Metabolism (and gene control lol)

Question 1

Define Metabolism

Answer 1

the sum of all catabolic (breakdown) and anabolic (build up) reactions in a cell or organism

Question 2

What are the differences between exergonic and endergonic reactions?

Answer 2

exergonic: energy is released
e.g. Combustion, bioluminescence, cell respiration

endergonic: energy is absorbed
e.g. photosynthesis

Question 3

What are the differences between anabolic and catabolic reactions?

Answer 3

Anabolic: uses energy to build large molecules from smaller molecules

Catabolic: release energy in the process of breaking down components into smaller molecules

Question 4

Where is the site for photosynthesis?

Answer 4

chloroplasts or folds in the cell membrane

Question 5

What is the first stage of photosynthesis?

Answer 5

-capturing light energy; occurs in the thylakoid membrane

Question 6

What is stage 2 of photosynthesis?

Answer 6

-light energy makes ATP + NADPH + H+; occurs in thylakoid membrane
-NADPH is a high energy intermediate
-the reduction of NADP+ is an endergonic and anabolic reaction
-2 H + NADP+ –> NADPH + H+

Question 7

What is stage 3 of photosynthesis?

Answer 7

-using ATP+NADPH+H+ to synthesize organic compounds (glucose) from CO2; process called Calvin cycle; occurs in stroma

6CO2 + 6H2O + light energy —> C6H12O6 + 6O2

Question 8

Describe Light energy

Answer 8

-light energy travels in wave packets called photons
-visible light has a wavelength of 380 nm to 750 nm

Question 9

Describe the photosynthetic pigments in plants

Answer 9

-clusters of photosynthetic pigments embedded in the thylakoid membrane absorb photons of a particular wavelength
-pigments are clustered in groups called photosystem

Question 10

What are photosystems?

Answer 10

pigments clustered in groups that are embedded in the thylakoid membrane
–> absorb photons of specific wavelength

Question 11

Describe chlorophyll

Answer 11

-has phytol tail/chain (hydrophobic) and porphyrin ring (hydrophilic head)

-absorb all wavelengths accept for green (is reflected)
–> in fall, chlorophyll is no longer produced and is broken down

Question 12

What does light do to chlorophyll?

Answer 12

photoexcitation

• electron are normally stable in their “ground state”, the lowest possible energy level
  -when a photon strikes a chlorophyll molecule, the electrons have energy added to them and are in a state of ‘excitation’
  -an excited electron has more energy than one in a ground state, but it will return to the ground state in 1 billionth of a second —-> when the electron returns to the ground state, it releases energy (heat and light) –> however instead of being released, they are captured by primary electron acceptor (chlorophyll is oxidized)

Question 13

describe photosystems in algae and plants

Answer 13

-both contain photosystems I and II
-II contains chlorophyll P680, enough energy to break water (photolysis)
-photosystem I contains P700
-are used to produce ATP and NADPH + H+

Question 14

Describe photolysis

Answer 14

-the Z protein (in thylakoid space) uses energy from light to split H2O
-2 electron are given to photosystem II
-2 H+ are released in thylakoid space and create electrochemical gradient
-O2 leaves chloroplast as waste

Question 15

Describe Chemiosmosis

Answer 15

-once the electrochemical gradient of H+ is formed, the H+ move down the concentration gradient
-H+ cannot diffuse across the membrane, so it instead uses ATP synthase to move from the thylakoid space to the stroma
-this movement down the concentration gradient causes the phosphorylation of ADP to ATP

Question 16

What are the differences between cyclic and non-cyclic phosphorylation

Answer 16

-cyclic phosphorylation makes some ATP for glucose synthesis and some ATP for other purposes
-only photosystem I is involved
-electrons from P700 are excited but eventually return to P700 (H2O and NADP reductase are not involved)
-b6-f complex still pumps hydrogen across the thylakoid membrane to create the electrochemical gradient needed to make ATP

Question 17

What is the purpose of the Calvin Cycle?

Answer 17

-Turns carbon dioxide from the air into glucose for various usages

Question 18

Where does the Calvin Cycle occur?

Answer 18

occurs in the stroma

Question 19

What’s the first phase of the Calvin Cycle?

