Chapter Thirteen Reading Journal

What accounts for genetic variation?
The fact that the chromosomal number is split during meiosis means that there are several possibilities of contribution from each parent that will come together. This refers to independent assortment of the chromosomes during meiosis 1 and random fertilization. The pairs of chromosomes are arranged independently and randomly along the metaphase plate for when they split during meiosis 1 this result in many combinations then they fertilize and combine with other gametes leaving endless possibilities for genes.

What are the distinct features of Meiosis?
Homolog pair during Meiosis 1 in mitosis sister chromatids are attached and they split. The kinetochore behavior is also unique because in meiosis both kineticores of the homolog pair attach to the same pole of the microtubles. In Mitosis the sister chromatids are attached to by cohesion, in meiosis the pairs are linked by the chaisma and then use the cohesion to keep the sister chromatids together until they spilt during meiosis 2.

What are the benefits and disadvantages of sexual reproduction?
The advantage is that there is more room for variation and therefore adaptation. With sexual reproduction organisms are not the same as their parents, which creates variety. In asexual reproduction parents make exact replicas of themselves, they do not need a second person to contribute this is an advantage, because it makes asexual reproduction easier to occur since they do not have to find a mate. This means though that if something in the environment changes an entire species of asexual reproducing organisms could die off, where sexually reproducing organisms would have certain people with enough variation for some to survive most likely. A disadvantage to sexual reproduction is also though that it is so variant because if a species is successful with certain characteristics their offspring may not have those same beneficial traits.

Five Facts:
-A locus is a gene’s specific location on a chromosome
-Karyotyping involves mapping chromosomes
-Haploid cells are gametes and they contain half the chromosomes of diploid also known as somatic cells they make up the majority of the organism
-All sexual reproduction involves meiosis
- Meiosis halves the chromosome number so that offspring do not have double the genes of their parents.



This diagram shows the steps of meiosis. Essentially chromosomes replicate like they would in mitosis but instead of separating once they pair off into homologs cross over with other pairs and then separate. Then the sister chromatids which are still attached but may have some pieces from another chromosome separate halving the chromosome number.

Summary: In sexual reproduction offspring inherit half their chromosomes from each parent this creates variation and quicker adaptations. In asexual reproduction one parent exactly duplicates themselves. In somatic cells there are 2n chromosomes in gametes there are n chromosomes. Gametes are produced by meiosis and they combine with gametes from the opposite sex of the same organism to form a zygote, which is diploid and continues to replicate. Because of the genetic variation caused by crossing over and independent assortment with meiosis evolution is far more efficient.

Chapter Twelve Reading Journal

Questions:

What is the difference between mitosis and the cell cycle?
Mitosis includes prophase, prometaphase, metaphase, anaphase, and telophase this only makes up about 10% of the cell cycle the rest of the cell cycle is interphase that consists of G1, G2, and S phases. Mitosis is when the cell is actually in the process of dividing the other part of the cycle involves growth and DNA synthesis, which is most of the cells life. Although often the cells are in Go phase when they are told not to divide by the G1 checkpoint.

How do cells control the cell cycle?
Different cells divide at different rates and certain cells once in maturity never divide examples of these cells are muscle and nerve cells. The cell cycle has checkpoint after each of the sub phases of interphase and after mitosis. The checkpoint after G1 is called the restriction point and if it doesn’t receive the go ahead at this checkpoint it is sent into the non-dividing state called Go. Besides the checkpoints there are other molecules that regulate cell division mainly protein kinases and cyclin. Cyclin is constantly present but usually in the inactive form its active form is in higher concentration during S and G2 phases but is much lower during mitosis. Cells also regulate their cell cycles by knowledge of external factors such as surrounding density and anchorage.

What is known about how cancer cells differ from healthy cells?
Cancer cells don’t have good regulation of their cell cycles so they divide far too often. The fact that they are not anchorage dependant means that they can move from different parts of the organism and start growing in other places. The fact that they lack density dependency is the reason tumors form because the cells just layer on top of each other without stopping. They most also lack the cellular control of aptopsis or else they would self destruct because of their dysfunction.

Facts:
- Somatic cells contain 46 chromosomes gametes (reproductive cells) have 23 chromosomes
- Chromosomes are copied to from 2 sister chromatids which are attached at the centromere
- The five main phases of mitosis are prophase prometaphase metaphase anaphase and telophase the DNA needed for this division is produced during the S phase of interphase
- Microtubules play a major role in cell division because they attach to kinetochores and then shorten to separate the chromosomes that aligned in the middle during metaphase
- A benign tumor are cancer cells that stay in the place they started growing malignant tumors inhibit the function of major organs



This figure breaks down the various steps of mitosis. Doesn’t need much explaining I’m putting it on here because it explains.

Summary:
Cells are made up of genetic information that is packaged into chromosomes that are duplicated and then separated during cell division. The chromosomes duplicate to chromatids that are held together by the centromere. During interphase the cell grows and replicates DNA. It reaches several checkpoints before continuing and responds to many outside regulators. Cancer is somehow deficient in its regulation so its cell cycle malfunctions.

Chapter Eleven Reading Journal

Questions:

What are the three basic steps of Cell signaling?
Reception comes first when a chemical signal is detected by the cell this may happen because of direct contact or because the cell is receiving a signal that has already been passed along and is finally reaching the target cell. Transduction occurs when the message is converted so that it can be passed along to other signal molecules this is either done through the use of g-proteins, tyrosine kinasases, or ion channels. Response is when the cell behaves the way that the signal intended to make the cell.

How do G-Protein receptors work?
These receptor are in the membrane of cells and G proteins are either in the in active state of GDP or the active state of GTP when a phosphate has been added. When the g-protein receptor receives the signal molecule it changes the g-protein to the active form the g-protein then travels to an enzyme that it activates and often changes the shape of the enzyme once banded to it. This either immediately bringing about the cellular response or continuing to transfer the response through other enzymes. This is one of the most widespread cellular signaling functions.

