Martin's Biology Project

Cells are enclosed by a plasma membrane. The plasma memrane is semipermeable, this means that it chooses which things to be let into or out or the cell. This membrane is made from two layers of lipids. Since lipids are insoulble in water, the membrane can move and flex without mixing with its enviroments, similarily to how oil and water don'n mix.

Lipids are made from glyserol and three fatty acids. If a phosphate group replaces one of the three fatty acids then a phospholipid is made. These phospholipids are primarily what make up the membrane. The phospholipids have a phosphate group head and two fatty acid tails.

One layer of the membrane is made from these phospholipids all conected at their heads with their tails all facing the same way. The second layer is the same thing but the tails are facing the opposite way, back to back with the first layer. The phosphate heads are polar, which makes them stick together. The fatty acid tails on the other hand are nonpolar.

This nonpolar layer in the middle helps to keep molecules that are polar out. For example, water can easily pass through the phosphate group since they are both polar, but it is stopped by the fatty acids because the fatty acids are nonpolar.

Cholesterol is also a part of the plasma membrane because it keeps the fatty acid tails from sticking together. Protein as well is used in the membrane as well as all throughout the cell for different purposes. In the membrane proteins are used to transport needed substandes into the cell and wastes out of the cell. For this reason these proteins are called transport proteins. In a way the proteins are what makes the membane selectively permiable because they are what actively move things into and out of the cell.

The cell can even move particles from an area of lower concentration to an area of higher concentration but the cell must use energy to do this. This movement against a concentration gradient is called active transport. Another type of transport is passive transport which is when particles move thought the membrane simply by diffusion. No energy is used in passive transport.

Facilitated diffution is another type of passive transport that uses transport proteins. The transport proteins can form channels for particles to pass through or they can carry the particles by changing its shape around the particle. However, neither of these forms of transport require energy.

The last parts of the plasma membrane are carbohydrates as well as other proteins that stick out of the cell and identify chemical signals so that cells can communicate.

This model of the plasma membrane is known as the fluid mosaic model because the phospholipids that make up the membrane move in a fluid motion, similar to how water moves in a current.

B. Students know enzymes are proteins that catalyze biochemical reactions without altering the reaction equilibrium and the activities of enzymes depend on the temperature, ionic conditions, and the pH of the surroundings.

Enzymes are important proteins found in living things. They act as catalysts in chemical reactions. A catalyst is something that speeds up the rate of reaction in a chemical reaction withoout changing itself. This means that they can be reused. Enzymes are used in nearly all metabolic processes. They speed up the reaction of food. However, they are also used im many other reactions throughout the cell.

An enzyme enables molecules, called substrates, to undergo a chemical change to form new substances. These new substances are refered to as products. Enzymes do not change the amount of product or anything else in the reaction. The only difference between a chemical reaction with enzymes and one without is the rate of reaction.

There is a spot on the enzyme that fits the shape of the substrate. This is known as the active site. The substrate bonds to the active site and the active site changes its shape slightly to fit the substrate exactly.

Once the substrate or substrates are bonded to the enzyme, the enzyme does its job and speeds up the reaction between the substrates. Once the reaction is completed the product is released and the enzyme goes back to its normal shape. The enzyme then goes to complete the same reaction over and over again.

C. Students know how prokaryotic cells, eucaryotic cells (including those from plants and animals), and viruses differ in complexity and general structure.

Cells come in two basic types. These types are eukaryotic and prokaryotic. These two different types are determined by two different things. The first difference is size. A Eukaryotic can be anywhere from one to one hundred times the size of a prokaryotic cell.

Another difference between the cell types has to do with the contents of the cell. Using microscopes you can see many small structures inside the cell. These structures are called organelles. Many of these organelles have their own membranes. Cells that don't contain membrane-bound organelles are considered prokaryotic.

Most unicellular organisms, such as bacteria, do not have membrane bound organells and are therefore called prokaryotes. Cells that do have membrane-bound organelles are called eukaryotic. Most multicellular organisms are composed of eukaryotic cells. However, some unicellular organisms are eukaryotic, such as amoebas, and some algae.

The eukaryotic cell has a few advantages over the prokaryotic. For one, the eukaryotic cell can carry out various operations and chemical reactions in its defferent organelles. Where as in the prokaryotic cell most of the metabolism takes place in the cytoplasm.

Another completely different kind of cell is a virus. Which technically isn't a cell at all. They are not even living. Viruses are made up of nucleic acids enclosed in a protein coat. They are smaller then the smallest of bacteria. And since they don't have any caracteristics of living things, many biologists do not find them to be living.

Viruses do not carry out respiration, grow, or develop. All a virus can do is replicate, and in order to replicate a virus needs the help of a living cell. The cells that the viruses use to replicate are called host cells.

