Chapter 5

Question 1

what is metabolism?

Answer 1

Metabolism
• The sum of all chemical reactions within an organism
• Includes exergonic and endergonic reactions
• Includes anabolic and catabolic reactions
• Includes oxidation and reduction reactions

Question 2

What is catabolism? What is an exergonic rxn?

Answer 2

Catabolism
• Reactions that breakdown larger molecules into smaller ones
• e.g., proteins into amino acids
• e.g, sugar into carbon dioxide and water
• Produce metabolites that serve as building blocks for larger molecules
• Characteristics:
• Most are hydrolytic (use water)
• Exergonic
o Energy stored in bonds of ATP, although most lost as heat (entropy)

Question 3

what is anabolism? what is an endergonic rxn?

Answer 3

Anabolism
• Reactions that synthesize large molecules from smalelr ones
• Carbon dioxide and water into sugars
• Amino acids into protein
• Characteristics:
• Involve dehydration synthesis (release water)
• Endergonic
o Require the input of ATP
o Which is produced during catabolic reactions

Question 4

what is the equation for total metabolism?

Answer 4

catabolic rxns + anabolic rxns = total metabolism

Question 5

what are redox reactions? is the electron acceptor reduced or oxidized?

Answer 5

Redox reactions
Many metabolic reactions are oxidation and reduction reactions
o involve the transfer of electrons
o Electrons carry energy, so this matters
o Redox rxns always occur simultaneously because an electron gained by one molecule is donated by another molecule.
o The electron acceptor is said to be reduced.
o The molecule that loses an electron is oxidized.

Question 6

what is reduction? what is oxidation? what is dehydrogenation?

Answer 6

• Reduction
o A chemical may be reduced by gaining either a simple electron or an electron that is part of a hydrogen atom
• Oxidation
o A molecule may be oxidized by losing an electron, losing a hydrogen atom, or gaining an oxygen atom
• Dehydrogenation—loss of a hydrogen atom—is typical is an oxidation rxn

Question 7

what is ATP?

Answer 7

ATP = Adenosine Tri-Phosphate
• The majority of energy in ATP is between the 2nd and 3rd phosphate; breaking the bond releases the energy and results in ADP
• However, can also break both bonds holding phosphates together (ATP—AMP)
• Think of ATP as an “energy carrier”
• The energy released from catabolic reactions is used to make ATP from ADP (called phosphorylation)
• Anabolic reactions use some of this energy by breaking a phosphate bond on ATP (thus becoming ADP again)
• This then takes us back to a catabolic rxn

Question 8

what is phosphorylation in ATP production?

Answer 8

ATP production

• Phosphorylation: the process by which phosphate (PO43- ) is added to a substrate

Question 9

in what 3 ways do cells phosphorylate ADP to ATP in 3 ways?

Answer 9

o Substrate-level phosphorylation describes the transfer of phosphate from a phosphorylated organic nutrient to ADP to form ATP.
• Occurs during glycolysis and Kreb
o Oxidative phosphorylation : energy from redox reactions of cellular respiration is used to attach inorganic phosphate to ADP
• Produces the majority of ATP during aerobic respiration
• Occurs in the inner membrane of mitochondria of eukaryotes and cell membrane of bacteria
o Photophosphorylation is the phosphorylation of ADP with inorganic phosphate using energy from light
• Occurs during the light dependent reactions of photosynthesis
• Occurs in chloroplasts of eukaryotes and cell membrane of bacteria

Question 10

what are enzymes?

Answer 10

Enzymes
• Most metabolic processes occur in a series of steps
o Called metabolic pathways
• Each step usually requires a specific enzyme
• Enzymes are organic catalysts
o Most are proteins
o Catalysts: speed up the rxn without being consumed by the rxn
• Enzymes work be lowering the activation energy
o EA = Activation Energy
o The energy required to kick-start a reaction
• Including exergonic reactions
o The energy required to disrupt electron configuration of molecules involved in a reaction
• Enzymes are extremely efficient
o can increase rate of reaction up to 108 to 1010 times
o without enzymes chemical reactions in your body would not be able to happen fast enough to sustain you

Question 11

Enzymes are often named for their ____?

