Law of Thermodynamics 

What are the main laws of thermodynamics?

⮚ Closed system; the earth is not a closed system, because the sun is providing energy for us and  we replenish our energy, however the universe is a closed system. These laws are applied to  only closed systems, closed systems are well insulated.

⮚ The Laws of Thermodynamics, describe the quantity (total amount) and the quality (the  usefulness) of energy.  

o First Law (Law of Conservation of Energy), energy cannot be created or destroyed, but  you can change the way or the form of energy.  

o Second Law: Entropy (disorder) increases. Once used, energy becomes less available  to do work. This drives diffusion. You must account for the total energy you can never  destroy or create it (first law). Once you have used the energy it is always in a less  useable form because disorder has increased. Once you use energy it will become less  usable, ALWAYS. Useful energy tends to be stored in highly ordered matter, and  whenever energy is used within a closed system, there is an overall increase in  randomness and disorder of matter.  

What is the definition of exergonic?

We also discuss several other topics like What is the meaning of chi­ squared?

⮚ Chemical Reactions, start with one set of molecules which have bonds by definition, you’re  going to take either a molecule or a set of molecules that you start with and you’re going to  reorganize the bonds in another set of molecules; the molecules that you start are called  reactants, and the molecules that you end with, the ones that you have reorganized, are called  products. Measuring energy over time. (When you make bonds you store energy, and when  you break bonds you release energy.)  Don't forget about the age old question of When public opinion is not stable, its movements can usually be explained by which of the following?

o Types

▪ Exergonic: something is coming out, you’re releasing energy. The energy is  going downhill. The reactants have more energy than the products, the energy  left because of heat that has been given off. (Ex. In the military, you explode a  bomb, that is an exergonic energy. This is why it explodes, your giving off  energy.)  

What is the definition of endergonic?

• energy of reactants -> energy of products.

• A + B -> C + D +energy

▪ Endergonic: The energy is going uphill. Not releasing energy, instead this is  storing energy. The reactants that you start with are lower than the products,  they have moved uphill.  

• Energy of products -> energy of reactants

• A + B + energy -> C + D

⮚ Coupled Reactions,  

o First: Exergonic reaction: A + B -> C + D +energy

o Second: Endergonic reaction: E + F + energy from above rxn. -> G + H

⮚ Energy Carrier Molecules (this is how you move energy around from one cell to another;  from exergonic to endergonic)

o ADP + P + Energy -> ATP (energy storage molecule) If you want to learn more check out When and why did the eu develop the european neighbourhood policy (enp)?
If you want to learn more check out What is the meaning of the information-processing approach?

▪ Adenosine Triphosphate (ATP), three  

o ATP + H20 -> ADP + P + energy (energy released)

o Energy Carriers

▪ e.g., NAD(+)+ 2E(-)+ H(+) (Oxidized form)-> NADH (reduced form) • Oxidized form: electron acceptor

• Reduced form: electron donor

• Also, FAD+ and NADP+

⮚ Catalyst, lowers activation energy, not a reactant or product.

o Therefore, they increase rate of reaction, do not change ratios of products or reactants,  and are not themselves changed by reaction.  Don't forget about the age old question of What is the field that uniquely identifies a given record in a table?

⮚ Life requires moderate temperatures

⮚ How are life processes maintained without self-destruction?

o Employ catalysts – Enzymes (almost exclusively composed of protein) ⮚ A + B + Enz -> ABEnz (substrate enzyme complex) -> C + D + Enz

⮚ Active Site, region of an enzyme molecule that binds substrates and performs the catalytic  function of the enzyme.  

⮚ Enzyme action consists of:

o Binding of substrate, the atoms or molecules that are the reactants for an enzyme  catalyzed chemical reaction

o Catalysis

o Release of products

⮚ Enzyme Regulation

o Limit amount of enzyme We also discuss several other topics like What is the meaning of peacekeeping?

o Store enzyme in inactive form; activate only when released.

o End product inhibition=product inhibits enzyme activity. (These are concentration  dependent)  

▪ Competitive inhibition = product competes for active site.

▪ Allosteric inhibition = product binds to site on enzyme which changes shape  of active site.

