LEARNING SUMMARY PAPER - · PDF fileRobert Maxwell 1 December 2013 Biology ... Since...

Keelie Bolton LEARNING SUMMARY PAPER

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Keelie Bolton

Robert Maxwell

1 December 2013

Biology 2107: Learning Summary Paper

The cell was first discovered by Robert Hooke in 1665. Hooke used a coarse, compound

microscope and examined thin slices of bottle cork. He originally thought to experiment with a

cork when he discovered that a cork was made up of a single unit. The findings in the

microscope were a multitude of tiny pores that Hooke remarked to look like the wall

compartments that a monk would live in. Thus, Hooke discovered the cell in nonliving things,

and claimed the name “cell”. He later furthered his experimentation into different plants which

resulted in discovering that cells form the tissue of a plant2. Since Hooke’s discovery, cell

research and experimentation has flourished and still happens today. Since then we have

discovered, among many great discoveries, that the cell is the fundamental unit of life.

Cell theory states that cells are the basic structural and psychological units of all living

organisms and that, cells are both distinct entities and building blocks of more complex

organisms. To be clear, living organisms or a living “thing” as a generic category are known to

be all the diverse organisms descended from a single celled ancestor that evolved almost four

billion years ago. It is important to note that there are shared characteristics found in all living

things. These shared characteristics are that living things can regulate their own internal

environment, living things contain genetic information and use that genetic information to

reproduce, living things are genetically related and have evolved, living things have the ability to

convert molecules obtained from their environment into new biological molecules, living things


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can extract energy from the environment and use it to do biological work, and last but not least

living things consist one or more cells.

By means of cell division and its intricate step by step processes, cells come from pre-

existing cells. The cell splits and divides, thus creating new cells. Functional properties of cells

derive from properties of the preexisting cell. Inside the cell’s nucleus is where the DNA is

located. DNA (deoxyribonucleic acids) is coupled subunits of nucleotides. Each DNA as a whole

unit is what codes for each and every individuals genetic information. It is commonly stated that

the “blue print” for existence is contained in the cell’s genome-the sum total of the DNA in a

cell. The DNA itself is made up of varying components, as is the cell made up of different micro

molecules each with a different function.

DNA has a three dimensional physical appearance. The shape is in the twist form of a

double helix where two complimentary polynucleotides, through hydrogen bonding, are

complimentarily paired (for a visual aid, if the two paired strands were to be un-twisted and lied

out the DNA would have the appearance of a ladder.) Nucleotides are what make up each DNA

strand. A nucleotide is composed of monomers each with a pentose sugar, phosphate group, and

a nitrogen containing base. There are four nitrogenous bases in DNA, adenine, cytosine, guanine,

and thymine (adenine and guanine are purines while thymine and cytosine are pyrimidine’s.)

RNA on the other hand, has adenine, thymine, and cytosine; but the adenine does not pair to

guanine but rather uracil instead. These nucleotides are the building blocks for nucleic acids; and

both DNA and RNA, (RNA being ribonucleic acid, a single stranded molecule) are types of

nucleic acids that are present in all living cells. Nucleic acids are polymers for the use of genetic

information and transmission between generations. DNA and RNA are polymers formed from a


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monomer. Through cell division DNA is copied and passed down genetically. DNA’s sequence

carries the information that RNA uses to specify primary protein structure.

Structurally speaking, amino acids are the building blocks of proteins; each has a

carboxyl function group, an amino functional group, and an alpha carbon. Attached to the alpha

carbon is a hydrogen atom and a side chain or an R group. When the amino acids polymerize, the

carboxyl and amino groups that are attached to the alpha carbon are the reactive groups on the

protein. Proteins can further be described as being polymers composed of varying sequences of

20 different amino acids. All proteins have polypeptide chains (which are polymers that are

covalently linked amino acids) and the exact composition of a protein depends on how many

different amino acids are present on each amino acid chain. Proteins do almost always consist of

more than one chain. The sequence of the amino acids in the chain determines the structure and

function of each protein. The structure and functions are, on a more microscopic level, based on

how the chain folds. Obviously then, there are different types of proteins, each with different

functions. First, defensive proteins; defensive proteins are antibodies. These antibodies have the

ability to recognize substances that the body did not make itself or a substance that is

inappropriately located in a cell. These antibody proteins then respond to that cell with by an

invasion of the outlying organism. Second, hormonal proteins; hormonal proteins are regulators

for physiological processes such as metabolism, reproduction, growth and development. For

example, a hormonal protein can control insulin secretion for metabolism. Third, receptor

proteins; receptor proteins receive signals and then respond to them at a molecular level. The

signals that they receive and respond to are both inside and outside of an organism. Fourth,

storage proteins; storage proteins store chemical building blocks for proteins and amino acids.

The substances being stored are for a later use. Fifth is structural proteins; structural proteins


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have a wide variety of functions including providing movement and stability to a cell. Sixth is

transport proteins; the role of transport proteins is almost self-explanatory; they carry substances

within an organism (for example hemoglobin carrying oxygen throughout the blood.) The last of

the major functioning proteins are genetic regulatory proteins; genetic regulatory proteins

regulate the expressionisms in a gene. For example, a genetic regulatory protein would tell an

expressed gene how, when, and to what extent a gene should express its designated function.

Catalytic proteins that speed up biochemical reactions are enzymes. An enzyme is a

protein containing of hundreds of amino acids and a single polypeptide chain or several subunits.

The physical appearance of an enzyme is that it has an active site and it selectively chooses the

right substrate to bond to it. When the enzyme binds to the substrate with an induced fit, it

changes shape and the product of the bound substrate is released. There are a few different types

of enzymes; for example digestive enzymes catabolize nutrients for digestion in the body

Proteins are non-covalently embedded into the phospholipid bilayer by their hydrophobic

domains. However, more information about the phospholipid bilayer will come later when the

lipids are being discussed.

Another type of macromolecule located in the cell is a carbohydrate. The biochemical

roles of carbohydrates are to be used as a source of stored energy. This stored energy can and

will later be transported within complex organisms and to later be rearranged to from new

molecules. There are four categories of carbohydrates: polysaccharides are polymers of hundreds

of monosaccharides, monosaccharides are simple sugars that form the larger carbohydrates,

disaccharides are two monosaccharides linked together by covalent bonds and oligosaccharides

are made up of several monosaccharides (fewer than polysaccharides). In a cell, the


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monosaccharides act as simple sugars such as glucose, the blood sugar that transports energy in

humans. Polysaccharides are used for energy storage and providing structural materials.

Polysaccharides are those such as starches, glycogen, and cellulose. Carbohydrates of all forms

are a crucial source of energy for a cell for both eukaryotic cells and prokaryotic cells alike.

Carbohydrates are located on the outside of the cell where they can react with external

substances.

Lipids, a third type of macromolecule in the cell, are composed of many nonpolar

covalent bonds, thus making the hydrocarbons that are insoluble in water. Fats are usually found

in the form of a triglyceride or a simple lipid; they typically are solid at room temperature.

Triglycerides are composed of a fatty acid (a long nonpolar hydrocarbon chain and a polar

carboxyl group) and a glycerol (a small molecule with three hydroxyl groups). Lipids are used to

store energy, play regulatory roles for hormones and vitamins, and are important for cell

membranes. Lipids have roles in energy conversion, regulation and protection within a cell.

Examples of lipids further include carotenoids, steroids, and vitamins.

