Bio 110 Exam 3

Metabolism

sum total of all chemical reactions occurring in a biological system at a given time, involve energy changes, involves building up and breaking down

2 types of Metabolism

Anabolic and Catabolic

Anabolic Reactions

complex molecules made from simple molecules (type of metabolism), energy required, often linked to catabolic reactions, driven by energy from catabolic reactions

Anabolic Reaction Example

bringing amino acids together to form polypeptide chains

Catabolic Reaction

complex molecules broken down to simpler ones (type of metabolism), energy released, energy released in catabolic reactions are used to drive anabolic ones, reactions are often linked

Oxidation-Reduction Reaction

electrons transferred between 2 molecules (OIL RIG), one substance transfers electrons to another substance, often associated with transfer of hydrogen ions

If a reaction is reduced…

it gains electrons (oxidizing agent)

If a reaction is oxidized…

it loses electrons (reducing agent)

Energy

capacity to do work, or the capacity for change, can be converted from one form to another, can go from potential to kinetic

Chemical, light, mechanical, electrical, heat

Forms of Energy

Law of Thermodynamics

apply to all matter and all energy transformations in the universe, helps us understand how cells harvest and transform energy to sustain life

1st Law of Thermodynamics

energy is neither created nor destroyed, when energy is converted from one form to another, the total energy before and after the conversion is the same

2nd Law of Thermodynamics

when energy is converted from one form to another, some of that energy becomes unavailable to do work, no energy transformation is 100% efficient, some energy lost to disorder, energy is still equal but not all usable, disorder increases due to energy transformations, disorder increases due to energy transformations

2 types of energy

kinetic and potential energy

Potential Energy (PE)

stored energy, stored as chemical bonds, concentration gradient, or charge imbalance, when ions move across membrane

ex.) cat gearing up for a jump

Kinetic energy (KE)

energy of movement/ motion, can be converted from one form to another (kinetic to potential)

ex.) cat jumping onto table

Chemical Reactions

occur when atoms collect enough energy to combine or change their bonding partners, energy is stored in bonds and energy s released when bonds are broken

Entropy (S)

measure of disorder in a system, takes energy to impose order on a system, everything moves toward disorder unless energy is applied to the system

Enthalpy (H)

total energy (H=G/TS)

Free Energy (G)

usable energy that can do work,

∆G=∆H-T∆S

Free energy equation

calories or joules

How is change in energy measured?

If ∆G is negative…

free energy is released

If ∆G is positive…

free energy is required

If ∆G is zero…

a reaction does not occur

Exergonic Reactions

release of free energy (-∆G), catabolism (exit), reversible

Catabolism

Complexity deceases (generates disorder), complex molecules→free energy+ small molecules (associated with exergonic reactions)

Endergonic Reactions

consume free energy (+∆G), anabolic (enter)

Anabolism

complexity (order) increases, free energy+ small molecules→complex molecules (associated with endergonic reactions)

Chemical Equilibrium

balance between forward and reverse reactions, ∆G=0, every reaction has equilibrium point, ∆G values near zero are characteristics of readily reversible reactions

ex.) state of no net change

ATP (energy currency)

Where does biochemical energy come from?

ATP

energy transfer in biochemical reactions, captures and transfers free energy, can be hydrolyzed to ADP and P¡, releasing a lot of energy for endergonic reactions

ATP+H20→ADP+P¡+free energy, break down with the addition of H20

ATP Hydrolysis Reaction

Formation of ATP is…

endergonic

Characteristics of ATP that allow for release of free energy when hydrolyzed

1) Phosphate groups have negative charges and repel each other

2) Free energy of the P\~O bond is much higher than energy of the O-H bond that forms after hydrolysis

ATP hydrolysis is…

exergonic

ATP coupling reaction

formation and hydrolysis of ATP couple or join endergonic and exergonic reactions

Enzymes

biological catalysts that act as a framework in which reactions can take place, most are proteins, lower the energy barrier by bringing reactants together, lower activation energy, speed up reactions

Function of enzymes

lower the energy barrier by bringing reactants together, 3-D shape of enzyme determines its specificity

1) They do not change final equilibrium

2) They do not change the difference in free energy (∆G) between reactants and products

3) They do not make reactions that wouldn’t otherwise happen

What don’t enzymes do?

