Biology Reviewer PDF

Biology – scientific study of life and living organisms ▪ Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phot...

Biology – scientific study of life and living organisms ▪ Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Molecular Biology - fascinating branch of biology that focuses on ▪ Movement toward a stimulus is considered a positive understanding the molecular basis of biological activity within and between response, while movement away from a stimulus is cells. considered a negative response. III. Reproduction Themes and Concepts of Biology ▪ Single-celled organisms reproduce by first duplicating their DNA. All living organisms share several key characteristics or functions: order, ▪ Genes containing DNA are passed along to an organism’s sensitivity or response to the environment, reproduction, growth and offspring. These genes ensure that the offspring will belong to development, regulation, homeostasis, and energy processing. When the same species and will have similar characteristics, such viewed together, these eight characteristics serve to define life. as size and shape. Properties of Life: IV. Growth and Development ▪ All organisms grow and develop following specific 1. Order instructions coded for by their genes. These genes provide 2. Sensitivity or response to stimuli instructions that will direct cellular growth and development, 3. Reproduction ensuring that a species’ young will grow up to exhibit many of 4. Growth and Development the same characteristics as its parents. 5. Regulation V. Regulation 6. Homeostasis ▪ Regulatory mechanism (nutrient transport and blood flow) 7. Energy Processing VI. Homeostasis ▪ The ability of an organisms to maintain internal balance. ▪ Organism needs to regulate body temperature through a I. Order process known as thermoregulation. ▪ Organisms are highly organized, coordinated structures that consist of two or more cells. Adaptive Mechanism: (these can also alter the genes) II. Sensitivity or response to stimuli i. Structural – habitual ▪ Organisms can respond to stimuli ii. Behavioral – capable of mimicking  iii. Physiological 4. Cells: The smallest unit of life, making up all living organisms. Cells are classified as prokaryotic or eukaryotic. VII. Energy Processing 5. Tissues: Groups of similar cells that perform a specific function. ▪ An organisms use a source of an energy for their metabolic 6. Organs: Structures composed of different tissues working activities. together to perform specific tasks. VIII. Evolution 7. Organ System: Groups of organs that work together to perform ▪ The process of gradual change during which new species arise from complex functions. older species. 8. Population: A group of individuals of the same species living in a ▪ As a population interacts with the environment, individual traits that specific area. contribute to reproduction and survival in the environment will leave 9. Community: Different populations of species living together in a more offspring. particular area. ▪ This process, change overtime is called evolution. 10. Ecosystem: A community of living organisms and their physical environment interacting as a system. 11. Biosphere: The global sum of all ecosystems, encompassing all Levels of Organization of Living Things life on Earth. Describe the biological levels of organization form the smallest to highest level. Human Taxonomy: 1. Atom: The basic unit of a chemical element. 2. Molecule: A group of atoms bonded together. 1. Domain: Eukarya Many molecules that are biologically important are 2. Kingdom: Animalia macromolecules, large molecules that are typically formed by 3. Phylum: Chordata polymerization (a polymer is a large molecule that is made by 4. Class: Mammalia combining smaller units called monomers, which are simpler 5. Order: Primata/Primates than macromolecules). An example of a macromolecule is 6. Family: Hominidae deoxyribonucleic acid (DNA), which contains the instructions 7. Genus: Homo for the structure and functioning of all living organisms. 