I.

Define Biology and its branches

The word Biology is from two Greek words Bio which means life and logos which denotes
the study. Biology is an exciting and rapidly developing subject area. It is the science of
life or living matter in all its forms and phenomena, especially with reference to origin,
growth, reproduction, structure and behavior. Below are some of the different branches
of biology.

Concept map:

Anatomy - That
Microbiology- is the study of
deals with the
microorganisms, those being
study of structure
unicellular (single cell),
of organisms and
multicellular (cell colony), or a
their parts.
Cell Biology- Is the study cellular (lacking cells).
of cell structure and Microbiology encompasses
function, and it revolves numerous sub-disciplines
around the concept that including virology, parasitology,
the cell is the mycology and bacteriology.
fundamental unit of life.
Ecology - is the branch of
Botany- Is the scientific
Biology biology that is responsible
of plants, including their for studying the relationship
physiology, structure, of living beings on the
genetics, and ecology. planet with their natural
habitat.
Zoologists study animals. Zoology is divided into
several specializations. Some zoologists examine
heredity, or the ways traits are passed from one
generation to the next. Some zoologists
investigate how animals interact with their
environment or the other species that share their
environment.

https://www.google.com/amp/s/www.bioexplorer.net/divisions_of_biology/amp/

II. Explain the interdependency of Biology to other branches of

science. Sight at least 3 examples.
 Biology is the study of living organisms. Physics is the study of matter
and the laws of nature to understand the behavior of matter and the
universe. The Biophysical Society explains that, when scientists
combine physics and biology, they learn more about biological
systems on a molecular or atomic level. By taking a quantitative
approach to biological questions, a scientist gains a better
understanding of patterns that occur in living organisms. Physics
provides the basis for biology. Without space, matter, energy and
time components that make up the universe living organisms would
not exist. Physicist Richard Feynman said that everything on earth is
made of atoms, basic units of matter, that constantly move. Since
biology has its foundation in physics, it applies physical natural laws
to the study of living organisms, according to Muskegon Community
College. For instance, physics helps explain how bats use sound
waves to navigate in the dark and how wings give insects the ability
to move through the air. The American Physical Society shares that
many flowers arrange their seeds or petals in a Fibonacci-like
sequence to maximize exposure to light and nutrients. In some
cases, biology helps prove physical laws and theories. Feynman
states that biology helped scientists come up with the law of
conservation of energy.

https://education.seattlepi.com/relationship-between-physics-
biology-4698.html

 Ecology is the branch of biology that explains the relationship

between organisms and their environments. A subfield of biology,
ecology does not merely study living things like many other subfields
do. Instead, ecology focuses on abiotic factors like mountains and
streams to understand how living things interact with their
environments. In addition, ecology has important applications in the
social sciences when studying the impacts of topics like climate
change.

https://education.seattlepi.com/branch-biology-explains-
relationship-between-organisms-environments-6654.html

 Biology Relation with Chemistry: Body of all living organisms s

made up of organic and inorganic compounds, dissolved in water.
All the metabolic activities inside the body of living beings involve
chemical reactions and chemical changes. Genetic materials DNA
and RNA are also chemicals. Enzymes and hormones produced in
the body of living organisms are also exclusively chemicals.
 https://www.slideshare.net/JuinMondal/interrelation-inter-
dependece-of-biology-with-other-subjects

III. Discuss the difference steps of scientific method.

Steps of the Scientific Method:

1. Ask a Question: The scientific method starts when you ask a question about
something that you observe: How, What, When, Who, Which, Why, or Where?

For a science fair project some teachers require that the question be something you can
measure, preferably with a number.

2. Do Background Research: Rather than starting from scratch in putting together a

plan for answering your question, you want to be a savvy scientist using library
and Internet research to help you find the best way to do things and insure that
you don't repeat mistakes from the past.

3. Construct a Hypothesis: A hypothesis is an educated guess about how things work.

It is an attempt to answer your question with an explanation that can be tested.
A good hypothesis allows you to then make a prediction:

"If _____ [I do this] _____, then _____ [this] _____ will happen."

State both your hypothesis and the resulting prediction you will be testing.
Predictions must be easy to measure.

