BIOS 1700 Exam 2

Enzyme, transition, lowers

______ binds to __________ state and ______ free energy

Catabolism

Large molecules broken down into component parts

Capture energy

-ΔG

Adenosine Triphosphate (ATP)

Cells convert chemical E in macromolecules to ATP

Bonds linking PO4 groups

Energetic Coupling

Two reactions occur together

Sum of the ΔG

(-) Total = can proceed

(+) Total = can NOT proceed

Transition State

Intermediate structure between reactants and products

Unstable

Enzymes

Enzyme Inhibitors

Molecules that decrease activity of enzymes

Irreversible: form covalent bonds and stay attached

Reversible: form weak bonds and can dissociate

Competitive Inhibitors

Bind to same site as substrate (active site)

Can be overcome with large amount of excess substrate

Noncompetitive Inhibitors

Bind at allosteric site (inhibitor site)

Enzyme is not active

Excess of substrate will not overcome

Metabolic Pathway

Series of chemical reactions

Gradually modify molecules

Each reaction requires different enzyme

Metabolism

Set of chemical reactions converting molecules to other molecules and transfer energy in organisms

Anabolism

Building up molecules

Use energy

+ΔG

Potential Energy

Energy from position

Cholesterol

Greatest potential energy

First Law of Thermodynamics

Energy is always conserved

Energy before = energy after

Some energy given off as heat

Second Law of Thermodynamics

Disorder (entropy) in universe increases

Some energy lost as heat

Transformation of energy = increase in entropy

Chemical Reactions

Involve breaking and reforming bonds

Gibbs Free Energy (G)

Energy available to do work

Usable energy for organisms

Endergonic / exergonic

Endergonic

Non-spontaneous

ex. Anabolism

+ΔG

Exergonic

Spontaneous

ex. Catabolism

-ΔG

Hydrolysis

Use water molecule to split another molecule in two

One product gets H+

One product gets OH-

Phosphates liked with high energy bonds

Enzymes

Biological catalysts

Increase rate of reaction and determine which reactions will proceed in the cell

Activation Energy (EA)

Energy required to form transition state

Substrate

Reactant (modified by enzyme)

Binds to enzyme at active site

Forms enzyme-substrate complex

Allosteric Enzyme

Activity controlled by binding of a molecule at other site

Regulation of pathways (on/off)

Catabolic Processes

Breakdown of fuel molecules

Many reactions (gradual)

Releases small amounts of energy at a time

Cellular Respiration

Glycolysis

Acetyl CoA Synthesis

Citric Acid Cycle

Oxidative phosphorylation

Redox Reactions

e- have energy

Transfer of e- and energy

Reduction

Gain e-

Oxidation

Loss of e-

Reducing Agents

Donate e-

Oxidized

Oxidizing Agents

Accept e-

Reduced

Glycolysis

Stage 1 of Cellular Respiration

Glucose sugar is broken down

Three phases: prep step, cleavage, "payoff"

2 NADH

2 Pyruvate

2 ATP

Phase 1 of Glycolysis

Prep Phase

2 ATP molecules used

Prepare glucose

Phase 2 of Glycolysis

Cleavage

Split glucose into two 3-carbon molecules

Phase 3 of Glycolysis

Payoff

2 of each reaction

4 molecules of ATP

2 molecules of NADH

Substrate-Level Phosphorylation

Transfer PO4 to ADP and from phosphorylated intermediate

Acetyl-CoA

Stage 2 of cellular respiration

Pyruvate goes into mitochondria

One carbon is cut off

+1 NADH

Acetyl made and attached to CoA

Krebs Cycle

Stage 3 of cellular respiration

2 acetyl-coA come in from stage 2

Citrate made

Carbon atoms released as CO2

ATP made by substrate level phosphorylation

e- Transport Chain

Stage 4 of cellular respiration

4 protein complexes pass e- along inter membrane

Used to pump H+ ions from matrix to intermembrane spaces

Electrochemical gradient is created

Final e- acceptor = O2

Final e- Acceptor

O2

Oxidative Phosphorylation

Electrochemical gradient = high potential energy

Release kinetic energy

1 NADH

2.5 ATP

1 FADH

1.5 ATP

Fermentation

Metabolic process converting sugar to an acid, gas, or alcohol

1. Lactic acid

2. Ethanol fermentation

Lactic Acid

Exercise

With O2 = e- transport chain ---> regenerate NAD+

Without O2 = NAD+ must be generated another way ---> NADH used to reduce used to reduce pyruvate

Glycogen

How animals store glucose

Stored in liver and in muscles

Starch

How plants store glucose

Disaccharides / Monosaccharides

Converted into intermediates in glycolysis

Beta-Oxidation

In mitochondrial matrix

2 carbon units removed sequentially

e- carriers are made when carbon is broken off

Produces lots of ATP

Citrate

1st product of citric acid cycle

Anabolic Process

Creation of carbohydrates from CO2

Requires energy input from sunlight

CO2

Low energy bonds

Most oxidized form of carbon

Photosynthetic e- Transport Chain

Energy captured by photosystems

Strips e- from H2O

Produces ATP and NADPH (e- carrier)

