Download 2. How we study biology • The scientific method requires controls

2. How we study biology
• The scientific method requires controls, reproducibility, reliability, and hypothesis
testing
• The non-scientific method does not require controls, reliability
• Research usually requires financial support
• Ethics regulate research activities
Biology may intimidate us at first, but the reality is that we have contact with it in our daily
lives. For example, biology studies digestion, reproduction, anger, athletic performance
death and how effective are medical treatments. Cannot get more intimate than that!
(Different disciplines such as psychology, business, and sports are manifestations of
subsets of biology. )
There are two forms of reasoning that are part of the world of studying.
1 - Inductive reasoning: begins with an observation not universally accepted
2 - Deductive reasoning: based on observations solidly accepted to reach a
particular conclusion and is derived from logic.
Biology is studied using the scientific method. The scientific method requires
1. Question: does Gatorade enhance athletic performance?
2. Hypothesis: a proposition formulated by data collection and information. In
other words, what is the question? Does Gatorade really help improve
performance or will water be just as effective.
3. Data Gathering: Collecting the data in a systematic method
4. Controls: Used in the experiment part of the scientific method and is designed to
compare whether something really has an effect or not. To study if Gatorade
really enhances your performance requires also a control in which you drink just
water or nothing at all. Without controls, it is difficult to generalize.
5. Analysis: Analyzing the data to ascertain if the controls and experimental groups
are really different. Did the data indicate that Gatorade drinkers did better or
not?
6. Reproducibility and reliability: Can another group reproduce the data?
Biology can also be studied by not using the scientific method. It is important to
remember that scientific research requires financial support. Also, activities during
biological investigations should be performed following ethical standards. Although it is
mentioned last in this presentation, ethics should be involved at each step of any
investigation to protect the participants.
3. Properties of life
• Energy capture involves oxidation / reduction reactions in which hydrogen ions
are involved in the production of ATP
• Reproduction is essential for species survival
• Natural death is genetically determined
• Chromosome change promotes evolutions of life forms
Biology is the study of life. But what is “Life”? Life can be defined as the ability to be born,
grow, reproduce, die, and over successive generations, evolve. Now is this the definition of
an individual or of a species? Life also means managing the internal resources of a living
being to adapt to the changes occurring around them by way of feedback loops.
Life is governed by the mutual operation of various chemical and physical processes of
which energy capture and storage plus reproduction are the ultimate goals. Evolutions can
only be successful if they follow these two goals. (Seems like Spock is speaking!)
Energy capture requires the oxidation and reduction of food. The oxidative state is the
stripping of hydrogen from the food. In many cases the oxidation requires oxygen. As long
as life forms can produce chemical energy from some form of hydrogen donor-life is good.
Reproduction is the method whereby the survival of the species is assured and at the
chemical level this requires the transfer of “information” either as DNA, RNA or some other
form of molecule to make protein. All species have a programmed time of cessation of
activity (death) which is ultimately determined by genetic information. Consider plant
forms that live to be 500 to 1,000 years old and humans who survive for 100 years to
viruses who live only hours to weeks.
4. Cells
• The nucleus controls reproduction and all chemical reactions
• Mitochondria makes energy-rich molecules such as ATP
• The transport system is an exchange system bringing and taking substance to the
cell
• Cells form tissues which form organs and organisms
If we look in a mirror, we will not be able to tell that our body is composed billions of cells,
but it is.Our entire body is made of cells. All cells are composed of a membrane, cytoplasm
and a number of organelles such as the nucleus, mitochondria, etc.
1 - The membrane has different receptors composed of protein.
2 - The cytoplasm has various organelles that control the production of energy which is
stored in the form of adenosine triphosphate (ATP). In addition, there are organelles that
play a major role in protein production and others in clearing up the molecular debris in
cells.
3-The nucleus controls reproduction and all chemical reactions that occur within the cell
by way of its production of enzymes which are chemical catalysts.
Organisms: Different kinds of cells form different tissues that compose an organ. The
organs work independently but their activities are coordinated by chemical and electrical
signals to form a multicellular organism.
5. Water
•
•
•
•
Certain pathological conditions are caused by osmotic changes which lead to
diarrhea or edema.
Concentration of water in cells is determined by osmosis and hormones
Water is a universal solvent for biological systems since it is essential for chemical
reactions
The chemical properties of water will influence temperature and pH of cells,
tissues and organisms
Water can be defined as the new global economy gold. Since 97% of the world's water
is salty, 2% is frozen in glaciers, so just 1% can be consumed by humans. We see water as
something of little value in our lives, because we live in a society in which marketing invites
us to drink all kinds of drinks harmful to our health, but the reality is that over time it is
becoming more difficult to obtain this vital resource in countries like Africa, Latin America,
and Mexico. The lack of drinkable water is not yet and issue in the United States but
elsewhere the shortage is becoming a catastrophe.
