EALS FINALS
Biology
A branch of science that deals with the study of life.
Helps to know about the diversity in the living world, the ways by which it can be conserved, more about ourselves.
The study of various aspects of living organisms and their interactions with the non-living components.
What is life?
The condition that distinguishes animals, plants, and microorganisms from inorganic matter.
Three Primary Branches of Biology:
Botany (study of plants)
Zoology (study of animals)
Microbiology (study of microorganisms)
Modern Branches of Biology:
Bioinformatics
Molecular Biology
Pharmacogenomics
Early Beliefs about the Origin of Life
Spontaneous Generation
Is the idea that life could appear from non-living material
Also known as abiogenesis
First person to propose the idea of spontaneous generation in the 4th century and held its position as the belief on the origin of life until the 17th century. (Aristotle 384-322 BC)
They thought:
Frogs developed from falling drops of rain
Mice could grow from wheat stored in the dark
An maggots from decaying meat
Biogenesis
Is the belief that life originates from preexisting life.
Redi’s Experiment
In 1668 - Francisco Redi, an Italian physician, did an experiment to see if the maggots on decaying meat came from fly eggs.
He concluded that life arose from living matter such as maggots from eggs, not from spontaneous generation in the meat.
Needham’s Experiment
In 1745-1748 - John Needham, a scottish clergyman and naturalist showed that microorganisms flourished in various soups that had been exposed to the air.
He then concluded that life in the broth caused spontaneous generation to occur.
In actuality, he did not heat it long enough to kill all the microbes from the broth.
Spallanzani’s Experiment
In 1765-1767 - Lazzaro Spallanzani, an Italian abbot and biologist tried several variations on Needham’s soup experiments.
He concluded that life occurred from something that entered the unsealed flask that it was the one responsible for life to grow.
Pasteur’s Experiment
In 1860- Louis Pasteur he designed flasks with long, specially curved, swanlike broth to be exposed to fresh air from the outside, but any microorganisms from the air would be trapped in a pool of water in the neck
Divine Creation
It is believed that life forms and everything in the universe were created through a supernatural power rather than naturalistic means.
Spontaneous Origin
He hypothesized that many gasses present in Earth’s early atmosphere, under very high temperatures, might have formed simple organic compounds such as amino acids.
These would have collected in lakes and seas as earth cooled, and over time, fueled by energy from lightning and UV radiation, could have formed larger molecules such as proteins.
Biogenetic Theory
The invention of the microscope and advances in science made it clear that living things created other living things.
Types of Cell
Prokaryotes/Prokaryotic Cells
Simple cells (no true nucleus)
Unicellular organisms
Eukaryotes/Eukaryotic Cells
Complex cells (with true nucleus)
Multicellular organisms
Plasma/Cell membrane
Controls what materials are allowed to enter and exit the cell
Made up of phospholipid bilayer
Cell wall
Serves as boundary between the cell and its external environment
Allows plant cell to change shape if needed
Can be made up of cellulose or chitin
Cytoplasm
The liquid portion of the inside part of the cell where all organelles are suspended
Nucleus
Serves as the control center of the cell/brain of the cell
Contains the DNA of an organism
Composed of the nucleus, nucleoplasm, nuclear pores and the nuclear envelope
Nucleolus
Found inside the nucleus
Site of ribosome production
Ribosomes
Made up of RNA and proteins
Site of protein production
Mitochondria or mitochondrion
Acts as the ‘powerhouse’ of the cell
Produces the energy (ATP) needed by the cell
Adenosine triphosphate (ATP)
Chloroplast
Site of photosynthesis
Contains the chlorophyll (green pigment in plants)
Endoplasmic reticulum (ER)
Forms compartments and vesicles
Participates in protein and lipid synthesis
Types: smooth ER, rough ER
> smooth ER
- without ribosomes
- site of lipid synthesis
> rough ER
- with ribosomes
- helps in the synthesis of proteins
Golgi apparatus/golgi complex
Packages proteins for export from the cell
Forms secretory vesicles
Vesicles
Carry materials in and out of the cell like food particles and waste particles
Vacuoles
Stores food, oil, carbohydrates, water
Helps the cell maintain its rigidity
Peroxisomes
Small vesicles around the cell that carry oxidative enzymes that require oxygen
Absorb nutrients that have been acquired by the cell
Play important roles in metabolism, reactive oxygen species detoxification, and signaling of the cell
Cytoskeleton
Serves as the bones of the cell
Provides support and allows movement of the cell
Centrioles
Helps animal cells to reproduce during cell division
Organize microtubules to form cilia and flagella
Cilia and Flagella
Found outside the cell
Locomotory organelles of the cell
Plasmodesmata
Numerous channels that pass between cell walls of adjacent plant cells, connect their cytoplasm, and enable materials to be transported from cell to cell, and thus throughout the plant.