What are Second Messengers?
Typically small water-soluble molecules or ions that are used to spread the signal within the cell. cAMP usually activates protein kinase A which typically spreads the signal by adding phosphorous to other proteins. This happens because the first signal that occurs in the membrane increases the levels of Camp to pass the signal along within the cell. Other cellular signals increase levels of ions most typically Ca + IP3 or DAG these work similarly to Camp in that the original signal triggers an increase in the ions which triggers further responses. Second messenger is a general term used for non-proteins used in the transductions pathways.

Facts:
- Cells have to communicate because they need to regulate cellular processes and respond to their environment as well as reproduce
- Cells perform apoptosis basically cell suicide when their DNA is coded improperly or they are about to stop functioning they do this to prevent damage to other cells
- Cell signaling can also stimulate certain genes within the nucleus to produce certain RNA
- Earl Sutherland discovered second messengers and the use of cAMp in epinephrine
- Ligands bind to receptors to promote the cellular response



This shows how signals can be transferred over a long distance. The original receptor activates a molecule that is able to activate other protein kinases. This works because a phosphate is added to the protein activating it then deactivates be transferring its P to another kinase, which is activated. Thus the reaction can move from molecule to molecule.

Summary:
Cell signals are either local or long distance. The main signal receptors are G-protein tyrosine kinnases and ion gated channels. To get from reception and response cells must undergo transduction pathways that either use phosphorylation cascade or secondary messengers. The response helps regulate transcription and other cellular functions this also helps them identify surrounding cells. The also use signaling to know when to self-destruct to prevent damage to nearby cells.

Chapter Ten Reading Journal

Questions-

How does Photosynthesis relate to respiration?
The general equation of Photosynthesis is the reverse of respiration. Photosynthesis uses energy to build molecules of carbs for energy storage. Plants also use respiration when they need ATP for their cells but they are able to use sunlight to formulate the glucose needed unlike heterotrophs that have to consume this by eating other organisms often plants. Both respiration and photosynthesis have many similarities the product of the steps of photosynthesis are reactants of respiration. Photosynthesis only has two major steps instead of the three in respiration, and it also contains a cycle and an electron transport chain some ATP is also produced during this process.

Explain the concept of wavelengths visible light and how they relate to photosynthesis?
Light behaves like a wave and a particle; the particle is called a photon. The distance between peaks of a wave of light is called the wavelength the shorter the wavelength the higher the energy of light and the greater energy photons of that light contain. The visible light spectrum is from wavelengths of 380 to 750nm. The Chloroplasts contain chlorophyll molecules that absorb light. The most effective visible light is violet-blue and red and the least effective is green since chlorophyll reflects that color. Accessory pigments such as carotenoids and xanthophylls help the plant absorb more colors of light making the process more efficient. The membrane of the thylakoid contains light harvesting complexes that use these pigments to excite electron and send them to the primary electron acceptor sending the energy from Photosystem 2 to Photosystem 1.

What are the evolutionary advantages of CAM and C4 Plants?
Most plants can be called C3 plants because they use a 3-carbon compound to start the Calvin cycle. Unfortunately when not very much Co2 is present the Calvin cycle will bind to O2 to produce more Co2 this can be seen as very wasteful because it consumes ATP. C4 plants have adapted to hot dry climates because they use PEP carboxylase to which has a very high affinity for CO2 to fix CO2 in the mesophyll cells before sending CO2 to the more contained bundle-sheath cells where the Calvin cycle takes place. This eliminates photorespiration and also lessens water evaporation. CAM plants leave their stomata open only during the night to avoid the excessive amounts of water evaporation that would occur during the day. They fix co2 with and acid known as CAM during the night and then use it during the day when the light reactions are occurring.

Facts:
-The O2 released during photosynthesis is a result of the water spitting during the light reactions
-NADPH and ATP are formed during the light reactions and these energy molecules are needed to fix co2 during the Calvin cycle
-Stomata are the pores in the leaf stroma is the liquid inside the chloroplast
- Photosystem 2 occurs first and best absorbs light with a wavelength of 680 Photosystem 1 occurs second but can also function independently and best absorbs light with a wavelength of 700.
- ATP synthase is used during the electron transport chain from photosystem 2 to photosystem 1 when a H+ concentration is formed within the tylakoid pumping ATP into the stroma where the Calvin cycle occurs.




This depicts the relationship between Photosystem 1 and Photosystem 2. Photosystem 2 absorbs light and splits water to send the excited electron to the electron transport chain that produces ATP while sending the electron to Photosystem 1. Photosystem 1 uses this energy to from NADPH, but it can also independently absorb light and form NADPH. This is why Photosystem 2 is said to use non-cyclic electron flow and Photosystem 1 uses cyclic electron flow.

Summary:
Plants are said to be the producers because they don’t need to live off other organisms they use photosynthesis to produce glucose. Inside the chloroplasts within the membrane of the thylakoid light energy is absorbed by the photosystems that produce NADPH and ATP the energy storing molecules needed for the Calvin cycle. The Calvin cycle uses CO2 to combine with Rubisco ATP and NADPH power the cycle and are recycled to NADP+ and ADP to be reused in the light reactions. The Calvin cycle produces G3P, which is converted into energy storing molecules.

Chapter Nine Reading Journal

Questions:
What is the basic summary of respiration?

The first step is glycolysis, which breaks down glucose and produces NADH, ATP and Pyruvate. In the energy investment phase the cell uses ATP to break glucose in G3P. In the energy pay off phase NADH and are produced along with Pyruvate, which makes it possible to move into the Krebs cycle. Through active transport the Pyruvate is moved into the mitochondria, once Coenzyme A is added CO2 and NADH are released forming Acetyl CoA. Acetyl CoA combines with oxaloacetate to start the Krebs cycle forming NADH and FADH2. These molecules are used as the electron transport chain, which creates a concentration gradient powering ATP synthase, which produces ATP.

What are the different types of fermentation?

Alcohol fermentation: Ethanol is converted to Pyruvate first CO2 is released forming acetaldehyde then its reduced by NADH to ethanol this recycles the NAD+ so the glycolysis can continue. Many bacteria and yeast use this for energy production.

Lactic Fermentation: Pyruvate is reduced to NADH forming Lactate. This is also used in bacteria and fungi, but also used in animal cells when they are short of oxygen. In humans lactate is taken to the liver and converted back to Pyruvate.

