A) Chemistry of Life (7%)

i) Water
(1) How do the unique chemical and physical properties of water make life on earth possible?

Water is often nicknamed the "universal solvent" as it can dissolve other substance. Those which dissolve well are hydrophilic (eg. salts, sugars, acids), where as those which do not are called hydrophobic (eg. fats, oils). Water has a high specific heat (the amount of energy needed to raise the temperature of 1 gram 1 degree Celsius) and a high heat of vaporization (the energy needed to turn a liquid into a gas) due to the many hydrogen bonds and then breaking the hydrogen bonds. The high specific eat allows water to keep the Earth's climate moderate, protecting us from any huge changes in temperature. The high heat of vaporization is important in humans when they sweat. The change from a liquid to a gas is what creates the cooling sensation. A high surface tension exists with water. Due to cohesion, water molecules have hydrogen bonds which attract to one another. This is important in transpiration, as the water molecules stick to each other as they move up a tree.

ii) Organic molecules in organisms
(1) What is the role of carbon in the molecular diversity of life?
Carbon is a key player in biochemistry because it can form four stable bonds to other atoms at once. This means it can form long chains and also bind reactive side groups that help it bend into useful shapes and elaborate structures. It is thought that if life develops on other planets it would probably have to be carbon-based or silicone-based because they are the only elements that can form such chains.
(2) How do cells synthesize and break down macromolecules?

2 monosaccharides, such as glucose and fructose, are hooked together by a process called dehydration synthesis. A larger molecule is synthesized by removing a water molecule from between them - an H from one and an OH from the other, freeing up a covalent bond on each. Two of those free bonds join together to make HOH (water), and the other 2 join to make the disaccharide called sucrose

(3) How do structures of biologically important molecules (carbohydrates, lipids, proteins, nucleic acids) account for their functions?

Carbohydrates- different types
- monosaccharides (glucose and company)
- disaccharides (maltose and sucrose, etc.)
- polysaccharide (starch and multiple monosarcharides bonded together)
These carbohydrates as used to make ATP via celluar respiration. It's basically a place for energy storage. It can also be used in cells as cell walls (chitin and cellulose are both carbohydrates). Their structure is appropriate, because it's purpose is an energy bank and thus getting the energy when it is needed would be helpful. All you have to do to get energy from polysaccharides is just add H2O and it'll become a simpler monosaccharide, easily able to be formed into ATP.

Lipids- Includes triglycerols, steriods, phospholipids, and fats.
Fats: fatty acids and glycerol, has a carboxyl group at the end. Fats help to protect organs, provide insulation, and to store energy.
Saturated and Unsaturated Fats: Saturated has kinks, Unsaturated has no kinks.
external image fattyacids.jpg
Phospholipids: Has a hydrophobic and hydrophlilic part. Vital to the fluid mosaic membrane model. It's structure keeps it so there are hydrophilic parts facing the water while the hydrophobic parts do not in the cell membrane.
Steriods: Hormones and stuff are included in this.
Triglycerols: make up body fat, good for storage of energy.

Proteins- Many different types and functions of proteins, including but not limited to:
- Structural proteins
- Storage proteins
- Transport proteins
- Enzymes
Primary structure is composed of amino acids; secondary structure are alpha helixes and beta sheets; Tertiary structure are folds of a-helixes and b-sheets, R group interactions make them fold; Quaternary structure have complex folds and twists, interaction between proteins with subunits.

Nucleic acids- Usually found in DNA/RNA, have genetic info stored in chains of nucleotides. Nucleotides: Adenine, Guanine, Cytosine, Thymine.

iii) Free Energy Changes
(1) How do the laws of thermodynamics relate to the biochemical processes that provide energy to living systems?
1st law of thermodynamics: Energy can be transferred and transformed, but NEVER destroyed or created (science, God would not be pleased). Second law is that entropy occurs everytime energy is transformed or transferred. Living organisms take in energy, then use some of it, and release most in heat and waste. During all processes of organisms, energy is never created/destroyed, it is merely converted from unusable to a usable form of energy.

iv) Enzymes
(1) How do enzymes regulate the rate of chemical reactions? they lower the activation energy required to start the reaction and due to feedback inhibition, they stop when their product overaccumulates

Feedback inhibition is when the end product of a metabolic pathway acts as an inhibitor of an enzyme which is acting in that pathway. The original substrate is changed so much, that when it binds to a different active site of the enzyme a second time, the original active site can no longer bind to the original substrate.