Cell Junctions
Allow neighboring animal cells to communicate with each other.
Types: tight junction, desmosomes, gap junction, adherens junction
Levels of organization
Adaptation
It is the ability to adjust to changes in the environment
Evolution
It refers to the changes in characteristics of a group of organisms (populations) over time
Evolutionary adaptation- gradual or rapid change
Charles Darwin
He published on the origin of the species by means of natural selection in 1859
Fossils and other evidence document the evolution of life on earth over billions of years
Chemical level
A unit of matter that comprises a chemical element
It is the smallest particle of an element
Cellular level
Cell is the basic organizational unit of life
It is the simplest organization of matter that exhibits the properties of life
The structure and function of a typical cell usually apply to all animals & plants
Tissue level
It is the level in which different cell types are joined together to form a structure called, tissue
Organ level
It is where different kinds of tissues are joined to form a structure of a body called organ
Organ system level
Different organs complete an organ system with a specialized function
Organism level
An organism is made up of different organ systems with individualized but coordinated functions
These communities exist in an environment affected by both living and nonliving components known as ecosystem
Biosphere make up all ecosystems on earth whether they support life on land, water, or lower atmosphere
The life’s hierarchy of organization from atom (simple) to biosphere (complex)
Organism interacts with other organisms of the same kind known as population
Community is an array of populations sharing their habitat
These communities exist in an environment affected by both living and nonliving components known ecosystem
Bisophere make up all ecosystems on earth whether they support life on land, water, or lower atmosphere
Three domains of life
The living world has three major divisions or domains: bacteria, archeria, and eukarya
Of the three domains, bacteria and archaea are prokaryotes, while eukarya are eukaryotes
Domain bacteria (the true bacteria)
Also known as eubacteria, or simply bacteria has very sturdy cell walls & simpler genome structure
The most present day bacteria
i.e cyanobacteria (blue-green algae) is one type of photosynthetic eubacteria that has been vital in the history of life on earth
Domain archaea (ancient bacteria)
Also known as archaebacteria, derived from the greek word for ‘ancient ones’
It comprise the first stages of life on earth
i.e methanogens (methane producing bacteria), grow only in an oxygen free environment because oxygen poisons them.
It lacks of peptidoglycan (a protein cross-linked carbohydrate material)
Domain eukarya (eukaryota)
It came from the greek words for ‘true’ and ‘nucleus’, because they possess an internal structure called a nucleus that encloses most of their genetic material
All organisms other than the bacteria are eukaryotes
Cell is the basic unit of life
1665 - English Scientist who discovered cells while looking at a thin slice of cork.
He described the cells similar to cellula or small rooms
He thought that cells only existed in plants and fungi.
Robert hooke
1673 - used a handmade microscope to observe pond scum & discovered single-celled organisms.