How does ATP synthase work?
NADH and FADH2 release their H+ ions to proteins in the membrane that pump the H ions across the membrane to create a concentration gradient. The H ions move back across the membrane to reach equilibrium through the protein ATP synthase that by the energy provided attaches P to ADP forming ATP. This is called oxidative phosphorylation. About 36 ATP are made through this process for every NADH 3 ATP can be produced and for every FADH2 2 ATP can be produced.

Facts:
*Glycolysis is one of the most wide spread metabolic pathways and is therefore the oldest.
*Cells are able to trigger the production of more ATP or make the process slow because of feedback inhibition.
* O2 acts as the final acceptor in the electron transport chain
* The general equation for glycolysis is C6H12O6 + 6O2 → 6CO2+ H20 + energy hydrogen is oxidized and the Oxygen is Reduced
* The majority of ATP is produced during ATP synthase/ electron transport chain, but it is made other times during respiration






This shows the Krebs cycle also known as the citric acid cycle. Acetyl CoA combines with the oxaloacetate to form citrate. As the cycle continues NADH and FADH2 are released as NAD+ and FADH are reduced. This is also the step in respiration where Co2 is released and it is considered a cycle because the same products will be produced every time allowing it to occur again in other words oxaloacetate will be produced allowing acetyl CoA to combine with it theoretically allowing it to continue forever.


Summary:
All cells need energy and they undergo a process called respiration to produce this energy. Respiration involves glycolysis, which can also be used for anaerobic respiration (respiration without O2) if O2 is present glycolysis moves to the Krebs cycle and then to the electron transport chain performing oxidative phosphorylation thus completing aerobic respiration. Fermentation is used in organism that produce energy either without the presence of a mitochondria or when O2 levels are depleted. Since glucose is not always available cells must perform respiration using other molecules such as fats and proteins by breaking them into either G3P, Acetyl CoA or as the case is only in proteins moving directly into the citric acid cycle.

Chapter Related Vids

Chapter One: (possible distant relative of the human?)

http://www.youtube.com/watch?v=eIW4lqLz_Rc

Chapter two: (difference between ionic and covalent bonds)
http://www.youtube.com/watch?v=ERy18NwemVc

Chapter three: (Properties of water resulting in H-bonds)

http://www.youtube.com/watch?v=Jh2qpsZe6GA

Chapter Four: (Enantiomers)
http://www.youtube.com/watch?v=G-eMr1kxorc&feature=related

Chapter Five: (protein structure)
http://www.youtube.com/watch?v=lijQ3a8yUYQ

Chapter Six: (cell tour)
http://www.youtube.com/watch?v=--NXZCX9VPA&feature=related

Chapter Seven (Cell membrane)
http://www.youtube.com/watch?v=GW0lqf4Fqpg&feature=related

Chapter Eight: (ATP Cycle)
http://www.youtube.com/watch?v=Ki9Tly-A-Rc&feature=related

Chapter Nine: (Cellular Respiration)
http://www.youtube.com/watch?v=x-stLxqPt6E&feature=PlayList&p=E705480FEF95FE96&playnext=1&playnext_from=PL&index=41

Chapter Ten: (Summary in song) http://www.youtube.com/watch?v=Q_1mxZdF2TY&feature=channel
http://www.youtube.com/watch?v=OYSD1jOD1dQ&feature=channel

Chapter eleven (G-proteins)
http://www.youtube.com/watch?v=NB7YfAvez3o

Chapter Twelve: (Cell cycle check points)
http://www.youtube.com/watch?v=QGx50C1w8YY

Chapter Thirteen: (Meiosis)
http://www.youtube.com/watch?v=uh7c8YbYGqo

Chapter 15: http://www.youtube.com/watch?v=H1HaR47Dqfw

Chapter 16: http://www.youtube.com/watch?v=teV62zrm2P0

Chapter 17: http://www.youtube.com/watch?v=41_Ne5mS2ls

Chapter 18: http://www.youtube.com/watch?v=g7CMWuIZ2So

Chapter 19: http://www.youtube.com/watch?v=MEdcXQvwxk4

Chapter 20: http://www.youtube.com/watch?v=QhUGguUNR7Q&feature=related

Chapter 21: http://www.youtube.com/watch?v=-gVh3z6MwdU

Chapter 22: http://www.youtube.com/watch?v=lqhlGaVxV3E

Chapter 23: http://www.youtube.com/watch?v=8r5dtUmAbeE&feature=related

Chapter 24: http://www.youtube.com/watch?v=YCoEiLOV8jc

Chapter 25: http://www.youtube.com/watch?v=QWVoXZPOCGk

Key terms

Chapter One:

Systems Biology- Studying biology by looking at one system at a time and seeing how it contributes to the whole

Eukaryotic cell- Make up plants and animals these cells are more complex and contain a membrane bound nucleus and organelles

Prokaryotic cell- Simpler kind of cells make up bacteria and archea lack a nucleus and membrane bound organelles

DNA- genetic material

Genome- The entire genetic sequence (DNA strands) of an organism

Bioinformatics- The use of technology to take lots of biological data and organize and group it

Negative Feedback- The production of something stimulates a reaction that will slow down the production

Positive feedback- Production of something stimulates the production of more of that substance

Inductive reasoning- Taking specific observations and making generalizations based on them

Deductive reasoning- Using general principles to make predictions about specific biological interactions/ processes

Controlled experiment- An experiment where one group doesn’t receive the experimental variation

Theory- A hypothesis that has been tested many times with the same outcome and usually a more broad

Chapter two:

Anion- Negatively charged ion

Cation- Positively charged ion

Isotope- A different form of the same element, the number of protons are the same but the number of neutrons differs

Covalent bond- A bond in which atoms share electrons

Ionic bond- Negatively and positively charged ions are bonded by their attraction to each other

Valence- the number of unpaired electrons needed to fill in the atom’s outmost valence

Van der Waals interactions- weak interaction between molecules; a result of very slightly charged regions

Orbital- The space where an electron is found 90% of the time

Electro negativity- The strength of the pull on atom puts on shared electrons

Nonpolar Covalent bond- covalent bonds where both atoms are equally electronegative

Hydrogen Bond- When hydrogen already covalently bonded to an atom is attracted to a slightly another electronegative atom

