1.) RNA and DNA. Although all cells must contain

1.)  
As the cell is the basic monomeric unit amongst
all things living, we are to observe many similarities in the cells’ structural
features across bacteria, plants and animal. All cells possess a plasma
membrane to keep their internal structures separate from their environment.
This encasement is typically made up of lipids and proteins. The lipid
component of the membrane more specifically creates a phospholipid bilayer. A
single unit of the bilayer consists of a phosphate- containing head that is
characteristically polar thus hydrophilic and two fatty acid tails that are
hydrophobic. The hydrophobic tails tend to aggregate towards each other to
avoid interacting with water thus organizing itself into a bilayer with the
hydrophilic heads both facing the outside and inside environment of the cell.
The proteins throughout the membrane have several functions such as creating
channels for the selective passage of ions and other material inside and
outside of the cell to maintain an equilibrium with its environment. To note,
the proteins and lipids do not bond covalently allowing for the flexibility to
accommodate changes in the physical properties of the cells such as size and
shape. In addition to the plasma membrane, bacterial and plant cells have a
cell wall providing further rigidity, structural support and osmotic
resistance. More specifically, bacteria have a cell envelope containing the
aforementioned cell membrane as well as a cell wall. Depending on the
morphology and certain structural components of the cell wall, bacteria can be
broken down into two classes: gram negative or gram positive. In gram positive
bacteria, there is a characteristically thick layer of peptidoglycan while gram
negative bacteria have a single layer of peptidoglycan and an outer membrane
made up of lipopolysaccharides also known as endotoxins. Plant cells possess a
cell wall typically made up of cellulose. Encased inside of the plasma
membrane, all cells have a cytoplasm that contains the specialized particles
that do work inside of the cell. Each cell must also contain protein
synthesizing particles such as ribosomes (smaller in bacteria, 70S vs 80S) as
well as enzymes, coenzymes, metabolites, RNA and DNA. Although all cells must
contain a DNA genome, how it is stored depends on whether or not it is a
prokaryote or eukaryote. In Eukaryotes the DNA is stored in the nucleus that is
surrounded in the highly selective, double layered nuclear membrane The nucleus
acts to store the genetic material and regulate all cell activity. In the place
of a nucleus, prokaryotes possess a membrane-less, DNA containing nucleoid.
Bacteria also have DNA containing plasmids completely separate from the
nucleoid. These circular, double stranded DNA vehicles typically code for
advantageous characteristics to improve the survival of the bacterium such as
toxin resistance. In general, bacterial cells are smaller than that of animal
and plant cells and lack the complexity and compartmentalization of the latter.
Plant and animal cells contain membrane bound organelles inside of their
cytoplasm each with their own specialized function. Both animal and plant cells
contain a DNA containing nucleus, protein synthesizing ribosomes, endoplasmic
reticulum (rough and smooth) for protein and lipid synthesis as well as folding
of proteins, golgi complex for packaging and sending proteins, RNA synthesizing
nucleolus and ATP producing mitochondria. While bacteria do not have a membrane
bound mitochondrion to produce their ATP for energy, using the Endosymbiont
hypothesis, one could say the entire bacterial cell acts, in a way, as a
mitochondrion producing its own energy. Plant cells tend to be larger and have
some significant membrane bound organelles to mention in addition to those they
share with animal cells. Most importantly, plants have chloroplasts that
capture sunlight and are lined with thylakoids to carry out photosynthesis
producing glucose and thus ATP through the process of cellular respiration. The
glucose produced can be briefly stored in the starch granule also present in
the plant cell.  …anaerobes and aerobes
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2.)  
Energy is required for all cellular processes
and cells may differ based on how the energy is sourced. Some cells extract
energy from light making them phototrophs and some cells produce energy through
oxidizing chemical fuels thus classifying them as chemotrophs. There are
subclasses of photo/chemotrophs known as autotrophs and heterotrophs.
Autotrophs or “self-feeders” can use light and inorganic substances such as CO2
to synthesize complex biomolecules while heterotrophs are not “self-feeding” so
they must consume organic compounds usually made by producers or other animals
to make energy. Most photoautotrophs are plants in which they use water to
reduce CO2 in oxygenic photosynthesis. Photoheterotrophs such as green/purple
non-sulfur bacteria use light and organic carbon sources to produce energy. In
regards to chemoautoptrophs, these organisms extract chemical energy from
inorganic sources such as CO2 and are typically found in hostile environments
such as the deep sea vents. Humans would be classified as Chemoheterotrophs as
they extract their energy from organic carbon sources that are premade by
producers or other animals. Using these carbon sources, human cells are able to
undergo cellular respiration starting in the cytoplasm and to completion in the
mitochondria utilizing oxygen as the final electron acceptor to produce energy
in the form of ATP.  ATP contains 2 very
high energy yielding phosphoanhydride bonds and when hydrolyzed, energy is
released and can be used to do cellular work. 
There are other chemoheterotrophs that do not use oxygen as a final
electron acceptor and instead can use other organic compounds (fermentative
bacteria) or inorganic compounds.

