Monthly Archives: September 2011

3.2 Carbohydrates, Lipids, Proteins

Condensation and Hydrolysis

Monosaccharide, amino acids, and nucleotides are subunits of polysaccharides, polypeptides, and nucleic acids respectively. For the subunits to combine, they go through condensation. This process involves loosing an OH from one molecule and an H from another molecule, and together they form H2O. So, condensation is a process that involves combining subunits and producing water and larger bonds. The new bond that is formed is called a peptide linkage. To split the bonds formed in this process, water is added to a reaction known as hydrolysis. Hydrolysis is a breakdown of a compound because of a reaction with water.

Polypeptides + water  –> dipeptides or amino acids

Polysaccharides + water –> disaccharides or monosaccharides

Glycerides + water –> fatty acids + glycerol


Lipids are a huge category of molecules that include steroids, waxes, fatty acids, and triglycerides. Triglycerides are fats that are solid at room temperature or they are oils if they are in liquid form at room temperature. To form this molecule, three fatty acids combine with a molecule of glycerol and when this happens, three water molecules are made. This is a condensation reaction and the breakdown of this occurs by hydrolysis. Triglycerides are used for energy storage and can serve can insulation.

Steroids serve as hormones, waxes serve as hydrophobic barriers on the surface of leaves, and fatty acids serve as structural components of the cell membrane. Both lipids and carbohydrates are used for energy storage but also have many differences. Lipids are used for long-term energy storage whereas carbohydrates are more soluble and easier to transport. Lipids have double the amount of energy per gram as carbohydrates do. Carbohydrates though, have a stronger impact on the osmotic balance. Lipids are insoluble in water so they do not cause osmotic problems but since carbohydrates do, they have an impact on osmosis.

Amino Acids

The general formula of amino acids is. The R is a group of amino acids can be non polar or polar and can be either positively or negatively charged. The bond between two amino acids in a dipeptide is known as a peptide bond.


3.1 Atoms, Molecules, Water


Elements are pure substances that are made up of just one kind of atom and have its individual unique chemical and physical properties. The most common elements are oxygen, nitrogen, carbon, and oxygen. There are many examples of elements that are important for many living organisms such as animals, plants, and prokaryotes. Sulfur is a component of amino acids. Secondly, phosphorus is a component of nucleotides in DNA and RNA. When two or more atoms combine chemically through a covalent bond, they can form a molecule. If an atom or molecule has a charge, they are called an ion.


Water is a molecule that if formed by a covalent bond between an oxygen atom and two hydrogen molecules. This bond involves unequal sharing of electrons, therefore it is a polar covalent bond. For this reason, water has an unequal charge distribution. Also, because it is polar, it repels the non-polar regions of the cell membrane (hydrophobic tails) but attracts the hydrophilic heads. This unequal charge distribution causes hydrogen to have a partial positive charge and oxygen to have a partial negative charge. This causes water molecules to stick together and form “hydrogen bond”

A hydrogen bond is a type of intermolecular force that forms when hydrogen in one polar covalent molecule is attracted to a partial negative atom of another polar covalent bond. Though it may be called a bond, this term is quite inaccurate in a few ways. Firstly, this is an interaction between the molecules, not a bond. Secondly, it does not lead changes to occur in the chemical properties of its particles like a covalent bond would. Lastly, it is considerably weaker than a covalent or ionic bond.

The properties of water

Cohesion is the binding of two molecules of the same type. An example of wter used in this is transport medium for the xylem of plants. Adhesion is the binding of molecules with different polar molecules.

The polar nature of water molecules form shells around charged and polar molecules, which prevent them from clumping together. Water is known as a universal solvent because so any materials are dissolved in water so water is the medium for metabolic reactions and can be used as transport mediums

Water also has a large heat capacity so large amounts of energy are needed to raise its temperature and is needed to break some hydrogen bonds. Blood, composed of water, is also used as a transport medium.

Water also has a boiling point, which is 100 degrees C because to change it from a liquid to a gas all of the hydrogen bonds need to be broken. As a liquid, water can act as the medium for metabolic reactions.

