Week 12 Reflection

This week we learned about the central dogma! The central dogma a two-step process of transcription and translation. This is when information in genes flows into proteins.

DNA → RNA → protein.

Transcription is the synthesis of an RNA copy of a segment of DNA.

Translation is the process by which RNA is used to produce proteins.

Image result for central dogma diagramImage result for central dogma diagram

Transcription has a three step process:

  • initiation
    • In Initiation RNA Polymerase attaches to a “promoter” region in front of a gene. These “promoters” have characteristic DNA sequences. 
  • elongation
    • The “Template Strand” of DNA is the one that the RNA transcript is being produced off of (has an opposite sequence to the transcript)
    • The “non template strand” of the DNA will have the same sequence as the RNA.
  • termination
    • Transcript production continues until the end of the transcription is reached

Translation also has a three step process:

  • Initiation
    • The mRNA attaches to the small ribosomal subunit and the ribosome assembles so that the start codon (AUG) is in the P-site.
    • This is called the “translation initiation complex”
  • Elongation
    • The next code is then available in the A-site for the next incoming charged tRNA. The next codon determines the next two amino acid to be brought to the ribosome. The incoming charged tRNA enters at the A-site and the growing polypeptide is transferred to the new tRNA molecule. 
  • Termination
    • When a stop codon (UAG, UAA, or UGA) is encountered, a release factor binds to the A-site, and the polypeptide chain is released so the ribosome disassembles. 

This video helps the summarize these two concepts that make up the central dogma:

We also briefly reviewed mutations:

  • There are 2 major types of DNA- level mutations:
    • Point mutations: one DNA base is replaced by another DNA base
    • Frame-shift mutations: DNA bases are inserted or deleted (“in/dels”)

On Thursday we did a packet to learn about two different kinds of operons:

  • inducible operons
    • an operon naturally in the off position. This is only turned on by using a chemical signal called an inducer.
  • repressible operons
    • an operon that is naturally in the on position. This only turns off once enough production has occurred and a co-reppresor molecule signals the repressible operon to turn off.
    • Image result for inducible and repressible operonsImage result for inducible and repressible operons
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Week 11 Reflection

This week in AP Biology we had a unit test on Monday! The test was on cellular respiration, and it had 10 multiple choice with a few short response. One of the short response questions was very confusing to me, and I looked at it afterwards to make sense of the process.

On Tuesday and Thursday we did a two part lab called: Photosynthesis and Cellular Respiration Kit, a ThINQ Investigation. This lab was very interesting and started out by refreshing our knowledge on both photosynthesis and cellular respiration. All organisms need energy and matter to survive, and energy cannot be created or destroyed in the process. The lab also reviewed the second law of thermodynamics which showed that energy not used in the process of photosynthesis or cellular respiration is then converted and released in the form of heat energy. On the first day of the lab we focused on what variable we could manipulate in order to measure the rate of photosynthesis in algae beads. Algae beads are small and eukaryotic which made them a good choice for our experiment. (eukaryotic means any organism whose cells have a cell nucleus and other organelles enclosed within membranes.) My group had a hard time getting our microscope adjusted but eventually we were able to see the different colors on the algae that represented how much light had been obtained and taken in by the plant.

Image result for algae beads bio rad

On Thursday we did the second half of the lab we used algae beads to measure rates of photosynthesis and cellular respiration. We compared the rate of color change of the CO2
indicator by comparing algae beads that were incubated under bright light and algae beads that were wrapped in foil to maintain darkness. The color/pH change of
the CO2 was measure by a computer spectrophotometer, and we then converted our measurements of nanometers by using the indicator color guide. The data we collected during this phase of the experiment was in 5 minute intervals over a 45 minute time period. Once all the data was collected we graphed both the dark and light data and then calculated slopes. My groups data was fairly inconclusive in its summary of the rate of color change as our graphs were very bumpy.

