NAME: ANDOG, QUEENCY P.

COURSE & YEAR:BS BIOLOGY-III

REFLECTION PAPER
[lesson 1]
REACTION KINETICS AND TRANSPORT PROCESSES; CONNECTING
THERMODYNAMICS AND KINETICS
Throughout this lesson I have learned that Thermodynamics tells us what can occur during a
process, while kinetics tell us what actually occurs. Some processes, such as the conversion
of diamond to graphite, are thermodynamically favored but kinetically unfavored. In these
cases, the processes do not occur to any measurable extent. Chemical kinetics can be defined
as “the investigation of chemical reaction rates and the molecular processes by which
reactions occur where transport is not limiting”.
The study of chemical kinetics examines how quickly chemical compounds change from
reactant to product species. The fundamental ideas of chemical kinetics are covered in this
article. Basic ideas about rate coefficients, reaction order, the rate expression, elementary
reactions, third-body reactions, and steady-state concentration analysis are introduced using
atmospherically relevant reactions. The rate coefficient and its temperature dependency are
described physically, drawing on the concepts of statistical mechanics and collision theory.
Methods for deriving rate parameters from experiments are discussed, emphasizing relative
rate calculations and pseudo-first order kinetic analyses.
I also learned that Chemical kinetics, is the branch of physical chemistry that is concerned
with understanding the rates of chemical reactions. It is to be contrasted with
thermodynamics, which deals with the direction in which a process occurs but in itself tells
nothing about its rate. Thermodynamics is time’s arrow, while chemical kinetics is time’s
clock. Chemical kinetics relates to many aspects of cosmology, geology, biology,
engineering, and even psychology and thus has far-reaching implications. The principles of
chemical kinetics apply to purely physical processes as well as to chemical reactions.
One reason for the importance of kinetics is that it provides evidence for the mechanisms of
chemical processes. Besides being of intrinsic scientific interest, knowledge of reaction
mechanisms is of practical use in deciding what is the most effective way of causing a
reaction to occur. Many commercial processes can take place by alternative reaction paths,
and knowledge of the mechanisms makes it possible to choose reaction conditions that favour
one path over others.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 2]
BIOMOLECULAR ENERGIES, FORCES AND BONDS
In this lesson I have learned that The human body is composed of roughly 30 trillion cells
that collectively perform the essential functions of life. The cells can perform these life-
sustaining tasks with the help of several organic molecules present in them. These organic
molecules are referred to as biomolecules. Carbon compounds have major involvement in the
formation of biomolecules. They covalently bind with other elements to form several other
compounds. Some biomolecules are considered derivatives of hydrocarbons, they’re formed
by replacing hydrogen atoms from functional groups like alcohols, amines, aldehydes,
ketones, and carboxylic groups.
The biomolecules have a wide range of sizes and structures, and they are involved in a vast
array of life functions. They are composed of more than 25 naturally occurring elements, with
the primary elements being carbon, hydrogen, oxygen, phosphorus, and sulfur.
Approximately 10,000 to 100,000 molecules are present in a cell to regulate bodily function.
But the four major types of biomolecules include carbohydrates, lipids, nucleic acids, and
proteins. Most of the other compounds are derivatives of these major primary compounds.
Every biomolecule has its characteristics and is designated to perform some specific function
essential for life. So, let’s see what they are all about.
Carbohydrates are a vital part of a healthy diet. They provide the energy required to do work.
Scientifically, it’s a polyhydroxy aldehyde or polyhydroxy ketone. Carbohydrates are the
most abundant biomolecules on earth. Proteins are unbranched polymers of amino acid
residues. There are about 22 amino acids that are involved in the synthesis of proteins
according to their location and function. Proteins are categorized into four groups depending
on their structural organization.
Nucleic acids are macromolecules present in cells and viruses, and they are involved in the
storage and transfer of genetic information. The nucleic acid was first discovered by Friedrich
Miesher in the nuclei of leukocytes. Later, further studies showed that it’s a mixture of basic
proteins and phosphorus-containing organic acid. Lipids are organic compounds that are
insoluble or poorly soluble in water but soluble in organic solvents (like dissolves like) such
as ether, benzene, or chloroform. They are hydrophobic and structurally composed of a chain
of hydrocarbons. They are chemically more diverse than other biomolecules, and they are
primarily involved in membrane structure and energy storage.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 3]
BIOMOLECULAR STRUCTURE; DNA, RNA, AND POLYPEPTIDE

In this lesson, I learned about, what makes a protein, DNA, or RNA molecule unique and
crucial to its function is its complex folded, three-dimensional structure, or biomolecular
structure. From the level of individual atoms to the interactions among complete protein
subunits, the structure of these molecules can be analyzed at various length scales. Proteins,
lipids, nucleic acids, and carbohydrates are the four main categories of biomolecules. These
main fundamental compounds are the source of the majority of other chemicals. Each
biomolecule has unique properties and is intended to carry out a particular task that is
necessary for life.