Answer 11

named for substrates

Question 12

what is a substrate? what are the 6 categories of these chemicals? (hint: HLILPOT)

Answer 12

o Substrates are the chemicals enzymes cause to react.
o There are six categories of enzymes based on mode of action
o hydrolyses add hydrogen and hydroxide from the hydrolysis of water (catabolic)
o lyases split molecules without using water (catabolic)
o isomerases rearrange atoms in a molecule but do not add or remove anything
o ligases or polymerases join molecules together (anabolic)
o oxidoreductases oxidize or reduce molecules
o transferases transfer functional groups, such an amino group of phosphate group, between molecules

Question 13

are protein enzymes complete in themselves? what is an apoenzyme? what is a cofactor? what is a coenzyme? what is a holoenzyme?

Answer 13

• Many protein enzymes are complete in themselves.
• Other enzymes are composed of apoenzymes—a protein portion—and one or more nonprotein cofactors.
• Inorganic cofactors include ions such as iron, magnesium, zinc, or copper
• Organic cofactors (called coenzymes) are made from vitamins and include NAD+, NADP+, and FAD
• The combination of both apoenzyme and its cofactors is a holoenzyme
• The apoenzyme is not active until it is bound to its cofactor

Question 14

what is an active site on an enzyme?

Answer 14

• Active site: specific region of protein where substrate attaches to enzyme
o Induced fit model

Question 15

What creates enzymatic activity?

Answer 15

Enzyme Activity
• Enzyme + Substrate interact

• Enzyme-substrate complex formed
o Induced fit
• Bonds within substrate are broken, forming two or more products (catabolic rxn)
o Or in anabolic—2 reactants are linked to form product
• The enzyme dissociates from products
o No longer “induced fit”
• Enzyme resumes its original configuration
o Ready to function again

Question 16

what are some factors that influence enzyme activity?

Answer 16

• Since most are proteins, they may be denatured by physical and chemical factors such as
o temp (in human body 37 degrees C)
o pH
can be temporary or permanent
• Enzyme and substrate concentration can also affect activity
o Enzyme activity proceeds at a rate proportional to the concentration of substrate molecules until all the active sites on the enzymes are filled to saturation
o After that, need to increase enzyme concentration

Question 17

how can enzymes be activated/inhibited? What is allosteric activation/inhibition?

Answer 17

Factors influencing enzyme activity
• Enzymes can be activated/inhibited by the binding of a cofactor to the allosteric site
o A site away from the active site
• Allosteric activation: the binding of an activator (such as a cofactor) to the allosteric site results in a shape change to the active, essentially making it active (ready to receive substrate)
• Allosteric inhibition: an inhibitor attaches to an allosteric site on the enzyme, distorting the shape of the active site, making it unable to receive substrate

Question 18

what are inhibitors? What are competitive inhibitors, noncompetitive inhibitors, and feedback inhibition?

Answer 18

Inhibitors : substances that block enzyme activity
•Competitive inhibitors
o Competes with substrate for access to active site
o How can this type of inhibition be overcome?
•Noncompetitive inhibitors
o attach to an allosteric site on an enzyme, distorting the active site so that it no longer accepts the normal substrate
•Feedback inhibition (negative feedback)
o occurs when the final product of a series of reactions is an allosteric inhibitor of some previous step in the series.
o Thus, accumulation of the end product “feeds back” a stop signal to the process.

Question 19

what is carbohydrate catabolism? What are the 2 processes?

Answer 19

• Most organisms oxidize carbohydrates as primary energy source for anabolic reactions
• Usually Glucose
• However, lipids and proteins and other carbs can also be used
2 general processes:
•Cellular respiration: complete oxidation of glucose
o Can be both aerobic and anaerobic in bacteria

•Fermentation: partial breakdown of glucose
o Summary of glucose catabolism

Question 20

what is aerobic cellular respiration? what are the 4 steps? what kind of respiration can bacteria perform?