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3.)  
Overall, there are 30 elements that are
necessary to sustain life. You can further break down these elements into bulk
and trace elements. Bulk elements are primarily consist of carbon, hydrogen,
oxygen, nitrogen, and sulfur along with sodium, calcium, potassium, phosphorus
and chlorine which can be considered “macrominerals”. Bulk elements are the
individual molecules that make up the four biological macromolecules that make
up a living organism; carbohydrates, proteins, lipids and nucleic acids. A
substantial amount of these elements must be consumed daily. The
“macrominerals” constitute the ions found in body fluid and play a structural
role as well. For example, phosphorus is an important element in the
phospholipid bilayers of all cells and is an important component of DNA, RNA
and ATP. Trace elements including magnesium, iron, copper, since, chromium,
selenium, iodine, fluoride, manganese, molybdenum, vanadium and tungsten. Trace
elements play important roles in regards to enzymes, enzyme activation and
enzymes activity, cellular transportation, protein folding/confirmation and
metabolism or microelements. These elements are consumed in very small
quantities. ??

4.)  
Carbons ability to form variety of single,
double and triple bonds allows for a plethora of organic compounds to exist.
Not only does the sequence in which the molecules are bound create unique set
of chemical and physical properties but the spatial arrangements can affect
their molecular function as well. Because carbon can form 4 single bonds to 4
different substituents, it can obtain a geometric property known as chirality.
Chirality indicates that the molecule is optically active which means that it
can rotate the plane of polarized light. A chiral carbon will have one mirror
image (an enantiomer) and one or more diastereomers. Enantiomers have identical
physical properties (except the direction in which it rotates light) and
chemical properties when reacting with achiral materials. Chirality is
especially important to consider in regards to its reaction in the body.

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5.)  
A. Methyl (-CH3) of the alkyl group is a
derivative of methane which is connected to 3 carbons and one substituent
group. It is non polar/hydrophobic by nature.

 

B. Phenyl (-C6H5) is an aromatic
structure that is practically benzene with one hydrogen detached. It is
hydrophobic/nonpolar. 

 

C. Amino (-NH2) an essential piece
of an amino acid making up the N-terminus. Typically has a lone pair making it
basic, however can bind to a third hydrogen to make NH3+.

 

D.Carboxyl (-COOH-) another
essential piece of an amino acid making up the C-terminus. It is polar and
acidic.

 

E. Phophoryl- (PO32-) a
derivative of phosphoric acid. Acidic and negatively charged by nature.
Important presence in ATP and DNA. ??

 

F.Phosphoanhydride bonds are
present between the three phosphate groups in an ATP molecule. This is a very
high energy bond and when broken by hydrolysis greate ADP and inorganic
phosphate it releases energy for the cell to do work.

 

6.)  
 b.) 
and when broken by hydrolysis greate ADP and inorganic phosphate it releases
energy for the cell to do work.