4. Test Your Hypothesis by Doing an Experiment: Your experiment tests whether

your prediction is accurate and thus your hypothesis is supported or not. It is
important for your experiment to be a fair test. You conduct a fair test by making
sure that you change only one factor at a time while keeping all other conditions
the same.
You should also repeat your experiments several times to make sure that the first
results weren't just an accident.

5. Analyze Your Data and Draw a Conclusion: Once your experiment is complete, you
collect your measurements and analyze them to see if they support your
hypothesis or not.
Scientists often find that their predictions were not accurate and their hypothesis
was not supported, and in such cases they will communicate the results of their
 experiment and then go back and construct a new hypothesis and prediction based
on the information they learned during their experiment. This starts much of the
process of the scientific method over again. Even if they find that their hypothesis
was supported, they may want to test it again in a new way.

6. Communicate Your Results: To complete your science fair project you will
communicate your results to others in a final report and/or a display board.
Professional scientists do almost exactly the same thing by publishing their final
report in a scientific journal or by presenting their results on a poster or during a
talk at a scientific meeting. In a science fair, judges are interested in your findings
regardless of whether or not they support your original hypothesis.

https://www.sciencebuddies.org/science-fair-projects/science-fair/steps-
of-the-scientific-method

IV. Research an article were biology is apply. (in any field)

“The ATGCs of DNA” 25 April 2018 by Jeremy Briton.

Sometimes I feel sad about how little I know of modern science...

I understand the scientific process all right, but the new discoveries often seem way out
of reach. I'm not equipped to really comprehend the Big Bang 13.8 billion years ago, the
warping of space time by a black hole, or force particles like the Higgs boson. I'm not
alone, and this isn't a new human condition. Science has always been working at the
frontiers, beyond common knowledge. Despite the learnings of the ancient Greeks, some
people two thousand years ago may have struggled with the idea of a round Earth. A
person two hundred years ago may not have been able to grasp the connection between
electricity and magnetism. Today these concepts are trivial. Perhaps general relativity will
be second nature to future generations. Does this make me feel better? Yes, I guess so,
a little bit.

I accept that I'm unlikely to ever fully understand in detail all the fantastic discoveries of
modern science. For some of the more impactful ideas, however, I want to at least
understand the basics. A couple years ago, I pushed myself to fathom the essence of
quantum physics. Then I tackled Einstein's gravity. I found a general approach to learning
that works well for me (more on this later...). Now I'm striving to wrap my mind around
the age-old inquiry: what is life and how does it work? Or more specifically: what is DNA
and how does it work?

“Watson and Crick”

In 1953, James Watson and Francis Crick built ball-and-stick models to help discover the
structure of deoxyribonucleic acid, or DNA. In this kind of model, the balls are atoms and
the sticks are bonds between them. I figure there's no better way for me to understand
what DNA is than to build a ball-and-stick model myself. Then I'll use another model to
simulate how DNA copies itself and how the DNA code is used to produce proteins.

On a Saturday in January, 2018, I'm sitting on the carpet in our guest bedroom where
there's room to lay out all the contents of the kit I bought online from the Molecular
Models Company. I feel excited, like I used to when I was a kid unpacking a new box of
LEGO on the floor and previewing the construction steps. The atoms are small plastic
balls with stubs where bonds will be (you might recall that atoms have a nucleus of
positive protons and neutral neutrons surrounded by shells of negative electrons, and
electrons in the outer shells can sometimes be shared between atoms to form bonds).
Hydrogen atoms are white. Carbon atoms are black. Oxygen atoms are red. Nitrogen
atoms are blue. Phosphorus atoms are purple. There are only these five elements in DNA.

The first step in the model instructions, which are nine pages long and include
illustrations, is to assemble the bases. A base is a molecule that tends to accept a proton
or donate an electron pair (an acid, which we'll run into later as the "A" in DNA, is a
molecule that tends to accept an electron pair or donate a proton). I'll be building 20
base molecules: five called thymine, five called adenine, five called cytosine, and five
called guanine. These bases are often referred to as T, A, C, and G. Their main structures
are flat rings built with carbon and nitrogen atoms—the nitrogen atoms make them bases
because nitrogen can donate an electron pair. T and C look alike. Both have one ring in
the shape of a hexagon, with four carbons and two nitrogen at the corners. I connect
each atom to its two neighbors using 20-millimetre-long grey tubes that slip over the
stubs on the atoms. These grey tubes represent strong covalent bonds formed by the
sharing of electrons. I adorn the rings around the outside by connecting single atoms or
simple molecules (of no more than four atoms) to most of the corners. The appendages
are composed of hydrogen, oxygen, carbon, and nitrogen atoms.