(2) How does the specificity of an enzyme depend on its structure?
each enzyme has exactly one substrate that it induce its structure to fit to yield a real product

*They have a tertiary structure with a HIGHLY specific ACTIVE site. The active site will only fit a SPECIFIC substrate. (If it wasn't it woudl start breaking down things it wasn't supposed to) It's described as a "induced-fit model": when the substrate enters the active site it alters slightly to better fit the substrate.

(3) How is the activity of an enzyme regulated?

Competitive inhibitor: primarily reversible and the inhibitor binds to the enzyme’s active site which keeps substrate from binding with the enzyme.
Noncompetitive inhibitor: primarily reversible and binds somewhere other than the active site of the enzyme, resulting in the enzyme’s active site changing shape so that the substrate can no longer bind with it.
Allosteric inhibitor: enzymes that are allosterically regulated are constructed from two or more subunits, each composed of a polypeptide chain having its own active site. The entire complex changes between two different shapes; an active form and a non active form. The binding of an allosteric inhibitor binds to one of the enzyme’s active sites and causes the non active form to stabilize and results in no more substrate binding to any of the active sites.

Heat- increased heat can make enzymes work at a faster rate
Increase in substrates- rate increases
increase in enzymes - rate increases

Each enzyme not only has an optimal temperature, but also has an optimal pH level. Most enzymes work best under pHs of 6 to 8. There are some exceptions, like pepsin, in the stomach, which works best at a pH of 2. If an enzyme with the optimal pH of 8 were placed in the stomach, it would denature.

B) Cells (10%)

i) Prokaryotic and eukaryotic cells
(1) What are their similarities and differences?
Prokaryotic cells:
· Less complex
· DNA is located in the nucleoid which is not membrane bond
  • Chromosomes are dispersed in the cytoplasm
  • No true nucleus and no membrane-bound organelles
  • Have circular chromosomes and lack histone proteins
  • Small - typically 0.1-1.0 micrometers in diameter
  • Have a primitive cytosketetal structures or don't have a cytoskeleton at all
  • Reproduce sexually by the transfer of DNA fragments through conjugation. Don't undergo meiosis.

Eukaryotic cells:

  • More complex
  • DNA is located in the nucleus, bonded by a double membrane
  • Contain true nuclei in which chromosomes are compacted as chromatin
  • Contain membrane-bound organelles
  • Have linear DNA and contain histone proteins
  • Larger - typically 10-100 micrometers in diameter
  • Have a complex cytosketeton
  • Reproduce sexually with the use of meiosis

ii) Membranes
(1) What is the current model of the molecular architecture of membranes?

The fluid mosaic model concept was introduced by Singer and Nicholson. The name arose because they believed there was a phospholipid bilayer where membrane proteins were able to move, rather than be static. The membrane mainly consists of lipids with hydrophobic tails and hydrophilic heads. Within this layer, there are many different proteins. These include integral membrane proteins, which are partially inserted and peripheral proteins which attach to the surface. There also is cholesterol imbedded and carbohydrates on the outer portion, used as markers. The membrane is selectively permeable, as it allows some small molecules to pass through, but keeps others out unless there are certain types of transport proteins which go through the membrane.
external image fluid.mosaic.jpg

(2) How do variations in this structure account for functional differnces among membranes?
membranes are made up of scattered proteins embedded in/associated with the phospholipid bilayer. but these scattered proteins are not incorporated into the membrane at random. there are different proteins with different structures, and therefore different functions that are embedded in different membranes. in the cell membrane, there are embedded proteins that function in transporting nutrients into the cell, and waste products out of the cell. in the membranes of your mitochondria, proteins are needed to serve as electron carriers (this makes the electron transport chain work). orientation of proteins in the membranes is important because when your mitochondria creates a proton gradient, all the protons must flow in the same direction. the ATP synthase protein directs this proton flow. if the ATP synthase were oriented backwards in the membrane or on a different cell, the protons would flow backwards or not at all and that would suck then we wouldn't be able to create energy.

(3) How does the structural organization of membranes provide for transport and recognition?

  • The fluidity of membranes
    • Membranes are held together by hydrophobic interactions
    • Proteins and lipids can move around laterally on one layer but rarely flip to the other side
      • Some move along cytoskeleton fibers
    • Membrane remains fluid as temperature decreases until the phospholipids settle into a closely packed arrangement
      • Membrane remains fluid longer if there are more phospholipids with unsaturated hydrocarbon tails
        • Separated more because of the kinks in the tails
      • Cholesterol
        • At higher temperatures, it makes the membrane less fluid
          • Restrains phospholipid movement
        • Lowers the temperature required for membranes to solidify because they are packed less tightly
        • Temperature buffer