Energy Use in Cells 

⮚ Light Dependent Reactions (Thylakoid processes)  

o Photosynthesis, process by which solar energy is trapped and stored as chemical  energy in the bonds of organic molecules such as sugar. Photosynthesis occurs in  plants, photosynthetic protists, and certain types of bacteria.  

o Light travels as photons

o Shorter wavelengths = more energy.

o Three things occur when a specific wavelength of light strikes an object.  o Two types of Pigments

▪ Chlorophyll, absorbs red and blue light, reflects green.

▪ Accessory Pigments, absorbs additional wavelengths of light energy and  transfer them to chlorophyll.  

• Carotenoids, absorb blue and green (reflect orange)

• Phycocyanins, absorb blue and green (reflect red)

o Results in a relatively broad absorption spectrum.

o Light boosts electrons in pigment molecules to high energy states. As they fall back  to original E state -> E released is used to synthesize ATP. Use electrons here to turn  useless light into energy.  

o Photosystem, a cluster of chlorophyll, accessory pigment molecules, proteins, and  other molecules that collectively capture light energy, transfer some of the energy to  electrons, and transfer the energetic electrons to an adjacent electron transport chain. ▪ P680: Photosystem 2 (proceeds and then feeds into photosystem 1)

• You get replacement electrons from water.  

▪ P700: Photosystem 1

• You get replacement electrons from photosystem 2.

▪ Energy transfer and the light reactions of photosynthesis:

o Three things that come out of the thylakoid process

▪ ATP, photosystem 2

▪ NADPH, photosystem 1

▪ Oxygen, plant gives off the oxygen.  

⮚ Light Independent Reaction (Stroma processes)

o Making glucose with ATP, NADPH, CO2 (Carbon fixation)

o Ribulose Bisphosphate  

⮚ Glycolysis, reactions carried out in the cytoplasm, that break down glucose into two  molecules of pyruvic acid, producing two ATP molecules; does not require oxygen but can  proceed when oxygen is present.  

o Two processes in cytoplasm

▪ Glucose activation: phosphates attached to glucose molecule, results in high  energy unstable molecule.

▪ Energy harvest: phosphates donated to ADP -> ATP

o Energy input per glucose molecule: 2ATP

o Energy Output:  

▪ 4ATP

▪ 2NADH

o Net energy yield = 2ATP + 2NADH

⮚ Fermentation, anaerobic reactions that convert the pyruvic acid produced by glycolysis into  lactic acid or alcohol and CO2, using hydrogen ions and electrons from NADH; the primary  function of fermentation is to regenerate NAD+ so that glycolysis can continue under  anaerobic conditions.  

o Under anaerobic conditions only.

o Glycolysis leads to buildup of NADH (run out of NAD+)

o Two methods to convert NADH -> back to NAD+

▪ Lactic acid fermentation (Strenuous exercise)

• Pyruvic acid + NADH -> lactic acid + NAD + (pH lowered in tissues) ▪ Alcoholic fermentation (Microbes such as yeast)

• Pyruvic acid +NADH -> ethanol (2C) +CO2 + NAD+

Molecular Genetics 

⮚ DNA structure and Replication

o DNA = genetic material

o Pneumococcus sp. (Pneumonia) and bacterial transformation (one of the first  experiments that gets people to question that protein is not the genetic material. There  are two major strains:  

▪ S strain = encapsulated form; causes pneumonia

▪ R strain = naked, encapsulated form; not virulent

▪ Example

• Inject encapsulated

• Inject naked  

• Inject heat killed encapsulated

• Inject heat killed encapsulated + naked

o Bacteriophages: Viruses that infect bacteria. Consist only of protein and DNA ▪ Phage attaches to bacterial cell wall.

▪ Phage DNA injected into bacterium.

▪ Phage genes take over and run cell  

• phage DNA copes manufactured  

• phage protein parts manufactured.

▪ Bacteria produces enzyme to burst cell and release new phages.  

o Hershey Chase Experiment

▪ Phage labeled with radioactive phosphorous (P32)->only label DNA

• Grow with bacteria

• Label turns up in bacteria

• Some new phages contain radioactivity.

▪ Phage labeled with radioactive sulfur (S35) -> only label protein

• Grow with bacteria

• No label turns up in bacteria

• No new phages agree radioactive  

o Clues on the Structure of DNA

▪ Quantity of DNA varies among species, but is constant between cells of a  given species.

▪ However, gametes have half amount of DNA found in other cells.