Firstly, Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are perhaps the most
important molecules in cell biology, responsible for the storage and reading of genetic
information that underpins all life. They are both linear polymers, consisting of sugars,
phosphates and bases, but there are some key differences which separate the two1. These
distinctions enable the two molecules to work together and fulfil their essential roles. Here,
we look at 5 key differences between DNA and RNA. Before we delve into the differences,
we take a look at these two nucleic acids side-by-side.
Besides I also learned that, DNA replicates and stores genetic information. It is a blueprint for
all genetic information contained within an organism. DNA consists of two strands, arranged
in a double helix. These strands are made up of subunits called nucleotides. Each nucleotide
contains a phosphate, a 5-carbon sugar molecule and a nitrogenous base. DNA is a much
longer polymer than RNA. A chromosome, for example, is a single, long DNA molecule,
which would be several centimeters in length when unravelled. The bases in DNA are
Adenine (‘A’), Thymine (‘T’), Guanine (‘G’) and Cytosine (‘C’).However, RNA converts the
genetic information contained within DNA to a format used to build proteins, and then moves
it to ribosomal protein factories. RNA only has one strand, but like DNA, is made up of
nucleotides. RNA strands are shorter than DNA strands. RNA sometimes forms a secondary
double helix structure, but only intermittently. RNA contains ribose sugar molecules, without
the hydroxyl modifications of deoxyribose. RNA shares Adenine (‘A’), Guanine (‘G’) and
Cytosine (‘C’) with DNA, but contains Uracil (‘U’) rather than Thymine.
A polypeptide is a continuous, unbranched chain of amino acids joined by peptide bonds. To
generate an amide, the peptide bond connects the carboxyl group of one amino acid to the
amine group of the next amino acid Proteins play an important part in biology, serving as the
building blocks of muscles, bones, hair, and nails, as well as creating enzymes, antibodies,
muscles, connective tissue, and a variety of other things. Peptides differ from polypeptides in
that they are made up of shorter chains of amino acids.
As a conclusion Biomolecular structure of DNA, RNA, and Polypeptide is very interesting.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 4]
BIOLOGICAL ENERGY: ENERGY CONSUMPTION, PHOTOSYNTESIS, ATP
In this lesson I have gained knowledge about Biological Energy. Scientists use the term
bioenergetics to describe the concept of energy flow through living systems, such as cells.
Cellular processes such as the building and breaking down of complex molecules occur
through stepwise chemical reactions. Some of these chemical reactions are spontaneous and
release energy, whereas others require energy to proceed. Just as living things must
continually consume food to replenish their energy supplies, cells must continually produce
more energy to replenish that used by the many energy-requiring chemical reactions that
constantly take place. Together, all of the chemical reactions that take place inside cells,
including those that consume or generate energy, are referred to as the cell’s metabolism.
Firstly, is a form of renewable energy that is derived from recently living organic materials
known as biomass, which can be used to produce transportation fuels, heat, electricity, and
products. In a process called "photosynthesis" (the reaction between plants, light, water and
carbon dioxide) plants capture sunlight and transform it into chemical energy. This energy
can then be converted into electricity, heat, or liquid fuels using a number of different
conversion processes.
Besides I have learned that, Without energy, our world stops. Each day millions of people
work to harvest energy sources like coal, oil and gas. And thousands of scientists develop
new energy sources that are needed to make the energy we use cleaner and more sustainable.
Life on earth is run by energy. We need energy in order to live and it is crucial to survival but
the world in running out of the energy sources we have been taught to use for decades.
I feel like I have a better understanding of how, where, and why photosynthesis occurs. I
believe using scientific method, method of data analysis , and drawing conclusion for this
process is what lead to this change. The other labs (Intro to Bio Lab, Investigating
Macromolecules, Osmosis & Diffusion. ect.) we completed so far this semester has
introduced me the rules of laboratory and different ways of thinking of science. It also
introduced me the ideas of analyzing data ,drawing conclusion , and dealing with
experimental uncertainties. When I attended high school, I was taught of photosynthesis,
diffusion and other biological process but we never had a hand on experiment(lab) with those
ideas. Physically doing experiments and observing really help me understand better. It give
me the chance to verified the idea myself. Also, using lab tool and instrument such as
spectrophotometer and computer program(Logger Pro, Excel) shows me the importance of
how a tool could be used in understanding biological process and testing theories. In a way,
scientific method helps me to enrich my critical thinking skills.