Answer 20

Equation: C6H12O6 + 6O2 —> 6H2O + 6CO2 + Energy

Includes the following stages:
•	Glycolysis (also fermentation)
•	Synthesis of Acetyl Co-A
•	Krebs Cycle
•	ETC/Chemiosmosis
•	Some bacterial species can perform anaerobic respiration

Question 21

what is step 1 of aerobic cellular respiration? where in the cell does this occur?

Answer 21

GLYCOLYSIS

Involves splitting of a six-carbon glucose into two three-carbon sugar molecules (called pyruvate or pyruvic acid)
• Also includes a net gain : 2 ATP molecules (via substrate-level phosphorylation), 2 molecules of NADH

Question 22

what is step 2 of aerobic cellular respiration?

Answer 22

SYNTH OF ACETYL-COA

• If oxygen is present (or other terminal electron acceptor…more on this later), moves on to Acetyl-CoA formation
• The synthesis of Acetyl-C0A
o Acetyl-CoA is formed when two carbons from pyruvic acid join coenzyme A.
• Results in
o 2 molecules Acetyl-CoA
o 2 molecules CO2 (decarboxylation)
o 2 molecules of NADH (electron carrier)
o *results are for every 2 molecules of pyruvic acid
• *results are for every 2 molecules of pyruvic acid
• Acetyl Co-A can now enter the Kreb Cycle

Question 23

what is step 3 of aerobic cellular respiration?

Answer 23

KREBS CYCLE

• A series of 8 enzymatic steps that transfers energy and electrons from acetyl-CoA to electron acceptors NAD+ and FAD
• Occurs in cytosol of prokaryotes and in matrix of mitochondria in eukaryotes
• Net gain of*:
o 2 ATP (via substate level phosphorylation)
o 4 CO2
o 6 NADH
o 2 FADH2
• *For every 2 molecules of Acetyl-CoA that enter the cycle

Question 24

what is step 4 of aerobic cellular respiration?

Answer 24

E- TRANSPORT AND CHEMIOSMOSIS

o This is where the most significant amount of ATP is produced

Electron Transport o	In this step, the NADH’s and FADH2 deliver electrons to the Electron Transport Chain (ETC) o	Located in the plasma membrane of  bacteria and mitochondrial membrane of eukaryotes o	The electron transport chain is a series of redox reactions that passes electrons from one membrane-bound carrier to another and then to a final electron acceptor.  o	Think of it as an exergonic fall of electrons o	The energy from these electrons is used to pump protons (H+) across the membrane  o	This establishes a proton gradient o	Also, ETC is where NAD+ gets recycled  o	When NADH delivers its electron to ETC, it becomes NAD+, which can go back to glycolysis and Krebs to pick up more electrons

Question 25

what are the 4 categories of carrier molecules in electron transport?