Chemical equilibrium- The concentration of reactants and products remain the same ratio because the rate of reaction is the same as the rate of decomposition

Chapter Three:

Adhesion- The attraction between a molecules and a different type of molecule

Cohesion- A substances attraction to its own molecules

Hydration shell- water molecules surrounding the individual ions of a dissolved solution so they wont reattach

Hydrophilic- Water loving

Hydrophobic- fear of water (substances that don’t mix well with water)

Colloid- A mixture where the particles too big to dissolve in water remain suspended in it

Molarity- Moles of solute/ liters of solution

Buffers- Minimize the concentration of acid or base in a solution brings the solution closer to neutral

PH- The concentration of H ions in a solution (low Ph acidic high Ph basic)

Specific heat- The amount of heat a substance has to absorb to change one gram one degree

Emergent properties- When alone these properties aren’t as important as they are when taken into consideration in relation to the whole

Surface tension- how hard it is to stretch or break the surface of a liquid

Chapter four:

Hydroxyl Group- Hydrogen and Oxygen

Carbonyl Group- Carbon double bonded to Oxygen

Carboxyl Group- Combination of hydroxyl and carbonyl

Amino Group- Two hydrogen bonded to nitrogen

Sulfhydryl Group- Sulfur bonded to Hydrogen

Phospate- Phosphorous bonded to four oxygen atoms (double bonded to one of them)

Methyl- Carbon bonded to three hydrogen

Isomer- A compound with the molecular formula but a different function because of different arrangement of atoms (geometric, structural, or enantiomers)

Hyrdocarbon- A compound made of only carbon and hydrogen

Functional Group- A common composition of molecules typically attached to a carbon skeleton giving it various properties

Chapter Five:

Dehydration reaction- A reaction that connects monomers forming polymers by the release of a water molecule

Hydrolysis- When adding a water molecule breaks the bonds of a polymer breaking them down into monomers again

Carbohydrates- Sugars; polymers of larger sugar formed from monosaccharides

Glycosidic linkage- The bonding between monomers of sugars of form polymer sugars

Starch- A polymer of glucose mostly found in plants

Cellulose- A polysaccharide common in plants that is not digestible by humans

Lipids- Group of polymers grouped together because they are all hydrophobic

Fat- Made of glycerol and a fatty acid

Triacylglycerol- Three fatty acids linked to one glycerol

Polypeptides- Polymers of amino acids; makes up proteins

Peptide bond- A bond between amino acids that forms polypeptides

Denaturation- When a protein unravels causing it not to function

Polynucleotides- Nucleic acids in polymer form


Chapter six:

Cytosol- the gel substance inside the cell where all the pieces of the cell reside

Plasma Membrane- The barrier between the inside of the cell and the outside allows the transport of certain substances

Nuclear Lamina- Proteins that help the nucleus maintain its shape by supporting the nuclear envelope

Ribosomes- Made of RNA and proteins carry out protein synthesis

Transport Vesicles- Sacs of membrane that transport products of the ER to the Golgi apparatus

Phagocytosis- When a cell engulfs a large particle or sometimes even another cell (endocytosis)

Cristae- The mitochondrion folding of the inner membrane

Mitochondrial Matrix- The space of the mitochondria that is enclosed by the inner membrane

Thylakoids- Sacs within chloroplasts that make up stacks called Granum

Stroma- The liquid within the inner membrane of chloroplasts

Cytoskeleton- The system that helps the cell maintains shape and stabilizes it for reproduction and movement

Centrosome- Found in animal cells organizes the microtubules

Chapter Seven:

Selective permeability- Allows certain substances to cross easier than others; a property of membrane

Amphipathic- Having hydrophobic and hydrophilic regions
Intergral Protein- Proteins that penetrate the hydrophobic core of the membrane

Peripheral Proteins- Proteins attached to the outside of the membrane

Glycolipids- A carb covalently bonded to a lipid

Glycoproteins- Carbs covalently bonded to protein

Aquaporins- Transport proteins that aid in water transport

Passive transport- transport that doesn’t require energy from the cell

Tonicity- the ability of a solution to cause a solution to gain or lose water

Osmoregulation- control of water balance

Membrane potential- The voltage across a membrane

Cotransport- A substance that has already left the membrane coming back across the membrane with another substance

Chatper eight:

Metabolism- All chemical reactions within the cell

Catabolic pathway- A metabolic pathway that breaks things down and releases energy

Anabolic Pathway- A metabolic pathway that builds things absorbing energy

Bioenergetics- The study of energy’s flow through an organism

Entropy- The measure of disorder or randomness a result of energy transfers

Free energy- Energy that do work within a system at constant temp and pressure

Energy couplings- The use of an exergonic reaction to power an endergonic reaction

Phosphorylated- A molecule that ATP has attached to

Substrate- The reactant an enzyme is going to speed up the reaction of

Active site- Where the substrate bonds to the enzyme

Chapter Nine:

Fermentation- anerobic respiration in other words the break down of sugars without oxygen
Oxidation- the loss of electrons from a substance during a reactions the substance that is oxidated is also the reducing agent

Reduction- Is the gain of electrons during reactions the reduced molecule is also known as the oxidizing agents

NAD- A coenzyme that carries electron in the electron transport chain of respiration

Glycolysis- Breaks down sugar in G3P and then Pyruvate

Citric Acid cycle- The cycle inside the mitochondria that starts by fixing Acetyl CoA to oxaloacetate to form citrate it releases NADH and FADH2

Oxidative phosphorylation- The ATP that is formed during the electron transport chain its named as such because it is the result of a redox reaction

Subsrate-level phosphorylation- Phosphorylation that occurs inside of an enzyme this type of ATP production occurs during glycolysis and the citric acid cycle

Acetyl CoA- This is an enzyme that Pyruvate transforms into upon entering the mitochondria it fixes to the citric acid cycle

Cytochromes- The protein complexes that are in the mitochondrial membrane and function in the electron transport chain

Chemiosmosis- The creation of a concentration gradient that powers cellular work

ATP Synthase- A protein that is in the membrane of the mitochondria it works like a small motor to power ATP synthesis