  • Major functions of proteins in the plasma membrane

    • Transport
      • Hydrophilic channel through the protein
      • Shuttle a substance from one side to the other by changing shape
    • Enzymatic Activity
      • May have an active site exposed to substances in the adjacent solution
    • Signal Transduction
      • May have a binding site with a specific shape that fits the shape of a chemical messenger, such as a horomone
      • May cause a shape change in the protein that relays the message to the inside of the cell
    • Cell-Cell Recognition
      • Some glycoproteins are identification tags that are recognized by membrane proteins of other cells
    • Intercellular Joining
      • Membrane proteins of adjacent cells may hook together in junctions
    • Attachment to the Cytoskeleton and Extracellular Matrix
      • Microfilaments may be bound to membrane proteins, which stabilizes the location of certain membrane proteins and maintain cell shape

(4) What are various mechanisms by which substances cross membranes?

Diffusion: moves from high to low concentration; no energy required

OSMOSIS- the movement of water through a membrane until reaching equilibrium. There are three different types of osmotic conditions. Hypertonic is the movement of water out of the cell. Hypotonic is the movement of water inside the cell in which the cell becomes turgid. The third type of osmosis is isotonic in which equal amounts of water move in and out of the cell.

Facilitated Diffusion: carrier proteins aid in moving the substrate through the membrane if the substance cannot diffuse directly through the membrane itself; continues, to move from high to low concentration; no energy required
Active Transport: Energy is required as it is going against the concentration gradient. Proteins can be uniports (moving a single type of solute in one direction), symports (two types of solutes moving in the same direction), or antiports (two different molecules in two different direction). Usually, symports and antiports are seen together

iii) Subcellular organization
(1)How does compartmentalization organize a cell's function?

Compartmentalization allows each compartment to perform specific functions without interference from other cell functions. For example, lysosomes can break down cell debris in a compartment without accidentally digesting the cell itself.

It also allow enzymes and substrates to reach higher concentrations than if everything was diluted by the entire cytoplasm. For example, the mitochondria accumulates a large electron gradient in order for the electron transport chain to work.

(2) How are the structures of the various subcellular organelles related to their functions?

They are directly related to their functions. The mitochondrial cristae have a higher surface area to facilitate cellular respiration. The phospholipid bilayer of a cell membrane allows nutrients and fat soluble vitamins across the cell membrane. Cilia and flagella function as propellers for locomotion. The rigid cell wall of plants provides structure.

In each of the above cases, structure influences function. Cells have evolved over time to efficiently carry out their respective functions.

(3) How do organelles function together in cellular processes?

Organelles such as the cell wall and membrane work with the rest of the cell by not letting in/out certain particles, and providing structural integrity. The nucleus works with the nucleolus by creating to make ribosomes, which are then transported to the rough endoplasmic reticulum. Proteins are then made. Proteins travel through channels in the endoplasmic reticulum and go to the golgi body. The golgi body packs and makes them ready to be transported to the border of the cell.

The nucleus is the organelle that functions as the command center. The nucleus contains the genetic code material, in the form of DNA, that coordinates the growth and function of the rest of the cell.An organelle that works very closely with the nucleus is the ribosome. The ribosome---through the molecule messenger RNA---obtains the codes from the DNA in the nucleus for building cellular proteins.A fairly large and extensive organelle is the endoplasmic reticulum. The endoplasmic reticulum is a complex series of folded membranes. It is connected to the membrane that surrounds the nucleus and extends out into the cell's cytoplasm. In doing so, it establishes a chemical communication pathway between the nucleus and the cytoplasm. One of its critical functions is to transport proteins within the cell. An organelle that is somewhat similar to the endoplasmic reticulum is the Golgi apparatus. It functions in a similar way except that it specializes in preparing materials, like proteins, for transport through the cell membrane to the exterior of the cell.

(4) What factors limit cell size?

Cell size is limited to the logistics of cellular metabolism: the plasma membrane functions as a selective barrier that allows sufficient passage of oxygen, nutrients, and wastes service the entire cell. The surface area to volume ratio is crucial in determining cell size as there is a limit to how much of a particular substance can cross a certain area per second. As a cell grows, it's volume increases more than its surface area. A high ratio of surface area to volume is especially important in cells that exchange a lot of materials with their surroundings.

iv) Cell cycle and its regulation

(1) How does the cell cycle assure genetic continuity?
When the cells divide, they must replicate every chromosome so the new cells have all the genetic material of the old cell. If a chromosome is missing, then the cell with the mutation would not be able to survive. This is similar to natural selection on a cellular level, as only those cells which are complete enough to survive will pass on their genetic material.