The virus has an inner core of nucleic acid, either RNA or DNA, and an outer protein coat called a capsid. Some of the larger viruses can have another layer called an envalope. The envalopes are made up of lipids, carbohydrates, and proteins, similar to the plasma membrane of a cell. The capsid is made up of just proteins. The arrangement and type of the proteins in the capsid determine the shape of the virus. The arangement also determines what types of cells can be infected by this virus and how the virus would go about infecting it.

When a virus replicates it enters the host cell. Before it can enter it must first recognize and atach to a receptor site on the membrane of the host cell. The process of recognizing and attaching is like two pieces of a jigsaw puzzle fitting togeter. The attachment proteins of a virus are usually shaped specially so that the virus can attach itself to a variety of cells.

After the virus is attached it enters the cell in one of two ways. It can either inject its nucleic acids into the host cell from outside the cell, or it can attach to the membrane and wait for the membrane to grow around itself. Once the membrane grows around the virus the cell makes a virus filled vacuole in the cytoplasm. Then the virus bursts out of the cell sand releases its nucleic acid into the cell.

The virus's genes then take over and alter the host cell to make new viruses. All of the cell's enzymes, raw materials, and energy goes into making copies of the viral genes. These genes along with viral proteins that are made in the host cell are assembled into new viruses. These new viruses then burst out of the cell, killing it. These new viruses can then repeat the cycle on new host cells until all of the cells are dead. This cycle is known as the lytic cycle.

There is another cycle that a virus can use to replicate itself. It is known as the lysogenic cycle. In this cycle the virus does not kill the host cell right away. It injects its nucleic acids and actually integrates its own DNA into the host cell's DNA. Viral DNA that is integrated into the host cells chromosome is called a provirus. The provirus then simply waits for the cell to divide itself a few times before it enters the lytic cycle and kills the cell. In the lysogenic cycle the cell helps spread the virus itself because all the cells that are duplicated from an infected cell are then infected themselves.

D. Students know the central dogma of molecular biology outlines the flow of information from transcription of ribonucleic acid (RNA) in the nucleus to translation of proteins on ribosomes in the cytoplasm.

The central dogma of molecular biology basically consists of DNA to RNA to protein. This is refering to how the DNA gets out of the nucleus to the ribosomes to make protein. DNA contains information that can be put to work through the production of proteins. Proteins have many different jobs in the cell including becoming important stuctures like the fillament of muscle tissue. As well as all of the jobs of enzymes such as the digestion of food and cellular respiration.

Since DNA contains all of the instructions for making proteins, and proteins run the cell, DNA controls the cell. Proteins are made of polymers of amino acids. The sequence of nucleotides in each gene contains information for assembliing the string of amino acids that make up a single protein.

But DNA is only found in the nucleus and proteins are only made on ribosomes which are found in the cytoplasm or on rough endoplasmic recticulum. So to get the information from the DNA to the ribosome RNA must be used. RNA is also a nucleic acid. But RNA is different from DNA in three ways. First, RNA is only one strand while DNA is two. The second differece is that the sugar in RNA is ribose and the sugar in DNA is deoxyribose. And thirdly, DNA contains a nitrogenous base known as thymine while RNA has a similar base known as uracil in its place.

The nucleus is surrounded by a double membrane. This membrane has small pores for things to pass through. DNA is too large to pass trough these pores, but RNA is small enough to fit through which is why it carries the information to the ribosomes. The process of copying the information to the RNA is called transcription. During transcription enzymes break apart the DNA and free RNA nucleotides form pairs with their complimentary nucleotides. Once the RNA strand is complete it breaks away from the DNA strand and the DNA strands rejoin. Then the RNA strand leaves the nucleus into the cytoplasm to find a ribosome.

This RNA that takes the information from the DNA to the ribosome is called messenger RNA or mRNA. The mRNA contains four different nitrogenous bases. But there are twenty different amino acids in proteins. So in order for the information from the mRNA to be usable it must be transilated. Translation is the process of converting the information in a sequence of nitrogenous bases in mRNA into a sequence of amino acids in protein. Translation occurs on the ribosome after the mRNA attaches to it.

There are certain codons which are are a group of three nitrogenous bases in mRNA code. For every codon there is a an anticodon which is the combonation of the compiments of the codon carried on molecules of transfer RNA or tRNA. The tRNA is also carries the amino acid that the codon specifies. After the tRNA finds a match with the codon, the amino acid it carries bonds with the previous amino acid and the tRNA molecule can find another amino acid to pick up.

Once there is a complete chain of amino acids they free themselves from the ribosome and twist and curl into complex three dimentional shapes. The same proteins always form the same shapes.