Lastly, water can evaporate when temperatures are below boiling point but for this, the hydrogen bonds must be broken. The heat energy needed for this is taken from liquid water, cooling it down, so water can be used as a coolant.

Because of the hydrogen bonds between water molecules and the individual covalent bonds within the water molecule, surface tension is created. This can be broken if a more dense material is put upon it. Because surface tension is so strong due to the bonds in water, when we land on our bellies in the water, it hurts us because the strong water tension is broken down.

Organic Molecules

The chemistry of living thins in based on carbon. When a molecule contains carbon, it is known as organic. The oxides of carbon are not categorized as organic. Structural formulas can show the atoms found in a compound and the way they are bonded. A covalent bond is shown as a straight line. In a condensed structural formula, because bonds with hydrogen atoms and other atoms are easy to predict, they are not included.

Macromolecules are large molecules that are created by long chains of repeating subunits known as monomers. For example the nucleic acid of RNA is made up of many nucleotides and the polypeptide is made of a long chain of amino acids. Compounds that do not contain carbon as inorganic compounds.


Carbohydrates are composed of carbon, hydrogen and oxygen and hydrogen and oxygen are expressed as 2H:1O. The monomers of carbohydrates are monosaccharaides such as ribose, fructose, and glucose. Carbohydrates with many monomers are polysaccharides.

2.5 Cellular Division

There are a few ways for the creation of new cells. They are growth, asexual reproduction, tissue repair and maintenance. In eukaryotic cells, when the nucleus divides to form two genetically identical nuclei, it is known as mitosis. When the cytoplasm divides to form two cells, it is known as cytokinesis. In prokaryotic cells reproduce by a process known as binary fission. In this process, a single circular chromosome replicates and then the two copies of the chromosome move to opposite sides of the cell and cytokinesis then follows.

The cell cycle is the ordered sequence of events for the life of a cell and refers to the events between one cell division and the next in eukaryotic cells. This cycle can be divided into two parts, interphase and cell division. Interphase is an active period in the cell life when metabolic reactions occur, including protein synthesis, DNA replication, and an increase in mitochondria and/ or chloroplasts. A cell can remain in interphase for a long time so it does not mean that it is the preparation stage for mitosis. Interphase has three phases, the G1 phase, the S phase, and the G2 phase. During the G1 phase, cells grow and DNA trasnscription and protein synthesis take place. During the S phase, the genetic material is copied so that there are two new cells with a complete set of genes. Lastly, during the G2 phase, the cell prepares for division.

Mitosis is the division of a eukaryotic cells’ nucleus into two genetically identical nuclei. Mitosis is needed during the growth of a cell, during embryonic development, when tissues are damaged and have to be repaired, and lastly to reproduce asexually. Before this can occur, there has to be two copies of each chromosome. Each chromosome consists of a single DNA molecule that has to be replicated so that there are two identical DNA molecules called sister chromatids. Though mitosis is a continual process, scientists have split it into four stages; prophase, metaphase, anaphase, and telophase.


In this early stage of this phase, the chromosomes coil and become shorter and fatter. To become short enough they have to coil repeatedly and this is known as supercoiling. At the end of this phase, the nuclear membrane breaks down and each chromosome (consisting of tow identical chromatids created in DNA replication during interphase) are held together by a centromere.

Microtubules grow from the piles of the cell from a structure called the microtubule organizing center (MTOC) to the chromosomes. They form a spindle shape and so the MTOCs together with the microtubules are referred to as the mitotic spindle. In prophase, the spindle microtubules extend from each pole to the equator of the cell.


The spindle microtubules attach to the centromeres. Chromosomes are then moved from the center of the cell to opposite ends, with the spindle microtubules attached to one of the sister chromatics from one pole, and the another spindle microtubules is attached to the other sister chromatid from the other pole.


In anaphase, the centromeres divide and the chromatids are now chromosomes. The pair of sister chromatids separate and the spindle microtubules bring them to the poles of the cell. Up until this point, the centromere has held them together. Because the sister chromatids are pulled to opposite poles, mitosis produces two genetically identical nuclei. To make sure of this, the centromeres of the sister chromatids must be attached in metaphase to spindle microtubules from different poles.