One specific and very important form of a lipid is a phospholipid. A phospholipid

structure is fatty acids bound to glycerol by ester linkages (a type of covalent bond.) The

phosphate functional group of a phospholipid or the “head” has a hydrophilic negative electric

charge, thus attracting polar water molecules. The two fatty acids acting of the “tails” of the

phospholipids on the other hand are hydrophobic thus avoiding and repelling water and similar

substances. Phospholipids are arranged so that the nonpolar hydrophobic tails are tightly in tact

with the phosphate heads facing outward where they would interact with the water molecules.

The result of such formation is a bilayer where two molecules form a thick sheet where water

can be excluded from the core. The bilayer allows for the phospholipids to coexist with water.


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The general design of the biological membrane is depicted in the fluid mosaic model, where the

lipids from the hydrophobic core of the membrane.

All macromolecules, carbohydrates, lipids, proteins and nucleic acids, work together in

the cell. The four macromolecules come together and are easily represented as a visual

interpretation called the fluid mosaic model. For biological membranes, proteins are embedded

into the phospholipid bilayer with functions such as moving materials through the membrane and

receiving chemical signals. Carbohydrates associated with the membrane, on the other hand, are

attached to a lipid or protein, however in the plasma membranes they are found on the outside of

the cell interacting with extracellular fluids. Lipids, phospholipids in-particular, make up both

the hydrophobic core of the membrane as well as the hydrophilic outside, thus making the

membrane (much like all membranes) semi-permeable (meaning that not all molecules can

diffuse across the lipid bilayer and that only some can.) Lipids in general total for approximately

half the mass of the cell membrane itself. Majority of the other half of the mass of a membrane is

accounted for by the proteins. One protein in particular, the transmembrane proteins, extends

completely through the phospholipid bilayer terminating on both ends of the membrane. Each

side of this protein has a different and specific proteins based on if it terminates facing inner or

outer sides of the membrane. Speaking in terms of movement, the transmembrane proteins have

the ability to move in the lipid bilayer providing that they move in a lateral direction. For most

living cells, proteins do not move freely, so this is a special characteristic to these proteins. The

fluid mosaic model as a whole is applicable to both the plasma membrane as well as the

membranes of organelles.

Membranes in general have a main goal to act as a barrier for the cell as well as acting as

a guard regulating which substances are permitted to come into and out of the cell. Diffusion (the


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process of random movement across a membrane to reach a state close to equilibrium) is a

passive process of membrane transport. Simple diffusion is when small molecules can easily pass

through the phospholipid bilayer. Electrically charged particles, however, do not pass as easily

because when trying to pass through the bilayer they form hydrogen bonds with the surrounding

water ions, thus preventing the substances from moving inward. So, although those larger

molecules such as amino acids, sugars and ions do not readily pass through, substances such as

hormones or immune mediators have the ability to do so due to other types of transmembrane

proteins that bind to these signals. These receptor proteins, as they are called, have a selective

shape and location for binding with only specific types of molecules, allowing for only those to

pass. Separately from the passive transport means such as diffusion, there are ways of active

transport across a membrane. The sodium potassium pump, for example, is an active way of

transporting molecules and establishing and maintaining chemical gradients on both the inside

and the outside of the cell. In the sodium potassium pump, sodium ions bind to the protein

channel and energy via ATP binds to the channel and allows the shape to be changed, thus

opening the other end of the channel allowing the sodium ions to exit the membrane and go to

the outside of the cell. One phosphate ion remains bound to the channel, so when potassium ions

attach to the newly shaped binding site, the phosphate group is released allowing the channel to

take its original shape as well as releasing the positively charged potassium ions allowing the

sodium ions to once again attach to the channel. Through these means the sodium and potassium

ions are moving from areas of low concentration to that of high concentration, or the ions are

moving against its concentration gradient.

There is some differentiation in terms of membranes for eukaryotic cells. Contrasting that

of prokaryotic cells, eukaryotic cells have two different types of membranes. They do not only


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have the plasma membrane that surrounds the entire cell; eukaryotic cells also contain

intracellular membranes that surround a few types of organelles within the cell. In addition to the

endoplasmic reticulum, the nuclear membrane, lysosomes, and the golgi apparatus that are a part

of the plasma membrane, mitochondria and chloroplasts are also surrounded by these

intracellular membranes. The intracellular membranes though are not just a single surrounding

membrane. They are composed of two membranes; one membrane allows for small molecules to

easily pass through the pores on the membrane, and another membrane holds the proteins

allowing a generation of energy as well as composing the electron transport chain. The double

membrane characteristics of these eukaryotic membranes resemble the origins of prokaryotes as

they are seen today.

Central dogma in a cell is the two steps of protein synthesis, transcription and translation.

On a vague spectrum, DNA being converted to mRNA is transcription and mRNA being

converted to a protein is translation. Three of the nitrogenous bases (every three nitrogenous base

is a codon) in DNA code for one amino acid. This DNA is copied and produces mRNA. The

polypeptide’s order of amino acids is determined by the three letter sequence code in mRNA. So,

transcription is the synthesis of RNA from a DNA template. Only one single strand of the DNA

is copied, however a single gene may be transcribed thousands of times over and over again. The

mRNA copy of the gene that encodes a protein is the gene’s transcript. For transcription to start,

the enzyme RNA polymerase creates RNA by copying the template DNA strand. Before the

process can officially begin in eukaryotes, transcription factor proteins bind to the promoter

region of DNA. RNA polymerase then binds to the transcription factors as well as the promoter.

For bacterial cells, the polymerase binds directly to the promoter; in these cells the assistance of

transcription factors are not necessary. The RNA polymerase, after binding, can unwind the


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DNA double helix and arrange the nucleotides so that they are complimentary to the DNA strand

that is being copied (this has to take place especially because RNA contains a uracil nucleotide

instead of the thymine that is found in DNA.) The direction of synthesis for transcription is 5’ to

3’. As transcription continues, multiple RNA polymerase molecules can transcribe a single gene

many times as one polymerase molecules continuously follows another. For bacteria as well as in

eukaryotic cells, a specific stop code is transcribed, thus signaling that the RNA polymerase

enzymes are now finished and they are to stop. For bacteria, however, there is a termination

sequence in the DNA that indicates specifically where transcription is to stop. After transcription

is complete, the mRNA transcript is processed, and translation can begin. Before translation

begins taking place, a ribosome is assembled into two ribosomal subunits, one of which attaches

to the 5’ end of the new transcript mRNA. The ribosome moves along the mRNA transcript until

it comes into contact with the start codon (AUG is the start codon for every mRNA strand.)

When the ribosome reaches the start codon, tRNA attaches to the mRNA and the other ribosomal

subunit also attaches. The tRNA molecule transports the next amino acid in every sequence, one

at a time, to the ribosome. A peptide bond is then formed and the growing polypeptide chain is

now attached to the tRNA. The ribosome continues to move down the mRNA strand via tRNA

and the amino acid chain continues to grow. A stop codon and its attached release factor cause

everything to dissociate as well as the release of the polypeptide chain.

An oxidation-reduction reaction occurs when there is a transfer of one or more electrons

form one substance to another, and in exchange there is a transfer of energy. Because reduction

is the gain of one or more elections and oxidation is the loss of one or more elections, it makes

sense that oxidation and reduction always occur together. As one chemical is oxidized the other

is being reduced. Oxidation and reduction are defined in terms of electron exchange; however it


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is also correlated or even easier to think about it in terms of hydrogen atom exchange. When a

molecule loses any number of hydrogen atoms, the molecule becomes oxidized; when a

molecule gains any number of hydrogen atoms, the molecule becomes reduced.