8. Species: Sapiens 3. Organelle: Which is composed of aggregates of macromolecules. The Diversity of Life Examples: The evolution of various life forms on Earth can be summarized in a phylogenetic tree using phylogeny. CHEMICAL FOUNDATION OF LIFE Phylogeny: the evolutionary history of an organism A phylogenetic tree is a diagram showing the evolutionary The chemical foundation of life refers to the essential elements and relationships among biological species based on similarities and molecules that make up living organisms and enable biological processes. differences in genetic or physical traits or both. Essential Elements A phylogenetic tree is composed of nodes and branches. Phylogenetic tree was constructed by microbiologist Carl Woese. Carbon ©: The backbone of organic molecules, forming the The tree shows the separation of living organisms into three structure of carbohydrates, proteins, lipids, and nucleic acids. domains: Bacteria, Archaea, and Eukarya. Hydrogen (H): Found in water and organic molecules, playing a Many organisms belonging to the Archaea domain lives under crucial role in energy transfer and chemical reactions. extreme conditions and are called extremophiles. Oxygen (O): Essential for cellular respiration and a component of 3 Domains: Bacteria, Archaea, Eukarya water and many organic molecules. 2 Domains: Prokarya and Eukarya Nitrogen (N): A key element in amino acids, proteins, and nucleic A. Bacteria acids. Examples: Phosphorus (P): Important for the formation of nucleic acids and 1. Aquifex ATP, the energy currency of the cell. 2. Thermotoga 3. Bacteroids Cythophaga Sulfur (S): Found in some amino acids and vitamins, contributing to 4. Planctomyces protein structure and function. 5. Green Flamentous Bacteria (algae family) Chemical Bonds and Interactions B. Archaea Examples: Covalent Bonds: sharing electrons between atoms 1. Halophiles Ionic Bonds: transfer of electrons 2. Methanobacterium C. Eukarya  Hydrogen Bonds: Weak bonds important for the structure of water, Key Terms proteins, and nucleic acids. atom: The smallest possible amount of matter which still retains its Van der Waals Forces: Weak interactions that contribute to the identity as a chemical element, consisting of a nucleus surrounded three-dimensional structure of molecules. by electrons. Water’s Role proton: Positively charged subatomic particle forming part of the nucleus of an atom and determining the atomic number of an Solvent: Water is a universal solvent, facilitating chemical reactions element. It weighs 1 amu. and transport of substances. neutron: A subatomic particle forming part of the nucleus of an Cohesion and Adhesion: Water molecules stick together and to other atom. It has no charge. It is equal in mass to a proton or it weighs 1 surfaces, aiding in processes like nutrient transport. amu. ATOMIC NUMBER AND MASS NUMBER OVERVIEW OF ATOMIC STRUCTURES Key Points Key Points Neutral atoms of each element contain an equal number of protons An atom is composed of two regions: the nucleus, which is in the and electrons. center of the atom and contains protons and neutrons, and the outer The number of protons determines an element’s atomic number and region of the atom, which holds its electrons in orbit around the is used to distinguish one element from another. nucleus. The number of neutrons is variable, resulting in isotopes, which are Protons and neutrons have approximately the same mass, about different forms of the same atom that vary only in the number of 1.67 × 10-24 grams, which scientists define as one atomic mass unit neutrons they possess. (amu) or one Dalton. Together, the number of protons and the number of neutrons Each electron has a negative charge (-1) equal to the positive determine an element’s mass number. charge of a proton (+1). Since an element’s isotopes have slightly different mass numbers, Neutrons are uncharged particles found within the nucleus. the atomic mass is calculated by obtaining the mean of the mass numbers for its isotopes. Key Terms half-life: The time it takes for half of the original concentration of an isotope to decay back to its more stable form. mass number: The sum of the number of protons and the number of neutrons in an atom. radioactive isotopes: an atom with an unstable nucleus, characterized by excess energy available that undergoes radioactive atomic number: The number of protons in an atom. decay and creates most commonly gamma rays, alpha or beta atomic mass: The average mass of an atom, taking into account all particles. its naturally occurring isotopes. radiocarbon dating: Determining the age of an object by comparing the ratio of the 14C concentration found in it to the amount of 14C in ISOTOPES