Answer 25

``` • Four categories of carrier molecules in the ETC o Flavoproteins o Ubiquinones o Metal-containing proteins o Cytochromes ```

Question 26

what does oxygen do in aerobic respiration? What does oxygen do in anaerobic respiration?

Answer 26

* aerobic respiration: oxygen serves as final electron acceptor * Bonds with H+ ions to form water, which clears out the chain for another oxygen •anaerobic respiration: molecule other than oxygen serves as final electron acceptor

Question 27

What is chemiosmosis (step 4 of aerobic cellular resp)? What is the protein channel called? How is ADP phosphorylated to ATP?

Answer 27

• This high level of protons on one side of the membrane has a proton motive force o They “want” to move back (into the bacteria) down their concentration gradient. • However, they need a protein channel to move thru o Called ATP Synthase • As the protons move down their concentration gradient thru ATP synthase, ADP is phosphorylated into ATP o via oxidative phosphorylation because proton gradient created by oxidation of components of ETC

Question 28

what is the total energy production from aerobic cellular resp? how many ATP in eukaryotes?

Answer 28

38 ATP •34 ATP during chemiosmosis o each NADH creates 3 ATP (10 NADH x 3) o each FADH2 creates 2 ATP (2 FADH2 x 2) • Plus 2 ATP from glycolysis and 2 from Krebs • A grand total of about 38 ATP from the entire process of aerobic cellular respiration o36 ATP in eukaryotes • because the NADH made in glycolysis have to be moved into the inner matrix; it costs 2 ATP to do this o Depends on amount of oxygen available • An oxygen shortage stops the flow down the ETC, reducing ATP yield o Depends on general efficiency of each step

Question 29

what is the Entner-Doudoroff (ED) pathway of metabolic diversity?

Answer 29

•Entner-Doudoroff (ED) pathway o Some bacteria substitute this pathway for the EMP pathway (glycolysis) o Discovered only in prokaryotes o ED pathway produces only one ATP, NADH, and NADPH.

Question 30

What is the pentose phosphate pathway of metabolic diversity?

Answer 30

•Pentose phosphate pathway o Alternative to glycolysis o Less energy efficient than glycolysis o Produces precursor metabolites and NADPH o Used to make DNA nucleotides, steroids, fatty acids

Question 31

What is anaerobic respiration? What is the ATP production compared to aerobic cellular resp or fermentation?

Answer 31

o Occurs among some prokaryotes o Occurs when something other than O2 serves as the final electron acceptor in the ETC o Examples • Some Pseudomonas and Bacillus use nitrate (NO3 -)and reduce it to N2 gas in a process called denitrification • Some bacteria use carbonate (CO3-2) and convert it to methane (CH4) in a process called menthanogenesis o NOT nearly as efficient as aerobic cellular resp. o NOT the same thing as fermentation o ATP yield: less than aerobic cellular resp but more than fermentation

Question 32

what is fermentation?

Answer 32

•Fermentation: partial breakdown of glucose to release energy using an organic molecule within the cell as the final electron acceptor • The essential function of fermentation is to regenerate NAD+ for use in glycolysis o Cells require constant source of NAD+ • Cells need a way to recycle NAD+ from NADH • NAD+ is an important electron acceptor during the oxidation of glucose • In aerobic cellular respiration, this is accomplished by the ETC • however, this requires oxygen • Fermentation pathways provide cells with source of NAD+ o when oxygen is not present, o or organisms lacks enzymes for the ETC o or the organism lacks the enzymes to tolerate oxygen (SOD, catalase, etc.) • Fermentation uses organic molecule within cell (usually pyruvate) as final electron accept o Thus reduces pyruvate to another molecule, such as lactic acid o Converts NADH back to NAD+ so that it can go back thru glycolysis o Net yield of fermentation is 2 ATP • Via substrate level phosphorylation during glycolysis

Question 33

what are 2 types of fermentation?

Answer 33

•Many types of fermentation ``` •Lactic acid fermentation o pyruvate --> lactic acid o occurs among Streptococcus and Lactobacillus o produces yogurt from milk o produces sauerkraut from cabbage o also causes food spoilage ``` •Alcohol fermentation o pyruvate --> ethanol + CO2 o occurs among yeasts (Saccharomyces) and some bacteria o used for beer brewing, wine making o baking bread (CO2 causes bread to rise, ethanol gives it aroma)

Question 34

how are lipids catabolized?

Answer 34

•Fats o Lipase breaks it down into glycerol and fatty acids, which enter the process at various stages o For example, fatty acids are catabolized by beta-oxidation reactions to form Ac