Nucleotides are indeed the building blocks of nucleic acids, but there are other purposes to

them as well. For example, ATP, an energy source, is a type of nucleotide with an important role.

The overall function of ATP (adenosine triphosphate) is to act as an energy transducer for

biochemical reactions including but not limited to the following: active transport, the Calvin and

citric acid cycle, chemiosmosis, energy release, fermentation, formation of mitochondria,

glycolysis, muscle contraction, and phosphorylation.

Metabolic pathways are where the product of one reaction having occurred becomes the

reactant for another reaction. Reactions taking place like this allow for the internal environment

of a cell to be regulated; in return helping the cell maintain homeostasis. Each metabolic reaction

is not an isolated process; they interact extensively throughout the cell. The pathways for each

reaction are each catalyzed by a specific enzyme. Metabolic pathways allow for things like the

catabolism of glucose to yield energy, carbon dioxide, and water as well as the metabolism of

lactose.

Chemotrophs and phototrophs obtain energy through different means. Chemotrophs, to

begin, obtain energy by the oxidation of electron donors that are found in their environment. So,

as previously discussed, oxidation is the loss of one or more electrons or hydrogen’s. There are

two types of chemotrophs; they can be either autotrophic (self-sufficient) or heterotrophic

(relying on another organism.) The autotrophic chemotrophs synthesize organic compounds from

carbon dioxide using inorganic sources. The heterotrophic chemotrophs lack the ability to fix


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carbon from their own compounds, so they utilize organic sources of energy via consumption

such as carbohydrates, lipids, and proteins. Phototrophs, on the other hand, are different because

they utilize solar energy instead of oxidation energy. Phototrophs rely on the solar energy to

carry out their necessary metabolic processes; they have to establish an electrochemical gradient

utilizing ATP, and then provide energy at a molecular level for the cell. Majority of the identified

phototrophs are autotrophs because they can fix carbon, but they are not to be confused with

chemotrophs.

The Calvin Cycle is when ATP and NADPH produced via light reactions power the

synthesis of carbohydrates. Through this cycle’s system, carbon dioxide is fixed, reduced, and

then regenerated for further fixation. In terms of acquiring carbon, autotrophs and heterotrophs

have different means of doing so. The autotrophs are completely self-feeding. The C-H covalent

bonds that can be found in the products of the Calvin cycle supply almost all of the energy

necessary to life for living organisms. Autotrophs use the products and then undergo glycolysis

and respiration to support themselves as well as a release of energy. Heterotrophs are not as self-

sufficient. They rely on other organisms for their energy supply. Heterotrophs cannot

photosynthesize like autotrophs can, therefore acquiring carbon by consumption rather than self-

making it.

Our fixation on the word “cell” is myopic: a biological unit, contained by a wall, with its

internal organelles and cytoplasm, producing various proteins for use by the organ to which the

cell is designed for. However, a cell is also one of many single units within a monastery, where

a monk resides to have a closer relationship with God. This etymology of this simple word and

its simple yet similar structure and purpose, within their respective systems, is where science and


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religion converge. The cell is the smallest unit where we can begin to examine the interplay of

those 8 characteristics. Through the construction of this paper it has occurred to me that there is

one other characteristic to be accepted: mortality. A cell, organelle, organ, and organism has a

limited lifespan. The unit ceases to be. This paper has broadened my perspective of the

scientific principle of the cell. However my fixation on the word “cell” has been myopic: a

biological unit, contained by a wall, with its internal organelles and cytoplasm, producing

various proteins for use by the organ to which the cell is designed for. However, a cell is also

one of many single units within a monastery, where a monk resides to have a closer relationship

with God. This etymology of this simple word and its simple yet similar structure and purpose,

within their respective systems, is where science and religion converge.

A reaction in which one substance transfers one or more electrons to another substance is

called an oxidation-reduction (redox) reaction. Reduction is the gain of one or more electrons by

an atom, ion, or molecule whereas oxidation is the loss of one or more electrons. Both processes

occur together. Oxidation and reduction can also be thought of in terms of the gain or loss of

hydrogen atoms. So, when a molecule loses hydrogen atoms it becomes oxidized. Generally

speaking, the more reduced a molecule is, the more energy is stored in its covalent bonds.

Metabolic processes that harvest energy in the chemical bonds of glucose are cellular respiration,

glycolysis, and fermentation. All three involve metabolic pathways composed of distinct

chemical reactions. Cellular respiration uses oxygen gas from the environment while each

pyruvate molecule is completely converted into three molecules of carbon dioxide gas via

pyruvate oxidation, the citric acid cycle, and the electron transport chain. Glycolysis begins

glucose metabolism in all cells. Through chemical rearrangements glucose is converted into two

molecules of pyruvate (a three carbon product) and a small abundance of energy for later use.


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Fermentation converts pyruvate into lactic acid or ethyl alcohol. Fermentation is similar to

Cellular respiration, however much less energy is released in fermentation.

Coenzyme NAD+ (nicotinamide adenine dinucleotide) is a key carrier in redox reactions. NAD+

exists in two chemically distinct forms; one is the oxidized from NAD+ while the other is

reduced NADH. The reduction reaction between the two (NAD+ + H+ + 2e- NADH) is

actually the transfer of a proton and two electrons. Oxygen is highly electronegative and readily

accepts electrons from NADH.

Glycolysis is a six step process. The energy-investing reactions 1-5 of glycolysis require ATP. In

reaction one, the enzyme hexokinase catalyzes the transfer of a phosphate group from ATP to

glucose, forming the sugar phosphate glucose 6-phosphate. In reaction two, the six-membered

glucose ring is rearranged into a 5-membered fructose ring. IN reaction three the enzyme

phosphofructokinase adds a second phosphate to the fructose ring, forming fructose 1,6-

bisphosphate. Reaction four opens up the ring and cleaves it to produce two different three-

carbon sugar (triose) phosphates: dihydroxyacetone phosphate and glyceraldehyde 3-phosphate.

In reaction five, the dihydroxyacetone phosphate product from reaction four is converted into a

second molecule of the other glyceraldehyde 3-phosphate. At this halfway point in the process,

two things have happened: ATP, two molecules of it, have been invested. Also, the six-carbon

glucose molecule has been converted into two molecules of a three-carbon sugar phosphate,

glyceraldehyde 3-phosphate. Continuing the process, reaction six produces NADH. Reaction six

is catalyzed by the enzyme triose phosphate dehydrogenase and its end product is a phosphate

ester 1,3-bisphosphate. This reaction is accompanied by a large drop in free energy. For each

molecule of G3P that is oxidized, one molecule of NAD+ is reduced to make a molecule of


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NADH. NAD+ must be recycled to allow glycolysis to continue. As the process furthers, NADH

is oxidized back to NAD+ in the metabolic pathways that follow glycolysis. Reactions seven

through ten are the ATP producing processes. In these reactions the two phosphate groups of

BPG are transferred one at a time back into molecules of ADP. The result is two molecules of

pyruvate for every mole of glucose that enters glycolysis. The enzyme-catalyzed transfer of

phosphate groups from donor molecules to ADP to form ATP is substrate-level phosphorylation;

phosphorylation being the addition of a phosphate group to a molecule. Reaction seven is an

example of substrate level phosphorylation, in which phosphoglycerate kinase catalyzes the

transfer of a phosphate group from BPG to ADP, forming ATP. In reaction eight the phosphate

groups on the two 3PGs move, forming two 2-phosphoglycerates (2PG). Reaction nine creates

two high-energy phosphoenolpyrucates through the two molecules of 2PG losing water. Finally,

in reaction ten, the two phosphoenolpyrucates transfer their phosphates to ADP, forming two

ATPs and two molecules of pyruvate. To summarize glycolysis, the energy-investing steps of

glycolysis use the energy of hydrolysis of two ATP molecules per glucose molecule. The energy-

releasing steps, however, produce four ATP molecules per glucose molecule, resulting in a net

production of two ATP molecules. The energy –releasing steps of glycolysis produce two

molecules of NADH.