the atmosphere. Key Points Isotopes are atoms of the same element that contain an identical THE PERIODIC TABLE – Dmitri Mendeleev (Russian) number of protons, but a different number of neutrons. Key Points Despite having different numbers of neutrons, isotopes of the same All matter is made from atoms of one or more elements. Living element have very similar physical properties. creatures consist mainly of carbon, hydrogen, oxygen, and nitrogen Some isotopes are unstable and will undergo radioactive decay to (CHON). become other elements. Combining elements creates compounds that may have emergent The predictable half-life of different decaying isotopes allows properties. scientists to date material based on its isotopic composition, such as The periodic table is a listing of the elements according to increasing with Carbon-14 dating. atomic number that is further organized into columns based on Key Terms similar physical and chemical properties and electron configuration. isotope: Any of two or more forms of an element where the atoms As one moves down a column or across a row, there are some have the same number of protons, but a different number of general trends for the properties of the elements. neutrons within their nuclei. The periodic table continues to expand today as heavier and heavier elements are created in laboratories around the world. Key Terms The properties of an element are determined by its outermost electrons, or those in the highest energy orbital. element: Pure chemical substances consisting of only one type of atom with a defined set of chemical and physical properties. Atoms that do not have full outer shells will tend to gain or lose electrons, resulting in a full outer shell and, therefore, stability. emergent properties: Properties found in compound structures that are different from those of the individual components and would not Key Terms be predicted based on the properties of the individual components. octet rule: A rule stating that atoms lose, gain, or share electrons in periodic table: A tabular chart of the chemical elements according to order to have a full valence shell of 8 electrons. (Hydrogen is their atomic numbers so that elements with similar properties are in excluded because it can hold a maximum of 2 electrons in its the same column. valence shell) electron shell: The collective states of all electrons in an atom having the same principal quantum number (visualized as an orbit in ELECTRON SHELLS AND NEILS BOHR MODEL which the electrons move). Key Points In the Bohr model of the atom, the nucleus contains the majority of Biological Macromolecules the mass of the atom in its protons and neutrons. Biological macromolecules are large, complex molecules that are essential Orbiting the positively-charged core are the negatively charged for life. They are built from smaller organic molecules and play crucial roles electrons, which contribute little in terms of mass, but are electrically in the structure, function, and regulation of living organisms. equivalent to the protons in the nucleus. The four major classes of biological macromolecules: In most cases, electrons fill the lower- energy orbitals first, followed by the next higher energy orbital until it is full, and so on until all 1. Carbohydrates: electrons have been placed. o Carbohydrates can be represented by the stoichiometric Atoms tend to be most stable with a full outer shell (one which, after formula (CH2O)n, where n is the number of carbons in the the first, contains 8 electrons), leading to what is commonly called molecule. the “octet rule”. o Function: Provide energy and structural support.  o Examples: Glucose, starch, cellulose. curren cy of o Structure: Made up of monosaccharides (simple sugars) that the can form polysaccharides (complex carbohydrates) through cell. glycosidic bonds. 2. Galactose o Carbohydrates are classified into three subtypes: 3. Fructose monosaccharides, disaccharides, and polysaccharides. 