Obligate Anaerobes- Organisms that only use fermentation or other form of anerobic respiration and can’t survive with oxygen

Facultative Anerobes- Can use either aerobic or anerobic respiration to survive

Beta Oxidation- Breaks down fatty acids into two carbon fragments and then enters the citric acid cycle as Acetly CoA

Chapter Ten:

Photosynthesis- the process by which plants make energy storing molecules from sunlight and water

Autotrophs- “self feeders” Organisms that can sustain themselves without consuming other living things

Heterotrophs- Organisms that survive by consuming other living things

Chlorophyll- The green pigment located in the cholorplasts that absorb sunlight

Mesophyll- The tissue in he interior of the leaf where most photosynthesis occurs

Stomata- The pores in the leaf of the cell where water is absorbed

Stroma- The fluid within the chloroplasts

Thylakoids- Membrane sacs inside the inner membrane of the chloroplasts

Light reactions- The reactions where water is split and ATP and NADPH is formed for use in the Calvin cycle

Calvin cycle- Where Co2 is fixed to form G3P and later large carb molecules

Photophosphorylation- The way in which the light reactions power the formulation of ATP

Carbon Fixation- The initial adding of carbon to organic compounds

Wavelength- The distance between the peaks of light shorter the wavelength the higher the energy

Electromagnetic Spectrum- The entire range of radiation

Visible Light- The radiation with wavelengths from 380-750nm

Photons- Particles of light

Carotenoids- Acessory pigments that are able to absorb violet and blue-green light making photosynthesis more efficient

Photosystem- Contained within the thylakoid membrane these absorb light and transfer electrons from one to the other

Reaction-center complex- Part of the Photosystem this is a protein complex that aids in the absorbtion of light and exciting of electrons

Light-harveting complex- Made up pigments that absorb certain wavelengths of visible light

G3P- A three carbon sugar that is made during the energy investment phase of glycolysis and produced as a product of the Calvin cycle

Rubisco- The enzyme that Co2 fixes to the Calvin cycle

Photorespiration- When the Calvin cycles fixes O2 instead of Co2 to produce Co2 for photosynthesis

Chapter Eleven:

Signal Transduction pathway- The steps that are taken to get a signal from the membrane to the cellular reaction

Local Regulators- Signaling molecules that only travel a short distance to regulate the functions of nearby cells

Hormones- Chemicals used for long distance signaling

Ligand- The signaling molecules that bind to the receptor

G protein- Binds to GTP to be activated or GDP in the inactive which then opens up the G-receptor for signals

Receptor tyrosine kinases- The type of receptor that is activated by forming a dimmer and then adding P

Ligand-Gate ion Channel- a membrane receptor that only works when the signaling molecule opens it up for ions to flow in

Protein Kinase- An enzyme that transfers P from ATP to a protein

Protein Phosphatases- Enzymes that can quickly remove P from proteins

Second messengers- Small non-proteins or ions that work in signaling pathways

Scaffolding protein- A large relay protein that several other relay proteins attach to at the same time

Apoptosis- Programmed cell death performed to protect surrounding cells and prevent the reproduction of DNA dysfunctional cells

Chapter twelve:

Cell division- The reproduction of cells

Genome- A cells genetic information

Chromosomes- What DNA molecules are packaged into

Somatic Cells- Non reproductive cells that have 46 chromosomes

Gametes- Reproductive cells that only have 23 chromosomes

Chromatin- Complexes of DNA and proteins that make up chromosomes

Sister Chromatids- Every time chromosomes are duplicated into two of these

Centromere- The region where the chromatids are attached

Mitosis- Division of the nucleus

Cytokinesis- The division of the cytoplasm

Meiosis- The cell division that results in reproductive cells that have only one set of chromosomes

Mitotic phase- The part of the cell cycle that includes mitosis and cytokinesis

Interphase- 90% of the cell cycle that includes growth and the copying of the DNA but not the actual division

Mitotic Spindle- Fibers made of microtubules and proteins that start to form during prophase it later plays a role in separating the chromatids

Chapter thirteen:

Heredity- The transfer of traits from one generation to the next

Genetics- The scientific study of heredity and hereditary variation

Gametes- Reproductive cells (haploid)

Locus- A gene’s specific location on a chromosome

Clone- A genetic exact copy of something else

Sex chromosomes- The X and Y chromosomes that determine the sex of an organism along with other genetic traits

Autosomes- all the chromosomes an organism contains besides the sex chromosomes

Diploid cell- has a single set of chromosomes (gametes) N= number of chromosomes

Haploid cell- Double the set of chromosomes (somatic cells) 2n= number of chromosomes

Chiasma- the X shaped region that the homlogs cross over and hold together

Chapter Eight Reading Journal

What is the function of an enzyme in metabolic reactions?
Most reactions within the cell have to occur once molecules have absorbed enough energy to become unstable. Once reactants reach the “transition state” they are able to form products but they need activation energy to reach this point, enzymes provide this activation energy. Enzymes aid reactions that would eventually occur, but they speed up the process.

How do Enzymes work?
An enzyme has only a specific shape that allows only certain reactants to fit into the enzyme. This shape or cut out is called the active site once the reactant(s) are inside the active site they enzyme is able to speed up their breaking apart and then release them as separate products. The enzyme either speeds up the process by allowing the optimal conditions (position Ph ect) for the reactions or by fitting into the active site it puts stress on the reactants decreasing their stability making it easier for them to react.

What is the difference between an Exergonic and endogonic reaction?
An exergonic reaction is also known as a spontaneous reaction it will just happen without the input of energy. It releases free energy that can be used for work or more reactions. These reactions start with a high energy potential and move to a lower more stable energy potential this is also know as it moving towards equilibrium. Endergonic reactions start with a lower potential energy and then as it absorbs energy it moves to a higher potential. These reactions take the free energy from their surroundings and essentially store it for a later exergonic reaction.