Pyruvate oxidation links glycolysis and the citric acid cycle. Through the process of pyruvate

oxidation, pyruvate is oxidized to the two-carbon acetate molecule, which is then converted to

acetyl CoA. Coenzyme A (CoA) is a complex molecule responsible for binding the two-carbon

acetate molecule. The formation of acetyl CoA is a reaction catalyzed by pyruvate

dehydrogenase. In eukaryotic cells, pyruvate is located in the mitochondrial matrix where it

enters the mitochondrion by active transport followed by a series of coupled reactions: first,


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pyruvate is oxidized to a two-carbon acetyl group (acetate) and carbon dioxide is released

(decarboxylation). Second, part of the energy from this oxidation is captured by the reduction of

NAD+ to NADH. And third, some of the remaining energy is stored temporarily by combining

the acetyl group with CoA resulting in the formation of acetyl CoA. The main role of acetyl CoA

is to donate its acetyl group to the four-carbon compound oxaloacetate, forming the six carbon

molecule citrate. This initiates the citric acid cycle.

Acetyl CoA is the starting point for the citric acid cycle. This eight reaction pathway completely

oxidizes the two-carbon acetyl group to two molecules of carbon dioxide. The free energy

released from these reactions is captured by ADP and the electron carriers NAD+ and FAD. As

the citric acid cycle has intermediate compounds enter and leaving, the concentrations of the

intermediates do not change much. In reaction one of the citric acid cycle, the energy that was

temporarily stored in acetyl CoA drives the formation of citrate from oxaloacetate. During this

reaction, the CoA molecule is removed and can be reused by pyruvate dehydrogenase. In

reaction two, the citrate molecule is rearranged to from isocitrate. In reaction three of the cycle a

carbon dioxide gas molecule, a proton, and two electrons are removed, converting isocitrate into

alpha-ketoglutarate. This reaction releases a large amount of free energy, some being stored in

NADH. In reaction four, alpho-ketoglutarate is oxidized to succinyl CoA. This reaction produces

CO2 and NADH. In reaction five, some of the energy in succinyl CoA is harvested to make GTP

(guanosine triphosphate) from GDP and P. This is another example of substrate level

phosphorylation. GTP is then used to make ATP from ADP and P. In reaction six, the succinate

released from succinyl CoA in reaction five is oxidized to fumarate. In this process, free energy

is released and two hydrogens are transferred to the electron carrier FAD forming FADH2.

Reaction seven is a molecular rearrangement where water is added to fumarate, forming malate.


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In reaction eight, the final reaction for the citric acid cycle, one more NAD+ reaction occurs,

producing oxaloacetate from malate. Between reactions seven and eight a carbonyl group is

generated and reduces NAD+ to NADH. The final product, oxaloacetate, is ready to combine

with another acetyl group from acetyl CoA and go around the cycle again. To summarize, the

inputs of the citric acid cycle are acetate in the form of CoA, water, and the oxidized electron

carriers NAD+, FAD and GDP. The outputs, on the other hand, are carbon dioxide, the reduced

electron carriers NADH and FADH2, and an overall release of two carbons as CO2 and four

reduced electron carrier molecules.

The electron transport chain, also know and recognized as the respiratory chain, transfers

electrons and releases energy. The electron transport chain is located in the inner mitochondrial

membrane and contains several interactive components. Uviquinone (Q) is a small, nonpolar,

lipid molecule that moves freely within the hydrophobic interior of the phospholipid bilayer in

the inner mitochondrial membrane. Cytochrome c is a small peripheral protein that lies in the

intermembrane space. It is loosely attached to the outer surface of the inner mitochondrial

membrane. Four large protein complexes, (I, II, III, and IV) contain electron carriers and

associated enzymes. In eukaryotes they are integral proteins if the inner mitochondrial membrane

and three are transport proteins. In the electron transport chain, NADH passes electrons to

protein complex I (also called NADH-Q reductase) which in turn passes the electrons to Q.

Complex II (succinate dehydrogenase) passes electrons to Q from FADH2 , which was generated

in reaction six of the citric acid cycle. Complex III (cytochrome c reductase) receives electrons

from Q and passes them to cytochrome c. Complex IV (cytochrome c oxidase) receives electrons

from cytochrome c and passes them to oxygen; then finally the reduction of oxygen to water

occurs. Two protons are consumed in this reaction, contributing to the proton gradient across the


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inner mitochondrial membrane. During the electron transport, protons are actively transported

across the membrane. In complexes I, III< and IV this results in a transfer of protons from the

matrix to the intermembrane space. Proton diffusion is coupled to ATP synthesis. All of the

electron carriers and enzymes of the respiratory chain, except for cytochrome c, are embedded in

the inner mitochondrial membrane. Transmembrane complexes I, III, and IV act as proton

pumps, resulting in the intermembrane space being more acidic than the matrix. This positively

charged proton results in both a concentration gradient as well as an electric charge across the

membrane. Combined the proton concentration gradient as well as the electrical charge

difference contributes to a potential energy source called the proton-motive force, which drives

protons back across the membrane. Because the hydrophobic lipid bilayer is essentially

impermeable to protons the potential energy of the proton motive force cannot be discharged. So,

protons can only diffuse across the membrane through a specific proton channel called ATP

synthase, which couples proton movement to the synthesis of ATP. Electron transport can be

summarized into two steps: first, electrons carried by NADH and FADH2 from glycolysis and the

citric acid cycle feed the electron carriers of the inner mitochondrial membrane, which pump

protons out of the matrix to the intermembrane space. Second, protom pumping creates an

imbalance of H+ and thus a charge difference between the intermembrane space and the matrix.

This imbalance is the proton motive force. Third, the ATP synthesis process, is when the proton

motive force drives protons back to the matrix through the H+ channel of ATP synthase. This

movement of protons is coupled to the formation of ATP.

Multicellular organisms probably would not exist without mitochondria. The inability to remove

electrons from the system and buildup metabolic end products restricts the utility of anaerobic

metabolism. Through exudative phosphorylation mitochondria make efficient use of nutrient


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molecules. They are the reason that we need oxygen at all. The double-membraned

mitochondrion creates distinct compartments with the organelle. The outer membrane is a

relatively simple phospholipid bilayer, containing protein structures making it permeable to

small molecules such as ions, nutrient molecules, ADP and ADP. The inner membrane is freely

permeable only to oxygen, carbon dioxide, and water. This highly complex structure includes all

of the complexes fo the electron transport chain, the ATP synthetase complex, and transport

proteins. The surface of the membranes are wrinkled (or folded/layered) to increase the surface

area of the inner membrane. The larger surface area makes room for more of the above-named

structures. The membranes create two compartments. The intermembrane space is the region

between the inner and outer membranes. It has an important role in oxidative phosphorylation,

the primary function of mitochondria. The mitochondrial matrix contains the enzymes that are

responsible for the citric acid cycle as well as containing dissolved oxygen, water, carbon

dioxide, and recyclable intermediates.