Image result for algae beads bio rad

Overall, this week we took a test, reviewed cellular respiration, photosynthesis and created an experiment to measure these things using algae beads as a mean of data collection.

Week 10 Reflection

This week we learned about ways in which an organism can make energy without oxygen. Three ways we learned are photosynthesis, anaerobic respiration, and fermentation.

Most cellular respiration requires oxygen to produce ATP. Without oxygen, the electron transport chain cannot operate. In this case glycolysis (sugar breaking) works with fermentation of anaerobic respiration to produce energy for the cell. Anaerobic respiration is able to use the electron transport chain with a final electron receptor other than oxygen (sulfur sometimes). Fermentation is separate and uses phosphorylation instead of an electron transport chain. The two types of phosphorylation are oxidative and substrate level phosphorylation. Substrate level phosphorylation is less efficient and takes more time to generate energy. Most often, fermentation uses oxidative phosphorylation.

Image result for oxidative and lactic acid phosphorylation

Fermentation consists of glycolysis reactions that work to generate NAD+, which is reused by glycolysis. The two types of fermentation are lactic acid fermentation, and alcohol fermentation. In alcohol fermentation pyruvate is converted into ethanol. this 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 carbon dioxide.Image result for fermentation and anaerobic respiration

Fermentation VS anaerobic respiration 

  • All use glycolysis (with a net ATP of 2) to oxidize glucose and harvest chemical energy of food.
  • In all three, NAD+ is used as an oxidizing agent that accepts electrons during glycolysis
  • the processes have different final electron receptors: an organic molecule in fermentation and oxygen in cellular respiration.
    • C3 plants do better in cool weather and suffer in warm/hot weather.
    • C4 plants seperate things spacially inside plant cells, and there are two different kinds of tissues.

There are two types of anareobes that carry out fermentation or anoerobic respiration (they die if the come in contact with oxygen). Yeast and many other bacteria are facultative anaerobes which means that they can survuve using either fermentation or cellular respiration. In facultative anaerobe, pryuvate is a “fork in the metabolic road” that leads to two alternate catabolic routes.

One thing that confused me before was thinking that plants only did photosynthesis and animals did cellular respiration, but in reality, plants use both photosynthesis and cellular respiration to generate ATP.

One thing that really made sense to me this week was learning about rubisco – “keep oxygen away from rubisco so rubisco only has eyes for oxygen.” (Look at your notes titles “plant lifestyle choices”)

Week 9 Reflection

CELLULAR RESPIRATION

This week we learned about aerobic cellular respiration.The three main stages in aerobic cellular respiration are: glycolysis, citric acid cycle, and oxidative phosphoryation. These three steps only occur if there is oxygen in the cell, and otherwise it is known as anaerobic respiration. Cellular respiration is used to create ATP (energy), and falls under big idea 2.

Cellular respiration is the process in which glucose and other organic molecule are broken down over a series of steps. Usually electrons from organic compounds are first transferred to NAD+. The NADH then passes the electrons to the election transport chain. Unlike an uncontrolled reaction, in the electron transport chain electrons are passed in a series of steps rather than in a single explosive reaction. The energy yielded from this process is then used to regenerate ATP.

The First Step in cellular respiration is glycolysis (means breaking down glucose-sugar). This is when glucose breaks down into two molecules of pyruvate. (Pyruvate is a key intermediate in several metabolic pathways.) these two molecules of pyruvate then enter the citric acid cycle to complete the break down of glucose. This leads to the final step which accounts for most of ATP synthesis and is known as oxidative phosphorylation. This process is powered by redox reactions and makes the most ATP (energy). For each molecule of glucose degraded to CO2 and water in this process, the cell makes up to 32 molecules of ATP. This is the process in our bodies that created energy from sugars.