▪ Amounts of nucleotide bases varies among species, but always show these  ratios:

• 1:1 Adenine and Thymine (Complementary Bases)

• 1:1 Cytosine and Guanine (Complementary Bases)

▪ X-Ray diffraction studies:

• Molecule is helical

• Uniform diameter of 2 nm

• Subunits separated by .34 nm

• Full turn of helix every 3.4 nm

• Backbone faces outside, bases face inside.

o DNA Replication

▪ Helicase and Topoisomerase -> unwind DNA helix

▪ Primase -> lay down RNA primer

▪ DNA polymerase III -> replication in 5’ to 3’ direction

▪ DNA polymerase I -> remove RNA primer, replace with DNA

▪ DNA ligase -> splice “primer” piece to rest of daughter strand.  

o Mutations, a change in the base sequence of DNA in a gene; often used to refer to a  genetic change that is significant enough to alter the appearance or function of the  organism.  

▪ Point Mutations, a mutation in wihich a single base pair in DNA has been  changed

• Mutation may not change code due to triplet redundancy. CTC  

changed to CTT: both code glutamic acid.

• Mutation may code for an amino acid that is functionally equivalent to  the original=neutral mutation. CTC changed to CTA: both code for  

hydrophilic amino acids (glutamate to aspartate).

• Mutation encodes for functionally different amino acid. CTC changed  to CAC: hydrophilic changed to hydrophobic amino acid (glutamate to  

valine); Ex. Sickle cell

• Mutation may produce stop codon.  

▪ Insertions (one or more pairs of nucleotides are inserted into a gene) and  Deletions (one or more pairs of nucleotides are removed from a gene)

⮚ Deciphering the Genetic Code

o Clues:

▪ There are 20 different amino acids possible in proteins.  

▪ There are four bases possible in DNA

o Solutions

▪ One to One: base to amino acid? Wrong! Could only code for one amino acid. ▪ Two bases per amino acid? 4^2=16 combinations. Wrong! Four combinations  too few.

▪ Three bases par amino acid? 4^3=64 combinations. Right! More than enough.  o Information within the Code:

▪ Each triplet of bases = one amino acid.

▪ Also “Start” (AUG) and “stop” (UGA, UAG, UAA) sequences.

▪ Great Deal of redundancy. Some amino acids have more than one codon.  ⮚ Frame Shift Mutation

⮚ Gene Regulation in Prokaryotes  

⮚ Gene Regulation in Eukaryotes

⮚ Human Alterations of Phenotype; Genetic Engineering

Law of Thermodynamics 

⮚ Closed system; the earth is not a closed system, because the sun is providing energy for us and  we replenish our energy, however the universe is a closed system. These laws are applied to  only closed systems, closed systems are well insulated.

⮚ The Laws of Thermodynamics, describe the quantity (total amount) and the quality (the  usefulness) of energy.  

o First Law (Law of Conservation of Energy), energy cannot be created or destroyed, but  you can change the way or the form of energy.  

o Second Law: Entropy (disorder) increases. Once used, energy becomes less available  to do work. This drives diffusion. You must account for the total energy you can never  destroy or create it (first law). Once you have used the energy it is always in a less  useable form because disorder has increased. Once you use energy it will become less  usable, ALWAYS. Useful energy tends to be stored in highly ordered matter, and  whenever energy is used within a closed system, there is an overall increase in  randomness and disorder of matter.  

⮚ Chemical Reactions, start with one set of molecules which have bonds by definition, you’re  going to take either a molecule or a set of molecules that you start with and you’re going to  reorganize the bonds in another set of molecules; the molecules that you start are called  reactants, and the molecules that you end with, the ones that you have reorganized, are called  products. Measuring energy over time. (When you make bonds you store energy, and when  you break bonds you release energy.)  

o Types

▪ Exergonic: something is coming out, you’re releasing energy. The energy is  going downhill. The reactants have more energy than the products, the energy  left because of heat that has been given off. (Ex. In the military, you explode a  bomb, that is an exergonic energy. This is why it explodes, your giving off  energy.)  

• energy of reactants -> energy of products.

• A + B -> C + D +energy

▪ Endergonic: The energy is going uphill. Not releasing energy, instead this is  storing energy. The reactants that you start with are lower than the products,  they have moved uphill.  