At the early stage of the phase, nuclear membranes are formed around the chromosomes at each pole. Also, the spindle microtubules break down. During the late stage of this phase, the chromosomes uncoil, the cell once again divides, and the two daughter cells enter interphase again and this cell cycle goes on again and again.

Sometimes, certain agents damage the way cell division is regulated, such as ultraviolet light, chemicals and carcinogens or viruses. When this happens, it can cause a change in the genes of a cell and as this cell divides on and on, the other cells inherit these genes. WHen this uncontrolled cell division occurs, it can produce tumors which are a mass of cells. These can grow to large sizes and spread to many areas of the body. This disease is known as cancer.

DBQ: cell size and the cell cycle

1a. DNA most likely occurs at about 2:00 and 3:00. This is because the S phase, which is the phase where DNA replication occurs, is at its peak and more than 50% of the population is in that phase during this time.

1b. Mitosis is most likely to occur when the G2+M stage is at its peak. This is because this occurs right before mitosis does. It will occur at 5:00, 3:00, and 6:00

2. Most of the increase in cell size occurs in the G1 stage of interphase.

3.  From the graph, it is evident that during the day when there is the most light, the cell is increasing in size. As it gets darker in the day, the cell decreases in size. For example, at from 12:00 to 18:00, the cell size in increasing and so is the light outside. However as it gets darker outside and the time falls to 6:00, the cell size decreases. This supports the claim that Emiliania hyxleyi take advantage of light resources for the timing of their cycle.

2.4b Membranes

In most cells, water is able to movie in and out of the plasma membrane freely while the movement of solutes is restricted. This means that the membrane is partially permeable to water. Sometimes with water molecules, there are an equal amount of molecules moving both in and out of the cell. However, sometimes, there are both molecules either moving in or out and this causes net movement known as osmosis. Simply put, osmosis is when water movies from higher concentrations of water to lower concentrations or vice versa. This is different from diffusion because diffusion is the process for particles to move in and out of the cell while osmosis is the process for water. Osmosis can only occur if there are solutes dissolved in the water. The water molecules bonded to solutes cannot move freely so the concentration of water is reduced. For this reason, regions with a higher solute concentration have a lower water concentration (hypertonic concentrations) than regions with a lower solute concentration. This also causes water to move from regions of lower solute concentrations to higher solute concentrations. This is a passive process meaning that no energy has to be used directly to make water move.

Sometimes cells take in substance with higher concentrations inside the cell than outside. This substance is absorbed against the concentration gradient. Rarely, cell pump out substances even if there is already larger concentrations outside. This type of movement is not diffusion because there is no energy required for it to happen so it must be active transport. Active transport moves molecules against their concentration gradients. For this, ATP, produced by cell respiration, supplies energy.

Globular proteins, known as pump proteins or transporter proteins, carry out this process. There are many different types of these proteins and this allows the cell to control the contents of its cytoplasm. For example, plant roots can absorb potassium and other ions by active transport.

A vesicle is a small, spherical sac of membrane with a droplet of fluid inside and is present is most eukaryotic cells. They are formed by larger pieces of the membrane. And since membranes are fluid, so they can change shape and move. Vesicles are formed when a small piece of membrane is taken from the rest of the membrane, and proteins using energy from ATP carry out this process. Endocytosis is when vesicles form at the inner surface of the plasma membrane and trap fluid from outside the cell.

Vesicles are used to move materials around inside the cell. One of the examples where this occurs is in secretory cells. Ribosomes synthesize protein on the rough endoplasmic reticulum and store it in the cisternae of rER. The vesicles then leave the cisternae and carry the protein to the Golgi apparatus where the vesicles fuse with the cisternae of the Golgi apparatus so that the protein is processed. The protein then moves through the cisternae and is released in more vesicles. These fuse with the plasma membrane and are the proteins are released from the cell. This is called exocytosis.

