to 2CO2, FAD reduced to FADH2 4. ETC and oxidative phosphorylation; oxidized NADH and FADH2 to NAD+ and FAD Photosynthesis: CO2 reduced to C6H12O6, H2O oxidized to O2

What type of a reaction is cellular respiration? What does this mean?

Cellular respiration is an exergonic reaction. It starts with higher energy reactants and ends up with lower energy products and it releases energy.

What are the different types of carbohydrates and what are some of their distinguishing features? What is a general chemical formula for a carbohydrate? How might you recognize the name of one?

Cellulose- structure (in plant cell walls) Starch- energy storage in plant cells Glycosidic Linkages are the bond. General Chemical Formula: CH2O (1:2:1 ratio) -ose ending.

What are similarities and differences between RNA and DNA? What are Chargaff's rules?

DNA contains thymine, deoxyribose (has one less oxygen), and is less polar. RNA contains Uracile, ribose (extra oxygen), and is more reactive because it is polar. (OH on 2' C). Chargaff's Rules; 1) The total number of purines = the total number of pyrimidines in DNA. 2) The total number of adenines = the total number of thymines, and the total number of guanines = the total number of cytosines.

What are some attributes of DNA's 2° structure? Basically, how does DNA replicate?

DNA- 2 antiparallel strands, double helix, hydrogen bonds form between G-C and A-T pairs, backbone is hydrophilic. RNA replicate: 1). Strand Separation- DNA strands separate when H bonds between complimentary base pairs are broke . 2). Base pairing with Template- each new strand created in 5' to 3' direction. 3). Polymerization- the original molecule has been copied.

What are the differences between the two types of muscle fibers? Under which circumstances would you want to have each? How does substrate-level phosphorylation factor into all of this?

Dark muscle fibers store more O2 for aerobic respiration, lots of mitochondria, for endurance. fast twitch. Light muscle fibers only use lactic acid fermentation to make ATP, for sprinting. Slow twitch.

What happens to each pyruvate before it heads into the citric acid cycle? How many times does this happen per glucose?

Each pyruvate converted to acetyl CoA (oxidized C to CO2, NAD+ to NADH, CoA- SH in). This happens 2 times per glucose.

For glycolysis specifically, what are the two major phases? What does this mean? Why is the third enzyme, phosphofructokinase, so important in the process? What happens if the cell already has plenty of ATP? What happens if the cell needs to make more ATP?

Energy investment (enzymes 1-6)/payoff (enzymes 7-10) phase. It must put in a little energy to get a lot out. Phosphofructokinase (3rd enzyme) is the point of no return. If the cell has plenty of ATP, either allosteric inhibition or feedback inhibition occurs. If it needs more, glycolysis proceeds.

What is energy? What is the relationship between potential and kinetic energy?

Energy is capacity to do work or supply heat. Potential energy is resting, an e- in an outer shell. Kinetic is in active motion, an e- falling to a lower energy shell, light or heat.

How does ATP work into all of this?

Energy is released when ATP is hydrolyzed in exergonic, and reversed for endergonic.

How is a fat constructed? How about a steroid and a phospholipid? Why is it significant that phospholipids are amphipathic?

Fats- 3 fatty acids linked to a glycerol by ester linkage Steroids- four carbon rings, differ by side groups attached to carbons Phospholipids- glycerol + phosphate group (polar) + 2 fatty acid tails (non polar) joined by ester linkages. Phospholipids are responsible for the plasma membrane, so its good they're amphipathic because they can move through membrane easily.

What are the types of lipids, and what are their characteristics?

Fats- more energy, non polar Steroids- hormones, amphipathic Phospholipids- hydrophilic head, hydrophobic tail Isoprene- 5 Carbon compound, consists of C atoms bonded to H atoms, can be linked to each other to form load hydrocarbon chains called isoprenoids.

How does feedback inhibition work? What is substrate-level phosphorylation?

Feedback inhibition, when there is an abundance of ATP (and is also the end product) tells the enzyme to slow down/stop the reaction rate. Substrate- level phosphorylation is the production of ATP from ADP + Pi.

What are the names and contributions of the people who were involved in elucidating the 2° structure of DNA? How does this demonstrate both collaboration and competition?

Franklin and Wilkins measure DNA using X- ray crystallography. Watson and Crick discovered double helix from Franklin's pictures. Franklin got no credit while Watson, Crick, and Wilkins won the Noble Peace Prize.

What do cellular respiration and fermentation processes have in common? How are they different?

Glycolysis, oxidize NADH, regenerate NAD+. Fermentation is anarobic, produces only 2 ATP.

What are the net yields of each step in respiration?

