Law of Thermodynamics

1
Law of Thermodynamics

• 1st energy is conserved
• 2nd - Increased disorder
• 3rd at absolute zero, entropy is zero

2
Reactions

• Exergonic reaction release of free energy.
  Spontaneous
• Endergonic require free energy from outside

3
Metabolism

• The key to survival
• The total of all the life activities required to
  sustain life.
• Each process is chemical (metabolic) in nature
• Anabolism is a constructive activity
• Catabolism is a destructive process

4
Homeostasis

• The key to the quality of life
• Life functions are carried out in an integrated
  way that results in the maintenance of a stable
  internal environment (internal dynamic
  equilibrium)
• This maintenance is known as homeostasis

5
Water

• Polar. Solvent.
• Density highest at 4oC. Leads to fall spring
  overturn.
• High heat of vaporization
• Water absorbs heat in phase change
• High heat capacity (specific heat)- can absorb
  lots of heat with only minimal changes in
  temperature
• Hydrogen bonds
• Dissipates heat when broken
• Prevents sudden temperature change

6
Lab 1 Diffusion and Osmosis

• Dialysis bag of sucrose (solution) was
• placed in distilled water. Water moved into
• the bag. There was a higher water
• potential outside the bag. Water moves
• toward a more negative water potential.
• The bag is hypertonic to the distilled water.
• The water is hypotonic to the sugar solution in
  the bag.

7
Lab 1 Cont.

• Adding sugar to the distilled water decreases the
  water potential there.
• Water potential is represented by ? psi
• ? ?p ?pi symbol
• At equilibrium the pressure (turgor) of the cell
  wall will balance out the negative potential of
  the solutes out of the cell.

8
pH etc

• pH scale is used to show relative amounts of H
  and OH- ions
• pH of 7 neutral (equal amounts of H and OH-
  ions)
• Acid (pH 0-7) a compound that dissolves in
  water to yield H a proton donor
• Base (pH 7-14) a compound that dissolves in
  water to yield OH- a proton acceptor
• pH 1/ logH -logH

9
Organic Compounds

• Contain both the elements carbon and hydrogen

10
Macromolecules

• Carbohydrates (sugars and starches)
• Lipids (fats, oils, and waxes)
• Proteins (functional and structural)
• Nucleic Acids (RNA and DNA)

11
Carbohydrates

• Consist of C, H, and O (21 ratio)
• Monomer monosaccharide
• Pentose sugar has 5 carbons

12
Lipids, Protein and Nucleic Acid

• Lipids
• Saturated fatty acid no double bonds
• saturated with hydrogen!
• Protein
• Monomers are amino acids
• Nucelic Acid
• Monomers are nucelotides
• (sugar, phosphate, and nitrogenous base)

13
Proteins

• Monomer amino acids
• 20 commonly found
• 4 levels of structure
• Primary structure
• Number, type, and sequence of amino acids
• Secondary Structure
• Due to hydrogen bonding
• A twist alpha helix, or pleat beta pleat
• Tertiary Structure
• 3D folding pattern due to interactions between
  the amino acids and their various charges
• Quaternary
• The way two or more folded subunits fit together
  (hemoglobin structure)

14
Enzymes

• Organic Catalysts
• Protein nature all enzymes are either all
  protein or protein with non-protein parts known
  as coenzymes. Coenzymes are often vitamins.
• Active site Enzyme molecules are usually much
  larger than the molecule they interact with.
• Enzyme substrate complex with induced fit.
• Factors influencing enzyme action
• Temperature
• In general as temperature increases, action
  increases
• Most efficient temperature is optimum temperature
• At high temperature enzyme denatures
• Relative amounts of enzyme and substrate
• Rate of enzyme action varies with the amount of
  available substrate molecules.
• When an excess of substrate is added to a system
  with a fixed concentration of enzymes, the rate
  of enzyme action tends to increase to a point
  then remain fixed as long as the enzyme
  concentration remains constant.
• pH
• Ranges and optimums differ