Water is necessary for all chemical reactions occurring in living systems. Osmosis is a
physical movement of water through a semipermeable membrane which is dictated by the
concentration of the solute. Water flows from an area of high concentration to an area of
low concentration. The amount of water is determined by the solute. The more the solute,
the less the water and vice versa.
There are different types of solutions:
1 - hyperosmotic: A solution having a higher osmotic pressure than another. One solution
relative to another has more solute than solvent.
2 - hypoosmotic: A solution having a lower osmotic pressure than another. One solution
relative to another has less solute than solvent.
3-isotonic: A solution that is in a state of equilibrium with its surroundings.One solution
relative to another which have the same amount of solute/solvent.
A solvent is a substance which causes the dilution of another substance at the molecular
level. The chemical properties of water influence the temperature change in the cells,
tissues, and organisms.
The lack of water for a prolonged period of between 3 and 5 days leads to death.
6. Glycolysis
• The method of anaerobic energy (ATP) production in all cells
• Anaerobic metabolic process generates a small amount of energy
• Enzymes are located in the cytoplasm
• Depending on the cell type, metabolic products may be lactic acid, ethanol, and gas
in the form of carbon dioxide
Whenever energy is needed in the body, glycolysis is the first process that occurs. It
naturally leads into another process called oxidative phosphorylation. Glycolysis also
occurs in other living systems and it is the oldest metabolic system.
Glycolysis is the method of producing energy found in all cells. It is an anaerobic
process (e.g. requires no oxygen) that generates a small amount of ATP. Aerobic respiration
process occurs after glycolysis when oxidative phosphorylation (the metabolic process that
utilizes the hydrogen ion released during the oxidation of nutrients) occurs.
The metabolic end product of glycolysis is the molecule, pyruvate. Pyruvate has
different metabolic destinations and can lead to fermentation or is the entry molecule for
the Krebs cycle also called the Citric Cycle which is the next step in oxidative
phosphorylation
Glycolysis is regulated by enzymes, so that when the amount of ATP is high, it will
adhere to the enzymes in the glycolytic pathway to inhibit further production of ATP. This
results in decreased cellular respiration and ATP. This phenomenon is an example of
negative feedback at a molecular level. Glycolytic enzymes are located in the cytoplasm and
their function is to catalyze a specific sequence of chemical reactions. Depending on the cell
type, metabolic products that may result from glycolysis is lactic acid in our muscles
(obtained through the fermentation of sugars), ethanol (obtained in solutions with yeast
and sugar and carbon dioxide gas.
Returning to the example of a person who exercises. Sprinters or weightlifters require
ATP that is not dependant on oxygen levels thus they rely on the process of glycolysis as
the main mechanism for their muscles getting ATP. The muscles in this group of individuals
are large so that the muscles can generate force quickly without relying on oxygen transfer
at the capillary level.
7. Oxidative phosphorylation
•
•
•
•
•
Hydrogen Ion + Oxygen are used by the mitochondria to make ATP
Mitochondria produces large amounts of ATP by way of oxidative
phosphorylation
Oxidation is the loss of electrons and associated hydrogen ion.
Hydrogen ion activates ATP synthase to combine ADP with P to make ATP.
Imagine a diver plunging into the depths of the ocean and when the diver goes
deeper, bubbles begin to rise. These bubbles are an example of the absolute requirement of
oxygen for oxidative phosphorylation.
All of our activities require large amounts of adenosine triphosphate (ATP) per
second, which provides power to all chemical reactions and mechanical movements of
living systems. The essential element of Oxidative Phosphorylation is oxygen. The
mitochondria is the organelle which produces large amounts of energy (ATP).
Phosphorylation refers to adding inorganic phosphate of adenosine diphosphate
(ADP) to make ATP. For this to occur, ATP synthase must be activated by Hydrogen ion.
The hydrogen comes from the electron transfer chain that receives it from the Citric Acid
cycle.
NAD and FAD transfer the Hydrogen and associated electron from the Citric Acid
cycle to the electron transfer chain. Oxygen is used to capture the electron which allows
hydrogen to increase in concentration which then drives ATP synthase. The movement of
hydrogen ion through the ATP synthase molecule is called reverse osmosis.