Glycolysis- 2 ATP, 2 NADH Pyruvate Processing- 2 NADH, 2 CO2 Citric Acid Cycle- 2 ATP, 6 NADH, 2 FADH2 Etc and Op- 25 ATP

What is glycoprotein (great example of an oligosaccharide) and what does it do?

Glycoprotein is a protein with one or more carbohydrates covalently bonded to it (oligosaccharides)

How do cells communicate over long distances? What are the different sequences of events, depending on whether the communicating molecule is hydrophilic or hydrophobic?

Hormones; Hydrophobic- 1. Signal arrives and diffuses 2. Signal receptor with conformational change 3. Direct signal response by changing DNA expression Hydrophilic- 1.Signal receptor 2. Signal transduction (conversion) often assisted by G proteins 3. Signal amplification 4. Signal response by changing DNA expression

What role does feedback inhibition play in the citric acid cycle?

It can shut down the CAC when ATP is abundant.

What does a phospholipid bilayer look like, and how does this work as a cell membrane?

It looks like 8=8 (sideways). The phospholipid bilayer is amphipathic. The heads (8) are hydrophilic, and the hydrocarbon tails are hydrophobic (=).

What are the major differences between the processes and products of the two types of fermentation?

Lactic Acid Fermentation- humans, no intermediate steps, pyruvate accepts e- from NADH (oxidized), produces 3 lactate. Alcohol Fermentation- yeast, 2 CO2 added to pyruvate to form 2 acetylaldehyde, produces 2 ethanol. Pyruvate is not reduced!

What is an N-terminus, and what is a C-terminus? How would you be able to recognize them?

N-terminus is the beginning of a polypeptide chain. C-terminus ends the chain.

How do NAD+ and NADH relate to each other? What are the net results of glycolysis?

NAD+ is the oxidized form of NADH (2 e-). Net results of glycolysis is 2 NADH, 2 ATP, and 2 3C pyruvate for every glucose.

What would be a final electron acceptor for an anaerobe to complete respiration?

Nitrate or Sulfate (can't be Oxygen!)

What is so important about the last stage of cellular respiration? (Another way to think about it - what would be missing if it were not completed properly?) What is meant by oxidative phosphorylation?

OXYGEN is produced! Oxidative phosphorylation is the production of ATP molecules by ATP synthase using the proton gradient established via redox reactions of an electron transport chain (NADH and FADH2).

Why is fermentation good for meeting all of a small organisms' energy needs, but not for big organisms?

Only 2 ATP are produced from lactic acid fermentation.

How can many of our cells function as facultative anaerobes? What is an obligate anaerobe?

Our cells function as facultative anaerobes (can live without O2 temporarily) by fermentation. An obligate anaerobe can not survive in the presence of O2.

How does this enzyme specifically exemplify the concept of an enzyme having an allosteric inhibitor?

Phosphofructokinase speeds up reaction when ATP binds but if ATP binds but if ATP binds somewhere other than the active site, process shuts off.

What are the 4 levels of protein structure and what happens in each? What happens in the primary structure of a person with HbS, and how does this affect their red blood cells? Why?

Primary- unique sequence of amino acids in a protein. Peptide Bonds join polymers. Secondary- H-bonds can form in same chain, forming secondary could and folds (alpha- helices or beta- pleated sheets). Tertiary- structure is determined by the interactions between the side chains on amino acids including H bonds, hydrophobic interactions. Quaternary- 2 or more polypeptide chains from one macromolecule. Proteins to fold just right.

Why is is significant that proteins may be amphipathic? What does this have to do with amino acids?

Proteins that are amphipathic are both hydrophilic and hydrophobic. They can go through the phospholipid bilayer.

What are the chemical reactions which link monomers (and which link fatty acids to glycerols) called? Be sure to know what type of bond results from each of these reactions in each category of macromolecule.

Proteins- peptide bond; Nucleic Acids- phosphodiester linkages (H bond between base pairs); Carbohydrates- glycosidic linkages Dehydration Synthesis: monomers joined by condensation reactions (active) Hydrolysis breaks polymers into monomers (passive)

Be sure to know the specific monomers for proteins, nucleic acids, and carbohydrates, and their corresponding polymers.

Proteins: monomer- amino acids polymer- polypeptide Nucleic Acids: monomer- nucleotide polymer- nucleic acids Carbohydrates: monomer- monosaccarides polymer- polysaccharides

What is Q, and how it is important? What is it similar to in photosynthesis?

Q is Ubiquinone, aka Coenzyme Q, lipid soluble and move efficiently throughout hydrophobic interior of inner mitochondrial membrane. Move electrons between complex 1 & 2 to 3. Similar to PQ

What roles do RNA and DNA play? What makes pyrimidines different than purines? Be sure to know the examples of each. How do they pair with each other? Why is this significant in the structure of DNA? How many H bonds are involved in each base pairing? What is significant about the 5' and 3' ends of a DNA molecule? Why is DNA "read' in this direction? How does antiparallel relate to all of this?