15
Enzyme Catalysis Lab 2

• In this lab you used the enzyme catalase to
  convert hydrogen peroxide (H202) to water and
  oxygen gas.
• The slope of the graph line in the early,
  constant period is called the initial velocity.
  It is the same for an enzyme and substrate when
  conditions are the same. It is used to compare
  one reaction with another. It is constant because
  at the beginning of the reaction, the number of
  substrate molecules is usually large compared to
  the number of enzymes. Increasing the substrate
  concentration will increase productive
  collisions.
• Rate of reaction pick any two points on the
  straight line portion. Divide the difference in
  product by the difference in time.
• uMoles2 uMoles1 30 -20 10
• t2 - t1 180 -120 60

0.17 umoles/sec
16
Mitosis and Meiosis Lab

• You calculated the relative duration of the
  phases of mitosis.
• Prophase was found to have the longest relative
  length (50 )
• Telophase was the shortest (12)
• You looked at meiosis and mitosis in the
  formation of ascospores within the asci of
  Sordaria fimicola.
• Meiosis reduces the chromosome number. It starts
  out 2n and ends up n. (n is the number of
  different chromosomes you have. In humans your n
  number is 23 and you have two of each (2n) for 46
  total.)
• 2n is called diploid
• n is haploid
• Sordaria is usually haploid. It is diploid only
  when the mycelia of 2 strains fuse to form a
  diploid nucleus. It must undergo meiosis to
  return to its haploid state.
• Meiosis (chromosomes double then divide, leaving
  one n)
• is followed by
• Mitosis two of each of the 4 cells from
  meiosis. Resulting in 8 haploid ascospores in a
  sac called an ascus (plural asci). Many asci are
  in a fruiting body called a perithecium.
• Synapsis (coming together) and crossing over
  frequency can be calculated because the alleles
  are independently expressed in the haploid state.

17
DNA

• In Progress

18
Central Dogma DNA-RNA-Protein

• Replication DNA to DNA (semi-conservative)
• Transcription DNA to RNA
• Primary Transcript-result of translation
• Must be processed
• Introns-Clipped out (think intervening)
• Exons-stuck together
• Translation RNA to Protein
• 3 nucleotides 1 amino acid

19
DNA Replication

• 1. Start at origins
• 2. DNA Polymerase adds nucleotides
• 3. Nucleotides are only added to the 3 end.
  Grows in the 5 to 3 direction.
• 4. Have a leading strand and a lagging strand.
• 5. DNA ligase joins the lagging or Okazaki
  fragments together.
• 6. Chains must be started with an RNA primer
  added by the enzyme primase.

20
Lab 6 Molecular Biology Part I

• There are 3 ways to move genes between bacteria
• Conjugation (mating)
• Transduction (virus transfer the genetic
  material)
• Transformation (direct uptake of DNA by cells)
• We did a lab on transformation.

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Lab 6 Molecular Biology Part ITransformation
with pGlo
0

• We made the cells competent- able to take up
  environmental DNA.
• We mixed the competent E.coli with plasmids.
• The plasmids we used were already made and
  carried
• 1. a gene for antibiotic resistance.
• 2. pGlo gene

We could tell if our transformation worked
because we grew the bacteria on plates full of
ampicillin. They could only grow there if they
contained the plasmid with the antibiotic gene
(therefore the plasmid). If the sugar arabinose
was present it turned on the gene which made the
glow in the dark protein. Positive Control LB
Negative Control LB/Amp- ( or the plasmid)
22
Lab 6 Molecular Biology Part IIRestriction
Enzyme Cleavage

• DNA can be cut with restriction enzymes. These
  have been isolated from bacteria and protect them
  from viral invasion.
• They recognize palindromes. Many leave sticky
  ends. These allow different pieces of DNA cut
  with the same restriction enzyme to combine due
  to base pairing.
• In this lab DNA from the bacteriophage (virus)
  lambda was cut with three different restriction
  enzymes. The results were electrophoresed (is
  that a word?)