Happens in thylakoid membrane

Calvin Cycle

Energy used to reduce CO2 to carbohydrates

Happens in stroma

1. Carboxylation

2. Reduction

3. Regeneration

Photosynthesis

Occurs in chloroplasts

1. Photosynthetic e- transport chain

2. Calvin cycle

Chloroplast

Outer membrane

Inner membrane

Thylakoid membrane

Grana

Lumen

Stroma

Cyanobacteria

Prokaryotes

Have both photosystems

Rubisco

Slow enzyme (selective for O2)

Most abundant plant protein

Chlorophyll

Pigment that absorbs light energy

Absorbs at specific wavelengths and reflects others

Accessory Pigments

Absorb wavelengths that chlorophyll absorbs poorly

Why leaves are green

Antenna Chlorophyll

Allow efficient absorption of light

Protein Complexes

Photosystem 1 / Photosystem 2

Light hits PS2 first and brings down to reaction center chlorophyll

Photosystem 1

Energizes e- enough to reduce NADP+ to NADPH

Light hits second

Photosystem 2

Strips e- from H2O

Light hits first

Plastoquinone

Carrier of e- from PS2 to cytochrome

Cytochrome

Energy and pumps proton to lumen

Plastocyanin

e- carrier from cytochrome to PS1

Photosynthesis

Low energy e-

Energized by light

NADPH produced

H2O = e- donor

O2 is produced

Redox reactions

Electrochemical gradient

Respiration

High energy e-

Low energy throughout

NADH used

O2 = last acceptor of e-

H2O produced

Redox reactions

Electrochemical gradient

Challenges of Photosynthesis

Too much light and calvin cycle can't keep up

Not enough NADP+ ---> will reduce O2

Cyclic e- Transport

Can send e- backwards in chain

More p+ pumped = more ATP

Anti-Oxidants

Detoxify reactive O2 species

Xanthophylls

Pigment molecules that reduce the rate at which energy and e- enter the e- transport chain

Activated by high proton gradient

Block e- transport at photosystem 2

Allows cyclic e- transport

More Photosystems

Lot's of thylakoid membrane

Photorespiration

Rubisco makes a mistake and adds O2 to RuBP instead of CO2

Cell uses up ATP and loses CO2

Communication Elements

1. Signaling cell

2. Signaling molecule

3. Responding cell

4. Receptor

Ligand

Signaling molecule

Binds specifically to a receptor

Endocrine Signaling

Signal travels through circulatory system

Cells are far away from each other

Moves through bloodstream (ex. Hormones)

Paracrine Signaling

Diffusing through to the next cell

ex. Cancer, nerve transmission

Autocrine Signaling

Signaling molecule is also responding cell

ex. Some cancers

Juxtacrine Signaling

Signaling cell = transmembrane protein

ex. Immune system

Signal Transduction

Signal changed within cell into a f or the cell can respond to

1. Signal binds to receptor

2. Signal transmitted to interior by transduction pathway

3. Cell responds and activates enzyme

4. Response terminated

Growth Factors

Stimulate cells to grow and divide

Serum and plasma

Serum

Needs growth factor to make cells grow

PDGF = platelet derived growth factor

Plasma

Clotting caused by platelet activation

Activated platelets release many different factors

Hydrophilic Ligands

Growth factors

Receptor on surface of cell

Hydrophobic Ligands

Steroids

Can enter cell

Receptor in cytoplasm / nucleus

Polar Ligands

Can't cross plasma membrane and rely on cell-surface receptors

Nonpolar Ligands

Freely pass through plasma membrane and activate cytoplasmic receptors

Steroid

Receptor complex

Binds to DNA in nucleus to regulate gene transcription

Signal Transduction

Pathways amplify signals as they pass downstream

One signaling molecule can activate several molecules of next

Small signal = large response

Turn themselves off

Protein Kinase

Enzymes that add phosphate to specific substrate proteins (Phosphorylation)

Membrane bound or cytoplasmic

Phosphorylation

Can affect target protein ---> activate, inactivate, change interactions, change location

G-Protein

Guanine nucleotide-bonding proteins in DNA/RNA

Molecular switches

G-Protein On

Bound to GTP

G-Protein Off

Bound to GDP

Second Messengers

Small molecules that diffuse rapidly within the cell

ex. Ca2+, cAMP

Enter through plasma membrane

Bind to enzymes causing them to become activated

G-Protein Coupled Receptors

Bind many signaling molecules

Regulate many processes

7 Transmembrane domains

Adrenaline Signaling

G-protein activates adenyl and makes cAMP

Protein kinase A (PKA) binds to cAMP

Amplification

Each receptor can activate many g-proteins

Each adenyl cyclase makes many cAMP molecules

Each PKA phosphorylates many target proteins