6.)  
ant
arbon mpeA.) Proteins are polymers made up of individual amino acids
that is folded into a unique conformation defining its biological function. It
is one of the four macromolecules of life. They assume many roles inside of the
cell and function as structural components such as in the cytoskeleton, enzymes
to reduce the activation energy thus increase the rate of reaction, regulation
of cell activity and aide in the selective transport through the cell membrane.

 

B.) Nucleic acids can be categorized as
deoxyribonucleic acid (DNA) or ribonucleic acids (RNA). The main role of DNA in
the cell is store the genetic material in a stable double stranded helical
structure. This genetic material contains the instructions for all chemical and
physical that act together to produce certain behavioral/functional/structural characteristics
of an organism. RNA, in a general overview, acts to copy the genetic material
stored in the DNA made up of a sequence of nucleotides, transfer it to the
cytoplasm, match it to the corresponding amino acid and synthesize the
designated protein. RNA has three main subtypes of RNA; messenger RNA, transfer
RNA, ribosomal RNA and small nuclear RNA.

 

C.) A polysaccharide is a polymer made up
of many monosaccharides. Polysaccharides have many functions in the cell
including acting as a structural support, cell to cell communication and energy
storage. The suffix “–ose”  is indicative
of a sugar. Cellulose is a complex carbohydrate that is the main component of a
plant’s cell wall. This gives the plant cell physical protection, structural
support and osmotic resistance. Polysaccharides have the ability to bind to
protein and lipids to become their corresponding conjugates. Glycoproteins are
often located on the outside of a cell to serve in cell to cell communication
and identification. This is especially important in regards to the immune
system and specific cell recognition. Glycolipids mainly function to stabilize
the cell membrane. Polysaccharides can also be stored most commonly in the
forms of glycogen or starch which can later be converted to glucose to be used
in glycolysis to produce energy for the cell.

 

D.) Lipids are made up mainly of glycerol
and fatty acid chains. They are known for being nonpolar and therefore
hydrophobic. Lipids have a role in energy storage as triacyglycerols in adipose
tissues, maintaining the separation of the intracellular environments by being
the main component of the phospholipid bilayer as well as glycolipids and play
a role in cell to cell signaling. 

 

7     
A.) When carbon is bound to four different
substituents groups via single covalent bonds creating asymmetry around the
carbon in question it becomes a chiral carbon. Chiral carbons are able to
rotate the plane of polarized light making them optically active. The plane of
polarized light can be rotated in a clockwise or counterclockwise direction in
which the chiral center can be denoted as R/D or S/L respectively, depending on
the notational system that is preferred.

 

B.) When comparing stereoisomers in which
it is found that the pair are exactly the same except for the configuration at
one chiral center, this isomer would be considered its epimer. 

 

C.) When determining the configuration of a
chiral center you can label it using one of two notational systems. The first
of mention would be the R and S system. R refers to rectus which is Latin
indicating right or the clockwise direction. S refers to sinister which is
Latin for left or counterclockwise. To determine whether a chiral center
rotates the plane of polarized light in the clockwise or counterclockwise
direction one must prioritize (highest to lowest atomic numbers) the
substituent groups connected to the chiral center. One must manipulate the
compound until the lowest priority group is on the dashed line, or in other
words, going into the page on a 2 dimensional plane. Once completed, the
substituent groups can be counted starting at the highest priority group to the
lowest in which the direction of rotation can be determined.

 

D.) The D and L notational system is
slightly different than that of the R and S system. The D and L system does not
indicate the character of the chiral carbons optical activity, instead you
denote a molecule as D or L depending on how its spatial configuration relates
to that of the standard glyceraldehyde enantiomers ((+/clockwise)
glyceraldehyde, (-/counterclockwise) glyceraldehyde). If it closely resembles
that of a (+) glyceraldehyde then the molecule is labeled as D and vice versa. To
note, this system is not used to label each chiral center of a compound rather a
compound as a whole.