The plasma membrane separates a cell from its surroundings. Sometimes cells leave components they have produced outside the plasma membrane using exocytosis and these components are known as extracellular components. Examples of extracellular components are the plant cell wall and glycoproteins. Cell walls are constructed by synthesizing cellulose fibers in vesicles which are then added to the inner structure of the cell. The plant cell walls help keep the cell’s shape, help it build high pressures without bursting, prevent it from bursting from osmosis, and use pressure to support and keep the cell rigid. Glycoprotein are proteins that have carbohydrates attached which form extracellular matrices. Glycoproteins support single layers of thin cells that could tear and help cell to cell adhesion.

DBQ: autoradiography

1a. The most radioactivity is located in the rough endoplasmic reticulum

1b. The reason that the most radioactivity is located in the rough endoplasmic reticulum is because of the ribosomes synthesizing proteins. Because this experiment adds radioactive amino acids on to tissue that is actively synthesizing protein form amino acids, and synthesizing occurs in the rough er, most of the radioactivity occurs there.

2. Proteins are carried through vesicles form the rough endoplasmic reticulum to the Golgi apparatus. This is because it is shown as the vesicles have the highest percentage of autodiographic grains after 7 minutes, then after 37 minutes the Golgi Apparatus does.

3. It takes the protein 7 minutes to be synthesized. After 117 minutes, it is sent to the large storage vesicle near the plasma membrane. This can be seen because at 7 minutes, there is a lot of radioactivity in the rough endoplasmic reticulum and vesicles between rough endoplasmic reticulum. This is showing that the protein is getting synthesized and processed. After 7 minutes, the radioactivity decreases in the rough endoplasmic reticulum and vesicles between it and the Golgi apparatus. After 117 minutes, we can see that the highest percentage of radioactivity is in the large vesicles showing that the proteins are sent there.

4.The reason this is occurring could be because the proteins are done synthesizing and have reached their maximum ability. Also, it could be possible that the cell is not releasing a large amount of proteins out of the cell therefore the radioactivity is not rising above 7.1%.

2.4a Membranes

Membranes are structures that separate the inside of the cell or organelle from the outside. They are involved in many cellular processes such as cell adhesion, cell signaling, and other processes as well. Phospholipids are a very important parts both the plasma membrane and the membranes inside the cell. Phospholipids have two regions, one that is hydrophobic meaning that the two hydrocarbon tails are not attracted to water and the other, the phosphate head, which is hydrophilic meaning that it is negatively charged and attracted to water. When mixed with water, the phospholipids are arranged in double layers with the heads facing outward and the tails facing inward. This structure is very stable because of the interactions between the water and the phosphate heads and the hydrophobic interaction between the tails (though this is one is a weak intermolecular interaction it is strong because of the huge of number of tails). Because of the many interactions, membranes are infrequently torn.

As well as phospholipids, proteins also compose the membrane. There are some proteins that are in phospholipid and are called integral proteins. Other proteins are loosely attached to the membrane surface and are called peripheral proteins. Membranes are asymmetrical and the ways the faces of the membrane are arranged are in terms of the proteins that are exposed. Proteins have many functions in the membrane. Some of these are the hormone binding sites, immobilized enzymes, cell adhesion, cell-to-cell communication, channels for passive transport, and pumps for active transport.

Liquids and gases are fluids for the reason that the particles in them flow together in a mass. In fluids, the individual particles move independently and the direction of the movement for particles are random. This random movement results in diffusion, a process where particles move randomly from areas of high concentration to areas of low concentration creating net movement. It can occur if the membrane is permeable to the particle. If the membrane allows some substance to diffuse but not others, they are known as partially permeable. Diffusion is an important process because oxygen and carbon dioxide move into and out of cells by diffusion.

One of the ways for passive transport across a membrane is simple diffusion. Simple diffusion across membranes is the passing of particles between the phospholipids in the membrane. This is only possible if the phospholipid bilayer is penetrable to the particles.  Ions with positive or negative charges cannot pass easily because the center of the membrane is hydrophobic. Molecules that have partial positive and negative charges such as polar molecules can diffuse but only at low rates. Also, smaller particles have an easier time passing through than larger molecules. Simple diffusion only occurs if there is a concentration gradient where the concentration of the particles is higher on one side of the membrane than the other side.