Chloroplasts are organelles in plant and algae cells. Their main function is to generate

photosynthesis (the process where chloroplasts capture the energy from sunlight and store it in

ATP and NADPH while freeing oxygen from water). They then use ATP and NADPH to make

organic molecules from carbon dioxide, aka Calvin cycle. Chloroplasts carry out other functions

including fatty acid synthesis, amino acid synthesis, and immune response in plants.

Chloroplasts, in land plants, have at least three membrane systems-the outer membrane, inner

membrane, and the thylakoid system. Inside the outer and inner chloroplast membranes is the

chloroplast stroma that make up for much of a chloroplasts volume, and in which the thylakoid

system floats.


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The chloroplast double membrane is often compared to the mitochondrial double membrane,

however this is not a valid comparison-the inner mitochondria membrane is used to run proton

pumps and carry out oxidative phosphorylation across to generate ATP. The chloroplast structure

that regulates metabolite passage and synthesizes some materials has no counterpart in the

mitochondrion.

The Calvin cycle is made up of three processes: dixation, reduction, and regeneration. The

Calvin cycle uses the ATP and NADPH made in the light to reduce carbon dioxide in the stroma

to a carbohydrate. Fixation, step one, is catalyzed by rubisco, and its stable product is 3PG.

Reduction of 3PG to form glyceraldehyde 3-phosphate (G3P). This series of reactions involves a

phosphorylation using the ATP made in the light reactions and a reduction using the NADPH

made in the light reactions. Regeneration is that of the CO2 acceptor, RuBP. Most of the G3P

ends up as ribulose monophosphate (RuMP) and ATP is used to convert this compound to RuBP.

The product of this cycle is glyceraldehyde 3-phosphatewhich is a 3-carbon sugar phosphate,

also called triose phosphate. More specifically, the Calvin cycle can be broken down into five

steps. First, CO2 combines with its acceptor, RuBP, forming 3PG. Second, 3PG is reduced to

G3P in a two-step reaction requiring ATP and NADPH. Third, about one-sixth of the G3P

molecules are used to makes sugars-the output of the cycle. Then, the remaining five-sixths of

the G3P molecules are processed in the series of reactions that produce RuMP. Fifth and last,

RuMP is converted to RuBP in a reaction requiring ATP. RuBP is ready to accept another CO2 at

this point. Six turns of this cycle produce the equivalent of one molecule of glucose (a hexose

sugar). Light stimulates the Calvin cycle. The Calvin cycle uses NADPH and ATP which are

generated using energy from light. Light-induced pH changes in the stroma activate some Calvin

cycle enzymes. Proton pumping from the stroma into the thylakoid causes an increase in the pH


20

of the stroma, favoring the activation of rubisco. The light induced electron transport reduces

disulfide bonds in four of the Calvin cycle enzymes, thereby activating them. The resulting

changes shapes and activates the enzymes and increase the rate at which the Calvin cycle

operates.

Like glycolysis and other metabolic pathways that harvest energy in cells, photosynthesis is a

process consisting of many reactions. These reactions are divided into two main pathways: light

reactions and light- independent reactions. The light reactions convert light energy into chemical

energy in the form of ATP and the reduced electron carrier NADPH (again, NADPH is NADH

but with an additional phosphate group attached to the sugar of its adenosine). NADPH acts as a

reducing agent in photosynthesis and other anabolic reactions. The light-independent reactions

(also known as the carbon-fixation reactions) do not use light directly but instead use ATP,

NADPH, and CO2 to produce carbohydrate. These reactions do not directly require light energy.

The reactions of both pathways proceed within the chloroplast, but they occur in different parts

of that organelle. Light behaves as particles, called photons; in plants and other photosynthetic

organisms, receptive molecules absorb photons in order to harvest their energy for biological

processes. When a molecule absorbs a photon, it becomes excited and one of three things could

happen: the photon may bounce off the molecule, the photon may pass through the molecule, or

the photon may be absorbed by the molecule. Either way, the photon’s energy cannot disappear.

When the molecule acquires the energy of the photon it is raised from a ground state with lower

energy to an excited state with higher energy. In plants, two chlorophylls are responsible for

absorbing the light energy that is used to drive light reactions: chlorophyll a and chlorophyll b.

both have a complex ring structure similar to that of the heme group of hemoglobin, and in the

center of the chlorophyll ring is a magnesium atom. Attached at a peripheral location on the right


21

is a long hydrocarbon tail which anchors the chlorophyll molecule to integral proteins in the

thylakoid membrane of the chloroplast. Excited chlorophylls in the reaction center act as electron

donors because chlorophyll has two vital roles in photosynthesis: absorbing light energy and

transforming it into excited electrons, and transferring those electrons to other molecules,

initiating chemical changes. Photosynthesis harvests chemical energy by using the excited

chlorophyll molecules in the reaction center as reducing agents to reduce a stable electron

acceptor. Two photostems are required in the thylakoid membrane for noncyclic electron

transport. Photostem I uses light energy to pass an excited electron to NADP+, reducing it to

NADPH. Photostem II, on the other hand, uses light energy to oxidize water molecules,

producing electrons, protons, and oxygen gas. The reaction center for photostem I contains a pair

of chlorophyll a molecules called P700 because it can best absorb light with a wavelength of 700

nm. Likewise, the pair of chlorophyll molecules in the photosystem II reaction center is called

P680 because it absorbs light maximally at 680 nm. Thus, photosystem II requires a little bit more

energetic photons that those that are required by photosystem I. For noncyclic acid transport to

keep going, both photostems must be constantly absorbing light, thereby boosting electrons to

higher shells which they can later be captured by different types of electron acceptors. It is

crucial to have both noncyclic electron transport as well as cyclic electron transport. Noncyclic

electron transport produces NADPH and ATP. Essentially, the excited electron is “lost from

chlorophyll and the transport process ends up with a reduced coenzyme. Cyclic electron transport

produces only ATP. Essentially, here, the transport process ends up with the excited electron

returning to chlorophyll after giving up energy to make the ATP.

Compartmentalization is the key to eukaryotic cell function. The membranous compartments of

eukaryotic cells, or the organelles, each have a specific role in its particular cell. The nucleus


22

contains most of the cell’s genetic material (the DNA). The replication of genetic material and

the first steps in expressing genetic information take place in the nucleus. The mitochondrion is

where energy is stored in the bonds of carbohydrates and fatty acids are converted into a form

that is more useful to the cell, ATP. The endoplasmic reticulum and Golgi apparatus are

compartments in which some proteins synthesized in the ribosomes are packaged and sent to

appropriate locations in the cell. Lysosomes and vacuoles are cellular digestive systems in which

large molecules are hydrolyzed into usable monomers. Chloroplasts (which are found only in

some cells) perform photosynthesis. The cells also have ribosomes for factories of protein

synthesis, a nucleolus, a region within the nucleus, where ribosomes begin to be assembled from

RNA and proteins. Protists, plants, fungi, and animals are all eukaryotes (or they are all members

in the domain Eukarya, meaning they all have eukaryotic cell organization). In contrast to

prokaryotes, the genetic DNA material of eukaryotic cells is contained in the nucleus, as well as

having other membrane-enclosed structures and compartments in which chemical reactions

occur. Prokaryotes, on the other hand, are organisms in Archaea and Bacteria, they have

prokaryotic cell organization. A prokaryotic cell does not have membrane-enclosed internal

compartments; specifically, a prokaryotic cell does not have a nucleus. Other membrane

enclosed organelles in the cell are peroxisomes (organelles that accumulate toxic peroxides that

occur as byproducts of some biochemical reactions), glyoxysomes (similar to peroxisomes but

are found in plants only), and vacuoles, occurring in many eukaryotic cells (that help with

storage, structure, reproduction and digestion). In addition to membrane-enclosed organelles,

there are a group of cytoplasmic structures without membranes. The cytoskeleton, first and

foremost, has many important roles: it supports the cell and maintains its shape, it holds cell

organelles in position within the cell, it moves organelles within the cell, it is involved with


23

movements of the cytoplasm called cytoplasmic streaming, it interacts with extracellular

structures, helping to anchor the cell in place. Most importantly, the cytoskeleton is important in

the cell structure and movement. The three compartments of the cytoskeleton are the

microfilaments, the intermediate filaments, and the microtubules. Microfilaments help the entire

cell or specific parts of the cell to move as well as determine and stabilize cell shape.