8. Loss of oxidative phosphorylation
(Any substance that interferes with ATP production is a poison)
•
•
•
•
Cyanide competes with oxygen for the capture of electrons at the electron transfer
system
Carbon monoxide reduces oxygen transfer into the mitochondria
Dinitrophenol alters hydrogen gradient so that it minimizes chemiosmosis.
Fluoroacetate disrupts the citric acid cycle
You are on the beach and suddenly you see the lifeguard drag someone from the sea.
Water has entered his lungs and he is no longer breathing. Now he cannot deliver oxygen to
his cells to produce ATP. He's unconscious and he might die. Why? The loss of oxidative
phosphorylation will lead to a decrease in ATP so that all systems in the body will go into a
standstill.
Loss of oxidative phosphorylation occurs when carbon monoxide minimizes oxygen
transfer into the mitochondria so that it interferes with chemiosmosis. After fluoroacetate
is converted into fluorocitrate, it disrupts the citric acid cycle (Krebs cycle) so that NAD and
FAD are not reduced. Fluoroacetate is a poison that affects cytochromes aka the electron
transport system so that Hydrogen cannot activate ATP syntheses. Dinitrophenol also
alters the gradient of hydrogen. Cyanide directly competes with oxygen so that
chemiosmosis is directly impacted. Chemiosmosis is the flow of hydrogen ions through the
enzyme ATP synthase. If oxygen is not available, chemiosmosis does not occur.
9. ATP (adenosine triphosphate)
• Energy currency which is the production of ATP or other high energy substrates is
necessary for promoting anabolism and catabolism
• Mitochondria produces ATP which is essential for all cellular functions
• Phosphorylation of proteins are catalyzed by protein kinases
• ATP causes a decrease in the free energy required for spontaneous chemical
reaction
ATP is used to provide the energy required to promote chemical processes in
biological systems. For example, our body movements require the action of our muscles
which is dependent on ATP. Another example is the growth of humans; tissue formation
(mitosis) requires energy which is supplied by the adenosine triphosphate (ATP). All
energy ultimately comes from the sun via plants. Plants convert select wavelengths of
sunlight into organic material which are used by animals to capture the energy stored in
certain organic compounds.
ATP promotes chemical reactions in living systems, in other words, it provides energy
to the cell. Its presence or absence determines life or death. This energy currency is
necessary for anabolism and catabolism which occurs in all living systems.
- Anabolism is the process that synthesizes complex structures from simpler
molecular substructures... This process is performed at the cellular level. It includes:
synthesis of structural proteins such as enzymes, muscles, lipid synthesis into
cholesterol and hormones and biosynthesis of carbohydrates into glycogen. These
chemical processes are complex and require vitamins and other chemicals.
- Catabolism is the metabolic process that transforms complex molecules into their
smaller component parts. The recycling of parts of the organism is one aspect of
catabolism. If you are starving, catabolism will breakdown your lipid stores to form
ATP. Molecular digestion of food e.g. proteins into amino acids is another example of
catabolism.
Mitochondria produce ATP which is essential for all cellular functions in the body.
ATP causes a decrease in the free energy required for spontaneous chemical reaction
thereby promoting chemical reactions that otherwise would not occur. For example,
phosphorylation of protein is the process of adding an inorganic phosphate group to a
protein and changing its three dimensional structure so that it can promote various
chemical reactions. Phosphorylation requires ATP.
10. Photosynthesis
• Certain wavelengths of sunlight activate the molecule, chlorophyll
• The resulting excitation of chlorophyll produces ATP used in the synthesis of proteins
carbohydrates and lipids by taking the hydrogen ion from water to produce ATP.
Oxygen is then released into the atmosphere.
• Results of the “Light Reaction”: is ATP, NADPH ,Oxygen
• Results of “Dark Reactions” is: proteins, carbohydrates, lipids and insecticides
Photosynthesis is the most important set of chemical reactions on the planet. The end
result is oxygen which is necessary for aerobic metabolism as well as key food groups such
as proteins, carbohydrates and lipids. Photosynthesis is the conversion of inorganic matter
into organic matter produced by a combination of the energy (ATP) provided by light
carbon dioxide and water.
The structure responsible for photosynthesis in a cell is the chloroplast. Within these
green organelles is a chamber containing a "stroma” which has the various enzymes that
transforms carbon dioxide into organic matter. Moreover, the chloroplast uses wavelengths
of light to drive the formation of ATP and NADPH. These compounds are subsequently used
for the formation of sugars and other organic substances
The module describes two phases: "Light Phase" and "Dark Phase". During
photosynthesis the inorganic matter is converted into organic matter, this is called the dark
phase. In this phase, the enzyme, Rubisco, is used to capture carbon dioxide from the
atmosphere to be used as the carbon backbone for the synthesis of various organic
products. This process is made possible by the ATP which is obtained through the solar
energy e.g. wavelengths of light by means of the electron transport chain in the "Light
Phase". The light phase strips the oxygen from the water molecule resulting in hydrogen
ion and its electrons which subsequently produce ATP similar to what occur in oxidative
phosphorylation in animals cells.
