Bio exam 2

Cellular respiration

Metabolism

sustaining chemical reactions in a cell

• conservation of food energy into cellular energy (ATP)

• energy that the cell can utilize

• complex process

What are the 2 types of metabolic pathways

Catabolic and anabolic

Catabolic Pathways

• Break down of cellular components

• Exergonic - release’s energy

• Spontaneous

• stored in ATP and NADH

• Larger molecules broken down into smaller molecules

Anabolic Pathways

• Synthesizing cellular components

• Endergonic

• Requires energy input to drive reactions

• makes larger macromolecules not available in food

• small molecules to large ones

ATP

• Has 3 phosphate groups

  • energy is stored in the bonds in phosphate groups

• lots of negative energy

• lots of potential energy

• cycle between ATP and ADP

• When bonds are broken that is when energy is used.

NADH

• Energy intermediate

• Accepts electrons and protons removed from organic molecules

• high energy

NAD+

• carrier molecule

• transfers electrons and protons to where they need to be in the cell

• Hydrogen is coming from glucose or other substrate molecules

• 2 electrons 1 proton

Redox reactions

reactions involving an electron transfer - changing the nature of a molecule

• oxidation - removal of electrons

• Reduction - Addition of electrons (reducing charge)

OILRIG oxidation is loss, reduction is gain

EX: Ae- + B —> A + Be-

• A is being oxidized B is being reduced

Gene Regulation

Turns genes on and off

Cell Signaling Regulation

cell signaling pathways often activate protein kinases

Biochemical Regulation

Feedback inhibition

Feedback inhibition

product of a pathway inhibits early steps to prevent over accumulation of a product

• many enzymes involved

• Structure = function

• living organisms maintain homeostasis

Overview of cellular respiration

Process by which living cells obtain energy from organic molecules

• used by plants and animals

• primary goal is to make ATP and NADH

Aerobic Respiration

uses oxygen

What are the 4 metabolic pathways

1. Glycolysis

2. Breakdown of pyruvate

3. Citric Acid Cycle

4. Oxidative phosphorylation

Glycolysis overview

stage 1 of cellular respiration

• only step that does not happen in the mitochondria

  • happens in the cytosol

• can occur with out oxygen but will not move on to the next stage

• Has 10 steps that will happen in 3 phases

Energy investment

Stage 1 in glycolysis

• 2 ATP hydrolyzed to create fructose 1, 6-bisphosphate

• steps 1-3

Cleavage

Stage 2 in glycolysis

• 6 carbon molecules broken down into 3 carbon molecules of glyceraldehyde 3- phosphate

• steps 4-5

Energy liberation

Stage 3 in glycolysis

• 2 glyceraldehyde 3- phosphate broken down into 2 pyruvate molecules that produce 2 NADH and 4 ATP

• Steps 6-10

• Net Yield: 2 NADH and 2 ATP because the other 2 ATP go back to the first stage

Breakdown of pyruvate

Stage 2 of cellular respiration

• pyruvate is transported into the mitochondrial matrix through the outer membrane channel

• Broken down via enzymes pyruvate dehydrogenates

• molecule of CO2 removed from each pyruvate

• Remanning acetyl group attached to CoA to make Acetyl CoA - this is what is left of pyruvate

• Yield = 1 NADH for each pyruvate (2)

Citric Acid Cycle

Stage 3 of cellular Respiration

• Metabolic cycle

  • some molecules enter while others leave

  • series of organic molecules regenerated in each cycle

• Acetyl CoA starts the cycle

• series of steps releases - 2CO2, 1ATP, 3NADH, 1FADH2 - per pyruvate so times 2

• Acetyl is removed from acetyl CoA and detached from the citrate

Oxidative Phosphorylation

stage 4 of cellular respiration

• high energy electrons removed from NADH and FADH2 to make ATP

• requires oxygen

oxidation by the electron transport chain

• protein complexes embedded in the inner mitochondrial membrane

• accepts and donates protons and electrons in a series of redox reaction

• movements of electrons generates an H+ electron gradient

• providing energy for the next step

• water is produced during movement of electrons through ETC

• oxygen is the final electron acceptor

Phosphorylation by ATP synthase

phosphorylation - the addition of a phosphoryl group to a molecule - makes ADP —> ATP

• protons can only pass through ATP synthase - only way hydrogen ions can move back across bilayer