Intermediate filaments anchor the cells in place as well as resist tension in the cell. Microtubules

form a rigid internal skeleton for some cells as well as acting as a framework along which motor

proteins can move structures within the cell. Although the cytoskeleton provides stable structure,

it still lacks the semirigid wall that is characteristic of plant cells. That is why many animal cells

are surrounded by or are in close contact with an extracellular matrix. This matrix is composed

of collagen (fibrous proteins) and proteoglycans (a matrix of glycoprote ins). The functions of the

extracellular matrix are holding the cells together in tissues, contributing to the physical

properties of skin, cartilage, and tissues, filtering materials passing between different tissues,

orients cell movements during embryonic development and tissue repair, and a role in chemical

signaling from one cell to another. Proteins that connect the cell’s plasma membrane to the

extracellular matrix span the plasma membrane and are involved with transmitting signals to the

interior of the cell allowing for communication between the extracellular matrix and the

cytoplasm of the cell.

Cells in the brain can send signals from one region of the brain to another. Nerve cells

communicate with each other at a junction called the synapse. At the synapse signals move from

one neuron to another. The synaptic cleft, a small space between two cells, is where all the action

takes place. The cell that will send the message is loaded with vesicles that are loaded with

vesicles that are filled with neurotransmitter molecules. The type of neurotransmitter used along


24

the reward pathway is dopamine. The cell that will receive the message is coated with dopamine

receptors. An electrical impulse triggers the vesicles in the sending cell to dump their contents

into the synaptic cleft. After the dopamine molecules are released into the synaptic cleft, they

lock into the dopamine receptors on the receiving cell. Receptors are shaped to fit a particular

type of neurotransmitter. In this case, the receiving cell is studded with receptors specific to

dopamine. When a dopamine is docked, thre receptor sets into motion resulting in the production

of a second messenger molecule. Once the dopamine has done its job, it is released from the

receptor and travels back to the sending cell through reuptake transporters where it will either be

packaged for reuse or broken down. Once produced, the second messenger initiates a nerve

impulse which travels down the axon of the neuron. Once the impulse reaches the end of the

neuron, vesicles with neurotransmitters are stimulated to dump their contents and the whole

process starts again. Now, the receiving cell has become a sending cell. The impulse stops if too

few neurotransmitters bind to receptors, causing the neuron to not fire an impulse. Also, if

certain types of neurotransmitters are inhibitory, the neurotransmitters prevent a nerve impulse

from being passed on. Cells communicate through chemical signals. Hormones and

neurotransmitters (described above) act like words telling the cell the message. Once the signal

binds to the receptor, that protein turns on a signaling cascade in the cell that ultimately leads to

the cell’s response. Each cell has different receptors to detect different signals.

Watson and Crick were the first to describe the double helix. English physicist Francis

Crick and American geneticist James D. Watson were both at the Cavendish Laboratory of

Cambridge University and used the model building to solve the structure of DNA. They

attempted to combine everything that had already been learned about DNA into a single model.

The technique of using molecular dimensions and known bond angles to make a molecular


25

structural diagram was originally applied to molecular structure studies by Linus Paulding.

Watson and Crick combined that, as well as Rosalind Franklin’s crystallography results to

diagram a suggestion of how nucleotides are oriented in DNA chains. Watson and Crick

demonstrated the four key features to define DNA structure (the double-stranded helix, it’s right-

handedness, the fact that it is antiparallel, and the outer edges of the nitrogenous bases being

exposed). This diagram was then used and analyzed to describe DNA in more detail as well as

DNA replication. DNA replication takes place in two general steps. Each replication in the cell

involves a number of different enzymes and other proteins. The first main step is when the DNA

double helix is unwound to separate the two template strands and make them available for new

base pairing. Then, as new nucleotides form complementary base pairs with the template DNA,

they are covalently linked together by phosphodiester bonds, forming a polymer whose base

sequence is complementary to the bases in the template strand. IN DNA replication, nucleotides

are added to the growing new strand at the three prime ends (the end at which the NDA strand

has a free hydroxyl group). In more detail: Because the DNA molecule is twisted over on itself,

the first step in replication is to unwind the double helix by breaking the hydrogen bonds by and

enzyme called helicase. Then, the exposed DNA strands for a y-shaped replication fork. DNA

replication begins at specific sites, origins of replication. Because the DNA helix twists and

rotates during replication, classes of topoisomerase enzymes cut and rejoin the helix to prevent

tangling. PNA polymerase is the actual enzyme that performs the addition of nucleotides

alongside the naked strand. DNA polymerase though can only add to the three prime ends; so to

start off at a five prime end it needs an RNA primer (a short strand of RNA nucleotides). Once

that is completed a leading strand is added continuously by DNA polymerase. The lagging strand

is simultaneously made discontinuously by Okazaki fragments. These fragments eventually


26

become linked together by the enzyme DNA ligase to produce a continuous strand. Finally,

hydrogen bonds form between the new base pairs resulting in two identical copies of the original

DNA molecule. But, when the DNA is replicated, the result is not two entirely new molecules.

Each new molecule is half the original molecule, hence it being called “semiconservative.”

SNP’s (single-nucleotide polymorphisms) exist as a DNA sequence variation occurring when a

single nucleotide in the genome differs between members of a biological species, or for a paired

chromosome in a human. Factors like genetic recombination and mutation rate affect

determining SNP density. These SNP’s are what result in genetic variation in DNA. These

variations in the sequences for humans can affect how humans develop diseases and respond to

pathogens, chemicals, drugs, vaccines and other agents. SNP’s can also result in deletions and

insertions within the genome, which, of course, can result in different diseases. The high

resolution of gene mapping related to the knowledge of SNP’s will help in understanding

pharmacodynamics.

DNA, we wouldn’t be here without it! It is always interesting to learn more about DNA

and what it is really about. People think DNA is nothing but the simplicity of a double helix, but

it is so much more than that.

