Section 8.1 Notes-How Organisms Obtain Energy 10-21-09

Transformation of Energy
-Energy:the ability to do work
-Thermodynamics: the study of the flow and transformation of energy in the universe.

Laws of Thermodynamics
-First law: Energy can be converted from one form to another, but it cannot be created nor destroyed.
-Second law: energy cannot be converted without the loss of usable energy (heat, friction, sound, light etc).

Autotrophs and Heterotrophs
-Autotrophs: organisms that make their own food. Ex. plants, some protists(algae), and some bacteria.
-Heterotrophs: organisms that need to ingest food to obtain energy. Ex. animals, fungi, some protist (amoeba, paramecia), and some bacteria.

Metabolism: All of the chemical reactions in a cell.

Photosynthesis: light energy from the Sun is converted to chemical energy (glucose) for use by the cell

Cellular Respiration: organic molecules (glucose) are broken down to release energy for use by the cell.

Glucose: C6 H12 O6 CH2 O

ATP: The Unit of Cellular Energy
- ATP-the "energy currency" of the cell
-ATP: stored and releases a small amount ($1) of energy for movement, transport and other active processes in the cell.
-Both heterotrophs and autotrophs use ATP as an energy storage molecule in their cells.
- ATP is used to power processes in the cell such as the Calvin Cycle of photosynthesis in which CO2 is converted into glucose.

Date:10-22-09

ATP:
-ATP is also used for movement wihtin the cell.
-It is produced during cell respiration when carbohydrates such as glucose are broken down.
-Energy is released when the third phosphate on ATP is romoved and transferred to another molecule.
-This leaves behin ADP (adenosine diphosphate).
- like a rubberband pulled back then released.
- ATP becomes ADP and a phosphate group.
- microtubules microfiliments

Section 8.2 - Photosynthesis

Photosynthesis: the process by which the energy of the sun is used to convert H2O and CO2 into high energy sugars (glucose).
-Importance: we need glucose and other carbohydrates for energy but we cannot produce them ourselves. We also need oxygen and this is produced during photosynthesis by plants and algae.
- Glucose and Oxygen are the biggest.

Light Energy:
-Light is a form of energy that travels in the form of particles or waves. The waves are measured in wavelengths, which vary in length. Humans can see violet through red wavelengths. (Remember "ROY G BIV"?)
- nanometer : 1nm=1x10 (-9) m
- Color: reflected light. We see color.
- Pigment: a molecule that absorbs light.
- Whatever colors the pigment does NOT absorb are what we see.
- the nucleus, mitochondria, and chloroplast are double rapped because they're so special.

Pigments:
- Chlorophyll A is a pigment that absorbs violet, red, and blue wavelengths of light.
- Green is reflected by chlorophyll A. That's why most leaves appear green to us.
- Other pigments called accessory pigments (chlorophyll B, xanophyll, and carotene) help chlorphyll A absorb a greater spectrum of light.
- Leaves know to change color because there isn't as much light.

Chloroplasts:
- Photosynthesis takes place in the chlorplast.
- Double-membraned, disk-shaped organelle.
- located inside this disk are stacks of sacks.
- Each sack is called a thylakoid.
- Inside each thylakoid is chlorophyll and other pigments.
- Stacks of sacks are called grana.
- Surrounding the grana is a fluid called stroma.

Date: 10-27-09

Phase Two: The Calvin Cycle
- In the second phase of photosynthesis, called the calvin cycle, energy is stored in glucose.
- "light indefendent reaction"
- happens in the stroma.
- GOAL: uses the ATP and NADPH from the light reaction to convert CO2 into carbohydrate (glucose).
- What Goes In: ATP, NADPH, CO2, RuBP (a sugar)
- Happening in the stroma.
- RuBP is in the kitchen! It's in the stroma already.
- What Comes OUT: Glucose (stored by the plant), ADP, P, NADP+ : (shuttle back to the light reactions to get "charged up" again.)
- Four main steps:
Step 1: Six CO2 molecules combine with six RuBP's to form twelve 3-carbon molecules called 3-PGA.
Step 2: ATP provides energy and NADPH provides H+ to transform the 3-PGA molecules into twelve high-energy molecules called G3P. One molecule of G3P is essentially a "half-glucose". Two G3P's (half-glucoses) leave the cycle to become glucose.
Step 3: An enzyme called rubisco converts the remaining ten G3P molecules back into 6 molecules of RuBP.
- rubisco is an enzyme with an exception.
Step 4: The 6 RuBP's combine with 6 new CO2's to continue the cycle.

Date: 10-27-09

Factors influencing the rate of photosynthesis:
1. Availability of water - plants want plenty of water, but not too much.
2. Intensity of sunlight - plants want sunlight, but not too much.
3. Temperature - plants want it warm, but not too warm or too cold.