Additionally, almost all the oxygen in the atmosphere is due to the process of photosynthesis.
If photosynthesis ceased, there would soon be little food or other organic matter on Earth,
most organisms would disappear, and Earth's atmosphere would eventually become nearly
devoid of gaseous oxygen.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 5]
BIOLOGICAL MEMBRANE
In this lesson I learned that, Biological membranes allow life as we know it to exist. They
form cells and enable separation between the inside and outside of an organism, controlling
by means of their selective permeability which substances enter and leave. By allowing
gradients of ions to be created across them, membranes also enable living organisms to
generate energy. In addition, they control the flow of messages between cells by sending,
receiving and processing information in the form of chemical and electrical signals. This
essay summarizes the structure and function of membranes and the proteins within them, and
describes their role in trafficking and transport, and their involvement in health and disease.
Techniques for studying membranes are also discussed.
Lipid molecules form a bilayer, or double sheet, that makes up biological membranes. The
term "phospholipid bilayer" is commonly used to describe this structure. Membrane proteins
and sugars are important constituents of the structure, in addition to the diverse lipid types
found in biological membranes. Because they support the structural integrity, organization,
and material flow through biological membranes, membrane proteins are essential to
membrane function. Sugars are exclusively present on one side of the bilayer and are
covalently bound to certain proteins and lipids. Three types of lipid are found in biological
membranes, namely phospholipids, glycolipids and sterols. Phospholipids consist of two fatty
acid chains linked to glycerol and a phosphate group. Phospholipids containing glycerol are
referred to as glycerophospholipids.
In addition, the main components of biological membranes are proteins, lipids, and
carbohydrates in variable proportions. Carbohydrates account for less than 10% of the mass
of most membranes and are generally bound either to the lipid or protein components. Myelin
has few functions and is made up almost entirely of lipids. In plasma membranes, the weight
ratio of lipid to protein is close to 1; in several specialized membranes (ie, mitochondrion and
bacterial cells) this ratio is near 2 or 3. Thus, there appears to be a correlation between the
number of activities performed by and the amount of protein in a membrane. The main
membrane lipids are phospholipids, cholesterol, and glycolipids. Glycolipids seem to be cell
antigens, and they, together with glycoproteins, may determine surface characteristics of a
cell which distinguish it from other cells. Approximately ten polypeptide chains of different
molecular weights make up most of the mass of protein in plasma membranes.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 6]
NERVE SIGNAL
The nervous system is in charge of identifying both internal and exterior circumstances. For
instance, our nervous system is in charge of informing our brain to yank our hand away from
heat when we come into contact with anything hot. The nervous system's communication
channels are called neurons. The characteristics of a neuron's plasma membrane are what
transmit signals.
I discovered that the body's main tissue type, neuron tissue, is made up entirely of neurons.
Communication between cells is facilitated by the neurons. Neurons come in three varieties.
They go by the names of interneurons, motor neurons, and sensory neurons. Sensations from
one part of the body are picked up by sensory neurons and sent to the spinal chord.
Interneurons act as a link between the main categories of neurons. Finally, multipolar neurons
make up motor neurons. They are in charge of the skeletal muscle contractions that happen in
reaction to stimuli.
I also discovered that the components of neurons are the axon, dendrites, and cell body. I was
rather curious to find out more about action potentials. I discovered that action potentials,
commonly referred to as nerve impulses, occur when a stimulus causes a neuron's resting
membrane potential to reverse. Every action potential deviates from its initial position. I was
curious to find out more about the spinal chord's role in transmitting information from the
PNS to the brain. I discovered that it functions like an elevator. It serves as the reflex control
center. It is made up of both white matter and gray matter from the neurological system.
The brain is composed of the hindbrain, cerebellum, the pons, and the midbrain. Each section
has different functions. The hindbrain houses the medulla oblongata which is the brain's
reflex center. The Cerebellum coordinates our body's movement and balance. The pons,
signals between the cerebellum and the forebrain. The midbrain houses the tectrum, which is
also known as grey matter, and the forebrain. The midbrain is responsible for coordinating a
reflex response to light and sound.