2. Disaccharid composed 1. Sucrose Types of Definition Examples es of two (table sugar) Carbohydrates monosacch 2. Lactose 1. Monosacch Monosacch 1. Glucose aride 3. Maltose arides arides are (C6H12O6) molecules the simplest ▪ Primar linked form of y together by carbohydrat source a glycosidic es, of bond. consisting of energy 3. Polysacchar Polysacchar 1. Starch a single for ides ides are 2. Glycogen sugar cells. complex 3. Cellulose molecule. ▪ produc carbohydrat 4. Chitin the n of es es made up carbons adeno of long usually sine chains of ranges from triphos monosacch 3-7 phate aride units (ATP), linked the together. energy  2. Lipids: ▪ Trans Fat – H are present in the different planes. o Function: Store energy, form cell membranes, and act as ✓ Omega-3 fatty acid and omega-6 fatty acid are essential for human signaling molecules. biological processes, but they must be ingested in the diet because they cannot be synthesized. o Types of Lipids: Triglycerides, Waxes, Phospholipids, Steroids Waxes - type of long-chain nonpolar lipid. They are typically esters formed o Examples: Fats, oils, phospholipids, steroids. from fatty acids and long-chain alcohols. o Structure: Composed of 3 fatty acids and glycerol. Since fats Composition: Natural waxes are composed of fatty acids and long- consist of three fatty acids and a glycerol they also called chain alcohols. For example, beeswax contains the ester myricyl triglycerides. They are hydrophobic and do not dissolve in palmitate. water. Sources: Waxes are produced by both plants and animals. Plants Glycerol Fatty Acids use waxes as protective coatings on leaves and stems to prevent ▪ Alcohol with 3 ▪ Have a long chained water loss. Animals, such as bees, produce waxes for constructing carbons, 5 of hydrocarbons with honeycombs. hydrogens and 3 a carboxyl group Properties: Waxes are hydrophobic, meaning they repel water. This hydroxyl group attached. makes them useful for waterproofing and protection. (3C:5H:3OH) ▪ Have 4-36 carbons however most of Synthetic waxes are derived from petroleum or polyethylene and consist of long-chain hydrocarbons that lack functional groups. them have 12-18 carbons. Uses: Beyond their natural roles, waxes are used in various industries, including cosmetics, food (like in chewing gum), and as lubricants. Saturated Fats & Unsaturated Fats Phospholipids - These lipids are a major component of cell membranes. ▪ Saturated – single bond ▪ Unsaturated – double bond ▪ They consist of two fatty acids, a glycerol unit, a phosphate group, Examples: Olive oil, Canola oil (plant-based) and an alcohol. ▪ Cis Fat – H are present in the same planes  ▪ Their amphipathic nature (having both hydrophobic and hydrophilic Functions: Steroids play various roles in the body, from structural parts) allows them to form bilayers in aqueous environments, which components of cell membranes to signaling molecules that regulate is essential for cell membrane structure. physiological processes. ▪ A single phospholipid molecule has a phosphate group on one end, called the “head,” and two side-by-side chains of fatty acids that make up the lipid “tails.” The head is hydrophilic while the tails is 3. Proteins are large, complex molecules that play many critical roles hydrophobic. in the body. They are made up of long chains of amino acids, which are the building blocks of proteins. Steroids - Unique class of lipids characterized by their structure of four Structure: Proteins are composed of one or more long fused carbon rings. Despite their distinct structure, they share the common chains of amino acids. There are 20 different amino acids lipid trait of being hydrophobic and insoluble in water. that can combine in various sequences to form a vast array Structure: Steroids have a core structure of three six-membered rings and of proteins. one five-membered ring fused together. Amino acids linked by peptide bonds, forming polypeptide chains that fold into specific three-dimensional Cholesterol: This is the most well-known steroid. It is essential for shapes. maintaining cell membrane fluidity and serves as a precursor for the Functions: Proteins perform a wide range of functions within synthesis of other steroids, including vitamin D, bile salts, and steroid organisms, including: hormones. o Enzymatic: Catalyzing biochemical reactions Steroid Hormones: These include sex hormones like testosterone, (e.g., digestive enzymes). estrogen, and progesterone, which are crucial for reproductive o Catabolic enzymes: enzymes that break down functions. Other important steroid hormones include cortisol, which their substrate regulates metabolism and immune response, and aldosterone, which o Anabolic enzymes: enzymes that build more helps control blood pressure. complex molecules from their substrates ▪ hormone: any substance produced by one tissue and Examples of enzymes: conveyed by the bloodstream to another to affect a) Amylase – mouth and small intestine physiological activity. Examples: insulin, estrogen and so on. b) Pepsin – stomach c) Lipase d) Trypsin  o Structural: Providing support and shape to cells and tissues Amino Acids – are monomers that make up proteins. (e.g., collagen in connective tissues). It consists of: o Transport: Carrying molecules across cell membranes (e.g., 1. Carbon hemoglobin transporting oxygen in the blood). 