Alternative Pathways - the H2O/Co2 problem
C4 plants:
- Adaptation to conserve water in hot regions.
- Instead of 3-Carbon stages (3-PGA and G3P). these plants fix CO2 into a 4-Carbon molecule.
- Able to keep stomata closed on hot days and Calvin cycle occurs only in special cells.
- Used by sugar cane and corn.
CAM Plants:
- Conserves water in dry regions.
- Only open stomata for CO2 at night.
- Holds the CO2 until daytime. Calvin cycle proceeds while stomata are closed.
- Used by pineapple and cacti.
(most plants are not C4 or CAM plants)

Section 8.3 - Cellular Respiration

Overall Goal: To completely break down glucose and transfer the energy to ATP
Location: In the cytoplasm and mitochondra of all eukaryotic cells.

Glucose +

- Cellular respiration occurs in two main parts.
  • Glycolysis
  • Aerobic respiration
Glycolysis:
- Glucose is broken down in the cytoplasm through the process fo glycolysis.
- Two molecules of ATP and two molecules of NADH are formed for each molecule of glucose that is broken down.
- Location: Cyoplasm
- Goal: To break glucose ($100) into 2 pyruvates ($50). Does not require Oxygen therefore it is anaerobic.
- What Goes In: Glucose + 2 ATP's ("invested")
- What comes out:
  • 2 pyruvates ($50 each)
  • 2 ATP's ($1) (net)
  • 2 NADH's ($10)
- 9 step process with 2 phases:
  • energy consuming/investing
  • energy releasing
- Glucose enters the cell by facilitated diffusion.
- 2 ATP's phosphorylate glucose which makes it more reactive.
- Glucose breaks down into two 3-Carbon molecules.

Section 12.1 – 1/28/10
Griffith and Transformation

  • 1st major experiment on genetic material, Frederick Griffith (1928)
  • Question 1: How do bacteria cause pneumonia?
  • Exp.: Griffith grew 2 slightly different strains of bacteria.
  • Only 1 strain caused pneumonia.
- Smooth edged colonies caused pneumonia.
- Rough edged colonies did not cause pneumonia.

  • Mice injected with smooth edged bacteria died, those infected with rough edged bacteria lived (surprise, surprise!)
  • Question 2: Did the smooth edged bacteria secrete a deadly toxin?
  • Exp: Griffith heat killed some smooth bacteria and then injected it into the mice. The mice lived.
- Then Griffith mixed some heat-killed smooth bacteria with living rough bacteria. Since both of these are harmless on their own, you might expect the mice to live.
- But they died.
- Conclusion: somehow the disease causing bacteria passed on a gene to the non-disease causing bacteria.
- This process is called transformation.

  • Griffith realized that some genetic factor was being transferred from the heat-killed smooth bacteria to the living rough bacteria.
  • Question 3: What was this genetic material made of?
  • This question was answered by Oswald Avery in 1944

Avery Follows Up

  • Avery followed up Griffith’s work to determine what molecule the genetic material was.
  • Exp. 1: Avery made an extract from the heat-killed bacteria and subjected samples of it to enzymes that would break down carbs, lipids or proteins.
  • Mixed each sample with living rough bacteria and injected one type of sample into each group of mice.
  • All of the mice died.
  • Conclusion: Transformation had occurred and the genetic material is NOT composed of carbs, lipids or proteins.
  • Exp. 2: Avery sunbected the extract to enzymes that broke down DNA.
  • He mized this sample with living rough bacteria and injected it into the mice. The mice lived.
  • Conclusion: DNA was the transforming factor and is responsible for passing on traits.

Hershey and Chase

  • Avery’s conclusions were not widely accepted by other scientists. Hershey and Chase attempted to verify in 1952.
  • They used bacteriophages, viruses that infect bacteria to confirm that DNA and not protein was responsible for the infection.
  • Viruses (strands of DNA or RNA surrounded by a protein coat, or capsid) were grown in cultures with the radioactive isotopes (32P and 35S).
  • Proteins do not contain much P and DNA has no S. So if S was found inside the bacterium it could be concluded that the infecting agent was a protein.
  • If P was found inside the bacterium, the infecting agent must have been DNA.
  • Nearly all radioactivity in the bacterium was P.
  • Hershey and Chases agreed with Avery that the genetic material was definitely DNA and not protein.

Next Questions

  • Once it was confirmed that DNA was the genetic material, the next step was to determine how:
- DNA could carry information.
- DNA could replicate easily.
- DNA could code for specific traits.


2-5-10

Translation
  • Def. – the actual synthesis of a polypeptide (protein) which occurs under the direction of mRNA.
  • You go into the code with
The Process:
  1. The mRNA molecule attaches to the ribosome at its start codon (AUG)
  2. The tRNA bearing the anticodon UAC on one of its ends and carrying the amino acid methionine on its other end, binds to the mRNA at AUG.
  3. As the ribosome moves along the mRNA molecule, each mRNA codon is paired with its tRNA anticodon and amino acid. This will continue until one of the stop codons is reached. Stop codons are UAA, UGA, UAG
  4. The amino acids attach to one another with peptide bonds.
  5. When the ribosome reaches the end of the mRNA molecule, the protein detaches from the ribosome.