Catalyst

increases rate of a chemical reaction

Activation Energy (Ea)

amount of energy required to start a reaction, can come from heating the system, associated with enzymes, heat can start chemical reactions, ∆G=+, requires energy

Transition State

reaction mode of the substrate (aka. reactant) after there has been sufficient input of energy to initiate the reaction, they want to react because they are unstable and want to become stable again (similar to valence shell)

Transition State Intermediates

unstable reactions with higher free energy, added energy to reaction to make it unstable, will become stable quickly and have higher free energy, not in end state, pushing them to react, must become less stable before change is possible, energy required to make unstable, releases free energy to get stable again

Substrates

reactants, molecule(s) on which an enzyme exerts (is working) its catalytic action

Active Site

place on an enzyme where substrate binds (where the enzyme is working)

1. Enzymes can orient substrates so they react (orientation) (substrates fit well into enzymes)
2. Enzymes can indue strain by stretching substrate (physical strain) (stretches and breaks up bonds, makes bonds unstable and more reactive)
3. Enzymes can temporarily add chemical groups (chemical charge) (adding a positive or negative charge can make enzyme unstable)

3 Mechanisms of Enzyme Action

1. regulation of gene expression- how many enzyme molecules are made (turn on gene in DNA)
2. regulation of enzyme itself- enzyme shape may change, or enzyme can be blocked by regulators (cells can turn enzymes off and on when needed)

2 ways to regulate enzymes

Reversible Inhibition

inhibitor bonds covalently to the active site, preventing substrate binding, doesn’t allow enzyme to bind (competitive, uncompetitive, noncompetitive)

Irreversible Inhibition

inhibitor covalently (strong) bonds to side chains in active site and permanently inactivates the enzyme

Competitive Inhibitors

compete with natural substate for binding sites, if substrate doesn’t get there first, it cant bind because of the inhibitor, competition for binding to active site, degree of inhibition based on concentration of substrate vs. inhibitor

Noncompetitive Inhibitors

bind to enzyme at site other than the active site, enzyme changes shape and alters active site (allosteric), changes shape of active site

Allosteric Regulation

an effector binds an enzyme at a site different from the active site, changing the enzyme’s shape, doesn’t allow enzyme to bind properly because shape of site is different, enzyme will function or not function based on new shape (tuns on or off) (active and inactive form)

Uncompetitive Inhibitors

bind to enzyme-substate complex, preventing release of products, cannot be overcome by adding more substate, holds substrate to enzyme (locks enzyme in place), not competing for active site

Commitment Step

first reaction, followed by other reactions in sequence, cell is committed to following pathway

Feedback Inhibition

final product acts as noncompetitive inhibitor of the 1st enzyme, shutting down the pathway

Ribozymes

catalytic RNAs that speed up reactions involving their own nucleotides

Induced Fit

enzyme changes shape when it binds substrate, altering shape of active site

every enzyme is most active at a particular pH, which influences ionization of functional groups

How does pH affect enzymes?

every enzyme has an optimal temp., at high temp, noncovalent bonds begin to break and enzymes lose tertiary structure and denature, enzymes adapted to higher temps do not denature because of covalent bonds in their tertiary structure, at low temps reactivity slows down

How does temperature affect enzymes?

Aerobic Respiration

the process of using glucose and oxygen to produce ATP, more efficient than anaerobic respiration

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Cellular Respiration Formula

opposite of cellular respiration (except light energy and ATP), linked to cellular respiration

Photosynthesis Formula

Photosynthesis

produces oxygen gas and glucose (potential energy)→cellular respiration→produces CO2 and H2O, opposite of cellular respiration

1. Complex transformations occur in a series of separate reactions (multiple step process)
2. Each reaction is catalyzed by a specific enzyme (need different enzymes in different pathways, reactions must happen quickly)
3. Many metabolic pathways are similar in all organisms
4. In eukaryotes, metabolic pathways are compartmentalized on specific organelles (different compartments for photosynthesis and cellular respiration makes it easier for all compartments to be in each compartment efficiently)
5. Key enzymes can be inhibited or activated to alter the rate of the pathway (pathway can be turned on and off)

