Weekly Reflection 4/9-4/13

Hello all! This week in AP Bio we focused on learning about the central  dogma and gene expression.

Initiation is when RNA polymerase attaches to a promoter region in front “upstream” of a gene. In prokaryotes, the RNA poly binds directly to the promoter. In eukaryotes, the RNA poly requires an assemblage of transcription factor proteins to be able to bind to the promoter.
Elongation is when RNA production occurs in a 5’ to 3’ direction. The template strand of DNA is the one that the RNA transcript is being produced off of complementary nucleotides. The nontemplate strand or coding strand of the dna will have the same.
Termination is when transcript production continues until end of the transcription unit is reached. There are multiple mechanisms of termination, teo examples from prokaryotes are:
-Rho-independent: the transcript based hydrogen bond with themselves, fold back and pull the transcript out of RNA polymerase.
-Rho-dependent: the rho protein destabilizes the RNA-DNA hydrogen bonding at RNA polymerase and ceases transcription.
What happens next? Many kinds of RNA. Unlike DNA, RNA plays many roles in the cell. There are around 10 described types of RNA , each with different functions, but there are three major types:
-Messenger RNA: carrried DNA sequence information to the ribosome
-Transfer RNA: carries specific amino acids to the ribosome
-Ribosomal RNA: major structural building block of ribosomes
In prokaryotes, the mRNA transcript is immediately translated. In eukaryotes, the mRNA is extensively processed in nucleus before it leaves to be translated.
Post-transcriptional mRNA processing happens in eukaryotes ONLY. There’s a 5’ cap and poly-A tail: A modified nucleotide is added to 5’ end, which gives it directionality, and a tail of several hundred adenine residues put on 3’ end of transcript, which allows it to move out of cell and gives it directionality.
In exon splicing, eukaryotic genes contain large stretches of non-coding DNA (introns) interspersed between coding DNA (Exons). To produce a functional protein, introns must be removed and exits must be spliced together prior to movement of mRNA transcript to nucleus. This process is accomplished by a spliceosome (a type of enzymatic RNA molecule).
Why introns? This is not answered. It could be evolutionary baggage or maybe S elfish genes. We know that having multiple exons in a gene allows eukaryotes to make multiple functional proteins from one gene (alternative splicing).

Translation:
Ribosomes are the S ite of protein synthesis. It’s the only “non-membrane” bound organelle. All cells have them. They’re composed of two subunits. They have three sites:
-A site: “aminoacyl”- where amino acids enter the ribosome
-P site: “peptidyl”- where the growing polypeptide is kept
-E site: “exit”- where empty tRNA molecules leave
tRNA transfers RNA molecules and are responsible for bringing amino acids to the ribosome. Amino acids are added to tRNA molecules through the action of “amino-acyl tRNA synthase” enzymes. A tRNA with an amino acid attached is said to be “charged”.
The genetic code is universal across all domains of life. The triplet code is when mRNA is read in united of three bases (codons). There are 64 possible codons (for 20 possible amino acids). The code is redundant and unambiguous, and has “start” and “stop”.

This week was interesting learning about all of this! Looking forward to diving deeper as it is still kinda confusing!

Weekly Reflection 2/5-2/10

Hey guys! This week starting on Monday we took a test on cellular respiration which ended up going pretty well for me so I was hyped!! The rest of the week we basically focused on this lab called, “Photosynthesis and Cellular Respiration Kit, a ThINQ Investigation.”

We first started the lab by answering a series of pre lab questions. But before that the lab basically gave a summary of information we had already learned about photosynthesis and cellular respiration so that kinda helped us answer some of the questions for the pre lab. We learned that organisms need matter and energy to live, we learned the 2nd law of thermodynamics, entropy and how that is controlled disorder, we learned that organisms need energy to survive, and that energy is capture in universal units of chemical energy. Our algae balls ended up dying during the pre lab process but we just used another group’s samples to look at under the microscope.

On Thursday what we did was specifically to see how light affects photosynthesis which was really interesting!!!! We learned that organisms need matter and energy to live, we learned the 2nd law of thermodynamics, entropy and how that is controlled disorder, we learned that organisms need energy to survive, and that energy is capture in universal units of chemical energy. I was kinda confused during the lab but my table mates helped me understand what was going on.

Weekly Reflection 1/29-2/04

Last week we covered Photosynthesis. Photosynthesis is the way plants get energy and nutrients to function. The equation for this reaction is represented by the following equation:

I am going to post below all of the notes I have been taking in class this week.