(2) How does mitosis allow for the even distribution of genetic information to new cells?
The genetic material is copied during the phase right before prophase, in the S (synthesis phase) of interphase, where the chromosomes are duplicated once. Mitosis then occurs, and it can be divided into 5 phases- prophase, prometaphase, metaphase, anaphase, and telophase. The genetic material is wound, and the copies are split up between the two new cells which are formed. Each new cell gets an exact duplicate of the genetic material.

(3) What are the mechanisms of cytokinesis?
Cytokinesis occurs after telophase and is the process where the cytoplasm of a eukaryotic cell is divided to form two daughter cells. In both animals and plants, it involves vesicles which are made by the Golgi apparatus and move along microtubules. In animal cells, a cleaveage furrow develops, separating the two nuclei. In plants, the vesicles create a cell plate, which develops into a cell wall separating the two nuclei. An exception to this process is in animal cells during oogenisis,where the ovum takes all the cytoplasm and organelles, leaving the polar bodies to die.

(4) How is the cell cycle regulated?
The cell cycle is regulated so that cells do not constantly undergo cell division and to signal the movement from one phase of the cycle to the next. There are two main proteins involved- cyclin-dependent protein kinases (Cdks) and cyclins. Cdks are enzymes which stimulate phosphorylation, signaling for the cell to move on to the next stage. They are dependent on being bound with cyclins. Cyclins are constantly being synthesized and degraded. When they exist, they bind to Cdks to form a cyclin-Cdk complex. The cyclin will eventually degrade, and signal exist from a stage. There are G1 cyclins and miotic cyclings (normally accumulate during G2). There also are cell checkpoints which prevent the cell cycle from progressing at certain points. The two main checkpoints exists between G1/S and G2/M.

(5) How can aberrations in the cell cycle lead to tumor formation?
If the cell cycle doesn't function properly, tumors may form. Some cell cycle inhibitors may mutate and cause cells to multiply uncontrollably, which forms a tumor. The cell cycle in these tumor cells is equal or longer than that of a normal cell, but the number of cells undergoing cell division is much higher.

B) Cellular Energetics (8%)

i) Coupled Reactions
(1) What is the role of ATP in coupling the cell's anabolic and catabolic processes?
Catabolic pathways are metabolic pathways that release energy, or ATP, by breaking down complex molecules into simpler ones (cellular respiration).
Anabolic pathways are metabolic pathways that consume energy, ATP, to build complicated molecules from simpler ones (photosynthesis).
Metabolic reactions are coupled so that the energy released from a catabolic reaction can be used to drive an anabolic one.

(2) How does chemiosmosis function in bioenergetics?

Cells often use an electron transport chain to separate electrons from hydrogen protons. The hydrogen protons are then used during chemiosmosis. A hydrogen ion gradient is formed and the hydrogen ions flow through the ATP synthetase molecule to the other side of the membrane. Hydrogen ions accumulate outside the inner mitochondrial membrane during cell respiration and in the inner membrane space of the thylakoid membrane of chloroplasts during photosynthesis. Bacteria use the outside plasma membrane as the surface to build up the hydrogen ion gradient. Therefore the energy from food is transferred to hydrogen ions, and the hydrogen ions transfer the energy to ATP via the ATP synthetase enzyme. Chemiosmosis is critical in ATP production in eukaryote cells as well as most prokaryote cells.

ii) Fermentation and cellular respiration

(1) How are organic molecules broken down by catabolic pathways?
Hydrolytic enzymes attack the bonds that are holding the subunits together. As molecules are being digested, other enzymes can remove side groups of units to prepare the molecules for the synthesis of new molecules, or complete oxidation through cellular respiration.
(2) What is the role of oxygen in energy-yielding pathways?
Cellular respiration brings hydrogen and oxygen together to make H20. The electron transport chain is used to break the fall of electrons to oxygen into several steps. Energy is cascaded down the chain from one carrier molecule to the next until the terminal electron receptor oxygen is reached. The oxygen pulls the electron down the chain in an energy-yielding tumble for the production of ATP.

Without oxygen, cellular respiration could not occur because oxygen serves as the final electron acceptor in the electron transport system. The electron transport system would therefore not be available.
Glycolysis can occur without oxygen. Although glycolysis does not require oxygen, it does require NAD+. Cells without oxygen available need to regenerate NAD+ from NADH so that in the absence of oxygen, at least some ATP can be made by glycolysis.