Image result for cellular respiration

In Glycolysis, chemical energy is harvested by oxidizing glucose into a pyruvate. This “sugar splitting” occurs in two major phases: the energy investment phase and the energy payoff phase. After the pyruvate is oxidized, the citric acid ycele completes the enrgy-yielding oxidation of organic molecules. In the prescense of O2, pyruvate enters the mitochondria, where the addition of glucose finishes. The citric acid cycle (krebs cycle) then finishes breaking down the pyruvate into CO2. This cycle also produces ATP, NADH and FADH2. The next step is phosphorylation and during oxidative phosphorylation, chemiosis couples electron transport to ATP synthesis.

Chemiosmosis is the electron transfer in the electron transport chin that causes proteins to pump hydrogen ions from the mitochondrial matrix into the inner membrane space.

Image result for chemiosmosis

This video helps me to summarize this information! Also this simple diagram helped me to understand the overall goal of cellular respiration “by which the chemical energy of “food” molecules is released and partially captured in the form of ATP.”Image result for what does cellular respiration do

 

Week 8 reflection

This week we learned about the structures and supports of a cell! Throughout a cells life, all cells must process matter, energy, and information to stay alive, but many cells also do other things.

The structure of each cell starts at the cytoskeleton, each component of a cytoskeleton is assembled by a network of structural proteins that extends throughout the cytoplasm.

There are three types of structural proteins: There job is the keep the cell in its a shape.

  1. Micro tubules: these are the largest types of structural proteins, they are made up of tubium. Their function is to pull chromosomes out of the cell during mitosis and miosis.
  2. Micro-filaments: These are made out of actin proteins, and they are the smallest type of structural proteins.
  3. intermediate filaments: these are the middle sized proteins associated with the nucleus. They help to anchor it to certain places in the cell!

The main function of all structural proteins is to keep the cell in its shape. But they also offer structural support, anchor organelles, and regulate movement of chromosomes and organelles during cell division.

Image result for kinesinWe also learned about Kinesin. Also known as motor proteins, these proteins move the vesicle along the microtubule of a cytoskeleton. They are powered by ATP. The way I have understood this, is to think of their job as delivering cargo.

The next protein we learned about is the Cilia and Flagella. They are motility related extensions of the cytoskeleton proteins that extend outside of the cell. Their job is to move the cell throughout space. By elongating one side and shortening one side it is able to create a power stroke (kind of like a flipper) that allows it to move.

Ciliary and Flageller movement

The Centrosome is an animal like cell that acts as a microtubule organizing center. it plays a large role in cell division.

Image result for centrosome

We also learned about the cell membrane and its functions. Such as creating the boundary of the cell, transporting material in and out of the cell, and communicating between the cell and its environment. Membrane phospholipids create a “selectively permeable membrane” this only allows small, nonpolar molecules to move through the phospholipid bilayer. Another aspect of the cell is cholesterol. It is a steroid lipid that acts as a temperature buffer to help maintain the fluidity of the cell.

We also covered the two kinds of membrane proteins:

  1. integral proteins: penetrate one or both bi-layers
  2. Peripheral proteins: associated with the membrane, but do not penetrate the bi-layer.

The functions of these proteins are to transport, enzymatic activity, signal transduction, cell to cell recognition, inter cellular joining, and attaching the cytoskeleton to the extracellular matrix.

Image result for membrane proteins

Finally, we also covered the ECM (“Extracellular Matrix”) – only animals have this

The structure of the ECM is a network of connective proteins and “proteoglycan” molecules that are attached to the outside of the cell membrane of animal cells. Their job is cell anchorage, and cell communication. Image result for extracellular matrix

This week in AP biology we covered a lot of new material on the cellular proteins and their functions. To help us understand these new concepts we watched this video:

Week 7 reflection

This week we learned about transport in a cell. We focused on three specific types of transport: Passive transport, Active transport, and Bulk transport.