• Fermentation anaerobic respiration enable cells to produce ATP without the use of oxygen
  • Most cellular respiration requires O2 to produce ATP
  • Without O2 the electron transport chain will cease to operate
  • In that case, glycolysis couples with fermentation or anaerobic respiration to produce ATP.
• Anaerobic respiration uses an electron transport chain with a final electron acceptor other than O2 for example sulfate
• Fermentation uses substrate-level phosphorylation instead of an electron transport chain to generate ATP
• Types of fermentation
  • Fermentation consists of glycolysis plus reactions that generate NAD plus which can be reused by glycolysis
  • Two common types of alcohol fermentation and lactic acid fermentation
  • In alcohol fermentation pyruvate is converted to ethanol in two steps
  • The first step releases CO2 from pyruvate and the second step reduces acetaldehyde to ethanol
  • Alcohol fermentation by yeast is used in brewing, wine making, and baking
• In lactic acid fermentation pyruvate is reduced by NADH forming lactate as an end product with no release of CO2
  • Lactic acid fermentation by some fungi and bacteria is used to make cheese and yogurt
  • Human muscle cells use lactic acid fermentation to generate ATP when O2 is scarce
• Comparing fermentation with anaerobic and aerobic respiration
  • All use glycolysis to oxidize glucose and harvest chemical energy of food
  • In all 3, NAD+ is the oxidizing agent that accepts electrons during glycolysis
  • The processes have different final electron acceptors an organic molecule in fermentation and O2 in cellular respiration
  • Cellular respiration produces 32 ATP per glucose molecule fermentation produces 2 ATP per glucose molecule
  • Obligate anaerobes carry out only fermentation or anaerobic respiration and cannot survive in the presence of O2
  • Yeast and many bacteria are facultative anaerobes, meaning that they can survive using either fermentation or cellular respiration
  • In a facultative anaerobe, pyruvate is a fork in the metabolic road that leads to two alternative catabolic routes  

• What are the key players in the Calvin Cycle
  • RuBisCo is an enzyme that takes carbon dioxide and sticks in onto Ribulose bisphosphate
  • The energy that eventually processes these things and then you get a three carbon molecule that becomes sugar
• C3 plants do great in cool weather but suffer in warm/hot weather-why?
  • Not enough moisture, the stoma evaporates the water away. These plants lose a ton of water in this kind of dry situations.
• What enzyme do we know about in photosynthesis that needs CO2 to function?
  • RUBISCO is not monogamous it can bind with CO2 and O2
• How can we even have plants in hot/warm locations?
  • We can prevent photorespiration by getting rid of the oxygen not letting it get to the rubisco
• Two strats for hot weather plants
  • C4 pathway and cam pathway also known as crassalacean acid metabolism
  • C4 photosynthesis separates things spatially
  • Xylem is a vascular tissue that transports water and phloem transports sugars
  • Cam separates things temporally leaf structure is the same as C3 it just has different enzymes and mechanisms

I actually find all of the stuff we are learning about super interesting and not too hard to understand!!!! I usually struggle with most concepts in biology but this past unit and the current one about plants is all really easy ish to understand

Weekly Reflection 1/22/1/26

Hi everyone! It has been a couple of weeks since I last posted because we have been so busy doing stuff in class! This week we worked on cellular respiration and its complicated steps. I’m going to post below all of the notes I took the other day in class.

Step Wise Energy Harvest Via NAD+ and the Electron

• NADH passes the electrons to the electron transport chain
• Unlike an uncontrolled reaction the electron transport chain passes electrons in a series of steps instead of one explosive reaction
• O2 pulls electrons down the chain in an energy yielding tumble
• The energy yielded is used to regenerate ATP

The stages of cellular respiration: a preview

• Glycolysis (breaks down glucose into two molecules of pyruvate)
• Pyruvate oxidation and the citric acid cycle (completes the breakdown of glucose)
• Oxidative phosphorylation (accounts for most of the ATP synthesis)
• Oxidative phosphorylation accounts for almost 90% of the ATP generated by cellular respiration
• A smaller amount of ATP is formed in glycolysis and the citric acid cycle by substrate-level phosphorylation
• For each molecule of glucose degraded to CO2 and water by respiration, the cell makes up to 32 molecules of ATP

Glycolysis harvests chemical energy by oxidizing glucose to pyruvate

• Glycolysis breaks down glucose into two molecules of pyruvate
• Glycolysis occurs in the cytoplasm and has two major phases
  • Energy investment phase and energy payoff phase
• Glycolysis occurs whether or not O2 is present
• The citric acid cycle also called the Krebs cycle completes the breakdown of pyruvate to CO2
• The cycle oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH and 1 FADH2 per turn
• The citric acid cycle has 8 steps, each catalyzed by a specific enzyme
• The acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate
• The next 7 steps decompose the citrate back to oxaloacetate, making the process a cycle
• The NADH and FADh2 produced by the cycle relay electrons extracted from food to the electron transport chain

During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis

• Following glycolysis and the citric acid cycle NADH and FADH2 account for most of the energy extracted from food
• These two electron carriers donate electrons to the electron transport chain, which powers ATP synthesis via oxidative phosphorylation

The Pathway of Electron Transport

• The electron transport chain is in the inner membrane of the mitochondrion
• Most of the chains components are proteins which exist in multiprotein complexes
• The carriers alternate reduced and oxidized states as they accept and donate electrons
• Electrons drop in free energy as they go down the chain are finally passed to O2 forming H20
• Electrons are transferred from NADH or FADH2 to the electron transport chain
• Electrons are passed through a number of proteins including cytochromes
• The electron transport chain generates no ATP directly
• It breaks the large free energy drop from food to O2 into smaller steps that release energy in manageable amounts