 

E.) As mentioned above, every chiral center
has a single non-superimposable mirror image known as the enantiomer. Such
pairs rotate the plane of polarized light by the same degree but in opposite
directions and otherwise have identical physical properties. When naming the
compound one would find that all of the chiral centers will have the exact
opposite R and S notations. They also have identical chemical properties when reacting
with achiral compounds.

 

F.) Diastereomers are not exact mirror
images of the compound in question rather it has a different configuration at
one or more of the chiral centers.

 

G.) The cis and trans naming system
indicate geometric isomerism. This is used for compounds that have double bonds
which act to restrict rotation of the molecule unlike single bonds. When there
are one or two matching substituent groups on either side of a double bond,
they can be in “cis” (same side of the double bond) or in “trans” (opposite
sides of the double bond). Often when large groups or highly charged groups are
attached to the double bond they will be in the trans configuration as it
increases the stability of the molecule. 

 

H.) As indicated by the “-ase” suffix,
isomerase is an enzyme that is involved in catalyzing conversion reactions of
one isomer to another.

 

  are equal parts of a er to another. ers. re
stable. o the double bond they will be in the trans configuration as it iI.)
When there are equal parts of R and S enantiomers of a designated asymmetric    carbon present it is known as a racemic
mixture. Because enantiomers rotate the plane of polarized light by the same
degree but in opposite directions, when they are equal amounts of each they
cancel each other out and the mixture is not optically active.

 

8.)        The binding sites of enzymes are highly
selective and are able to recognize stereoisomers which allows for them to
exhibit distinct biological functions.  . e number 4 carbon is the chiral center of
the compond, roles.

 isomers and would not allow for the other to
bind thus produce For example, Maleic acid and Fumaric acid cis, trans
isomers of each other respectively. The binding site of an enzyme would be
specific for only one of these isomers and would not allow for the other to
bind thus produce no effect giving these two compounds two differentiated
roles.

 

9.)        A.) The number 4 carbon is the chiral
center of the compound. Isoproterenol binds to the Beta 1 or 2 receptors found
in the bronchioles and lungs. These receptor binding sites have unique binding
pockets that can only physically fit one stereoisomer and are stereospecific to
produce a particular biological activity. If bound to the L isomer, the
products produced would be different and therefore the action it would have on
the receptor would be different. ????

 

B.) Benzedrine
is a racemic mixture of amphetamine which means it contains equal parts of the
biologically active D form and inactive L form of the compound while Dexedrine
is enantiopure. When encountered with a racemic mixture, one must prescribe
double the dose to produce the same effect as the enantiopure drug thus 10
mg/day of Benzedrine is equivalent to 5 mg/day of Dexedrine.

 

10.)
     The relationship between free energy
(G), enthalpy (H) and entropy (S) can be represented by the mathematical
equation, .
To start, free energy is the energy available in a system to be converted (as
it is not created or destroyed) to do in this case cellular work. The change in
such energy, whether it is positive or negative, is indicative of the direction
of the reaction. When is
negative the reaction is favorable and will spontaneously occur, when  is positive the reaction is unfavorable.
Enthalpy is the amount of energy in the system or, in this case, inside of the
cell. In the aforementioned equation, the change in heat energy or the enthalpy
of the reaction is designated by a .
Whether  is positive or negative indicated whether the
reaction in the cell was endothermic (absorbed heat) such as photosynthesis or
exothermic (released heat) such as the hydrolysis of ATP observed in cellular
respiration. Based on the second Law of Thermodynamics, spontaneous reactions
are those that create greater disorder. Cells constantly absorb energy from the
environment whether chemically or through light to fuel themselves to do work.
As they do work to increase order in their system (decrease their entropy) they
produce bi-products such as heat and metabolites that increase the disorder of
their surroundings (increasing entropy). As long as the net entropy is positive
(,
these reactions will be spontaneous based on the second Law of Thermodynamics.
A reaction with positive enthalpy can be favorable as long as the temperature
and/or net entropy is great enough to compensate and make  negative based on the equation given above.
Negative or positive free energy only indicates whether the reaction is favorable
and will go spontaneously or not, it does not give any information about the
rate of reaction. So no, those with free negative energies won’t always go
immediately, that’s where enzymes come into play. 

