Law of Thermodynamics

• 1st – energy is conserved

• 2nd - Increased disorder

• 3rd – at absolute zero, entropy is zero

Reactions

• Exergonic reaction – release of free energy. Spontaneous

• Endergonic – require free energy from outside

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

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

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

Lab 1 – Diffusion and Osmosis

Dialysis bag of sucrose (solution) wasplaced in distilled water. Water moved intothe bag. There was a higher waterpotential outside the bag. Water movestoward a more negative water potential.

The bag is hypertonic to the distilled water.The water is hypotonic to the sugar solution

in the bag.

Lab 1 Cont.

• Adding sugar to the distilled water decreases the water potential there.

• Water potential is represented by Ψ “psi”

• Ψ = Ψp + Ψpi symbol

• At equilibrium the pressure (turgor) of the cell wall will balance out the negative potential of the solutes out of the cell.

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/ log[H+] = -log[H+]

Organic Compounds

• Contain both the elements carbon and hydrogen

Macromolecules

• Carbohydrates (sugars and starches)

• Lipids (fats, oils, and waxes)

• Proteins (functional and structural)

• Nucleic Acids (RNA and DNA)

Carbohydrates

• Consist of C, H, and O (2:1 ratio)

• Monomer – monosaccharide

• Pentose sugar has 5 carbons

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)

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)

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

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

Rate of Enzyme Catalysis

05

101520253035

1 2 3 4 5 6 7

Time (minutes)

Prod

uct (

in m

oles

)

0.17 umoles/sec

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.

DNA

• In Progress

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

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.

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.

Lab 6 Molecular Biology Part ITransformation with pGlo

• 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

BacteriaBig ring of DNA-one circular chromosome

The little ring of DNA is a plasmid.

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)

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?)

Lab 6 Molecular Biology Part IIRestriction Enzyme Cleavage

Eco RI HIND III No Enzyme

Distance CmNum

ber

of B

ase

Pai

rs (

log)

Plot the known, say HIND III

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).

Respiration

• Glycolysis-No oxygen needed

1. Glucose is broken into 2 pyruvate molecules.

2. Nets 2 ATP molecules by phosphorylation .

2 molecules of NAD+ are reduced to NADH

3. In fermentation pyruvate is converted to lactate, ethanol, etc.

4. Occurs in the cell cytoplasm.

Respiration (Cellular)

1. Occurs in mitochondria2. Pyruvate (See last slide) goes into the Krebs cycle

(AKA the Citric Acid Cycle).3. In a series of steps enzymes transfer electrons to

coenzyme acceptors NAD+ and FAD, CO2 released.4. 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.

Respiration (Cellular) ATP Ledger

Glycolysis 4 ATP’s -2 ATP = 2

Krebs 2 ATP’s = 2Chemiosmosis 34 ATP’s

3 per NADH 2 from glycolysis* = 4

2 from Acetyl CoA = 66 from Krebs cycle = 18

2 per FADH22 from Krebs cycle = 4

36* 2 ATP needed to move NADH from glycolysis across the mitochondrial membrane.

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.

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)

O2

Consumed

ml

Time (minutes)5

Germinating

Non-germinating

Colder-slower respiration

Warmer-faster respiration

Germinating- faster respiration

Dormant- Slower

25º

10º

25º10º

Photosynthesis• Light hits chlorophyll (strikes the antenna complexes on thylakoids in the chloroplast-photons

are funneled to the reaction center of the photosystem).

1. First occurs in the P680 reaction center in Photosystem II.2. Water is cleaved to replace the excited electrons which leave the reaction center. Oxygen is

released.3. The electrons move down the ETC. ATP is made.4. Last acceptor is P700 reaction center in Photosystem I.5. 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.

PhotosynthesisLight-Independent: AKA Calvin-Benson cycle: AKA

Dark Reaction (in the stroma)1. CO2 is converted to carbohydrate.2. CO2 is fixed as it reacts with ribulose

biphosphate( RuBP).3. The above is catalyzed by the enzyme ribulose.4. 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 plantC4- thrive in arid conditions (less photorespiration due to

special leaf anatomy)CAM-also thrive in arid conditions