I personally found the nervous system to be the most complex system we learned about in
this class. I had no idea how much goes on inside of our body in a mere .5 seconds that it
takes us to respond to a stimuli, such as touching something that is too hot and jerking our
hand away to prevent inury. The body is truly incredible.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 7]
MEMORY
My cognitive class this year has been a worthwhile educational experience. Cognitive refers
to the way our knowledge is processed. The manner in which it grows and the role it plays in
our bodies. It has to do with how our minds work when it comes to remembering, decision-
making, and regulating our emotions and volition. There are now three main processes
involved in memory. Encoding, storing, and retrieval come first. Here are the three methods
for creating new memories. Information must be transformed from its unusable form in
memory. It happens as a result of the encoding process that our brains use to know. We are
able to store memories in people's conscious minds through this retrieval process.
It is classified into numerous categories, based on memory. These categories—starting with
time, function, and category—store memory. When it comes to brain memory, there are
numerous layers. In order for the brain's various processes to operate correctly, it has been
represented.
Nowadays, working memory is capable of temporarily storing information from memory and
employing it to accomplish various tasks that need to be completed. The brain areas that
enable working memory can support it. It is referred to as the parietal and frontal lobes.
Working memory is now divided into four categories. The phonological loop, or verbal short-
term memory, is where it all begins. All verbal content is stored in brief storage, which is
used for language processing, practicing verbal problem solving, and arithmetic.
Memories occur when specific groups of neurons are reactivated. In the brain, any stimulus
results in a particular pattern of neuronal activity—certain neurons become active in more or
less a particular sequence. Memory is a system or process that stores what we learn for future
use. Our memory has three basic functions: encoding, storing, and retrieving information.
Encoding is the act of getting information into our memory system through automatic or
effortful processing. “Memories may be beautiful and yet, what 's too painful to remember we
simply choose to forget, so it 's the laughter that we will remember.
I have discovered that my study skills and memory has changed over the years. During my
youth I did have a vivid photographic memory (eidetic imagery); presently, I can see the
contents of a picture or of a page in a book, it is just not as clear as it once was. I keep up on
current events (semantic memory)
Memory is essential for our sense of self. It is through our memories that we define who we
are, our experiences, and our relationships. Without memory, we would be lost and unable to
make sense of the world around us. Memory is also important for our emotional well-being.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 8]
BIOMECHANICS
Every living thing on Earth, including humans, is continuously affected by forces both within
and outside the body by the global force of gravity. The form, function, and motion of human
bodies can be investigated through the study of these forces' interactions and the
consequences they have, and the knowledge that is gained can then be used to improve
quality of life. Human movement is made possible by the intricate and highly coordinated
mechanical interaction between the bones, muscles, ligaments, and joints that make up the
musculoskeletal system. This interaction is regulated by the nervous system and occurs under
the influence of gravity and other loads. Any damage or lesion to any one of the
musculoskeletal system's component parts will alter the mechanical interaction and result in
degeneration, instability, or mobility impairment. On the other hand, harm can be avoided,
abnormalities can be corrected, and healing and rehabilitation can proceed more quickly
when the mechanical environment is appropriately modified, altered, and controlled.
The study of biological systems' loads, motion, stress, and strain as well as the mechanical
influences on the size, shape, and structure of the body is known as biomechanics.
Continuum mechanics is the study of loads, motion, stress, and strain of solids and fluids.
There are several degrees of mechanical influence on biological systems, ranging from the
molecular and cellular to the tissue, organ, and system levels. Thus, the study of human
biomechanics encompasses everything from the structure and function of the body's
neuromusculoskeletal system to the internal workings of individual cells and the mechanical
characteristics of both soft and hard tissues.
Moreover, the integration of biomechanics with other disciplines, such as genetics,
neuroscience, and materials science, will unlock new frontiers. Combining genetic
information with biomechanical data will enhance our understanding of individual variability
in movement and injury susceptibility, leading to personalized treatments and interventions.
Furthermore, advancements in biomaterials and tissue engineering will enable the
development of bioengineered constructs that closely mimic the mechanical properties and
functions of natural tissues and organs.
Biomechanics is an exciting and dynamic field that unveils the intricacies of movement,
structure, and function in biological systems. Its applications span sports science,
rehabilitation, ergonomics, and biomedical engineering, contributing to enhanced
performance, injury prevention, and improved healthcare outcomes. As technology continues
to advance, the future of biomechanics holds tremendous potential, paving the way for
personalized interventions, bio-inspired designs, and a deeper understanding of the mechanics
underlying life itself.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 9]
PROTEIN FOLDING
Proteins are a necessary component for cell growth and structure in all tissues, including
blood, muscles, skin, and hair. In addition, they have the ability to function as hormones or
enzymes. Hormones are typically composed of carbon, hydrogen, oxygen, phosphorus, and
sulfur. There are only roughly 20 different types of amino acids, which are the fundamental
structural building blocks of all proteins. These amino acid molecules, which can include
anywhere from 50 to 5,000 amino acids, couple up to come together into a form akin to a
chain through peptide bonds. When the carboxyl group of one amino acid combines with the
amino group of the subsequent amino acid in the sequence, peptide connections are formed.