ATP synthase

• chemmiosmosis - chemical synthase of ATP as a result of pushing H+ across membrane

• ATP synthase captures free energy as H+ ions flow through

• Big energy pay off

• NADH and FADH oxidation makes most of the cells ATP

  • NADH and FADH oxidation makes most of the cells ATP

• Yield up to 30-36 ATP - rarely achieve maximal amounts because

  • NADH is also used in anabolic pathways

  • H+ gradient used for other purposes

Where does glycolysis occur

Cytosol

what is the end product of glycolysis

pyruvate

What is the net yield of energy containing molecules per 1 glucose in glycolysis

• 2 ATP

• 4 NADH

Where does the breakdown of pyruvate occur

mitochondria

what is the end product of the breakdown of pyruvate

Acetyl CoA

What is the net yield of energy containing molecules per 1 glucose in the breakdown of pyruvate

2 NADH

Where does the citric acid cycle occur

mitochondria

what is the end product of the citric acid cycle

oxolacitate is regenerated

What is the net yield of energy containing molecules per 1 glucose in the citric acid cycle

• 4 Co

• 2 ATP

• 6 NADH

• 2 FADH2

Where does oxidative phosphorliation occur

inner mitochondrial membrane

what is the end product of oxidative phosphorliation

• NAD+

• FAD+

• H2O

What is the net yield of energy containing molecules per 1 glucose in oxidative phosphorliation

30-36 ATP

Anaerobic organisms

• do not need oxygen

• are used for anaerobic respiration and Fermentation

  Ex: bacteria

Facultative Anaerobe

uses aerobic respiration when there is oxygen but can survive anaerobic

Anaerobic respiration

• Bacteria and archaea can us other e- accepters

• has donners besides glucose

• substituting oxygen with different electron receptors

• Still use ECT and ATP synthase in the mitochondrial membrane

Fermentation

• has 2 steps

  • glycolysis

  • Regeneration of NAD+

What are problems with fermentation

• high concentrations

  • NADH haphazardly donates it protons and electrons to other molecules

• decrease in NAD+

What are the solutions to fermentation

• Lactic acid fermentation

• alcohol fermentation

Lactic Acid fermentation

• pyruvate is reduced to make lactate

• electrons are used to reduce pyruvate are derived from NADH which is oxidized to NAD+

alcohol fermination

• pyruvate is turned into alcohol

• pyruvate is broken down into Co2 and 2 carbon molecule — acetaldehyde

• acetaldehyde is then reduced by NADH to make ethanol

• NADH in then oxidized to NAD+

How many ATP can fermentation make

2 ATP

What are the 2 trophic levels

• heterotroph

• Autotroph

What is a heterotroph

must eat food to sustain life

Autotroph

makes organic molecules from inorganic sources

• most are photoatrophes that use light as enegy

Mesophyll cells

• where a majority of photosynthesis occurs

• most of the cells in a plant

Stomata

carbon dioxide enters and oxygen exits through pores in the leaf

• oxygen can leave trough them to

chloroplast

organelle in plants and algae that caries out photosynthesis

• chlorophyll is found in here

Thylakoid (Chloroplast anatomy)

• a third membrane

• contains pigment molecules

• membranes form thylakoids

Granum (Chloroplast anatomy)

stack of thylakoids

Stoma (Chloroplast anatomy)

fluid filled region between thylakoid membrane and inner membrane

Lumen (Chloroplast anatomy)

region inside the thylakoid membrane

What are the two stages of photosynthesis

• light reaction

• Calvin Cycle

Light energy

light is a type of electromagnetic reaction

• travels as waves

  • short to long wavelengths

• behaves as particles called photons

  • discrete packets

  • shorter wavelengths have more energy

Photons

• discrete packets

• shorter wavelengths have more energy

• can be absorbed transmitted or reflected when they strike an object

Pigments

molecules that absorb only certain wavelengths of light

Electrons capturing light energy

• absorption boost energy to higher energy levels

• after an electron absorbs energy it is in an excited state and usually unstable

  • it does not want to be here

How does an release energy (3 ways)