Passive Transport: In Passive transport, we learned about the movement of materials from high to low concentration. During this type of transport there is no energy needed. Also during this type of transport is the action of diffusion. This is when molecules move across a semi permeable membrane (this type of diffusion is inescapable.) Osmosis is the specific type of diffusion of water, when water moves through the membrane from left to right. I thought this was very interesting because this leads to what can cause death if someone drinks too much water, and the concentration gradient on the outside of the cell is too high, the cell can explode.

Transport proteins:

  • channel proteins: allow water to freely move in and out of cell
  • carrier proteins: revolving doors for the cell
  • facilitated diffusion: transport proteins

 

Image result for passive transport

Active Transport: Active transport is the movement of material from low to high concentration. This type of transportation needs energy, and ATP fills this energy requirement. One way this type of transport works is with the sodium potassium pump . This is a very important system because without it, the human body would not have a nervous system. Tonicity (a relative measure of solution concentration) is also very important as a high tonicity could have serious consequences for the cell.

 

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Three types of solutions in the cell regarding tonicity:

  • Hypotonic solution: the cell has less water than the surrounding solution. The solute is diluted and then the cell can pop!
  • isotonic solution: Concentration is the same on both sides of the cell.
  • hypertonic solution: more solutes inside the cell outside the cell. (solute = water)

Bulk Transport: There are two key types of bulk transport: endocytosis, and exocystosis.

  • Endocytosis is the intake of large molecules, and it has three types:
    • Phagocytosis (cell eating)
    • Pinocytosis (cell drinking)
    • receptor-mediated endocytosis (cell being picky)
  • Exocystosis is the release of large cellular products into the outflowImage result for bulk transport

This week was a lot of new information, and we also did a very interesting lab learning about concentration gradients and cell membranes. Here a links to a couple helpful videos on this new material.

http://www.bozemanscience.com/015-cell-membrane

http://www.bozemanscience.com/016-transport-across-cell-membranes

 

Week 6 Reflection

This week we learned about Proteins and Enzymes! We did two labs that helped us understand these new concepts.

PROTEINS are the most complex biological molecules. They are made up of carbon, Hydrogen, oxygen, nitrogen and a little sulfur. All proteins are polymers of amino acid monomers, and all amino acids are joined by peptide bonds. Amino acids are a simple organic compound containing both a carboxyl (—COOH) and an amino (—NH2) group. There are 21 known amino acids, and each is bonded to a central “alpha” carbon. The structure of the R group in an amino acid varies in each amino acid.

Image result for amino acid  

Primary Structure: The sequence of amino acids in one typical polypeptide chain, peptide bonds between amino acids.

Secondary Structure: regular and repeating 3D structures which are found in all polypeptide chains. There are hydrogen bonds between the atoms in CN backbone of the polypeptide. (but no R groups in the part)

Tertiary Structure: The 3D folding pattern in a protein

Quaternary Structure: protein structure of proteins with more than one amino acid chain.

Proteins also denature (denaturation is the change in the structure of a protein.) Image result for denaturation

ENZYMES are proteins that catalyze, they accelerate chemical reactions.  The higher the temperature the more likely that a reaction will occur, and the lower the temperature, the lower the likelihood that a reaction will occur. Enzymes reduce the amount of activation energy so that the reaction is more likely to occur. The enzyme model is seen below and can be described best a a “lock and key model.” The activation site is filled with substrates (the reactants). These are molecules that are waiting to undergo reaction. A certain substrate can only fit in a certain enzyme, this is just like a key and lock.

There are two types of runs, anabolic and catabolic. Anabolic runs build things up, and catabolic runs break things down. Things that effect the reaction rate are substrate concentration, enzyme concentration and temperature.

Image result for enzymes

Negative feedback loop – body uses something up and starts using it again (a way to turn something off in your system.) Something happens that causes something else to happen, then the last thing goes back and turns off the first.

Image result for negative feedback loop

This week we mostly talked about Big Idea 2 (Biological Systems Using Energy to Maintain Homeostasis for Survival.) We talked about how energy is used in maintaining homeostasis which can be seen by enzymes. Homeostasis is “the tendency toward a relatively stable equilibrium between interdependent elements, especially as maintained by physiological processes.”