(3) How do cells generate ATP in the absence of oxygen? In the absence of oxygen, cells can still generate ATP in the initial process of glycolysis. Oxygen is not required for glycolysis and a net 2 ATP is made for every molecule of glucose which is broken down in that process.
Fermentation: glycolysis and reactions that regenerate NAD + - which you need to accept electrons! The two different types are Alcohol Fermentation and Lactic Acid Fermentation.
Alcohol Fermentation: converts pyruvate into ethyl alcohol and carbon dioxide. Yeast do this, and that's how beer is made.
Lactic Acid: Pyruvate is reduced to form lactic acid. Human skeletal muscles do this. We used to think it was bad, but now it's thought to be beneficial. .

iii) Photosynthesis
(1) How does photosynthesis convert light energy into chemical energy?

Photosynthesis starts with the light reactions, where photons from the light hit photosystem II, exciting electrons to a higher energy level and moving them down the electron transport chain. The electrons move down to photosystem I, where NADPH captures them while the hydrogen ions (which were pumped into the thylakoid through the electron transport chain mechanism) go through ATP synthase to create ATP. Both the ATP and NADPH are used in the Calvin Cycle (the dark reactions). The Calvin Cycle takes place in the stroma where three CO2 molecules enter and bind with RuBP , creating molecules of G3P. Only one of the six G3P molecule exits, however, while the others go back through the cycle to form 3 RuBP molecules for the next three carbons. This process continues, using up NADPH and ATP along the way.

It takes 6 cycles through the calvin cycle to create 1 glucose molecule. Every calvin cycle only produces 1 excess G3P molecule. ^ are actually created but 5 of them must be recycled and turned into RuBP by ATP.

2) How are the chemical products of the light-trapping reactions coupled to the synthesis of carbohydrates?

The chemical products ATP and NADPH that are produced in the light dependent reactions are used to fuel the following light independent reaction cycle (the Calvin Cycle), which produces one G3P molecule at a time to form full carbohydrates once enough G3P molecules have accumulated.

(3) What kinds of photosynthetic adaptations have evolved in response to different environmental conditions?

The C4 photosynthetic adaptation has allowed plants living in conditions with low CO2 to keep their stomata open less often since PEP Carboxylase fixes the CO2 immediately into OAA (oxaloacetate) once it enters the plant cell and transfers it into mesophyll cells. The OAA is then converted into malate with the help of NADPH, which is then taken to the chloroplasts in specialized bundle sheath cells. The four carbon malate then breaks into a CO2, three carbon pyruvate, and NADPH. The CO2 then enters the calvin cycle, producing the sugars like normal. The pyruvate re-enters the mesophyll cells, reacts with ATP, and is converted back to PEP so the whole cycle can start over again.

CAM plants open their stomata to fix CO2 only at night, using PEP carboxylase to form the CO2 into OAA, just like in C4 plants. THe OAA is converted to malate, which is then stored in vacuoles. When the stomata are closed during the day, CO2 is removed from the malate to enter the Calvin cycle.

(4) What interactions exist between photosynthesis and cellular respiration?

They both make energy for the organism, the product of photosynthesis, g3p (6 of which make glucose) is the reactant for respiration, which uses that glucose to make cellular energy. As it's product, respiration produces water and CO2, which photosynthesis needs in order to make the sugar.

The oxygen and water released by cellular respiration are used as reactants for photosynthesis. The two processes are essentially the opposite of each other in regard to the equations. Both animals and plants perform cellular respiration, but only plants perform photosynthesis.

Photorespiration: C3 plants sometimes get their rubisco bound with O2 rather than CO2, and when this happens it diverts photosynthesis in a) No ATP is produced (unlike regular respiration)
b) No G3P is produced (unlike regular Calvin Cycle)
The products of photorespiration are broken down and are useless. It's basically a vestigial function from the old days when the atmosphere had no oxygen to bind with rubisco and thus allow this to occur.

(5) How can aberrations in the cell cycle lead to tumor formation?

Each point of transition in the cell cycle from one phase to another is governed by multiple proteins which serve as either "accelerators" or "brakes" for the cell cycle. These proteins are coded by DNA,. The mutation in the protein-specific DNA creates either no protein, overactive protein, or underactive protein. In any case, it creates a disruption to the cycle, which disturbs orderly cell growth and division. This problem can lead to cancer.

Cancers are diseases in which there is a defect in the regulation of the cell cycle. Cancer cells are rapidly dividing cells that no longer are controlled. Cancer cells can form tumors due to this unchecked growth.

Normal cells have a characteristic called "contact inhibition" which limits the division of cells when the space is very crowded. Normal cells also are limited by the number of times that they may divide, therefore limiting their life span. Unlike normal cells, cancer cells lack the contact inhibition that limit their growth. They also are immortal cells and are not limited by the number of times they can divide.