There are numerous tasks that proteins strive to complete.
Protein folding is a process by which a polypeptide chain folds to become a biologically
active protein in its native 3D structure. Protein structure is crucial to its function. Folded
proteins are held together by various molecular interactions. During translation, each protein
is synthesized as a linear chain of amino acids or a random coil which does not have a stable
3D structure. The amino acids in the chain eventually interact with each other to form a well-
defined, folded protein. The amino acid sequence of a protein determines its 3D structure.
Folding of proteins into their correct native structure is key to their function. Failure to fold
properly produces inactive or toxic proteins that malfunction and cause a number of diseases.
In this lesson I also learned that the correct three-dimensional structure is crucial to function,
although some segments of functional proteins may stay unfolded. Failure to fold into the
salubrious structure produces dysfunctional proteins that are usually toxic to the cell. Several
neurodegenerative diseases are believed to result from the accumulation of amyloid fibrils
formed by misfolded proteins. Inappropriate folding of protein or maintaining it corresponds
to numerous malfunctions of cell operations that lead to disease
The proteins in our bodies are easily confused with the protein in food. There are similarities
and links between the two — for example, both consist of amino acids. But, when scientists
talk about proteins in biology, they are talking about tiny but complex molecules that perform
a huge range of functions at a cellular level, keeping us healthy and functioning as a whole.
Scientists will often talk about proteins "folding" and say that when they fold properly, we're
OK. The way they fold determines their shape, or 3D structure, and that determines their
function but, when proteins fail to fold properly, they malfunction, leaving us susceptible to
potentially life-threatening conditions.
NAME: ANDOG, QUEENCY P.
COURSE & YEAR: BSBIOLOGY-III
REFLECTION PAPER
[LESSON 10]
MOLECULAR CHAPERONES
Throughout this lesson I have learned that, the longevity of an organism and the health of its
cells are closely related to protein homeostasis, or proteostasis. An imbalance in the
landscape of protein folding can be brought about by aging, exposure to physiological and
environmental stress, and the expression of mutant and metastable proteins. This can lead to
the formation of non-native protein aggregates that put the proteostasis network (PN) to the
test and raise the risk of diseases linked to misfolding, aggregation, and aberrant regulation of
cell stress responses.
Molecular chaperones have central roles in each of the arms of the PN (protein synthesis,
folding, disaggregation, and degradation), leading to the proposal that modulation of
chaperone function could have therapeutic benefits for the large and growing family of
diseases of protein conformation including neurodegeneration, metabolic diseases, and
cancer. In this review, we will discuss the current strategies used to tune the PN through
targeting molecular chaperones and assess the potential of the chemical biology of
proteostasis.
The proteostasis network (PN), a conserved cellular system, is essential to all free-living
prokaryotes and eukaryotes for supporting all elements of protein synthesis, adapting to a
complex and changing environment, and determining organismal lifetime. In addition to
being crucial for biological fidelity, quality control mechanisms and cell stress responses—
which recognize and respond to both acute and long-term imbalances—are also necessary for
evolutionary robustness. Proteostasis, the process that integrates signals and controls flux
from synthesis to folding, transport, and clearance, is an example of this for proteins and
ensures the overall health of cells, tissues, and organisms.
Because of molecular chaperones' enormous cellular abundance, widespread expression,
evolutionary conservation, and essential functions in every stage of protein synthesis, the idea
that they could be targeted for therapeutic benefit was initially viewed with skepticism. The
development of small-molecule proteostasis regulators for cancer and neurodegenerative
illnesses highlights the therapeutic usefulness of altering the protein folding landscape
through pharmacological effects on molecular chaperones. The discovery of small-molecules
that can directly affect the function of isolated chaperone proteins or control the production of
several molecular chaperones at once has received a lot of attention.
Lastly, Molecular chaperones are a group of proteins that assist in the proper folding of other
proteins. They help in the conformational folding or unfolding of large proteins or
macromolecular protein complexes 1. There are several classes of molecular chaperones, all
of which function to assist large proteins in proper protein folding during or after synthesis,
and after partial denaturation 1. One major function of molecular chaperones is to prevent the
aggregation of misfolded proteins, thus many chaperone proteins are classified as heat shock
proteins, as the tendency for protein aggregation is increased by heat stress.