Ions and other particles that are not able to diffuse between phospholipids can pass in or out of the cells if there are channels, or holes with a narrow diameter, through the plasma membrane for them. The walls of these channels have either a single protein molecule or a group of proteins. The diameter and chemical properties of the channel enable only one type of particle to pass through. This process is known as facilitated diffusion because the channels help the particles pass through the membrane and from areas of high or low concentrations to the opposite concentration. Cells can decide what type of channels are created so they can control which substances diffuse in and out of the cell.

Plasma membranes are permeable to water, so the passive movement of water across membranes is different from diffusion across membranes because water is a solvent, or a liquid, which particles dissolve. A solute is dissolved particles. The concentration of the solutes rather than the concentration of the water molecules control which direction the water moves so it is known as osmosis not diffusion. In osmosis, water moves from an area of lower concentration of solutes to an area of higher concentration of solutes across a partially permeable membrane.

DBQ: patch clamp analysis

 1a. The size of the current flowing through the membrane when the ions are closed is 0 because there is no flow of ions. The membrane is non-polar, but the ions are charged so they can’t go through the membrane because there are no channels for them to pass through.

1b.There are 1 trillion Pico amps in one amp.

2a. The maximum length of time the channel remains open is 50 ms. This can be determined by measuring the scale. The scale, which is 200 ms, is 10 mm. This means that 1mm is 20 ms. The channel stays open for 2 ½ mm so this means that it stays open for 50 ms.

2b. The size of the current flowing when an ion channel is open is 4 pA which can also be determined using the scale. The scale on the side is 8 mm which is 4 pA.

3. The natural sources of Ach in living muscle fibers are vitamin B and sugar. This is because acetyl is two carbon fragments taken from sugar and choline is vitamin B.

4a. Higher concentrations of Ach increased the frequency of opening the channels because if you have more ACh, there are more proteins to which ACh binds to therefore more channels are opened. If there are more signal molecules, there will bind to more receptor molecules, therefore opening more channels.

4b. Higher concentrations of ACh do not increase the time it is open. This is because when right after ACh opens a channel, it is degraded by an enzyme so the time doesn’t change because no matter how many times it opens a channel, it will still be degraded by an enzyme right after.


Trace (i) Trace (ii)
Intensity of the current across the membrane Lower Greater
Duration of time the current is flowing through the membrane Lower Greater
Frequency of the current flow Lower Greater

5b. There are a few reasons for the differences between the traces. Firstly, two different species are used. In trace (i) the data is taken from a human while in trace (ii), the data is taken from a mouse. Additionally, there are taken from different tissues of the species with trace (i) being from muscle fiber of a human and trace (ii) being spinal neuron from a mouse. Also, there are different triggers for both. Trace (i) uses acetylcholine (Ach) while Trace (ii) uses glycine and since different proteins are making the channels, they respond differently

Store Analysis

As you enter 7-11, the first thing I noticed was that the entrance faces away from the cashier. This can be a way for the store to make sure the customers look at the whole store before they decide to exit the shop.


When you enter, the first thing you see are things that are necessary at times but are not edible items. This makes customers decide to roam around the store to find food or drinks if that is the reason they came to the store. This can be another way for the store to make sure you look around.



The aisles are not that wide or narrow which allows at most two people to go at the same time. This way, people may not feel overwhelmed by aisles that are too narrow where they can barely walk through or too wide.


The last thing I noticed was that after a customer passes and pays at the register and is walking towards the exit, they pass the sweets. The sweets are colorful and attract many customers so they may be kept there to make the customers buy even more items or for those who didn’t buy anything, buy a few things.


Hypothesis: I think that 7-11 wants its customers to buy a few things. When a customer first enters, they are faced in the opposite direction of the register so this can cause them to want to look at the whole store. As well as this, there are also other incentives to stay in the store. Lastly, when you are exiting after paying, there are even more items that most people want to buy. All of these facts show that 7-11 stores want quite a few items bought.