• heat

• light

• excited electrons can be transferred to another molecule

Chlorophyll pigments

• are the most common

• red and blur photons can be absorbed

• work in groups

  • 200-300 chlorophyll molecules and accessory pigments organized by many proteins to form antenna complex

what are some accessory pigments

• Chlorophylls

• Carotenoids

• xanthophylls

what do light reactions use

• light energy

• H2O

What do light reactions produce

• O2

• NADPH

• ATP

What is NADPH used for in light reactions

an electron carrier

What is ATP used for in light reactions

can store and transport energy

What are the 2 main components in the structure of photosystems

• antenna complex

• reaction Center

Antenna complex

• directly absorbs photons

• energy transferred via resonance energy transfer

Reaction Center

• energy is transferred quickly

• Electron transfers to a primary electron acceptor and captured

• PSII P680 —> P680* (P680* is relatively unstable)

• PSI P700 —> P700* (P700* is relatively unstable)

Photosystem II

• The initial step in photosynthesis

• light excites an electron

• releases energy via the electron into the electron transport chain

What does photosystem II create

oxygen

oxygenic photosynthesis

• happens in photosystem II

• Is the only protein complex able to break water apart in this way

Electron transport chain (photosystems)

happens in steps 2-4 of photosystem

• leave PSII and into the ECT

  • series of molecules that carry electrons

  • energy released drives H+ into the lumen

    • via the cytochrome complex

  • Used to make ATP

Photosystem I

• Primary role to make NADPH

• the same electron from PSII is now being re-excited by light

  • Same process but now uses a different reaction center

• Electron combines with NADP+ and a H+ to form NADPH

• the enzyme in NADP+ reductase

  • Aids in the process of turning NADP+ into NADPH

Z Scheme

Zigzag shape of energy curve

ATP synthesis in chloroplasts

• achieved by a mechanism called photophosphorlation

• Driven by the flow of H+ from thylakoid lumen into stroma via ATP Synthase

what are the 3 ways H+ gradient

1. ^ H+ in thylakoid lumen by slitting of water

2. ^ H+ by ETC pumping H+ into lumen

3. (down) H+ in stroma from formation of NADPH

What are the 3 chemical products in light reactions

1. oxygen,O2

2. NADPH

3. ATP

Synthesizing carbohydrates via the Calvin cycle

• CO2 incorporated into carbohydrates

  • precursors’s to other organic molecules

  • energy storage

• Requires massive energy input

In the calvin cycle how many ATP and NADPH must be used for every 6 CO2

• 18 ATP

• 12 NADPH

What is the final product of the calvin cycle

glyceraldehyde-3-phosphate

• glucose is later made from G3P in separate process

What is the first phase of the Calvin cycle

Carbon Fixation

What is carbon Fixation

CO2 incorporated into RuBP using ribisco

• reaction product is six-carbon intermediate that splits into 2 3-phosphoglyceralde

What is phase 2 of the calvin cycle

Reduction and carbohydrate production

what is Reduction and carbohydrate production

• ATP is used to convert 3PG into 1,3bisphosphoglycerate

• NADPH electrons are reduced to glyceraldehyde - 3 phosphate

• 6 CO2 —> 12 G3P

  • only 2 G3P molecules used to make carbs

  • 10 G3P molecules must be used for regeneration of RuBP

What is phase 3 of the calvin cycle

Regeneration of RuBP

what is Regeneration of RuBP

• 10 G3P are converted into 6 RuBP using 6 ATP

what is the CO2 fixing enzyme is

• Ribulose 1,5 bisphosphate carboxylase/oxygenase

What is rubisco

• Found in all photosynthetic organisms that use the calvin cycle to fix carbon

• thought to be the most abundant enzyme on the earth

What are environmental conditions that can cause variations in photosynthesis

• light intensity

• temperature

• water availability

when are stomatas usually open and closed

• open during the day

• closed during nights

What does closing the stoma cause

• CO2 delivery, and thus the calvin cycle stoping

Photorespiration

using oxygen instead of CO2

• this is not efficient

C3Plants

• plants that require 3-phosphoglycerate

• 90% of plants

C4 photosynthesis

• used in hot and dry climates

• spatial separation of 2 carbon fixation paths

CAM ( crassulacean Acid Metabolism)

• temporal separation of 2 carbon fixation pathways

• open stomata at night

  • conserve water

• CO2 enters and is converted to oxaloacate

• oxaloacate converted to malate

• malate broken down into CO2 to drive calvin cycle during the day

Mesophyll cells in C4 plants

• co2 enters via stomata and 4 carbon compound formed

Bundle sheath cell

• 4 carbon molecule transformed that releases steady supply of CO2 minimizing photorespiration