He called them “animalcules”
Anton van leeuwenhoek was the first man to witness a live cell under a microscope
Seven characteristics of life
Movement
Most animals can move from one place to another by walking, flying, swimming, gliding or jumping. Such movement is called locomotion or motility
Some animals such as sponges, cannot locomote but can move parts of their bodies. Plants also show slow movements of body parts like in flower blooming, tendrils clinging for support, shoots bending toward light, and vines creeping as they grow
Irritability/sensitivity
external factors or stimuli affect living things
Tropism or response - reaction of an organism to respond appropriately against stimuli
Sensitivity or irritability - ability of an organism to respond appropriately against a stimulus
Growth
It is an increase in size and volume by converting food to become a part of body cells
Living things exhibit growth from within the cells in a process called intussusception
Nonliving things sometimes also grow but only by accretion, which is growth by external addition of substances
Development
All living things undergo defined stages in their life cycle called development, which starts with birth and ends in death. No organism is immortal, but all living things have ways of making sure that their species survive. This is achieved by the ability to reproduce their own kind.
Reproduction
It is a process by which genetic information is passed on from one generation to another organisms produce offspring that resemble their parents
Heredity
Animals, plants and microorganisms carry the common genetic material DNA, which is the molecule of life that carries the instructions for assembling the proteins responsible for forming a variety of structures.
Organisms reproduce in two ways:
Sexual reproduction - two individuals contributing their sex cells to produce a unique individual of their kind
Asexual reproduction - occurs when an organism makes copies of their usually in lower life form.
Deoxyribonucleic acid (DNA) - is used as a physical carrier of the transferred genetic information that is passed from parent to offspring by a process called sexual reproduction
Cell theory of development
All organisms are composed of one or more cells. (Schleiden & Schwann) (1838-39
The cell is the basic unit of life in all living things. (Schleiden & Schwann) (1838-39)
All cells arise from pre-existing cells. (Omnis cellula e cellula) (Virchow) (1858)
Prokaryotic cells
It is characterized by the absence of nucleus or other membrane-bound organelles. Thus, the cell’s DNA is suspended in the cytoplasm. Though prokaryotic cells are simpler, they adapt very quickly to changing environments and have been present on the earth for the past 3 billion years. A bacterium is an example of a prokaryote
Eukaryotic cells
Another type of cell is the eukaryotic cell, which has nucleus and other membrane bound organelles. The nucleus encloses the DNA. due to the presence of these membrane bound organelles, chemical reaction takes place in a compartmentalized manner
Eukaryotic cells may come in different sizes, shapes and appearance depending on their type and the functions that they play. Animal and plant cells, being both eukaryotic, have similar organelles present. However, there are some organelles that are only present in animal cells but absent in plant cells or vice versa
A cell has three major parts: the cell membrane, the cytoplasm, and the nucleus.
Cell membrane - this structure is made up of lipid bilayer with large protein molecules that control the flow of substances into and out of the cell
Cytoplasm - this constitutes about 90% of the cell and houses the organelles. It is a jelly-like clear substance that is composed primarily of water and also contains proteins, amino acids, glucose, and salts. It is also a site for many chemical reactions in the cell
Nucleus - this structure is enveloped by a nuclear membrane and contains the DNA and nucleolus. This nuclear membrane has pores that allow the molecules to pass between the nucleus and the cytoplasm. The chromosome inside the nucleus, contains the genes carrying instructions for protein synthesis
Mitochondrion - this organelle is shaped like a bean and made up of two membranes. The inner membrane is folded and these infolding are called cristae, which partitions the matrix and the intermembrane space. The mitochondria supply the energy for the cell
endoplasmic reticulum - this organelle is made up of interconnected thin folded membranes that are found throughout the cytoplasm of the cell. There are two types of ER
Rough ER - with ribosomes
Smooth ER - without ribosomes
3. Golgi apparatus - this organelle consists of layered stacks of flattened membranes that process, sort, and deliver proteins. It also packages protein. Some of the proteins are sorted within itself, distributed to the other organelles, and secreted outside the cell
4. Ribosomes - this small round structure found in the cell consists of large small subunits made up of RNA and protein. These organelles can be found attached to the ER or floating in the cytoplasm. This is the site of protein synthesis