Facts:
-All chemical reactions within organisms are referred to as metabolism
- Most energy within the cell is produced by ATP (exergonic reaction)
- A substrate is what an enzyme is aiding in reaction
- If a cell reached metabolic equilibrium it would die the system keeps it from reaching equilibrium so the cycle of energy can continue
- Inhibitors prevent a substrate from bonding with the enzyme thus preventing enzymatic processes



This figure describes the process of ATP breaking down in order to produce energy for the cell. Since ATP is at an unstable energy level the original reaction occurs from the desire for energy equilibrium and so one of the phosphates breaks off forming ADP and an a single phosphate. The first reaction is exergonic and then the cell uses energy from other sources such as food intake or photosynthesis to take the ADP and by an endergonic reaction reform ATP. In this cycle the ATP→ADP + P→ATP so the energy is continually recycled within the cell.

Summary:
Energy is the ability to do work and all living organisms need energy to live energy is constantly being released and absorbed by chemical reactions within the cell also called metabolism. Metabolism follows pathways either catabolic (breaking down) or anabolic (building molecules). There are three types of energy kinetic (motion), Potential energy, or activation energy (energy needed to get kinetic energy going). There are two laws of thermodynamics: 1. Energy can’t be created or destroyed only transferred into a different form 2. Transfers of energy increase entropy.

Free energy is the energy able to do work in the cell and reactions move one of two ways either from high potential energy to low potential energy releasing free energy in the process or from stable potential energy to high potential energy essentially absorbing free energy and storing it. The cell needs to break down things with stored energy and enzymes aid in this process by bonding to the molecule and creating conditions optimal for it to react.

Chapter Seven Reading Journal

What is the Membrane composed of?
The main component of the membrane is the Phospolipid bilayer. Phospolipids double up so that their hydrophilic heads are on the outside of the cell and the inside of the cell and their hydrophobic regions are in the middle. Proteins are also major components of the membrane some go through the entire membrane and some are merely attached to the outside. The proteins are useful in identifying other cells and transporting things from one side of the membrane to the other. Cholesterol is also embedded in the membrane to act as a temperature regulator. Carbohydrates and other lipids also attach themselves to the outside of the membrane as markers.

What is the difference between Intergral Proteins and Peripheral proteins?
Intergral proteins go into the core of the membrane some go all the way through to the other side where some just reach the hydrophobic middle. Those that go all the way through have hydrophobic and hydrophilic regions to match up with the corresponding portions of the bilayer. Peripheral Proteins are just attached to the surface of the membrane.

Explain the difference between active and passive transport?
Transport is the way that substances move from one side of the membrane to the other. Passive transport doesn’t require energy from the cell. Forms of passive transport include: diffusion, osmosis, and facilitated diffusion. Active transport goes against the concentration gradient and therefore requires cell energy.

Facts
- Fluid mosaic model is the most common model of the membrane
- One of the most important characteristics of the membrane is that is hydrophobic and hydrophilic
- A membrane that is exposed to colder temperatures will have more unsaturated fatty acids because they are liquid at lower temperatures
- The membrane is selectively permeable
- Transport proteins can aid diffusion without using cell energy




This diagram shows the process of osmosis in which water moves from the side of a membrane with a lower concentration of solute to the side with the higher concentration of solute to balance out the concentrations. It can also be said that water moves from hypotonic solutions to hypertonic solutions. It does this until there is equilibrium (the same concentration on both sides) this is also called an isotonic solution.

Summary:
The membrane maintains fluidity because of the level on unsaturated fatty acids in the phospholipids as well as cholesterol keeping a stable temperature. Proteins also make up a large portion of the membrane they help the cell with transport, provides enzymes, creates signals, and is useful in allowing cells to recognize each other. The membrane is selectively permeable and small nonpolar molecules have the easiest time making it from one side to the other. Thing also cross through processes of diffusion or osmosis or active transport through energy release from the cell. Things can also be transported through endocytosis or exocytosis.

Chapter Six Reading Journal

What are major differences between plant cells and animal cells?
Plant cells have a cell wall that helps keep the plant cell in a more solid shape both types of cells have a cytoskeleton plant cells just have this extra structure because animal cells need more mobility. Along with the cell wall plant cells have pasmodesmata, which helps their walls to attach to the walls of other cells. Plant cells also have chloroplasts, which animal cells don’t contain. A vacuole is also very common in plant cells this does the job lysosomes usually do in a animal cell. Thus a plant cell lacks lysosomes and animal cells lack a central vacuole. Animal cells usually have a flagellum, which enables them to propel themselves. Animal cells also contain a centrosome, which produces microtubules.

What is the Cytoskeleton composed of and why is it important to the cell?
The cytoskeleton is made out of microtubules, microfilaments, and intermediate filaments. The cytoskeleton helps a cell maintain its shape, enables it to move, and aids in cell division. Microtubules are tubes like structures made from the protein tubulin this supports cell shape, separate chromosomes during cell division, and create a track so that organelles can move along it. Microfilaments are rod like structures formed from the protein actin responsible for the gel consistency of outer cytoplasmic layer. Intermediate Filaments are cable-like made from various proteins depending on the type of cell. The help keep certain organelles in place such as the nucleus.

What major cell structures produce energy for the cell?
The mitochondria are one of the most important structures in a eukaryotic cell. A cell can have one central mitochondrion or many mitochondria. It has a double membrane the inner membrane folds in on itself multiple times so that is has more surface area for respiration to occur. Enzyme and ATP reactions within the structure produce energy for the cell. In Plant cells chloroplast are extremely important for the production of energy. Chloroplasts convert sunlight into sugar in the cell. Peroxisomes also produce energy they are singularly membrane bound. They take the hydrogen out of certain compounds and combine it with oxygen forming hydrogen peroxide. This is used to break molecules down that then can be made into energy.

Facts:
- SEM is an electron microscope that scans the surface of a specimen
- TEM is an electron microscope that goes through a specimen (must be dead)
- Lysosomes are used to digest things in the cell
- The Golgi apparatus receives proteins from the ER and package them for use within the cell
- The Nucleus is the brain of the cell



This shows the structures within flagella and cilia. These projections grow out of animal cells and they help the cell to move. They grow out of the cytoskeleton of a cell and increase surface area. There is usually only one flagella and it moves in a snake like manner. If a cell has cilia it typically has several of them they move back and forth and also aid cell mobility.