23
Lab 6 Molecular Biology Part IIRestriction
Enzyme Cleavage
Eco RI
HIND III
No Enzyme
Plot the known, say HIND III
Number of Base Pairs (log)
Distance Cm
If one of the enzymes produced pieces of known
size (Like HIND III- data was given), the size of
pieces cut with a different restriction enzyme
can be determined. To find the size of pieces
cut with ECO RI measure the bands and find the
base pairs from the intersecting line (See the
red line).
24
Respiration

• Glycolysis-No oxygen needed
• Glucose is broken into 2 pyruvate molecules.
• Nets 2 ATP molecules by phosphorylation .
• 2 molecules of NAD are reduced to NADH
• In fermentation pyruvate is converted to lactate,
  ethanol, etc.
• Occurs in the cell cytoplasm.

25
Respiration (Cellular)

• Occurs in mitochondria
• Pyruvate (See last slide) goes into the Krebs
  cycle (AKA the Citric Acid Cycle).
• In a series of steps enzymes transfer electrons
  to coenzyme acceptors NAD and FAD, CO2 released.
• Electron Transport Chain
• The electron energy from NADH and FADH2 is
  retrieved and stored in ATP.
• ETC is made of a series of pigment containing
  cytochrome compounds that serve as electron
  carriers.
• Cytochromes are embedded in the inner membrane of
  the mitochondria.
• Making ATP from ADP this way is oxidative
  Phosphorylation.

26
Respiration (Cellular) ATP Ledger
2 ATP needed to move NADH from glycolysis
across the mitochondrial membrane.
27
Respiration (Cellular)Mitchell Hypothesis

• Chemiosmotic coupling hypothesis
• Movement of electrons through the ETC is
  accompanied by a protein pumping mechanism that
  sets up an energy gradient consisting of hydrogen
  ions (protons) across the inner mitochondrial
  membrane. These are pumped from the inner
  mitochondrial matrix to the outer compartment.
  As they flow back through the molecule known as
  ATP Synthase, free energy is released and
  conserved as ATP.

28
Lab 5Cell Respiration

• In this lab you compared germinating with
  non-germinating peas and their rate of
  repiration. You also looked at the effect of
  temperature.
• As plants respire they use up oxygen. You
  measured how fast they used it up.
• Non-germinating seeds are alive but dormant.
• To take CO2 out of the equation a CO2 absorbent
  was used (KOH)

Germinating
25º
Non-germinating
O2 Consumed ml
10º
Colder-slower respiration Warmer-faster
respiration Germinating- faster
respiration Dormant- Slower
25º
10º
5
Time (minutes)
29
Photosynthesis

• Light hits chlorophyll (strikes the antenna
  complexes on thylakoids in the chloroplast-photons
  are funneled to the reaction center of the
  photosystem).
• First occurs in the P680 reaction center in
  Photosystem II.
• Water is cleaved to replace the excited electrons
  which leave the reaction center. Oxygen is
  released.
• The electrons move down the ETC. ATP is made.
• Last acceptor is P700 reaction center in
  Photosystem I.
• Photons boost electrons again. 2e- are energized
  and reduce NADH forming NADPH. NADP is reduced
  to NADPH. (OIL RIG)
• Steps 1-5 is the light reaction.
• ATP and NADPH will be used in the dark reaction.
• Photophosphorylation is the term for making ATP
  from the movement of electron excited by light,
  as they move down the electron transport chain.
• Remember there is also Substrate level
  phosphorylation and oxidative phosphorylation.
  They all involve adding a phosphate. Substrate is
  a direct transfer, oxidation is when the energy
  comes from breaking down food.

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PhotosynthesisLight-Independent AKA
Calvin-Benson cycle AKA Dark Reaction (in the
stroma)

• CO2 is converted to carbohydrate.
• CO2 is fixed as it reacts with ribulose
  biphosphate( RuBP).
• The above is catalyzed by the enzyme ribulose.
• RuBP is regenerated so the cycle may continue.
• Photorespiration-an inefficient form of the dark
  reaction O2 os fixed instead of CO2. No
  carbohydrates are produced.
• C3- typical plant
• C4- thrive in arid conditions (less
  photorespiration due to special leaf anatomy)
• CAM-also thrive in arid conditions