Answer 19

Carbon fixation
-a CO2 is added to a 5-c RuBP to form 6-C intermediate–> splits into two 3-c molecules of PGA
-rubisco is involved (enzyme)
6(5-C RuBP) + 6CO2 –> 12(3-C PGA)`

Question 20

What is the second phase of the Carbon Cycle

Answer 20

Reduction reactions
-PGA is phosphorylated to (BPG) using ATP
-BPG is reduced to G3P by NADPH+H
-it takes 2 molecules of G3P to create glucose –> 1 molecule of G3P for every 5 G3P leaves the cycle

Question 21

What’s the third phase of the Calvin Cycle

Answer 21

RuBP regeneration
-5 molecules of 3-C G3P are converted into 3 molecules of 5-C RuBP
-2 Pi are removed and 3 ATP are consumed, 2 H2O must be added for the H and OH groups to add to the molecules

Question 22

What is the overall equation of the Calvin Cycle

Answer 22

3CO2 + 9ATP + 6(NADPH+H+) + 5H2O + 3RUBP –> 9ADP + 8Pi + 6NADP+ + G3P + 3RuBP

Question 23

What is photorespiration?

Answer 23

-When it is hot and dry, stromata closes to reduce water loss due to transpiration
- [CO2] leaves and [O2] increases
-oxygen binds to rubisco thus decreasing the production of carbs –> photorespiration is bad

Question 24

What is the overall equation of cellular respiration?

Answer 24

C6H12O6 + 6O2 –> 6CO2 + 6H2O + energy (ATP and heat)

Question 25

What is the purpose of Cellular respiration?

Answer 25

To convert energy trapped within glucose to energy available to do work in a cell in the form of ATP

Question 26

What is the order of the steps of cellular respiration

Answer 26

1. Glycolysis 2. Pyruvate oxidation 3. Kreb's cycle 4. electron transport chain and chemiosmosis

Question 27

Where does glycolysis occur?

Answer 27

Cytoplasm

Question 28

Where does pyruvate oxidation occur?

Answer 28

mitochondrial matrix

Question 29

Where does the Krebs Cycle occur?

Answer 29

mitochondrial matrix

Question 30

Where does the electron transport chain/chemiosmosis occur?

Answer 30

inner mitochondrial membrane

Question 31

State a summary of glycolysis

Answer 31

-glucose is broken down into 2 molecules of pyruvate -in order to break down glucose, it is first destabilized by the addition of 2 Pi from the addition of 2 ATP -Once the destabilized molecule breaks in half, it released enough energy to replace the 2 ATP and make an additional 2 ATP -NADH + H+ is also produced

Question 32

What is the overall reaction of Glycolysis? It's net energy?

Answer 32

glucose + 2 ATP + 2 ADP + 2Pi + NAD+ --> 2 pyruvate + 4 ATP + 2(NADH+H+) + H2O net energy = 2 ATP (used immediately) and 2 NADH (processed to obtain more ATP) --> overall 2 ATP is created

Question 33

What are the enzymes used in order (look at diagram to help)

Answer 33

phosphorylase, isomerase, phosphorylase, isomerase, dehydrogenase and phosphorylase (at the same time, phosphorylase, isomerase, dehydrase, phosphorylase

Question 34

Give summary of Pyruvate Oxidation

Answer 34

-only occurs in the presence of oxygen even though oxygen is not a substrate -If ATP levels are low, acetyl-CoA goes into krebs cycle to produce more ATP -if high, it goes to produce lipids

Question 35

What is the equation for pyruvate oxidation

Answer 35

pyruvate + NAD+ + CoA-SH --> acetyl-CoA + NADH + H+ + CO2

Question 36

Summarize the Krebs cycle

Answer 36

-only occurs if oxygen is present -oxaloacetate is a reactant and a product (cyclical) -the equation of krebs cycle is doubled as 2 acetyl-CoA molecules are produced per molecule of glucose.

Question 37

What is the purpose of pyruvate oxidation?

Answer 37

main purpose of pyruvate oxidation is to oxidize pyruvate to create the acetyl-CoA needed to be the intermediate of the Kreb's cycle.

Question 38

What's the equation of the Kreb's cycle?

Answer 38

oxaloacetate + acetyl-CoA + 3NAD+ + FAD + H2O + ADP + Pi ---> 2CO2 + 3NADH + 3H+ + FADH2 + CoASH + ATP + oxaloacetate (doubled)

Question 39

What's the purpose of the krebs cycle?

