BIO 215 Exam 2

Energy

the capacity to do work (to cause change)

potential energy

stored energy

includes chemical energy, concentration gradient, gravitational energy and stored mechanical energy

kinetic energy

energy associated with motion

includes electrical energy, radiant energy, thermal energy, motion energy, and sound

chemical energy

potential energy stored in bonds of atoms and molecules

concentration gradient

potential energy stored in concentration differences across a membrane

electrical energy

movement of charged particles (ex: electrical charge flowing through wires)

radiant energy

electromagnetic energy that travels in transverse waves

thermal energy

(heat) internal energy in substances (ex: vibration and movement of atoms and molecules within a substance)

motion energy

movement of objects from one place to another

types of change that require cellular energy

1. Synthetic work

2. Mechanical work

3. Concentration work

4. Electrical work

5. Generation of heat

6. Generation of light

autotroph

organism that produces organic compounds from inorganic molecules

heterotroph

organism that produces organic compounds starting from other organic molecules

photrophs

able to capture light energy and transform it into chemical energy

chemotroph

organism that extracts energy by oxidizing inorganic chemical compounds and uses carbon dioxide to synthesize its own organic molecules (food).

Photoautotroph

organism that captures light energy form the sun and uses carbon dioxide to synthesize its own organic molecules

energy flow through the biosphere

• Sun → Earth

• Light energy captured by photoautotrophs → used to convert inorganic carbon into organic carbon 

  • Some energy is lost as heat

• Heterotrophs and autotrophs convert organic carbon into usable energy 

  • Some energy is lost as heat

(open system)

matter is recycled within the biosphere

• Between phototrophs and heterotrophs and vice versa

(closed system)

thermodynamics

the study of how energy is transformed; cells/organism extract energy and use it to preform work

1st law of thermodynamics

the study of how energy is transformed; cells/organisms extract energy and use it to perform work

1st Law of Thermodynamics

Principle of Conservation of Energy; energy can be transferred and transformed, but it cannot be created or destroyed

2nd Law of Thermodynamcis

Every energy transfer always increases the entropy (the disorder) of the universe ie some energy is unstable (lost as heat)

Free energy

measure of thermodynamic spontaneity of a system (amount of energy available to do work)

spontaneous process

occurs on its own under a specific set of conditions (doesn’t require input of energy)

∆G

Free energy of a system

∆G < 0

reaction is spontaneous (exergonic) – energy available to do work 

∆G > 0:

 reaction is nonspontaneous (endergonic)

∆G = 0

system has reached equilibrium; system is in it’s MOST stable state; zero free energy available, cannot do work

∆H > 0

 endothermic reaction; unfavorable for spontaneity; heat is absorbed

∆H < 0

exothermic reaction; favorable for spontaneity; heat is released

∆S > 0

more disorder; favorable for spontaneity 

∆S < 0

less disorder; unfavorable for spontaneity 

∆H < 0, ∆S > 0

always spontaneous

∆H > 0, ∆S < 0

Never spontaneous

Equilibrium

• rate of forward reaction = rate of reverse reaction

• constant concentration of products are reactions

• stable reaction

• does zero work

equilibrium constant

[products]/[reactants]

Tells us: if there are more product or reactants at equilibrium & predict direction of a system not at equilibrium

before spontaneous change

more free energy, less stable (FAR from equilibrium), greater work capacity

during a spontaneous change

system moves toward equilibrium as free energy released is use to do work

after a spontaneous change

less free energy, more stable (closer to equilibrium), smaller work capacity

transition state

the highest-energy configuration of a molecular system along a reaction pathway. It represents the exact moment when old bonds are actively breaking and new bonds are forming; must be reached in order for product to be formed

activation energy

amount of energy reactants must have in order for a reaction to take place (ie in order to reach to transition state); determines rate of reaction

metabolism

total collection of chemical reactions that take place in the cell

anabolism

synthesis pathway (endergonic)

ex: aerobic respiration

catabolism

breakdown pathway (exergonic)

ex: photosynthesis

energy coupling

combing exergonic with endergonic reactions so that the exergonic reaction drives the endergonic reaction making OVERALL ∆G negative

glutamine formation coupled to ATP hydrolysis

energy coupling reaction: Glutamic acid + ammonia + ATP + H2O → Glutamine + ADP + inorganic phosphate