Finally, it is important to highlight the role of insecticides. Plants produce their own
insecticide to protect themselves from predators including insects. Some insecticides
include: cocaine, nicotine, caffeine, and marijuana. Cocaine is a poison but in turn activates
the pleasure center in our brain. Cocaine which is produced by plants activates specific
brain cells that dopamine, the hormone that makes us feel happy. Cocaine works on
neurons in insects and in humans. The active ingredient in marijuana called THC also
affects the same area of the brain. It must be remembered that these insecticides may cause
irreversible damage to the neural systems of insects.
11. Digestive system, liver, molecules of life
• The digestive system has four basic functions including motility, secretion, digestion,
and absorption of food
• The nutrients and water are absorbed in the small intestine and are transferred to
the liver by way of the portal circulation
• The pancreas is an example of a gland that secretes hormones that regulate the level
of glucose in the blood and also digestive enzymes that do not travel in the blood but
are secreted into the intestine
• The liver is the body's metabolic brain since it modifies all the food that we eat. In
addition there are more neurons in the intestinal tract than in the brain.
The digestive system has four basic functions including motility, secretion, digestion,
and absorption of food:
- Motility: contractions of the smooth muscle layers, mixes food with secretions and moves
it through the GI tract. The two common types are motion: segmentation and peristalsis.
- Secretion: exocrine glands secret chemicals, digestive enzymes, which mix with food in
the intestinal tract and break their molecular structure.
- Peristalsis: when rings of circular muscles contract behind a mass of food material and
relax in front of it to advance it forward.
- Segmentation: occurs in the intestine. Smooth muscle rings contract and relax to create a
reciprocating motion that mixes the contents of the lumen consistently and pushes against
the absorptive surface of the intestinal wall.
- Digestion: Digestion is completed in the small intestine where most of the nutrients and
water are absorbed. The large intestine is home to millions of bacteria that influence all our
bodily functions. In addition, final water absorption of the processed food occurs here.
- Absorption: the nutrients are absorbed in the small intestine (the small intestine has
three parts to it: duodenum, jejunum and ileum) and also water from both the small and
large intestine.
-Nervous innervation in the intestinal tract as well external control motility and secretion
of different hormones some of which control satiety. (Why do you feel full?)
The pancreas secretes hormones that regulate the amount of glucose in the blood and
also secretes digestive enzymes. The ducts of the pancreas and liver flow together into the
duodenum. Exocrine cells that secrete enzymes dump into the pancreatic duct and from
there pass into the duodenum. Its function is the digestion of carbohydrates, fats, and
proteins. The stomach secretes pepsin to digest the proteins and the pancreas secretes
trypsin and chymotrypsin to digest protein into peptide fragments. The pancreas also
secretes bicarbonate ions to neutralize the HCl which comes from the stomach. This
neutralization is necessary for the function of pancreatic enzymes. The pancreas also has
an endocrine function that produces hormones. The pancreas secretes insulin and glucagon
from the islets of Langerhans.
The liver is the body's metabolic brain. The liver is the largest glandular organ in the
body it stores fats and carbohydrates for energy, regulates glucose levels in the blood, the
synthesis of blood proteins, iron storage and vitamins, the conversion of toxic ammonia
into urea, and detoxifies harmful substances, such as nicotine and alcohol.
The digestive system is designed to break up or catabolize certain molecules.
Biological molecules commonly contain carbon, hydrogen, oxygen and nitrogen atoms.
These atoms are combined to form a number of large molecules that are found in every
earth organism. Carbon in biological molecules forms four covalent bonds which form the
backbone of the macromolecules of life. The macromolecules are made up of smaller
subunits called monomers [a small molecular weight molecule that is bound to other
monomers with sometimes hundreds or thousands of chemical bonds. Covalent
macromolecules are usually called polymers]. Enzymes can break up, catabolize, only
certain molecules based on their configuration. Although trees are made from cellulose – a
sugar- enzyme systems in our intestinal tract cannot break up, catabolize, the sugar as a
source of hydrogen ions to make ATP.