• Energy of products -> energy of reactants

• A + B + energy -> C + D

⮚ Coupled Reactions,  

o First: Exergonic reaction: A + B -> C + D +energy

o Second: Endergonic reaction: E + F + energy from above rxn. -> G + H

⮚ Energy Carrier Molecules (this is how you move energy around from one cell to another;  from exergonic to endergonic)

o ADP + P + Energy -> ATP (energy storage molecule)

▪ Adenosine Triphosphate (ATP), three  

o ATP + H20 -> ADP + P + energy (energy released)

o Energy Carriers

▪ e.g., NAD(+)+ 2E(-)+ H(+) (Oxidized form)-> NADH (reduced form) • Oxidized form: electron acceptor

• Reduced form: electron donor

• Also, FAD+ and NADP+

⮚ Catalyst, lowers activation energy, not a reactant or product.

o Therefore, they increase rate of reaction, do not change ratios of products or reactants,  and are not themselves changed by reaction.  

⮚ Life requires moderate temperatures

⮚ How are life processes maintained without self-destruction?

o Employ catalysts – Enzymes (almost exclusively composed of protein) ⮚ A + B + Enz -> ABEnz (substrate enzyme complex) -> C + D + Enz

⮚ Active Site, region of an enzyme molecule that binds substrates and performs the catalytic  function of the enzyme.  

⮚ Enzyme action consists of:

o Binding of substrate, the atoms or molecules that are the reactants for an enzyme  catalyzed chemical reaction

o Catalysis

o Release of products

⮚ Enzyme Regulation

o Limit amount of enzyme

o Store enzyme in inactive form; activate only when released.

o End product inhibition=product inhibits enzyme activity. (These are concentration  dependent)  

▪ Competitive inhibition = product competes for active site.

▪ Allosteric inhibition = product binds to site on enzyme which changes shape  of active site.

Energy Use in Cells 

⮚ Light Dependent Reactions (Thylakoid processes)  

o Photosynthesis, process by which solar energy is trapped and stored as chemical  energy in the bonds of organic molecules such as sugar. Photosynthesis occurs in  plants, photosynthetic protists, and certain types of bacteria.  

o Light travels as photons

o Shorter wavelengths = more energy.

o Three things occur when a specific wavelength of light strikes an object.  o Two types of Pigments

▪ Chlorophyll, absorbs red and blue light, reflects green.

▪ Accessory Pigments, absorbs additional wavelengths of light energy and  transfer them to chlorophyll.  

• Carotenoids, absorb blue and green (reflect orange)

• Phycocyanins, absorb blue and green (reflect red)

o Results in a relatively broad absorption spectrum.

o Light boosts electrons in pigment molecules to high energy states. As they fall back  to original E state -> E released is used to synthesize ATP. Use electrons here to turn  useless light into energy.  

o Photosystem, a cluster of chlorophyll, accessory pigment molecules, proteins, and  other molecules that collectively capture light energy, transfer some of the energy to  electrons, and transfer the energetic electrons to an adjacent electron transport chain. ▪ P680: Photosystem 2 (proceeds and then feeds into photosystem 1)

• You get replacement electrons from water.  

▪ P700: Photosystem 1

• You get replacement electrons from photosystem 2.

▪ Energy transfer and the light reactions of photosynthesis:

o Three things that come out of the thylakoid process

▪ ATP, photosystem 2

▪ NADPH, photosystem 1

▪ Oxygen, plant gives off the oxygen.  

⮚ Light Independent Reaction (Stroma processes)

o Making glucose with ATP, NADPH, CO2 (Carbon fixation)

o Ribulose Bisphosphate  

⮚ Glycolysis, reactions carried out in the cytoplasm, that break down glucose into two  molecules of pyruvic acid, producing two ATP molecules; does not require oxygen but can  proceed when oxygen is present.  

o Two processes in cytoplasm

▪ Glucose activation: phosphates attached to glucose molecule, results in high  energy unstable molecule.