The packing of chromosomes is an incredible process on a very microscopic level. There

is about one hundred trillion meters of DNA packed into each human. Certain proteins are used

to compact chromosomal DNA into the microscopic space of the eukaryotic nucleus. These

proteins, called histones, provide the energy to fold DNA and result in the DNA-protein

complex, chromatin. The basic repeating structural and functional unit of chromatin is the

nucleosome, which contains nine histone proteins and hundreds of base pairs. The Chromatin are

coiled into higher-order structures. A piece of DNA that is one meter long becomes a “string of


27

beads” chromatin fiber of just about six inches in length. The chromatin are still too long to fit

into the nucleus, so they are further coiled into a shorter, thicker fiber. Chromosomes are most

compacted during metaphase. The process of packaging starts when DNA is wrapped around

histones. The combined loop of DNA and protein (nucleosome) are packaged into a thread,

chromatin. This fiber is then looped and packaged. The end result is a tightly packed

chromosome structure. On the contrary, bacteria contain genophores, They are the chromosome

equivalent in viruses, prokaryotes, and certain organelles, however they lack associated histones.

Learning about chromosomes is something that has always been interesting to me. It is

incredible to think that so much DNA and genetic material is coiled to fit into such a small area.

And that each cell hosts that much information. It’s fascinating.

The period between cell divisions is the cell cycle. The cell cycle is divided into

mitosis/cytokinesis ad interphase. During interphase the cell nucleus is visible and typical cell

functions occur. This phase of the cell cycle begins when cytokinesis is completed and ends

when mitosis begins. Interphase has there subphases: G1, S, and G2. During the G1 phase, a cell

is preparing for S phase. So, each chromosome at this stage is a single un-replicated structure.

During the G1 to S transition (the restriction point, R) the commitment is made to DNA

replication and subsequent cell division. In the S phase DNA replication occurs, hence the

importance of this phase. Each chromosome is duplicated and thereafter consists of two sister

chromatids joined together and awaiting segregation into two new cells. In the G2 phase of cell

division the cell makes preparations for mitosis. Progress through this cell cycle depends on the

activities of cyclin-dependent kinases. By catalyzing the phosphorylation of certain target

proteins, CDK’s play important parts at various points in the cell cycle. Cyclin bonding activates

CDK; binding of a cyclin changes the three dimensional structure of an inactive CDK, making it


28

an active protein kinase. Each CDK complex phosphorylates a specific target protein in the cell.

By acting as checkpoints, the activated and different CDK complexes regulate the orderly

sequence of events in the cell cycle.

Mitosis results in two new nuclei that are genetically identical to each other and to the

nucleus from which they were formed. During the S phase of interphase, the nucleus replicates

its DNA and centrosomes. During prophase the chromatin coils and supercoils, becoming more

and more compact and condensing into visible chromosomes. The chromosomes consist of

identical paired sister chromatids. Centrosomes move to opposite poles at the end of prophase. In

prometaphase the nuclear envelope breaks down. Kinetochore microtubules appear and connect

the kinetochores to the poles. Next, in metaphase, the centromeres become aligned in a plane at

the cell’s equator. In anaphase, the next phase, the paired sister chromatids separate and the new

daughter chromosomes begin to move toward the poles. IN the final phase, telophase, the

daughter chromosomes reach the poles. As telophase concludes, the nuclear envelopes and

nucleoli re-form, the chromatin de-condenses, and after cytokinesis, the daughter cells enter

interphase once again.

Meiosis, on the other hand, is broken down into Meiosis I and Meiosis II. In meiosis one

there six sub-phases. The first of these sub-phases, early prhophase I, is when the chromatin

begins to condense following interphase. Next In mid-prophase I synapsis aligns homologs and

chromosomes condense further. In late prophase I, the last of the prophase stages for Meiosis I,

the chromosomes continue to coil and shorten. The chiasmata reflect crossing over, the exchange

of genetic material between nonsister chromatids in a homologus pair. It is here when the nuclear

envelope breaks down. In metaphase I of meiosis I (Meiosis I as a whole being when the genetic

recombination occurs) the homologus pairs line up on the equatorial plate. Then in anaphase I


29

the homologus chromosomes (each with two chromatids) move to opposite poles of the cell. In

the final stage of Meiosis I, telophase I, the chromosomes gather into nuclei, and the original cell

divides. It is after this that Meiosis II can begin. In prophase of Meiosis II the chromosomes

condense again, following a brief interphase of interkinesis in which DNA does not replicate. In

metaphase II the centromeres of the paired chromatids line up across the equatorial plates of each

cell. Then, in the following phase, anaphase II the chromatids finally separate, becoming

chromosomes in their own right and are pulled to opposite poles. Because of crossing over and

independent assortment, each new cell will have a different genetic makeup. In telophase II, the

final stage of Meiosis, the chromosomes gather into nuclei, and the cells divide. Each of the

resulting four cells has a nucleus with a haploid number of chromosomes. The crucial result of

Meiosis is four genetically varying haploid daughter cells. Meiosis is what creates genetic

diversity, and as history has proven a lack of genetic diversity is no good for it results in an

increase of genetic dysfunctions. During metaphase I, homologous chromosomes may fail to

remain together and then migrate to the same pole as anaphase I. This is called nondisjunction

and it results in a production of aneuploidy cells (aneuploidy is a condition in which one or more

chromosomes are either lacking or present in excess). An example of this is a trisomic for

chromosome 21. A child with an extra chromosome 21 has the symptoms of Down syndrome.

Summary of meiosis and mitosis: this is a section where I feel as though my knowledge of

the topic wasn’t necessarily deepened or expanded. The simplicity of mitosis and meiosis can

only be taught so many ways, and after reading and reflecting on this portion it felt more like a

review then it did learning more about the topic.

Gergor Mendel, and Austrian monk, spent seven years working out principles of

inheritance in plants. Mendel made crosses with hundreds of plant and noted the resulting


30

characteristics of 24,034 progeny. His meticulously gathered data suggested to him a new theory

of how inheritance might work. When he presented his work and findings, it was ignored.

However, by 1900 when meiosis had finally been observed, his work was finally noticed and

recognized for being a remarkable discovery before genes and meiosis had even been seen.

Mendel’s work was a study with pea plants. He controlled pollination and fertilization of his

parent plants by manually moving pollen from one plant to another. Thus, he knew the parentage

of the parentage of the offspring. He studied pea plants that produced male and female gametes

in the same flower. If untouched, they naturally self-pollinate. So, Mendel began to examine

different varieties of peas and looked deeper for well-defined contrasting alternative traits.

Mendel’s first low, the law of segregation, states that when any individual produces gametes, the

two copies of a gene separate, so that each gamete receives only one copy. Thus, every

individual in the offspring from a cross between parents inherits one gene copy from each parent,

and has the genotype Ss. (A genotype is what is not seen, is is the the allele combinations that get

placed into the Punnet square. The phenotype on the other hand is the visually demonstrated

characteristic of the genotype.) Mendel’s second law says that copies of different genes assort

independently. He concluded this after performing a dihybrid cross. Charles Darwin, whose

theory of evolution by natural selection was predicated on heritable variations among

individuals, failed to understand the significance of Mendel’s findings. He actually performed a

breeding experiment similar to Mendel’s work. However, he failed to question the assumption

that parental contributions blend in the offspring. It was not until that later he studied and

accepted Mendel’s Laws of Inheritance to complement his work on natural selection. The

combination of Mendel and Darwin’s work has lead us to the modern synthesis evolutionary

thought.


31

Mendelian Genetics is something that I thought used to be so simple; all it was to me was

Mendel crossing pea plants. But, I came to develop a deeper understanding of his detailed and

precise experiment as well as how it has helped develop our current understanding of biology.

The most interesting part to me about Mendel and his scientific times is that when he first

presented his ideas to the society, they were rejected because nobody was taking a mathematical

approach to the biological sciences. It took so many years for him to finally be appreciated for

all the work that he did. And, his later connections to Darwin’s work also helped him a lot. This

section made me look at myself and helped me realize that there is always more to learn and

understand than just what it may seem is on the surface.