“Purines and Pyramidines”

The T and C bases are called pyrimidines, and the bigger A and G bases are called purines.
Each purine has a pyrimidine-like hexagon with a pentagonal ring attached by sharing
two adjacent corner carbon atoms.

The next step is to join the bases into pairs using hydrogen bonds. A hydrogen bond is a
weak electrostatic attraction between a partially positive hydrogen atom and a partially
negative atom such as oxygen or nitrogen. Hydrogen bonds are represented by 30-
millimetre-long clear tubes in the model. The weaker the bond, the longer the bond
length—recall the stronger covalent bond is represented by a 20-millimetre-long tube.
The base pairs in DNA need to be approximately the same length in order to fit within
the double helix structure I'll be making later. The sizes of the four bases and the exact
appendages of atoms on the hexagonal rings make it such that T and A pair and C and
G pair. T and C don't pair because they are both small pyrimidines. Likewise, A and G
don't pair because they are both large purines. If the base pairs need to be the same
length, we need one pyrimidine and one purine per pair. Why doesn't T pair with G, and
C with A? The appendages of atoms on the hexagonal rings don't favor these
combinations. It turns out T pairs with A via two hydrogen bonds and C pairs with G via
three hydrogen bonds. I let this sink in overnight.

The following day I'm at it again. The instructions tell me to assemble 18 phosphate
molecules and 20 deoxyribose sugar molecules. I make the phosphates by attaching four
red oxygen atoms to a central purple phosphorus atom using grey tubes (covalent bonds).
Then I make the deoxyribose sugars by building covalently bonded pentagonal rings of
four carbons and one oxygen, with attachments on the perimeter composed of hydrogen,
oxygen, and carbon atoms. The "d" in deoxyribose is the "D" in DNA.

This is easy and relaxing work. It's Sunday afternoon and, while it's cold outside, I'm
warmed by unobstructed sunlight flooding in through a southern window. The bedroom
is quiet and peaceful and cozy. Constructing the phosphates and sugars is a repetitive
exercise. My hands slide plastic stubs into tubes over and over while my mind wanders.
I wonder why DNA is an acid when yesterday I built all those bases. After finishing all the
molecules, I take a break to look this up. The phosphates I made are phosphoric acid
without the hydrogen atom nuclei. In phosphoric acid, three of the oxygen atoms bonded
to the central phosphorus atom are also bonded to single hydrogen atoms, the positive
nuclei (i.e. protons) of which can be donated. Because the pyrimidine and purine bases—
as I am about to see—are on the inside of DNA, and the phosphoric acids are on the
outside, the phosphoric acids dominate and DNA is overall acidic.

“Piles of bases...”

I now have tidy piles of base pairs, phosphates, and sugars, and I'm ready to put them
all together into the macromolecule DNA. I should say that the order of construction
specified in the model instructions (thoughtfully designed for human hands) is not the
order of construction in reality. In living organisms, the building block of DNA is the
nucleotide: a phosphate attached to a sugar attached to one of the four bases. The
human body makes nucleotides from scratch in the liver, or salvages them from degraded
RNA (to be introduced later) and DNA.

The model stand that will support the DNA is a 23-inch-tall rod on a 15-inch-diameter
wood base. The rod penetrates 10 shelves of acrylic glass spaced 2 inches apart vertically.
The model instructions specify the sequence of base pairs to be placed on each shelf
from bottom to top. I follow it, not wanting to make a mistake. The flat base pairs rest
easily on the shelves. At one point I question why I'm worried about following the
sequence; the base pairs are approximately the same length and can be placed with any
of the four bases on the left and any on the right. The truth is the order doesn't matter
for the model, but for real DNA, as we shall see in the next model, the order is the code
of life.
With the 10 base pairs in place, I begin attaching sugar molecules. A carbon atom on
each sugar covalently bonds to a nitrogen atom on the end of each base. The final step
is to insert and connect the phosphates between the sugars to produce the two sugar-
phosphate backbones. Before I do this, all the shelves are oriented in the same direction.
For the phosphates to fit between the sugars, I have to rotate the shelves. I start inserting
phosphates on one side only, from the bottom up. I know that each backbone of DNA is
in the shape of a helix, but I'm surprised by the amount of twisting of the shelves I have
to do to fit the phosphates. I feel like I'm being overly aggressive. I carry on—trusting
the instructions which have not let me down so far—and of course, it turns out just right.
The finished backbone makes approximately one helical turn. I insert the phosphates on
the other side to complete the second backbone, and I'm done. I spend some time
comparing the model to diagrams of DNA in a textbook. Yes, it's correct!