5. Vacuole - this organelle is a fluid-filled sac that stores substances needed by the cell, which may include water, food, ions, and enzymes. Small numerous vacuoles are found in an animal cell; however, a large central vacuole is found in the plant cells. The vacuole in plant cell is filled with watery fluid which strengthens the cell and helps support the entire plant
6. Peroxisome - this structure contains enzymes involved in digesting fatty acids. They also absorb nutrients which the cell has acquired . They also play part in the way organisms digest alcohol (ethanol). In affect, you would expect liver cells to have more peroxisomes than most other cells in the human body
7. Vesicle - this small membrane bound sac functions to transport materials from one place to another inside the cell. They also function in metabolism and enzyme storage as well
Centriole - this is a cylinder-shaped organelle that is made up of microtubules arranged in a circle. There are nine microtubules. They help the cell to divide during mitosis and meiosis
Lysosome - this membrane bound organelle is basically a specialized vesicle that contains a variety of enzymes. It is used to digest food or break down the cell when the cell dies. It also defends the cell from bacteria and viruses
Cell wall - this structure is a rigid layer found not only in plant cells but also in algae, fungi, and most bacteria. Cell walls also allow plants to grow to great heights. A tree uses strong cell walls to maintain its shape so it can grow very high
Chloroplast - this organelle is made up of outer and inner membranes. They found closed compartments of stacked membranes called grana (singular for granum) each granum contains thylakoids which contains chlorophyll - a light absorbing molecule that plays an important role in photosynthesis
Photosynthesis
Is the process of trapping light energy and converting that energy to chemical forms that can be utilized for fuel by biological systems. In photosynthesis, light energy causes water and carbon dioxide to synthesize carbohydrates, which store chemical energy, releases oxygen as waste products
The leaf
Plant leaves absorb sunlight to manufacture plant sugars through a process called photosynthesis. In order to get enough light, leaf surfaces have a big area.
The blade is a thin expanded structure on either side of the midrib and is the largest part of leaf
The leaf is attached to the stem by a petiole. The base of the petiole is attached to the node of the stem. The node where a petiole meets a stem is called a leaf axil. You can also see a pair of appendages at the base of the petiole called stipules. Stipules protect the young leaf and may be modified into spines and tendrils
> the word chloroplast is derived from the greek word “chloros” meaning green and “plastes” meaning the one who forms. Chloroplasts are small organelles located inside the plant cells. The process of photosynthesis in plants and algae occurs in chloroplasts. Chloroplast can be compared to factories since these organelles can provide plants with food and energy
Internal structure of chloroplasts
Outer membrane - it is a semi-porous membrane and is permeable to small molecules and ions, which diffuses easily. The outer membrane is not permeable to larger proteins
Inner membrane - the inner membrane of the chloroplast forms a border to the stroma. It regulates passage of materials in and out of the chloroplast
Stroma - it is an alkaline, aqueous fluid which is protein-rich and present within the inner membrane of the chloroplast. The space outside the thylakoid space is called stroma
Thylakoid system - it is suspended in the stroma. The thylakoid system is a collection of membranous sacks called thylakoids. The chlorophyll is found in the thylakoids and is the sight for the process of light reaction photosynthesis to happen
Granal thylakoids - grana thylakoids are arranged in the grana. They are pancake shaped circular discs, which are about 300-600 nanometers in diameters
Stroma thylakoids - stroma thylakoids are in contact with stroma. They are form in helicoids sheets
The process of photosynthesis
The light - dependent reactions
Units of light called photons strike a molecule of chlorophyll in PS II. The light is absorbed by two electrons (2e) in the chlorophyll a which gives them enough energy to leave the molecule. At the same time, water (H2O) splits producing the following
Two electrons, which replace the electrons loss of chlorophyll a in PS II during light absorption
Two hydrogen ions (2H+), which are positively charged, and are released inside the interior space of the thylakoid membrane
One oxygen (O) atom that combines with another oxygen atom, producing one oxygen molecule (O2), which is released into the atmosphere as a waste product
2. Light - independent reactions
The second stage of photosynthesis happens in the stroma surrounding thylakoids in the chloroplast. The reactions in this stage occur without the direct use of energy from light, hence they are often called dark reactions. In 1961, a scientist Melvin Calvin won a nobel prize by discovering this reaction. In this cycle, chemical energy NADPH and ATP from light reactions are used to create glucose.