This week in AP biology was the most new material for me of any other week so far, after reviewing my notes I know better understand this new information.

Week 5 Reflection

This week in AP Biology we learned about macromolecules.  By doing two different labs I was better able to understand the structures and functions of amino acids, nucleic acids, proteins and lipids. I learned that all of these macromolecules are built out of monomers through the process known as dehydration synthesis. Our homework this weekend included a packet that taught me about ions, as well as the Ph scale of bases and acids. Image result for types of macromolecules

Nucleic Acids are polymers built out of monomers, which are called nucleotides. They store, transmit, and express hereditary information. They allow for genetic information to carry down through generations. Nucleotides are composed out of three main parts: nitrogenous base, five carbon sugar (pentagon), and phosphate groups. Basically nucleic acids build up the DNA and RNA within your body. One thing that I found confusing at first was how to explain their directionality, I now understand the system in which there are three prime sugars at one end, and 5 at the other.

Proteins are made out of amino acids. They are defined as a biological functional molecule that consists of one or more polypeptides folded and coiled into a specific three-dimensional structure. Examples of proteins are enzymes which are found in our bodies.

Lipids are composed primarily of fatty acids and glycerol, and are categorized as a diverse group of hydrophobic molecules. These macromolecules are grouped together because they do not mix well with water (think hydrophobic). Fatty acids have long carbon chains and mostly non polar C-H bonds.

Carbohydrates are monosacharides, and they encompass sugars, and starches. They are designed to fuel your body as a building material. Different alpha and beta groups are  determines the directionality of this molecule.

Image result for macromolecules diagrams

VOCAB:

Dehydration Synthesis: The process of joining two molecules, or compounds together following the removal of water.

Nucleotides: a compound consisting of a nucleoside linked to a phosphate group. Nucleotides form the basic structural unit of nucleic acids such as DNA.

Macromolecules: a molecule containing a very large number of atoms, such as a protein, nucleic acid, lipids and carbohydrates.

hydrophobic molecules: tending to repel or fail to mix with water.

Finally, in the homework we learned about acids and bases, and the pH scale. Things I learned about the pH scale are:

  • pH declines as the number of hydrogen molecules increases.
  • a solution of pH 10 has ahydrogen ion concentration of 10↑-10.
  • ACIDS add hydrogen ions to a solution and remove hydroxide ions
  • BASES takes away hydrogen ions from a solution and adds hydroxide ions.

Image result for pH scale

Week 4 Reflection

This week in AP Bio we learned about speciation, classifications, and cladistics.

Speciation is the process of developing new species. Species are created by a series of evolutionary processes. Defined by Ernst Mayr, a species is a population whose members can interbreed and produce viable, fertile offspring. Other definitions of species include: morphological (based on appearance), Ecological (based on niche), and Paleological (based on fossils). These different definitions are useful for different different situations and needs. Two types of speciation are Allopatric and Sympatric:

Allopatric Speciation: A populations is isolated from other populations due to a physical barrier. When given enough time the populations evolve separately and become reproductively isolated.

Sympatric Speciation: The populations are in the same physical area, yet still become reproductively isolated from other populations due to things like mutations, mistakes in miosis, and diversifying selection.

Species barriers are various mechanisms that prevent successful interspecies reproduction. Two types of barriers are Prezygotic and Postzygotic:

Prezygotic: -habitat isolation, mechanical isolation, behavioral isolation, temporal isolation, and gametic isolation.

Postszygotic: reduced hybrid visibility, reduced hybrid fertility, hybrid breakdown.

The rate of speciation has been an ongoing debate, but combining the two mechanisms we can see that it is a combination of gradualism and punctuated equilibrium. I thought this was really interesting because I had learned about natural selection in the past but I have never been taught how it led to the creation of new species.

Classifications: This describes how we organize species.