Before I move on to the next model, let me describe my recent pattern of learning. I fell
into it a couple years ago as I struggled to understand quantum mechanics, a modern
marvel of science. Physicists talk about wave-particle duality. Engineers use it to design
computers. Quantum mechanics is surely a bizarre and important thing, but what the
heck is it?! I wanted to know.

I read popular science books. There are many good ones. And from these books, I
garnered a clue. But I wanted more than a clue, so I looked for other ways to learn. I
decided to focus my attention on the double-slit experiment, which embodies the main
concepts of quantum mechanics. I read technical textbooks, pushing myself to continue
even when I wasn't comprehending much. I watched online lectures. As a last resort, I
consulted Wikipedia (don't tell my wife; I tell her anybody can write anything on there).

All this passive learning helped. I turned the corner in understanding, however, when I
decided to try to perform the double-slit experiment myself. I did it at home with a laser
pointer. Now things were starting to make sense. I drew the interference pattern of light.
I played with the math of waves. Neurons in my brain were firing. Emboldened, I
contacted universities in search of a lab with the double-slit experiment apparatus. I flew
across the country from my home in Portland, Oregon to Providence, Rhode Island to
observe the experiment performed one photon at a time at Brown University. I reached
my level-of-understanding goal by active learning.

Making a project out of it—that was the key.

To learn about general relativity, I witnessed scientists reproduce Sir Arthur Eddington's
famous 1919 eclipse experiment during the solar eclipse of August 21, 2017. By finding
out how light from distant stars bends as it passes the massive sun, I came to appreciate
the tenets of Einstein's theory of gravity.

Now I'm on to DNA: what it is and how it works. I started with popular science books
(e.g. DNA by James Watson), textbooks (e.g. Molecular Biology of the Gene by Watson,
Hopkins, Roberts, Steitz, and Weiner), and a video lecture series (Understanding
Genetics: DNA, Genes, and Their Real-World Applications by David Sadava). Then I began
my project: model building. First I built the ball-and-stick model, as you've seen. Now I'm
working on a model that shows how DNA copies itself and how proteins are made.

The Lab-Aids DNA-RNA Protein Synthesis Model Kit I purchased online is designed to be
used by students in a classroom under the guidance of a teacher. As I'm unpacking the
plastic pieces of the kit on the carpet in our guest bedroom, I feel like a teacher working
through the model to make sure I know what I'm doing before leading the students
through it. I do have the Teacher's Guide!

Step one is to build the DNA molecule, which will be much simpler than the ball-and-stick
model I built before. In this model, each base, phosphate, and sugar is one piece of
plastic. Each base molecule is a 25-millimetre-long soft tube. T is green, A is orange, C is
blue, and G is yellow. Each phosphate molecule is a 25-millimetre-long soft white tube.
Each sugar molecule is a small black pentagon with stubs.

The instructions say to make 18 nucleotides. I know what a nucleotide is from the
previous model: a phosphate attached to a sugar attached to one of the four bases. I
make each nucleotide by sliding a phosphate tube and a base tube onto stubs of the
sugar pentagon. Five nucleotides are made with T, five with A, four with C, and four with
G. I know from the previous model that T pairs with A and C pairs with G, so the number
of T bases equals the number of A bases and the number of C bases equals the number
of G bases (this is Chargaff's rule of base pairing).

I make two "half-ladders" of nine nucleotides each. Then I lay them side by side and
connect the base pairs using small rods—representing hydrogen bonds—that slip into the
base tubes. The result is an 11.5-inch-long DNA molecule in the shape of a ladder, with
nine base pair rungs. It's flat. The Student's Guide doesn't say anything at this point
about the shape of the DNA molecule. After consulting the Teacher's Guide, I gather that
this is an opportunity to ask the students about the shape. Because the model is
constructed using flexible plastic tubes, it can be twisted into the form of a double helix.
I do it again and again; it never gets old.