Overall ∆G = 3.4 kcal/mol - 7.3 kcal/mol

ATP (adenosine triphosphate)

• “energy currency of the cell”

• type of nucleotide

• Adenine + ribose + 3 organic phosphates (alpha phosphate, beta phosphate, gamma phosphate)

• hydrolysis of phophanhydride bond releases energy!

Phosphoanhydride bond

a high-energy covalent linkage between two phosphate groups

phosphodiester bond

covalent bond between ribose and alpha phosphate

movement of motor proteins

example of how cells use ATP hydrolysis to do work

• Motor protein binds ATP

• ATP hydrolysis (releasing ADP + inorganic phosphate) causes conformational change in motor protein 

• Conformation change physically moves motor protein along cytoskeletal element

benefits of ATP

1. opposing charges between adjacent phosphates

2. decreased resonance stabilization

3. free energy of ATP hydrolysis

opposing charges between adjacent phosphate

opposing charges INCREASES free energy within molecule (more repulsion, more destabilization) 

decreased resonance stabilization

 formation of bonds between phosphate and ribose makes molecule stable by eliminating resonance structure (and delocalized electrons), increases free energy of system

free energy of ATP hydrolysis

has intermediate amount  of energy (Goldilocks): release a good amount of energy while requiring a reasonable amount of energy to be resynthesized 

enzymes

catalytic protein (not consumed in reaction) that speeds up chemical reactions by lowering activation energy; name ends in “ase”, interacts with substrate (reactant) at active site; serve as biological catalysts in many important reactions

substrate

reactant that reacts with enzyme

active site

cavity grove in tertiary or quaternary structure where substrate fits

• Created by folding pattern 

• Arrangement of amino acids is crucial for substrate interaction

• Well-matched substrate fits into active site’ many non-covalent bonds form to enable transient E-S binding 

specificity of substrate binding

• Molecules in cell encounter each other due to continual random thermal motion

• Well-matched surfaces can withstand thermal vibrations and stay bound together allowing reaction tao take place (happens in enzyme binding site to unsure specificity)

• Poorly matched surfaces will NOT withstand vibrations

• Well-matched substrate fits into active site’ many non-covalent bonds form to enable transient E-S binding

hydrolysis of sucrose by substrate enzymes

1. Active site available 

2. Substrate enters active site and binds to enzyme using noncovalent interactions, binding lowers activation energy

3. Substrate is converted into product 

4. Products are released

• Uncatalyzed rate: 4 * 10^-11 Ms^-1 (½ t ~ 500 years)

• Catalyzed rate : 10^4 Ms^-1

• Catalyzed rate 200 trillion times faster

environment regulation

enzymes only function under specific conditions; changing conditions changes structure (and function!) of enzymes

pH optimum

pH environment in which enzymes can reside

pepsin

pH optimum in acidic environment, functions in stomach

trypsin

pH optimum in basic conditions, functions in small intestine

metabolic pathway

series of chemical reactions within a cell, each step it catalyzed by an enzyme

feedback regulation

activity of pathway enzymes influenced by concentration of substrates and/or products

positive feedback regulation

output increases original stimulus

negative feedback regulation

products SLOWS initial stimulus (supply and demand); maintains homeostasis

occurs when there IS a demand

• products of pathway are consumed

• pathway continues to supply products

occurs when there IS NOT a demand

• products start to build up

• accumulation of products serve as feedback signal to stop/slow down supply

competitive inhibition

• inhibitor and substrate BOTH capable of binding to active site

• binding of inhibitor prevents enzyme from binding to the substrate

noncompetitve inhibition (negative allosteric inhbition)

inhibitor binds to allosteric site, distorting enzyme so that substrate cannot bind to active site

positive allosteric activation

allosteric activator binds to regulator site, making it so that substrate can bind more effectively, increasing product; active site unavailable in unbound formation