▪ Energy harvest: phosphates donated to ADP -> ATP

o Energy input per glucose molecule: 2ATP

o Energy Output:  

▪ 4ATP

▪ 2NADH

o Net energy yield = 2ATP + 2NADH

⮚ Fermentation, anaerobic reactions that convert the pyruvic acid produced by glycolysis into  lactic acid or alcohol and CO2, using hydrogen ions and electrons from NADH; the primary  function of fermentation is to regenerate NAD+ so that glycolysis can continue under  anaerobic conditions.  

o Under anaerobic conditions only.

o Glycolysis leads to buildup of NADH (run out of NAD+)

o Two methods to convert NADH -> back to NAD+

▪ Lactic acid fermentation (Strenuous exercise)

• Pyruvic acid + NADH -> lactic acid + NAD + (pH lowered in tissues) ▪ Alcoholic fermentation (Microbes such as yeast)

• Pyruvic acid +NADH -> ethanol (2C) +CO2 + NAD+

Molecular Genetics 

⮚ DNA structure and Replication

o DNA = genetic material

o Pneumococcus sp. (Pneumonia) and bacterial transformation (one of the first  experiments that gets people to question that protein is not the genetic material. There  are two major strains:  

▪ S strain = encapsulated form; causes pneumonia

▪ R strain = naked, encapsulated form; not virulent

▪ Example

• Inject encapsulated

• Inject naked  

• Inject heat killed encapsulated

• Inject heat killed encapsulated + naked

o Bacteriophages: Viruses that infect bacteria. Consist only of protein and DNA ▪ Phage attaches to bacterial cell wall.

▪ Phage DNA injected into bacterium.

▪ Phage genes take over and run cell  

• phage DNA copes manufactured  

• phage protein parts manufactured.

▪ Bacteria produces enzyme to burst cell and release new phages.  

o Hershey Chase Experiment

▪ Phage labeled with radioactive phosphorous (P32)->only label DNA

• Grow with bacteria

• Label turns up in bacteria

• Some new phages contain radioactivity.

▪ Phage labeled with radioactive sulfur (S35) -> only label protein

• Grow with bacteria

• No label turns up in bacteria

• No new phages agree radioactive  

o Clues on the Structure of DNA

▪ Quantity of DNA varies among species, but is constant between cells of a  given species.

▪ However, gametes have half amount of DNA found in other cells.

▪ Amounts of nucleotide bases varies among species, but always show these  ratios:

• 1:1 Adenine and Thymine (Complementary Bases)

• 1:1 Cytosine and Guanine (Complementary Bases)

▪ X-Ray diffraction studies:

• Molecule is helical

• Uniform diameter of 2 nm

• Subunits separated by .34 nm

• Full turn of helix every 3.4 nm

• Backbone faces outside, bases face inside.

o DNA Replication

▪ Helicase and Topoisomerase -> unwind DNA helix

▪ Primase -> lay down RNA primer

▪ DNA polymerase III -> replication in 5’ to 3’ direction

▪ DNA polymerase I -> remove RNA primer, replace with DNA

▪ DNA ligase -> splice “primer” piece to rest of daughter strand.  

o Mutations, a change in the base sequence of DNA in a gene; often used to refer to a  genetic change that is significant enough to alter the appearance or function of the  organism.  

▪ Point Mutations, a mutation in wihich a single base pair in DNA has been  changed

• Mutation may not change code due to triplet redundancy. CTC  

changed to CTT: both code glutamic acid.

• Mutation may code for an amino acid that is functionally equivalent to  the original=neutral mutation. CTC changed to CTA: both code for  

hydrophilic amino acids (glutamate to aspartate).

• Mutation encodes for functionally different amino acid. CTC changed  to CAC: hydrophilic changed to hydrophobic amino acid (glutamate to  

valine); Ex. Sickle cell

• Mutation may produce stop codon.  

▪ Insertions (one or more pairs of nucleotides are inserted into a gene) and  Deletions (one or more pairs of nucleotides are removed from a gene)

⮚ Deciphering the Genetic Code

o Clues:

▪ There are 20 different amino acids possible in proteins.  

▪ There are four bases possible in DNA

o Solutions

▪ One to One: base to amino acid? Wrong! Could only code for one amino acid. ▪ Two bases per amino acid? 4^2=16 combinations. Wrong! Four combinations  too few.

▪ Three bases par amino acid? 4^3=64 combinations. Right! More than enough.  o Information within the Code:

▪ Each triplet of bases = one amino acid.

▪ Also “Start” (AUG) and “stop” (UGA, UAG, UAA) sequences.

▪ Great Deal of redundancy. Some amino acids have more than one codon.  ⮚ Frame Shift Mutation

⮚ Gene Regulation in Prokaryotes  

⮚ Gene Regulation in Eukaryotes

⮚ Human Alterations of Phenotype; Genetic Engineering