Summary:
In order to see the details of cell structure we use light or electron microscopes. Electron microscopes show the cell in more detail. Eukaryotic and Prokaryotic cells differ in that prokaryotic cells are much simpler and lack a membrane bound nucleus and organelles. Eukaryotic cells are also typically larger. Plant and animal cells share most of the same organelles (see question 1) since they are both Eukaryotic.

The nucleus is the brain of the cell and its is enclosed in the nuclear envelope. The nucleus contains the DNA of the cell. Ribosomes are subunits of proteins some of them are free in the cell and other are in the ER. ER is composed of smooth ER and Rough ER. Smooth ER aids in metabolism. Rough ER has ribosomes attached to it and therefore synthesizes proteins. The Golgi Apparatus functions as the packaging center of materials made by the ER. Lysosomes contain enzymes and are used as digestion centers. A vacuole serves the same function as the lysosome but it is only present in plant cells. Mitochondria, Chloroplasts, and Peroxisomes provided energy sources for the cell. The cytoskeleton helps the cell keep its shape and aid it in moving without falling apart as well as reproduction.

Chapter Five Reading Journal

Questions:

What are the differences between fats, phospholipids, and steroids?

Fats are made from three fatty acids bonded to a glycerol by what is called an ester linkage. Fats are non-polar and used to store energy. Phospholipids are made of two fatty acids and phosphorous bonded to glycerol. They are polar at the top where the phosphorous is and non-polar at the bottom where the two fatty acids are. Phospholipids make up cell membrane. Steroids are composed of four fused rings of carbon skeletons the function of a steroid is determined by the functional group that is attached to the rings.

What is an Amino Acid and why is it important?
An Amino acid is a molecule with the amino group and carboxyl group bonded to a central carbon, this carbon is also bonded to single hydrogen. This leaves one bonding site off the carbon which bonds to one of twenty different molecules. These twenty amino acids bond together to from polypeptides and proteins are made of either one polypeptide or several polypeptides bonded together.

Why are carbs, lipids, proteins and nucleic acids called macromolecules?
They are all named this way because they are huge molecules. They are all composed of many monomers that bond together through a dehydration reactions creating polymers. Many of these organic compounds are formed from these polymers or thousands of monomers bonding to other polymers.

Facts:
- Dehydration reactions form polymers
- Hydrolysis reactions break polymers apart
- Carbohydrates are composed of saccharies
- Lipids main common property is hydrophobia
- Nucleic acids are the macromolecules that are responsible for genes





This shows the structure of Phospholipids that consist of only two fatty acids compared to fats that are composed of three fatty acids. The third bonding site of the glycerol in the phospholipids is bonded to a phosphorous. This gives phospholipids different properties than fats because instead of the whole molecule being hydrophobic, one side is hydrophilic and the “tails” of fatty acids are hydrophobic. This property is important for the cell because layers of phospholipids make up the cell membrane and the hydrophilic portions are able to interact with the aqueous portions of the cell and the hydrophilic part of the phospholipids creates a barrier between the internal and external environment of the cell.

Summary: There are four main groups of large organic molecules called macromolecules, each group is very important for the functions of life. Carbohydrates are made up of saccharides and provide energy for the cell. Lipids are mostly common in that they are hydrophobic. Fats are used for energy storage and composed of three fatty acids and a glycerol. Phospholipids form the cell membrane and are made from two fatty acids and phosphorous. Steroids are made of four fused rings of carbon structures examples: cholesterol, hormones.

Proteins are composed of twenty different amino acids that form polypeptides. Proteins are formed from one or more polypeptides. Proteins have many functions. Nucleic acids are used to store and transmit genetic information. They made up DNA, which stores the information and RNA, which transmits the information.

Chapter Four Reading Journal

What is an isomer and what are the three types of isomers?

An isomer is a compound that has the same ratio of molecules but a different structure. Structural isomers have different structures made out of the same molecules. Geometric isomers have the same structures with different atoms attached to the different bonding sites. Enantiomers are mirror images of each other.

What are hydrocarbons and why are their main characteristics?
Hydrocarbons are molecules made up of only hydrogen and carbon atoms. They are mostly hydrophobic because bonds between hydrogen and carbon are virtually nonpolar. Typically reactions involving hydrocarbons release a large amount of energy. These are the framework of the most complex organic molecules.

What are the functional groups?
Different groups of chemical compounds that attach to a carbon skeleton. All but methyl are hydrophilic to they increase the organic compounds’ ability to dissolve in water. The seven most important most important of these groups are: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl.

Facts:
- Organic chemistry is deals with compounds containing carbon
- Bond angles when carbon forms four single bonds are 109.5
- Carbon has four valence electrons in its outmost shell this contributes largely to its diversity
- Isomers of a compound can have complete opposite effects of the original when reacting with living things
- ATP (cells energy source) is made of three phosphate groups bonded together










The diagram above shows that a very slight change in chemical structure can have a huge impact. These two molecules only differ in functional the group they have attached to them at one end, but they have opposite effects. One is a male hormone and one is a female hormone this is an example of form fitting function organisms are very sensitive to even slight changes in molecular structure.


Summary:
Organic compounds are those made of carbon and they are prominent in living things therefore important to the study of biology. Carbon is very diverse because it has four valence electrons. Very often organic compounds with the same molecular formula have different properties because they are arranged differently (isomers). Functional groups contribute to the properties of an organic compound because they all have properties of their own.

Chapter Three Reading Journal

Questions:

What main thing can account for the properties of water that make it so conductive to life?
- Hydrogen bonding is responsible for the special qualities that water possesses. Hydrogen bonding is responsible for the adhesion and cohesion of water that makes the transport of water within plants so successful. Hydrogen bonding is also what makes water able to maintain relatively consistent temperatures and keeps it from evaporating as quickly as most liquids. This is also a main reason that water makes such a great solvent.

What is PH?
- PH is an expression that helps us see the concentration of H+ and OH- ions in a substance. The lower the PH the higher the concentration of H+ ions and the higher the PH the more OH- ions are present. The PH scale only ranges from 1-14 because it is based on logarithms. A PH of 7 is neutral.

What is a buffer?
- A buffer is something that is able to balance the PH of a substance. A buffer is able to attach some of the H+ ions to itself as well as adhere OH- ions to itself. Buffers are able to do this by being a substance that has an acidic portion and basic portion balancing the excess of either H+ or OH- ions. Buffers within living things are very important for example the presence of buffers within human blood keeps blood at a PH of 7.4 and prevents it from changing PH quickly.