2. Amino Group (-NH2) o Signaling: Acting as hormones and receptors to transmit 3. Carboxyl Group (-COOH) signals within and between cells (e.g., insulin). 4. Hydrogen o Defense: Forming antibodies to protect against pathogens Types of Amino Acids (e.g., immunoglobulins). 1. Nonpolar (Hydrophobic) Amino Acids: o Actin and Tubulin protein form cell structures o Valine o Keratin forms the structural support for dead cells to o Methionine fingernails and hair. o Alanine o Immunoglobins fight pathogens o Leucine o Actin and Myosin allows the muscle to contracts. o Isoleucine o Albumin nourishes the embryo or seedling. o Phenylalanine Synthesis: Protein synthesis occurs in the ribosomes of cells, where amino acids are linked together in a specific sequence dictated by o Tryptophan the genetic code. o Proline Dietary Importance: Proteins are essential nutrients that must be 2. Polar (Hydrophilic) Amino Acids: obtained from the diet. They are found in a variety of foods, including o Serine o Threonine meat, dairy products, nuts, and legumes. o Cysteine o Tyrosine Examples: Enzymes, antibodies, hemoglobin. o Asparagine o Glutamine Characteristics of Amino Acids shape determines the protein’s function, from digesting protein in the stomach to carrying oxygen in the blood. 1. Peptide Bond - Each amino acid is attached to another amino acid Pepsin, the enzyme that breaks down protein in the stomach, only by a covalent bond. operates at a very low pH. 2. Polypeptide Chain - a polypeptide is technically any polymer of amino acids. Key Points Protein Structure Proteins change their shape when exposed to different pH or temperatures. 4 Levels of Protein Structure: The body strictly regulates pH and temperature to prevent proteins 1. Primary Structure – sequence of a chain of amino acids such as enzymes from denaturing. 2. Secondary Structure – hydrogen bonding of the peptide backbones causes the amino acids to fold into a repeating pattern. Some proteins can refold after denaturation while others cannot. α-Helix – a right-handed coil where each amino acid residue Chaperone proteins help some proteins fold into the correct shape. forms a hydrogen bond with the fourth amino acid ahead of it in the chain. Key Terms β-Pleated Sheets - consists of beta strands connected chaperonin: proteins that provide favorable conditions for the laterally by at least two or three backbone hydrogen bonds, correct folding of other proteins, thus preventing aggregation forming a sheet-like arrangement. denaturation: the change of folding structure of a protein (and thus 3. Tertiary Structure – three-dimensional folding of protein due to side of physical properties) caused by heating, changes in pH, or chain interactions. exposure to certain chemicals 4. Quaternary Structure - the orientation and arrangement of subunits in a multi-subunit protein. Protein consisting of more than one amino acid chain. 3. Nucleic Acids: Proteins: Denaturation and Protein Folding o Function: Store and transmit genetic information. Each protein has its own unique sequence of amino acids and the o Structure: Composed of nucleotides, which include a sugar, interactions between these amino acids create a specify shape. This a phosphate group, and a nitrogenous base. There are two main types of nucleic acids: Location: Found in the cell nucleus, cytoplasm, and ribosomes. ▪ DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Nucleotides Acid). Components: Each nucleotide has three parts: 1. Nitrogenous Base: This can be a purine (double ring) or a DNA (Deoxyribonucleic Acid) pyrimidine (single ring). Discovered by: James Watson and Francis Crick 2. Pentose Sugar: This is either deoxyribose (in DNA) or ribose Structure: Double-stranded helix. (in RNA). Components: Made up of nucleotides 3. Phosphate Group: One or more phosphate