In prokaryotes, genes are regulated through conserving energy. A cluster of genes with a

single promoter is called an operon, and the operon that encodes the three lactose-metabolizing

enzymes in E.coli is the lac operon. The lac operon promoter can be very efficient but mRNA

synthesis can be shut down when the enzymes are not needed. There are two types of regulation:

positive and negative. In positive regulation the gene is normally not transcribed; an activator

protein binds to stimulate transcription. In negative regulation, the gene is normally transcribed;

binding of a repressor protein prevents transcription.

This genetic regulation category is something that I wish I developed a stronger

discussion and understanding of. There is so much to learn about genetic regulation and its ties

to signal transduction. This is a category that I am going to take the time to develop a deeper

understanding of it.

Epigenetics refers to changes in the expression of a gene or set of genes that occur

without changing the DNA sequence. These changes are reversible, but sometimes are stable and


32

heritable. Epigenetics includes two processes: DNA methylation and chromosomal protein

alterations. Cytosine residues in the DNA are chemically modified by the addition of a methyl

group to the five prime carbon to form 5-methylcytosine. This covalent addition is catalyzed by

the enzyme DNA methyltransferase. The effect of DNA methylation is extra methyl groups in a

promoter attracting proteins that bind methylated DNA. These proteins are usually involved in

the repression of gene transcription; thus heavily metnylated genes tend to be inactive. This form

of genetic regulation is epigenetic because it affects gene expression patterns without altering the

DNA sequence. Another mechanism for epigenetic gene regulation is the alteration of chromatin

structure. DNA is packaged with histone proteins into nucleosomes, which can make DNA

physically inaccessible to RNA polymerase and the rest of the transcription apparatus. Each

histone protein has a tail of amino acids that sticks out of the compact structure and contains

certain positively charged amino acids. Acetyl groups are added to these amino acids and their

charges are changed.

The most interesting category/topic where my knowledge of epigenetics was expanded is

in the different types of methylation as an epigenetic regulation. This is something that I don’t

think I could necessarily grasp on a deeper level, but I still think it would be interesting to learn

more about.

One reason for sequencing genomes is to compare different organisms; another reason is

to identify changes in the genome that result in a disease. An enormous undertaking of

successfully completing the Human Genome Project was completed in 2003. The sequence

information is now used to: open reading frames, the coding regions for genes, amino acid

sequencing of proteins, and regulatory sequencing such as promoters and terminators for

transcription, RNA genes, and other noncoding sequences that can be classified into various


33

categories. The genome sequences for many prokaryotes (that are recently discovered) are of

great benefit to microbiology and medicine. As genomes have been sequenced and described, a

number of major differences have emerged between eukaryotic and prokaryotic genomes

including: eukaryotic genomes are larger than those of prokaryotes and they have more protein-

coding genes, eukaryotic genomes have more regulatory sequences and more regulatory proteins,

much of eukaryotic DNA is noncoding, and eukaryotes have multiple chromosomes. Two new

fields have emerged to complement genomics and take a more complete snapshot of a cell and

organism-proteomics and metabolomics. The proteome is the sum total of the proteins produced

by an organism, and is more complex than its genome. The metabolome, on the other hand, is the

quantitative description of all the small molecules in a cell or organism (including primary

metabolites (involved in normal processes, such as intermediates in pathways like glycolysis.

Also including hormones and signaling molecules.) and secondary metabolites (which are unique

to particular organisms and are often involved in special responses to the environment.)). Both

the proteome and the metabolome can be analyzed using chemical methods that separate and

identify molecules.

My learning experience about the genome: I feel as though I have a better understanding about

this topic. Before this point I did not realize how important and helpful the Human Genome

Project was. I knew it was important, but I thought its only purpose was to be a visual aid of the

genome, not to help with pharmaceutical developments in medicine and disease. As I was doing

my research on this topic I realized, and it was sometimes even stated, that the career world for

genome research is a growing field. And I found that to be very interesting especially because

much of the research being done is privately funded.


34

Works Cited

1Sadava, David E. Life: The Science of Biology. Sunderland, MA: Sinauer Associates, 2011.

Print.

2 Waggoner, Ben. "Robert Hooke." Robert Hooke. N.p., n.d. Web. 29 Sept. 2013.

3 Maxwell, R. (Director) (2013, September 26). cellular energetics. Biology 2107. Lecture

conducted from Georgia State University , Atlanta .

4 Maxwell, R. (Director) (2013, September 24). Central dogma . Biology 2107. Lecture

conducted from Georgia State University , Atlanta.

5 Maxwell, R. (Director) (2013, September 19). Cell membranes. Biology 2107. Lecture

conducted from Georgia State University , Atlanta .

6 “Animation: How the Sodium Potassium Pump Works." Animation: How the Sodium Potassium

Pump Works. N.p., n.d. Web. 29 Sept. 2013.

7 "Gene Expression: Transcription and Translation." Transcription and Translation. N.p., n.d.

Web. 29 Sept. 2013.

8 "Crossing the Divide: How Neurons Talk to Each Other." Untitled Document. N.p., n.d. Web.

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9 Newman, Jacalyn, and David E. Sadava. Study Guide to Accompany 'ninth Edition, Life : The

Science of Biology [David E. Sadava ... [ Et Al.]] . Gordonsville, VA: W. H. Freeman, 2011.

Print.

10 Maxwell, R. (Director) (2013, October 8). Glycolysis . Biology 2107. Lecture conducted from

Georgia State University , Atlanta.


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11 Maxwell, R. (Director) (2013, October 10). Citric Acid Cycle . Biology 2107. Lecture


12 Maxwell, R. (Director) (2013, October 15). Photosynthesis . Biology 2107. Lecture conducted

from Georgia State University , Atlanta.

13 Maxwell, R. (Director) (2013, October 17). Cells, Reception, Cell Types . Biology 2107.

Lecture conducted from Georgia State University , Atlanta.

14Annunziato, Anthony T. "DNA Packaging: Nucleosomes and Chromatin." Nature.com. Nature

Publishing Group, 2008. Web. 01 Dec. 2013.

15Maxwell, R. (Director) (2013, November 10). Chromosomes . Biology 2107. Lecture


16Maxwell, R. (Director) (2013, November 12). The Cell Cycle . Biology 2107. Lecture


17Brewer. 2012. BIOL 2107/2108-Principles of Biology Laboratory Manual. Data Analysis

Laboratory: Analysis of Photosynthetic Pigments Using Paper Chromatography and

Spectrophotometry. Atlanta, Georgia. Georgia State University.

18Newman, Jacalyn, and David E. Sedava. Study Guide to Accompany 'ninth Edition, Life : The

Science of Biology [David E. Sadava ... [ Et Al.]] . Gordonsville, VA: W. H. Freeman, 2011.

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Photosynthesis. New Comprehensive Biochemistry, Vol 15, pp 125–158. Elsevier, Amsterdam


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20Gest H and Favinger JL (1983) Heliobacterium chlorum, an anoxygenic brownish-green

photosynthetic bacterium containing a ‘new’ form of bacteriochlorophyll. Arch Microbiol 136:

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21Otsuka J, Miyachi H and Horimoto K (1992) Structure model of core proteins in Photosystem I

inferred from the comparison with those in Photosystem II and bacteria; an application of

principal component analysis to detect the similar regions between distantly related families of

proteins. Biochim Biophys Acta 1118: 194–210

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