Question 35

how are proteins catabolized?

Answer 35

•Proteins o Bacteria secrete enzymes (proteases) that breakdown proteins into amino acids outside the cell wall o The amino acids cross the plasma membrane and are used to build larger proteins or are deaminated (conversion to other organic molecules) to substrates for the Krebs cycle

Question 36

what is the equation for photosynthesis? what kind of reaction is this? (anabolic or catabolic?) what are the 2 main rxn stages of photosynthesis?

Answer 36

Equation: 6CO2 + 6H2O + light energy —> C6H12O6 + 6 O2 • The conversion of light energy into chemical energy (stored in chemical bonds) • Organisms use light energy to convert inorganic CO2 into organic glucose • This is an anabolic reaction • Performed by cyanobacteria, algae, and green plants o all form the base of food webs o Without them…we would have no food! Takes place in two main stages: •light dependent reactions o Uses sunlight to synthesize the energy products (ATP and NADPH) for the light reaction; releases oxygen gas •light independent reactions o Calvin-Benson cycle o produces glucose from CO2

Question 37

in a light dependent reaction, what is a photosystem composed of, and what is at the center of it all? Regarding protons, how does this reaction go down?

Answer 37

•2 photosystems (I and II) o A photosystem contains a mix of chlorophyll, other pigments, within a protein matrix o A light harvesting complex contains a variety of pigments that absorb various wavelengths of visible light from the sun o Within a photosystem I, there is a reaction center chlorophyll • a special chlorophyll molecule which is excited by transferred energy absorbed by the light harvesting complex. o Excited electrons from the reaction center are captured by a primary electron acceptor of an electron transport chain o Protons are pumped across the membrane of the ETC and ATP is generated in a process called photophosphorylation

Question 38

what are the 2 kinds of photophosphorylation?

Answer 38

•Cyclic photophosphorylation o Electrons return to the original reaction center chlorophyll after passing down the electron transport chain. o PSI is only functioning o The resulting proton gradient produces ATP only •Noncyclic photophosphorylation o PS I and II work together to produce both ATP and NADPH (an electron carrier) o The electron flowing down the ETC from PSII to PSI is captured by the reaction center of PSI o Therefore, in noncyclic photophosphorylation, a cell must constantly replenish electrons to PS II. • In oxygenic organisms, the electrons come from H2O, and oxygen gas is released. • In anoxygenic organisms, the electrons come from inorganic compounds such as H2S.

Question 39

what are light independent reactions? ATP and NADHP are generated to produce what? What enzyme is involved? what kind of reaction is are light indp? what are the 3 steps?

Answer 39

Light-Independent Reactions • Also called Calvin-Benson Cycle • Do not require light directly • Use ATP and NADHP generated by light-dependent reactions to ultimately form glucose from carbon dioxide • Involves the enzyme rubisco o Most abundant enzyme in the world, but terribly inefficient • Endergonic reactions (requires energy) o Supplied by the light dependent reactions •Three steps o Fixation of CO2 (carbon fixation) o Reduction o Regeneration of RuBP

Question 40

What are the 3 steps of the C-B cycle?

Answer 40

The 3 steps of the C-B cycle •Carbon fixation o CO2 is reduced o Carbon dioxide joins with ribulose bisphosphate (RuBP) to form PGA; required enzyme rubisco o Basically, carbon dioxide, which is inorganic, gets incorporated (or “fixed”) into an organic molecule •Reduction o Of PGA by NADPH to form molecules of G3P •Regeneration o of RuBP from G3P to continue the cycle o Every once in awhile, a G3P is “spit” out of the cycle o 2 G3P’s form 1 glucose

Question 41

what is an anoygenic reaction and what performs this?

Answer 41

A variation on photosynthesis • Occurs among purple and green sulfur bacteria (anoxygenic) • Use H2S (hydrogen sulfide) rather than water during the light dependent reactions • do not produce O2

Question 42

what are amphibolic reactions? how is this different than anabolic reactions?

Answer 42

•Amphibolic reactions are metabolic reactions that can proceed toward catabolism or toward anabolism depending on the needs of the cell. o Examples: the biosynthesis of carbohydrates, lipids, amino acids, and nucleotides. * Because anabolic reactions are synthesis reactions, they require energy (ATP) and metabolites (precursors) * both of which are often the products of catabolic reactions.