5 principles of Metabolic Pathways

Burning/ Metabolism of Glucose Formula

Metabolism of Glucose

cells OBTAIN energy from glucose, reaction is extremely exergonic (-∆G value), drives endergonic formation of many ATP molecules

How cells break can break down glucose from energy:

1) Glycolysis (anaerobic, oxygen absent) (always start with glycolysis followed by cellular respiration or fermentation depending on presence of oxygen)

2) Cellular Respiration (aerobic, oxygen present)

3) Fermentation (anaerobic, oxygen absent)

3 Catabolic processes that harvest energy from glucose

Transfer of electrons is associated with…

transfer of hydrogen ions

When a molecule loses H atoms…

it becomes oxidized

Electron carrier molecules

NADH, FADH2, NADPH

Electron Carrier Molecule Definition

garbs electrons from one molecule and moves to another molecule, shuttles electrons from one place to another

NADH and FADH2

Which electron carrier(s) are used for cellular respiration?

NADPH

Which electron carrier(s) are used for photosynthesis?

glycolysis, pyruvate oxidation, citric acid cycle, respiratory chain/ATP synthesis, fermentation

5 energy-yielding metabolic pathways

Aerobic

oxygen is present

Anaerobic

oxygen is absent

In the cytoplasm

Where does glycolysis occur in eukaryotic cells?

In the cytoplasm

Where does fermentation occur in eukaryotic cells?

In the matrix of the mitochondria

Where does the citric acid cycle occur in eukaryotic cells?

In the matrix of the mitochondria

Where does pyruvate oxidation occur in eukaryotic cells?

In the inner membrane of the mitochondria

Where does the respiratory chain/ ATP synthesis occur in eukaryotic cells?

In the cytoplasm

Where does glycolysis occur in prokaryotic cells?

In the cytoplasm

Where does fermentation occur in prokaryotic cells?

In the cytoplasm

Where does the citric acid cycle occur in prokaryotic cells?

On the cell membrane

Where does pyruvate oxidation occur in prokaryotic cells?

On the cell membrane

Where does the respiratory chain/ ATP synthesis occur in prokaryotic cells?

Glycolysis, Pyruvate Oxidation, Citric Acid/ Krebs Cycle, Electron Transport chain/ATP synthesis

Which pathways occur when oxygen gas (O2) is present?

Glycolysis and Fermentation

Which pathways occur when oxygen gas (O2) is absent?

Glycolysis

takes place in the cytoplasm and has to move to the mitochondria, converts glucose into 2 molecules of pyruvate, produces 2 ATP and 2NADH (to be used in electron transport chain), occurs in 10 steps: first 5 require ATP energy input, last 5 yield NADH and ATP

Oxidative Phosphorylation

ATP is synthesized by reoxidation of electron carriers in the presence of O2

2 Stages of Oxidative Phosphorylation

1) Electron transport-add phosphate to ADP to make the remaining 28 ATP molecules (electrons dumped, occurs in inter membrane space

2) Chemiosmosis

Chemiomosis

protons (hydrogen ions) flow back across the membrane (mitochondria) through a channel protein with the concentration gradient, from the matrix to the inter membrane space and back, energy released is uses to make ATP

ATP synthase

couples the diffusion with ATP synthesis, producing ATP

NADH and FADH2 donate their electrons to the electron transport chain

Electron transport chain- Where do the electrons come from?

Energy from electrons are used to produce many ATP

Electron transport chain- What are electrons used for?

As electrons travel through the transport chain, carrier molecules use the potential energy of the electrons to transport hydrogen ions into the inter membrane compartment

Electron Transport chain- Importance of proton/H+ gradient

Proton-motive force

force generated across a membrane having 2 compartments- a chemical potential plus an electric potential due to the electrostatic change on a proton

At the end of the transport chain, electrons are donated to an oxygen atom, which combines with hydrogens to form H2O

Electron Transport Chain- Final electron acceptor

If oxygen isn’t present, electrons can’t be donated and everything gets “backed up”- FAD and NAD+ cant be produced, which are required for the Krebs cycle

Why are pyruvate oxidation and Krebs cycle considered aerobic?