The endoplasmic reticulum is the site of cellular chemical reactions. The endoplasic reticulum is a series of highly folded membranes in the cytoplasm. The endoplasic reticulum is folded very tightly so that more surface area for chemical reactions is available without taking up as much space.

Some endoplasic reticulum have ribosomes attached to the surface, where they carry out protein synthesis. This endoplasic reticulum is refered to as rough endoplasic reticulum. Endoplasic reticulums that do not have ribosomes attached to them are refered to as smooth endoplasic reticulum. The smooth endoplasic reticulum is involved in many biochemical activities, including the production and storage of lipids.

After the proteins are made they are moved to the golgi apparatus. The golgi apparatus is a flattened stack of tubular membranes that modifies the proteins. The golgi apparatus sorts proteins into packages and packs them into membrane-bound structures, called vesicles. Once the proteins are in the vesicles they can be sent to anywhere they are needed.

You hear alot about energy that the cells are constantly using for their vaious activities. To get this energy the cells must first acqure it and then turn it into a usable energy known as ATP. Plant cells have a special process for this known as photosynthesis.

The word 'photosynthesis" can be broken down into its two root words; photo which means light, and synthesis which means to make. Together these two words mean to make out of light. Which is exactly what photosynthesis does. It captures the sunlight and turns it into energy for the cell to use.

Photosynthesis starts in the chloroplasts. A chloroplast is an organelle found only in plant cells that capture light energy and convert it to chemical energy. The chloroplast has two membranes. The inner membrane is folded like up into sacs called grana. This membrane is called the thylakoid. The grana is where the sunlight is caught. Around the grana is a fluid called stroma. Chlorophyll is the actual molecule that captures the sunlight. Chlorophyll is a plastid, an organelle found in plants for storage. They are either used for storing lipids and starches or they are pigments. Chlorophyll is a pigment and it is what gives leaves their green color.

The energy from the sunlight then is either turned directly into ATP energy for the use of the cell immediately, or it is turned into simple sugars to be saved for later. Some of the energy must be saved in order for the cell to have energy at night when there is no sunlight. This energy in the form of sugars is then converted into energy in the form of carbohydrates and stored in vacules or golgi bodies until it is needed.The

G. Students know the role of the mitochondria in making store chemical-bond energy available to cells by completing the breakdown of glucose to carbon dioxide.

Animals cannot convert light energy to sugars so they have to get sugars by ingesting them. But in order for the sugars to be converted into ATP energy they have to be processed by the mitochondria. This process of breaking down food to ATP energy is known as cellular respiration. cellular respiration takes place in three steps; glycosis, the citric acid cyle, and the electronic transport train.

Glycosis is a series of chemical reactions in the cytoplasm of a cell that breaks down glucose. Glucose is a six-carbon compound and glycosis breaks it down into two molecules of pyruvic acid, a three-carbon compound. Glycosis only produces two molecules of ATP for every glucose molecule which doesn't make it very effective. Before the process can move onto the citric acid cycle the pyruvic acid must enter the mitochondria.

The mitochondria is the powerhouse of the cell. It has two membranes. The inner membrane is folded many times as in the endoplasmic reticulum to increse surface area. Energy-storing molecules are produced on the inner folds.

Once the pyruvic acid enters the mitochondria it is involved in a few more chemical reactions. In these reactions the pyruvic acid gives off a molecule of CO2 and bondes with a molecule called coenzyme A. The reaction with coenzyme A also produces a molecule of NADH and a H+.

Calvin cyle in the way that the molecule used in the first reaction is also one of the end products. For every rotation of the citric acid cyle one molecule of ATP is produced as well as two molecules of CO2. Also, three NADH, three H+, and one FADH2 are formed during this cycle.

The last part of cellular respiration is the electronic transport train. In the electronic transport train NADH and FADH2 deliver energized electrons at the top of the chain. The energized electrons are then passed from protein to protein down the chain. As they are being passed down they loose some of their energy. This energy can be used to form ATP directly or it can be used to pump H+ ions into the mitochondria. The mitochondria then becoms positively charged and the exterior of the membrane is negatively charged which attracts more H+ ions. The last electron acceptor is oxygen. The oxygen reacts with four H+ ions to form H2O. The electron transport train adds thirty-two molecules of ATP to the four already produced by the first two steps.

H. Students know most macromolecules (polysaccharides, nucleic acids, proteins, lipids) in cells and organisms are synthesized from a small collection of simple precursers.

Polysacharides are many sugars put together. They are composed of carbon, hydrogen, and oxygen with a ratio of about two hydrogen atoms and one oxygen atom for every carbon atom. Polysaccharides are forms of carbohydrates which are used for energy.