Facts:
- Water is a polar molecule making it conductive for hydrogen bonding with other water molecules
- Cells are made up of 70-95% water
- Water is able to moderate air temperature by absorbing heat from the air surrounding it and then releasing back into the air at cooler times during the day
- The fact that ice is less dense than water allows marine creatures to survive even when a body of water freezes because it does so only at the top layer
- Water’s ability to be a solvent makes it conductive to life especially within cells





This shows the crystal like structure that water forms when it freezes. The fact that the molecules spread out when frozen makes water less dense in its solid state. This is structure is very important to organisms that live in bodies of water. Since the ice is less dense than the rest of the water it floats to the top allowing life to continue under this top layer of ice if this were not the case winter would kill off creatures that live in bodies of water.

Summary:
Water’s polarity results in hydrogen bonding. The behaviors of hydrogen bonding gives water many of its special properties. Water is so conductive to life because of its ability for cohesion, its control of temperature within cells and in large bodies of water, the crystal structure formed when frozen (explained above), and its many uses as a solvent. Water and other liquids are greatly affected by their PH levels, which are determined by the amount of H+ ions. Industrial pollution creates great risk to the planets health by making the ocean and other bodies of water more acidic.

Chapter Two Reading Journal

Questions:

Why is Chemistry important to Biology?
- Chemical reactions within the systems of organism are often essential to the basic functions of life. Carbon, Oxygen, Hydrogen, and Nitrogen account for 96% of living matter. Medically speaking chemistry helps doctor study the more intricate functions of metabolism with the use of radioactive isotopes. Understanding chemical reactions gives us a better understanding of organisms internal functions as well as the effect they have on external things (i.e. other organisms or other surroundings)

What’s the difference between a Polar and Non-Polar Bond?
- A polar bond is a covalent bond in which the electrons are pulled towards the nucleus of one atom more strongly than the other. In a non-polar bond the electro negativity of atoms is equal meaning that the electrons are completely evenly shared.

What is a Hydrogen Bond?
- This is a bond made when Hydrogen is already involved in a polar bond and the molecule formed from that bond is then attracted to another atom that is electronegative. These bonds often occur within the cells with Oxygen or Nitrogen atoms being the other involved elements.

Facts:
- The mass number is the sum of protons and neutrons
- The farther an electron is from the nucleus the more potential energy it has
- The chemical behavior of an atom depends mostly on the number of electrons in the outermost shell
- An atom’s valence is typically equal to the number of unpaired electrons needed to fill the atom’s outer valence
- The strongest chemical bonds are ionic and chemical, but the weakest chemical bonds are equally important in the function of a cell





The diagram above displays how important the shape of molecules is. Molecules within organisms only attach to molecules if they have the right structure. The portion of endorphin molecules that attach to the brain cell is very similar to a portion of the morphine molecule. These similarities in structure allow morphine molecules to attach the brain and have similar effects on the brain to that of an endorphin. This makes morphine very useful in prescribing for people that aren’t producing enough endorphins in times of stress.

Summary:
All matter is made up of elements and combinations of elements called compounds. Carbon, Hydrogen, Oxygen and Nitrogen are amongst the key elements within living things. Trace elements are also essential to living things but need in smaller amounts than the above-mentioned elements. Atoms are the smallest unit of matter that can still be considered an element; atoms consist of neutrons protons and electrons. Isotopes are formed when an element has more neutrons than protons. Electrons are the key to chemical bonding. Covalent bonding is determined by the number of electrons in an atom’s valence shell. Ionic bonds occur when negatively and positively charged atoms are pulled together. There are a number of weaker bonds that occur and also have a large impact on cells and organisms as a whole. The creation and the decomposition of chemical bonds make up the chemical reactions that keep living things functioning.

Chapter One Reading Journal

Questions:

What are the themes of Biology?
-There are said to be seven themes of Biology. The themes are: Evolution, New properties emerge at each level of biological hierarchy, Organisms interact with their environments exchanging matter and energy, Structure and function are correlated at all levels of biology, cells are an organisms basic unit of structure and function, The continuity of life is based on hereditary information passed through DNA, Feedback mechanisms regulate biological systems.

What is the Difference between Hypothesis and Discovery science?
-Discovery science is used when scientists make specific observations about the world around them and from those observations make assumptions about what would happen on a larger scale. Hypothesis based science occurs when scientists observe things ask questions about them and create experiments to help answer the questions.

Why is evolution so important to the themes of Biology?
- Evolution is said to be the core theme of biology because it accounts for the unity and disunity amongst living things. All species evolved from other species creating their differences but their ancestry tracing back also makes them similar.
Facts:
- Evolution is the core theme of biology
- Domains Bacteria and Archaea are prokaryotic and domain Eukarya has organisms with eukaryotic cells
- Eukaryotic cells have a membrane around the nucleus something that prokaryotes don’t posses
- All living things are connected through their evolutionary history and therefore common ancestry
- A theory is much broader and has much more evidence backing it up than a hypothesis






Prokaryotic and Eukaryotic cells are different in their size and in the presence of a nucleus in Eukaryotes. These cells are a good example of the theme of unity and disunity. The cells are clearly different in a few ways but they also share many similarities in that they both contain: plasma membrane, cytoplasm. DNA, and Ribosomes. This is a good indicator that the themes of biology apply even amongst the smallest pieces of it.

Summary: The themes of biology help us to better understand biology as well as to correlate the various occurrences. It helps us link different topics because all of the themes reoccur within the different topics and this helps us to group them together. Evolution is the overshadowing theme of all of biology and it provides a connection between all living things. Evolution accounts for the difference and similarities amongst organisms.

There are two types of scientific study Discovery and Hypothesis- based science. Discovery science comes to conclusions about general things after making specific observations. Hypothesis science asks questions and then develops experiments to explain observations. Effective experiments are created using control groups in order limit the number of variables affecting the results. Science is limited in that hypothesis must be testable and it must be possible to prove them wrong as well.

First Assignment of the Year

So here it is....I have created my bio blog for all things bio!