Genus: always capitalized         species: always lowercase

Hierarchy of life: Moving in order of domain to species, the number of possible groups increases. There are three domains:Bacteria, Eukarya, and Archea. These are classifications based on cell anatomy. There are also five kingdoms: monera, Protista, fungi, plantae, and animalia. These are based on cell anatomy and nutritional modes. The five kingdoms are what I have been taught most in my life. The old style of classification includes 7 kingdoms, and was a problem because the number of kingdoms kept changing, also the separations were based mostly off of visual observation. The new style of classification is Phylogeny. This is when the “DNA revolution” came to classification. This is when we discovered that DNA is a reliable indicator of relatedness and as species diverge, their DNA sequences diverge too. This changed the way scientists defined classification.

Image result for classificationThis is the old style of classification.

Cladistics: The grouping of organisms according to the number of shared characteristics, using a cladogram.

The rules of Maximum Parimony: all other things being equal, the simplest explanation is true = characteristics are most likely to evolve once.

Maximum Likelyhood: assuming mutation rates are equal in different lincages, more closely related organisms will have fewer differences in genetic sequences. This is an example of a cladogram. They are helpful visual representations of relationships between species.

This week in AP Biology, we learned a lot of different new things. This is a video that helped me understand these new concepts:

Week 3 Reflection

This week we reviewed important vocabulary words, and studied the Hardy-Wienburg theroem!

Genes: determines a trait.

Allele: a variant of a gene. (all sexually reproducing organisms have 2 allele for a trait).

Dominant: an allele that will show a trait, regardless of the other allele.

Recessive: an allele that will only show a trait if both alleles are recessive.

Homozygous: any individual with 2 copies of the same allele. It can be homozygous dominant, or recessive.

Heterozygous: any individual who has 1 copy of a dominant allele and 1 copy of a recessive allele.

Population: a localized group of interbreeding individuals.

Gene Pool: The collection of alleles in the population (different between alleles and genes).

Evolution: a change in allele frequencies in a population.

The Hardy-Weinberg situation describes a hypothetical environment in which there is no evolution, and none of the 5 means of evolution (mutation, gene flow, non-random mating, genetic drift, and natural selection). It is used as a model for comparison (a null hypothesis) which means no change. This is best used to measure changes in a population and how forces are acting on a population. Within the theorem you must assume 2 alleles: B and b. The frequency of the dominant allele (B) is equal to P, and the frequency of the recessive allele (b) is Q. These frequencies must add to 100% which means P+Q=1.

Image result for hardy weinberg equationsImage result for hardy weinberg equations

The frequency of homozygous dominant = PxP

The frequency of heterozygous recessive = QxQ.

The frequency of heterozygotes = (PxQ) + (Q+P) = 2PQ

These three frequencies also must add up to 1, which means that: P²+2PQ+Q²=1

The next thing we learned about this week was the difference between Phenotypes and Genotypes. Phenotypes are the physical traits such as blonde hair, while a genotype is the allele to create said Phenotype. When solving the Hardy-wienburg theorems these two terms come into play. When you are given the genotypes then you follow this equation, P²+2PQ+Q²=1, with each separate value, yet when solving for phenotypes, you must group it differently, P²+2PQ+=1.

Image result for phenotypes vs genotypes

This week we had a homework sheet with different practice problems on these equations, and many of them were confusing to me before talking about them in class. The parts I struggled with involved phenotypes and the different solving methods they require.

This week we also did a lab called Lab Population Genetics. In this lab we all had cups which contained two sets of different colored beads (meant to represent a heterozygous individual). We then were instructed to go “mate” around the classroom, and each round of mating had different specifications. This was a really good representation to me of the evolutional process. The takeaway I got from both this lab and class this week is the ability to measure evolutions effects, and to prove that natural selection cannot be the same as the Hardy-Wienburg theorem.

Link to helpful video: http://www.bozemanscience.com/solving-hardy-weinberg-problems