DNA is contained in chromosomes in the nucleus of cells. This gives us the "N" in DNA.
Human cells have 23 pairs of chromosomes, one set of 23 from Mom and one set of 23
from Dad. For a cell to divide into two cells, each possessing 23 identical pairs of
chromosomes (a process called mitosis), DNA must replicate.

“DNA replication”

Before I simulate DNA replication, I pretend I'm a liver and make 18 more nucleotides.
Then, to begin replication, I unzip the DNA molecule along the weak hydrogen bonds
between base pairs. As the double helix splits into two separate strands, I attach the
bases of the new nucleotides to the freshly unpaired bases on each strand. As always, T
pairs with A and C pairs with G. I started unzipping at the "top". Half-way through the
process, the model looks like the letter "Y": the original double helix is at the bottom and
two new double helices are branching off at the top. When I'm done, I have two identical
copies of the original DNA.

Prove to yourself that the copies are identical: Suppose the first three base pairs in the
original DNA are T-A, C-G, A-T. The two unzipped strands would be T-_, C-_, A-_ and _-
A, _-G, _-T. knowing that T pairs with A and C pairs with G, pencil in the new bases.

It is critically important that when a cell divides, each new cell retains the exact same
version of DNA as in the original cell, because DNA is the code for making the proteins
that do the things we recognize as life. Proteins provide the structures of cells and
therefore of bones, muscles, skin, and hair. Other proteins, called enzymes, provide
shapes that facilitate chemical reactions. The DNA code is used to create proteins through
the processes of transcription and translation.

Proteins are not made in the nucleus, where DNA is. They are made in ribosomes in the
cytoplasm of the cell. The cell needs some way get the code from the nucleus to the
ribosomes. This is where we first meet ribonucleic acid, or RNA. RNA is different from
DNA in two ways. The sugar molecule in RNA is ribose, which is very similar to, but not
exactly the same as, deoxyribose. And instead of thymine (T), RNA uses the pyrimidine
uracil (U). RNA comes in different flavors. Messenger RNA, or mRNA, transcribes the code
from DNA in the nucleus and delivers it to the ribosomes.

“Transcription”

I start the transcription exercise by building nine nucleotides. These will eventually form
the mRNA, so I use purple pentagons for ribose and lavender tubes for U instead of black
pentagons for deoxyribose and green tubes for T. Then I unzip one of my DNA molecules
from the replication activity. As the double helix splits into two separate strands (as it did
during replication), I attach the bases of the mRNA nucleotides to the freshly unpaired
bases on one of the strands (which goes AGTCTAGCT). U pairs with A, A with T, C with
G, and G with C. The mRNA nucleotides are now side by side, and covalent bonds form
between the neighboring sugar and phosphate molecules. As the new strand of mRNA
forms, I unzip it from the DNA strand and zip the two DNA strands back together. Voila,
I now have a single strand of mRNA, and the DNA molecule is restored. In a real cell, at
this point the mRNA would leave the nucleus through pores in the membrane and travel
to a ribosome in the cytoplasm.

My mRNA strand contains only nine bases (UCAGAUCGA). A real mRNA strand would be
much longer. The DNA in each human chromosome contains millions of base pairs, which
group into hundreds to thousands of genes. A gene, which contains hundreds to
thousands of base pairs, is an important unit of code. It used to be thought that each
gene is translated into one protein; now we know it's about three proteins on average.
In the transcription exercise, I unzipped the entire DNA molecule, which was no big deal
since it had only nine base pairs. In real life, transcription does not involve unzipping an
entire DNA molecule with its millions of base pairs; only a segment corresponding to a
specific gene unzips and is transcribed. The mRNA carries the code of this specific gene,
with its thousands of bases, out to the ribosomes.

I place the mRNA strand with nine bases on a flat piece of purple plastic in the shape, I
presume, of a ribosome. The ribosome is purple like the ribose sugar pentagon because
ribosomes, as you might tell from the name, contain ribose. Its structure, which I guess
is complex, will have to be a lesson for another day.