Carbon fixation - carbon fixation occurs when carbon dioxide (C02) from the atmosphere combines with a simple five-carbon (5-C) sugar compound, ribulose bisphosphate (RuBP), forming an unstable sir-carbon (6-C) molecule. The 6-C molecule is immediately broken down into two three-carbon (3-C) sugar phosphate known as 3-phosphoglycerate (3-PGA)
Reduction reactions - the 3-PGA molecules gain energy from the ATP and NADPH from the light reactions, and rearrange themselves to form glycerate 3-phosphate (G3P). This molecule also contains three carbon atoms but is more stable than 3-PGA. A single G3P molecule goes on to form into glyceraldehyde 3-phosphate, the three-carbon (3-C) carbohydrate precursor of glucose and other sugars. The rest of the G3P proceed to the regeneration step.
Regeneration of RuBP - the remaining G3P molecules then use more ATP to convert back into RuBP, completing the cycle. Converting the G3P molecules to the RUBP allows the cycle to repeat.
Also known as the anaerobic pathway of obtaining energy which consists of three stages: glycolysis, krebs cycle, end electron transport chain
Refers by which cells release the stored energy in glucose to make ATP
Cellular respiration
The primary goal of this life process is to convert the stored energy into usable form (ATP) for the cells to carry out their functions. Cellular respiration involves many chemical reactions. The reactions can be summed up in the following equation:
C6H12O6+6CO2+6HZ0+ energy (in ATP)
Kreb’s cycle or citric acid cycle
Also known as the citric acid cycle since the first molecule formed is citric acid
It takes place in the matrix of the mitochondrion
Glycolysis
Is the first stage of aerobic pathway
A series of enzyme-controlled reactions that occur inside the cytoplasm
The process that breaks down glucose molecules of 6-C glucose into 3-C pyruvate or pyruvic acids. It also releases four molecules of ATP
It does not require oxygen
It begins by breaking down glucose from food and only produces a small amount of energy in the form of ATP molecules.
glucose +2ATP+2NAD+>2aTP+2NADH+2 pyruvate
A pyruvic acid from glycolysis is broken down into a two-carbon molecule and a molecule of carbon dioxide which is expelled. NADH is formed as high energy electrons are transferred from the two-carbon molecule to NAD+
The coenzyme a binds with the two-carbon molecule and enters the krebs cycle
The two-carbon molecule is added to the four-carbon compound, thereby forming a six-carbon molecule called citric acid
A five-carbon molecule is formed from the breakdown of six-carbon molecule-citric acid. Along, with this carbon dioxide and NADH are produced
Carbon dioxide is removed again from a five-carbon molecule, making it a four carbon molecule. Along with this, NADH and ATP are formed. NADH leaves the Krebs cycle, while carbon dioxide is given off.
The four-carbon molecules are rearranged and the high energy electrons are released. NADH and FADH2 ( electrons carried) are produced. The four carbon compound will remain in the krebs cycle
electron transport chain
It is the third part of the process of obtaining energy
In this process the energy carrying molecules from glycolysis and krebs cycle are used and more number of ATP molecules are produced
It takes place in and across the inner membrane of the mitochondrion