RNA makes proteins, DNA determines the primary structure of the proteins. Purines are six- membered ring + five- membered ring (guanine, adenine). Pyrimidines are a single six- membered ring (cytosine, uracil, thymine). Pairs: A-T(U) (U in RNA, T in DNA)———— G-C (3 H-bonds) are equal and numbers of A&T(U) (2 H- bonds) are equal.

What does RNA's 2° structure look like? Why might this have been the first life form?

RNA- results from complimentary base pairing w/ bases on the same strand by H bonds. Folds in stem and loop hairpin structure. First form because RNA can make its own protein and replicate itself.

What is a reducing agent? What is an oxidizing agent? Make sure that you keep ALL of your vocab. straight!

Reducing agent is the e- donor, being oxidized (losing e) Oxidizing agent is the e- acceptor, being reduced (gain e)

What is a redox reaction? How can you remember which part is which? What are examples of coenzymes that function as electron acceptors? You should be very familiar with 3 of them. How do they work? What also comes along, when an electron is donated or accepted?

Reduction-oxidation reactions involve the loss or gain of e-. Coenzymes include FAD (flavin adenine dinucleotide), NAD+ (nicotinamide adenine dinucleotide), NADP+ (nicotinamide adenine dinucleotide phosphate). They attract electrons and a H+ follows (reduction), turn into FADH2, NADH, NADPH.

What does it mean that cell membranes are selectively permeable? How does this relate to unsaturated and saturated fats? Which has more chemical energy? What is a trans fat?

Selectively Permeable means that some substances cross a membrane more easily than others. Small non polar are quick, large/charged are slow, if at all. Short and unsaturated hydrocarbon tails = higher permeability and fluidity because it is spread out. Long and saturated hydrocarbon tails = lower permeability because they are packed closer together. A trans fat is an artificial unsaturated fat.

What other molecules work with enzymes, and what type of regulation are enzymes subjected to? How does each work?

Some enzymes work with inorganic metal ions. Others need organic coenzymes (NADH, FADH2) Regulation includes: 1. Competitive inhibition- directly blocks the active site so enzymes can't work. 2. Allosteric Regulation 2 types (allosteric inhibition & allosteric activation): regulatory molecule binds at a different site, changing shape of enzyme, making the active site either unavailable (inhibition) or available (activation).

What are the types of storage polysaccharides in plants and animals, and how does their structure relate to their function? How about with structural polysaccharides in plants, animals, fungi and bacteria? How does this affect how bacteria react to antibiotics? What are some special things about cellulose in particular?

Storage: Starch- energy storage in plant cells Glycogen- energy storage in animal cells Structural: Cellulose- structural support in cell walls of plants and algae (most abundant chemical compound on earth) Chitin- structural support in cell walls of fungi and external skeletons of insects and crustaceans Peptidoglycan- structural support in bacterial cell walls Gram positive cells have a thick cell wall and stain purple and respond to antibiotics. Gram negative cells have a thin cell wall, stain pink, and are more likely to be poisoned. Cellulose is a linear molecule held together by multiple H- bonds.

How does the structure of a protein lead to its function? Why it is a bad thing when a protein becomes denatured? What is a prion? How do they occur and what do they do? What was the name of the scientist who did a lot of the work to figure this out?

The order in which the amino acids are formed determines function, in the primary level. The proteins are then either formed into a alpha-helix or a beta-pleated sheet. Proteins have to fold just right! Denaturation is caused by heat, pH, salt, solvents, and these make the proteins unfold & unable to function. A prion is a protein folded into an infectious, disease causing agent. Normally cause spongiform encephalopathies, sponge-brain-illness (Mad Cow Disease). Stanley Prusiner discovered this.

How can prokaryotes perform cellular respiration if they do not have mitochondria?

They have ETC and ATP synthase in the cell membrane.

Why do fatty acids have more free energy than carbohydrates?

They have more C - H bonds.

How efficient is respiration? How do some poisons affect this process?

Very efficient 60/40 (compared to our cars 25/75); Rotenone, cyanide, carbon monoxide; break up flow of e-

What does ∆G stand for? What are endergonic and exergonic reactions, and how do they relate to ∆G? How can cells use the energy given off by one, to help the one that needs energy to occur?

∆G stands for the change in Gibbs Free Energy. Endergonic- non spontaneous reactions, needs energy, when ∆G is greater than 0. reduction (gain of e-). Exergonic- spontaneous reactions, releases energy, when ∆G is less than 0. oxidation (loss of e-).