There are four types of macromolecules:
1- Proteins: formed by amino acids (enzymes, muscles, hair)
2- Carbohydrates: are made of glucose molecules (sugar, starch, chips)
3- Lipids: formed by fatty acids (fats, oils, cholesterol, cell membrane)
4- Nucleic acid: consist of nucleotides (RNA, DNA)
12. Proteins
•
•
•
•
Twenty different amino acids are commonly available to make different kinds of
protein
Amino acid sequence and structure make a protein and define its function
Peptide bonds are molecular links connecting amino acids to form proteins
Proteins have many biological functions
Proteins have many functions: allow movement (skeletal muscle), provide structures
(cartilage and bone), help us fight disease (immunoglobulins), and digestion of the food
(enzymes).
An amino acid consists of a central carbon atom bonded to four different groups. The
four groups are nitrogen (containing an amino group), a carboxylic acid group, a hydrogen
atom, and functional side group designated R .Twenty different amino acids are commonly
available for making a protein. The amino acid sequence determines the structure and
function by the connection of peptide protein bonds. There are four ways that proteins are
structured: primary, secondary, tertiary, and quaternary.
- Primary structure: amino acid sequence forming a particular polypeptide chain and is the
primary sequence of a protein.
- Secondary structure: each amino acid of a polypeptide that interacts with its neighbor
causes the protein to fold into coils which are termed alpha-helices and beta pleated sheets.
Folding patterns are known as secondary structure of the protein.
- Tertiary bonds: allow the protein to assume a three dimensional shape and is referred to
as the tertiary structure.
- Quaternary: resulting from interactions between two or more polypeptide chains in some
proteins making a globular or fiber-like shape.
13. Carbohydrates
• The monosaccharides are mainly in cyclic form (as a ring structure) and form
polysaccharides.
• Sugars (sacccharides) are a source of energy since its hydrogen is used to make ATP
• Polysaccharides have many roles in biology
• Plants and animals store carbohydrates as starch and glycogen respectively
Carbohydrates (saccharides) are the most abundant of the four major classes of
biomolecules (proteins, carbohydrates, lipids and nucleic acids). They have many functions
in living things, such as the storage of energy (starch, glycogen) and they are also part of
the structural component (cellulose in plants and chitin in animals). Carbohydrates are the
most common source of biochemical energy. Note: Due to the number of hydrogen ions it
has, carbohydrates have the least amount of energy of the biomolecules that humans use
for energy. Lipids have the most.
Sugars are a form of energy biochemistry. Monosaccharides are the most basic unit
of carbohydrates. They are the simplest form of sugar and are generally colorless, solid,
crystalline, and water soluble. Monosaccharides are cyclical like rings. Other carbohydrates
are polysaccharides: polymeric carbohydrate structures that are formed of repeating units
(mono or disaccharide) linked by glycosidic bonds. Polysaccharides are linked to many
roles in biology due to their various configurations such as glycogen, cellulose, and chitin.
Plants and animals store carbohydrates as starch and glycogen. Other forms of
carbohydrates are starches, also known as complex carbohydrates which consist of
glucose polymers.
14. The Lipids
•
Lipids are classified into three categories: phospholipids, steroids, oils etc.
•
•
•
Categories are based on the number of carbon-carbon double bonds
Fatty acids(saturated and non saturated) are a source of biochemical energy
The cell membrane is mainly composed of phospholipids and cholesterol from a
lipid point of view. It also has proteins and carbohydrates.
Most of us enjoy Mexican food "taco shops", but we almost never agree on the amount
of fat we eat to enjoy this delicious meal. Lipids are fats. The meals we consume in our daily
lives contain lipids. Most meats, poultry, seafood, and fish contain this type of fat. Most
dairy products also contain fats. Some examples are: milk, cheese, and other products.
Cooking oils and even salads contain fat. Eggs also contain fat, but only the yolk. Also junk
food like chips, sodas and pastries are high in fat.
Lipids can be classified into three main classes:
- Phospholipids: oil are structurally similar and contain phosphorus, nitrogen, carbon,
hydrogen, and oxygen. These are the major component of the cell membrane and as a result
the membrane is hydrophobic.
- Steroids: Fused ring structures in which an example would be hormones. In addition,
cholesterol is an essential molecule in the steroid as found in all of them.
- Oils, fats and waxes: are similar in structure containing only carbon, hydrogen, and
oxygen. Vegetable oils are commonly used for cooking.
There are two kinds of fatty acids:
- Saturated fatty acids: when all the carbon atoms in a molecule are bonded to maximum
number of hydrogen atom and there are no double bonds.
- Unsaturated fatty acids: contain double bonds between some of carbon molecules and as a
consequence have less hydrogen ions. They are less caloric because they have fewer
hydrogen atoms. Butter is an example of saturated fats whereas olive oil is an example
unsaturated fats.