Transcriptional regulation

determines which genes are translated

includes chromatin remodeling, regulation of transcription initiation

post transcriptional regulation

determines types and availability of mRNAs to ribosomes;

variation in pre mRNA processing, removal of masking proteins, variations in rate of mRNA breakdown, RNA interference

translational regulation

determines rate at which proteins are made

includes variation in rate of initiation of protein synthesis

post translational regulation

Variations in rate of protein processing, removing of masking segments, varieties in rate of protein breakdown

includes phosphorylation and dephosphorylation

restricted localization

subcellular structures help bring order to metabolic pathways. In eukaryotic cells, some enzymes reside in specific cells

cofactors

non-protein components of proteins needed for protein to function properly

coenzyme

organic cofactor

gastroesophageal reflux (acid reflux)

• upward flow of acidic stomach continent into upper tract

  • Some pepsin remains in upper GI tract following a reflux event 

  • Subsequent reflex events reactivate pepsin (low pH)

  • Results in degradation of mucosal lining 

  • Secreted enzymes go through cotranslational import 

enzyme kinetics

study of enzyme-catalyzed reaction works

• important because understanding how enzymes work helps us regulate them

medical/pharmaceutical/industrial applications

application of enzyme kinetics! includes penicilin antibiotics, HIV protease inhibitors, viagra, RoundUp (herbicide)

spectrophotometry (enzyme kinetics application)

• sample tub: substrate (s) -enzyme→ product(s)

• Light passed through sample

• Detector measures absorbance: how much light absorbed by sample 

  • Either measuring: disappearance of reaction or appearance of product  

absorbance

how much light is absorbed by a sample

single substrate enzyme catlyzed reaction

E+S ←→ ES ←→ E+P

Basis for the Michalis-Menton equation and plot

Mechalis-Menten Equation

v = (vmax [S])/(Km + [S])

Michalis-Menten Plot

direct plot of Km vs Velocity used to explain enzyme action

• difficult to determine and vmax and Km from plot directly

• hyperbolic shape

vmax

maximum reaction rate; occurs when enzyme is saturated with substrate; determine by catalytic mechanism and concentration of substrate present

Km

tells us substrate-enzyme affinity; rate of ES breakdown/rate of ES formation; substrate concentration at ½ vmax; allows us to predict whether or not reaction will be affected by substrate availability

very low [S]

v = Vmax[S]/Km

very high [S]

• V = Vmax[S]/[S] = Vmax

[S] = Km

V = vmax[S]/2[S] = ½ Vmax 

Lineweaver-Burke Plot (double reciporcal)

x-axis 1/[S]

y axis 1/v

x-intercept = -1/Km

y-intercept = 1/v

competitive inhibitor (reaction rate and Km influence)

• can reach same max velocity as enzyme and substrate without competitive inhibitor, but will require more substrate (to outnumber inhibitor)

  • Same vmax

  • Different Km

noncompetitive inhibitor (reaction rate and Km influence0

• cannot reach same max since inhibitor binds to allosteric site (increasing [S]) will not relieve inhibition; enzyme substrate affinity remains the same since non-competitive inhibitor binds to allosteric site

  • Different vamx

  • Same Km 

functions of membrane

1. boundary/barrier 

2. organization/localization of specific functions

3. Transport

4. Signal detection/communication

types of lipids

• fatty acids

• phospholipid

• triglyceride

• steroids

• glycolipids

fatty acids

• carboxylic acid (polar) head + hydrocarbon (nonpolar)

• valuable energy source, can be thought of as building block for other lipids

saturated fatty acids

hydrocarbon tail composed entirely of single bonds

• straight molecules, pack closer together, more intermolecular forces at work

• solid at room temperature

• higher melting point

unsaturated fatty acid

hydrocarbon tail contain one or more double bond

• double bonds cause kinks, fewer intermolecular forces

• liquid at room temp

• lower melting point

cis-unsaturated fatty acid

unsaturated fatty acid with bulky groups on same side, prevents close packing