Elsewhere in the cytoplasm, another type of RNA called transfer RNA, or tRNA, is
gathering amino acids. The tRNA molecules are different from the mRNA molecules. One
side of tRNA does look like mRNA, but much shorter: it holds a string of only three bases.
The other side looks like a keyhole. The key that fits the keyhole is a part of an amino
acid.

“Translation: from gene to protein”

Amino acids are the building blocks of proteins. There are 20 of them. The human body
can make some; the rest we get from food. All amino acids have a central carbon atom
covalently bonded to four characters: a hydrogen atom, an amino group, a carboxylic
acid group, and a "side chain." The side chain is the only character that differs among
the 20 amino acids. It is the key of the amino acid. Each of the three amino acids in the
model has a different key: rectangle, triangle, and half-circle.

Each of the three tRNA model pieces has, on one side, a keyhole slot for either a
rectangle, triangle, or half-circle. The other side has stubs for three bases. Together, the
three bases form a unit that is called a triplet. There is a specific relationship between
the base triplet, tRNA with its keyhole, and amino acid with its key. Bear with me; this is
going to be awesome.

The bases on the three tRNA molecules have to pair with the bases on the mRNA, which
is waiting patiently on the ribosome. The first three bases on the mRNA are U, C, and A,
so the bases on the first tRNA have to be A, G, and U. I put these bases onto the first
tRNA. This tRNA has, on its other side, a rectangular keyhole holding an amino acid with
a rectangular key. The next three bases on the mRNA are G, A, and U, so the bases on
the second tRNA have to be C, U, and A. The second tRNA has the triangular keyhole
holding the amino acid with the triangular key. The last three bases on the mRNA are C,
G, and A, so the bases on the last tRNA have to be G, C, and U. The last tRNA has the
circular keyhole holding the amino acid with the circular key. I consult a textbook to find
that tRNA molecules with base triplets AGU, CUA, and GCU always have, on their other
sides, the amino acids serine (rectangular key), aspartic acid (triangular key), and
arginine (circular key), respectively.

Now I attach the bases of the three tRNA molecules to the bases of the mRNA molecule
using hydrogen bonds. In this arrangement, the three amino acids are side by side, with
the amino group of one next to the carboxylic acid group of another. I make covalent
bonds between the neighboring amino acids using grey tubes. Finally, I detach the string
of three bonded amino acids from the tRNA molecules. I now have a representation of a
very short protein molecule. In real life, a long string of hundreds of amino acids would
fold into a specific protein dictated by the exact type and sequence of the amino acids.

“The genetic code”

Let's catch our breaths and summarize what has happened. When we unzipped the DNA
molecule for transcription, these bases were exposed: AGT, CTA, and GCT. The
corresponding mRNA molecule had the following bases: UCA, GAU, and CGA. During
translation, the corresponding tRNA molecules had the following bases/amino acids:
AGU/serine, CUA/aspartic acid, and GCU/arginine. Here is the same information in a table:

DNA bases AGT CTA GCT

mRNA bases UCA GAU CGA

tRNA bases AGU CUA GCU

Amino acids serine aspartic acid arginine

Serine, aspartic acid, and arginine then bonded to form part of a specific protein molecule.
These are the broad strokes of how the DNA code is used to produce proteins. I am in
awe that we know how this works.

It's the end of another Sunday. My legs ache from sitting for so long on the carpet. I pull
open the curtain; it's almost dark outside. Tomorrow I have to go to work.

I'm done with both models, which is sad because I really enjoyed them. I do still have a
lot of questions. Different kinds of enzymes are required for all the processes I learned
about. I've acquired only a vague sense of how enzymes work. The compositions of
ribosomes and tRNA molecules are still mysterious to me. This was beyond the scope of
the Lab-Aids model kit. I don't know how mRNA and tRNA find their way to ribosomes.
Even though I'm tired—it's painstaking work keeping track of all those bases and their
letters—I scour Molecular Biology of the Gene looking for answers. Despite the amazing
learning experience I just had, I leave the guest bedroom a little frustrated at some of
the details I still don't know.

After a good night's sleep, I wake up with the proper perspective. I remember my
objective: to develop a basic understanding of what DNA is and how its code is used to
make proteins. Mission accomplished. Molecular biologists say that life obeys chemistry,
and now I can appreciate how. If I want to learn more, I have the foundation to do so.

https://www.thenakedscientists.com/articles/science-features/atgcs-dna