Answer 39

-produces energy -transfers high energy electrons to the ETC to then create the energy substrates needed for the krebs cycle

Question 40

Name the order of the enzymes used in the krebs cycle

Answer 40

hydrase, isomerase, dehydrogenase and decarboxylase (both at the same time), dehydrogenase and decarboxylase once more, phosphorylase, dehydrogenase, hydrase, dehydrogenase

Question 41

Provide an overview of the Electron Transport Chain

Answer 41

- a series of oxidation-reduction reactions convert the stored energy in NADH + H+ and FADH2 indirectly into ATP -the process involves moving electrons between proteins within the membrane which results in the movement of protons across the membrane

Question 42

What are the sources of FADH2 and NADH + H+

Answer 42

Krebs cycle in mitochondrial matrix = 6(NADH + H+), 2FADH2 pyruvate oxidation in mitochondrial matrix = 2(NADH+ H ) glycolysis in cytoplasm = 2(NADH + H+)

Question 43

what happens on the membrane, when NADH + H cannot pass through the membrane into the matrix?

Answer 43

energy stored in NAHD can be passed across the membrane with the electrons to a molecule of FADH2

Question 44

Go through the process of ETC (use diagram to help!)

Answer 44

NADH dehydrogenase: accepts 2 efrom NADH + H+ and passes them onto protein Q, 2H+ (p+) follow the e- and pass through the inner membrane into the intermembrane space protein Q (ubiquinone): accepts 2 e from NADH dehydrogenase or FADH2, then passes them onto cytochrome b-c1 complex cytochrome b-c1 complex: accepts 2 e from protein Q and passes them onto cytochrome c, 2H+ (p+) follow the e- and pass through the inner membrane into the intermembrane space

Question 45

Go through an overview of how chemiosmosis can apply to the ETC

Answer 45

during the ETC, protons (H+) accumulate in the intermembrane space; this creates an electrochemical gradient which is a potential difference (voltage) across the inner membrane (just like a battery)  the H+ cannot diffuse through the phospholipid bilayer  the enzyme ATP synthase embedded in the membrane allows H+ to pass through it  as the H+ pass through ATP synthase, ADP + Pi--> ATP  this process is called oxidative phosphorylation

Question 46

How much ATP is produced in ETC per product of each step of cellular respiration?

Answer 46

glycolysis: produces 4, however requires 2, from energy product, 4 ATP is produced pyruvate ox: no ATP is required or produced, from energy product, 6 ATP is produced in ETC Krebs cycle: 2 ATP is produced, from energy product 18 is produced from NADH + H+ and 4 is produced from FADH2

Question 47

What is fermentation?

Answer 47

-the metabolism of glucose in the absence of oxygen -NADH is oxidized by producing lactic acid or ethanol -lactic acid occurs in animal cells in temporary absence of oxygen, ethanol occurs in yeast in absence of oxygen

Question 48

Describe what a promoter, operator, repressor protein, and inducer

Answer 48

* promoter – a sequence of DNA that RNA polymerase binds to; located ‘upstream’ from the TAC ‘start’ signal on the DNA * operator – a sequence of DNA beside the promoter that a repressor protein binds to; if the repressor protein binds to the operator, the RNA polymerase cannot bind to the promoter and no transcription occurs * repressor protein – binds to the operator and prevents transcription * inducer – a molecule that binds to the repressor, changes it shape, and prevents the repressor from binding to the operator; RNA polymerase can bind to the promoter and transcription can occur

Question 49

Describe the lac operon

Answer 49

* the repressor protein is LacI protein * the inducer is lactose * lactose is a rare sugar in the environment, so the lac genes are usually OFF (b-galactosidase is not produced) * if lactose is present, it binds to LacI and allows transcription to occur

Question 50

Describe the trp Operon

Answer 50

* tryptophan is an amino acid that is rare in the environment * gene to produce trp is normally ON * if trp is present, it binds to the repressor protein and changes its shape so that it can bind to the operator * result: operator blocks transcription (gene turns OFF)

Question 51

Describe the trp Operon

Answer 51

* tryptophan is an amino acid that is rare in the environment * gene to produce trp is normally ON * if trp is present, it binds to the repressor protein and changes its shape so that it can bind to the operator * result: operator blocks transcription (gene turns OFF)