 

11.)
A reaction with a positive 0′
can go forward in the cell as long as summation of all the s
for that reaction pathway is negative and therefore product favoring. If the
overall  is still positive, this unfavorable reaction
can be coupled with an exergonic reaction so that the energy released by the
latter reaction can be used to make the unfavorable reaction go.

 

12.)
ATP contains two very high energy phosphoanhydride bonds that cause the
molecule to have a very high potential energy. ATP hydrolysis has a negative
change in free energy indicating that it will go spontaneously and is typically
coupled to other reaction via enzymes using the energy released by the high
energy bonds to do work. With these bonds broken the electrostatic repulsion
between the formally adjacent oxygen atoms is relieved and a lower energy, more
thermodynamically stable state is achieved. This reaction also forms smaller,
more disorganized end products than the starting molecule thus increase entropy
which is consistent with the second Law of Thermodynamics.

 

13.)     With
the help of enzymes, an uncountable number of specific chemical reactions occur
in a cell every second in order to sustain life. If enzymes would cease to exist
some biological reactions would take up to billions of years to occur spontaneously.
They are also the catalyzing tools involved in the degradative and synthesizing
pathways that constitute cellular metabolism. Enzymes are highly biologically
practical because they increase the rate of reaction under mild conditions
found in the human body, are highly specific, do not part take in side
reactions to produce unwanted products, can be regulated by the body, help to
couple reactions with ATP hydrolysis so that unfavorable but necessary
reactions can occur and participate in substrate channeling, all without ever
being consumed by the reaction. ??

 

14.)
Feedback inhibition ensures that the enzymatic activity is regulated and that
the amount of each intermediate and end products of enzymatic pathways
appropriately meet the requirements of the cell. The cell will make a given
product with the use of enzymes until the need is met. Once met, the cell will
begin to accumulate unused product (acting as feedback) which will in turn
inhibit the first enzyme of the metabolic pathways from catalyzing the reaction
and therefore stop production. If this type of regulation wasn’t set in place
the efficiency of the cell would be significantly lowered.

 

15.)
A.) The idea behind RNA world is that it is thought that RNA came before DNA
and protein for several reasons. Primitive Earth had very hostile conditions in
which only simple compounds could be produced and of those were short RNA
sequences. The fact that RNA can act as a catalyst in a reaction held in the ribosome
in cell this far down the line of evolution, means that they could’ve acted as
their own catalyst allowing for self-replication in the beginnings of life. After
so much replication, there is room for mutation which promoted natural
selection towards those self-promoting RNA molecules that have the ability
synthesize small proteins which later on become more prevalent in RNA
replication. Eventually the more stable DNA molecule that were complementary to
the RNA molecules came into play and took over the role of genetic storage.

 

            B.) The Central Dogma is the
simplified, step wise explanation of how genetic information flows within a
living organism. The genetics instructions are stored in the DNA which are
transcribed and translated by RNA and turned into proteins.

 

            C.) The early more primitive
eukaryotes carried out anaerobic metabolism which generates less than 1/10th
the energy produced in aerobic metabolism. At some point an aerobic
bacterium was engulfed by the primitive eukaryote and was allowed to replicate.
Together they were able to carry out aerobic catabolism. The eukaryotic cell
benefits from the energy production and the bacterium benefits from the shelter.
Over the many years of evolution, the engulfed aerobic bacterium was modified
enough to become the mitochondria of the chemoheterotrophic cells we know today
in which the two pieces become completely dependent on one another and thus
inseparable. At some point along the way, the aerobic eukaryotic cell engulfed
a cyanobacterium capable of photosynthesis. In a much similar way, the cyanobacterium
formed a mutually beneficial relationship with the eukaryotic cell, multiplied,
and some of the genes were transferred to the nucleus of the eukaryotic cell again
making that inseparable, dependent bond. After many years of evolution, it
became the chloroplast producing ATP and carbohydrates by harvesting energy
from sunlight.