groups are attached. ▪ Nucleotides monomer compromising DNA and RNA. It contains a pentose sugar, a phosphate group, and Structure nitrogenous bases. Numbering: The carbon atoms in the sugar are numbered 1′ to 5′. Function: Stores genetic information used for the development, Attachments: functioning, and reproduction of all living organisms and many viruses. o The base attaches to the 1′ carbon of the sugar. Location: Found in the cell nucleus and mitochondria. o The phosphate attaches to the 5′ carbon of the sugar. RNA (Ribonucleic Acid) Formation of Polynucleotides Structure: Typically single-stranded. Linking Nucleotides: When nucleotides join to form a chain, the 5′ phosphate of one nucleotide connects to the 3′ hydroxyl group of the Components: Made up of nucleotides, each containing a pentose next nucleotide. sugar, a phosphate group, and one of four nitrogenous bases (adenine, uracil, cytosine, guanine). Differences Between DNA and RNA Function: Various types of RNA play roles in protein synthesis (e.g., Sugars: mRNA, tRNA, rRNA) and gene regulation. o DNA: Contains deoxyribose (lacks an oxygen atom at the 2′ position).  o RNA: Contains ribose (has an OH group at the 2′ position). DNA provides the code for the cell ‘s activities, while RNA converts that code into proteins to carry out cellular functions. Bases: The sequence of nitrogen bases (A, T, C, G) in DNA is what forms an o Purines: Adenine (A) and Guanine (G) - double ring organism’s traits. structure. The nitrogen bases A and T (or U in RNA) always go together and C o Pyrimidines: Cytosine ©, Thymine (T) in DNA, and Uracil (U) and G always go together, forming the 5′-3′ phosphodiester linkage in RNA - single ring structure. found in the nucleic acid molecules. Five Carbon Sugars Key Terms DNA has a sugar called deoxyribose. nucleotide: the monomer comprising DNA or RNA molecules; RNA has a sugar called ribose. consists of a nitrogenous heterocyclic base that can be a purine or The difference between these sugars is: pyrimidine, a five-carbon pentose sugar, and a phosphate group genome: the cell’s complete genetic information packaged as a o Ribose (in RNA) has an OH group (hydroxyl) on the second carbon. double-stranded DNA molecule o Deoxyribose (in DNA) has just a H atom (hydrogen) on the monomer: A relatively small molecule which can be covalently second carbon. bonded to other monomers to form a polymer. The carbons in the sugar are numbered 1′, 2′, 3′, 4′, and 5′ (read as “one prime,” “two prime,” etc.). The DNA Double Helix Key Points Key Points The two main types of nucleic acids are DNA and RNA. The structure of DNA is called a double helix, which looks like a Both DNA and RNA are made from nucleotides, each containing a twisted staircase. five-carbon sugar backbone, a phosphate group, and a nitrogen The sugar and phosphate make up the backbone, while the nitrogen base. bases are found in the center and hold the two strands together.  The nitrogen bases can only pair in a certain way: A pairing with T Key Terms and C pairing with G. This is called base pairing. nucleosomes: The fundamental subunit of chromatin, composed of Due to the base pairing, the DNA strands are complementary to a little less than two turns of DNA wrapped around a set of eight each other, run in opposite directions, and are called antiparallel proteins called histones. strands. histones: The chief protein components of chromatin, which act as spools around which DNA winds. Key Terms mutation: any error in base pairing during the replication of DNA DNA (Deoxyribonucleic Acid) sugar-phosphate backbone: The outer support of the ladder, forming strong covalent bonds between monomers of DNA. Role: DNA is the genetic blueprint of all living organisms. base pairing: The specific way in which bases of DNA line up and Location: bond to one another; A always with T and G always with C. o In eukaryotes (like plants and animals), DNA is found in the nucleus, chloroplasts, and mitochondria. DNA Packaging o In prokaryotes (like bacteria), DNA is not enclosed in a membrane. A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called Structure: DNA is made up of building blocks called nucleotides. the nucleoid. Key Points RNA (Ribonucleic Acid) In eukaryotic cells, DNA and RNA synthesis occur in a different Role: RNA mainly helps in making proteins (protein synthesis). location than protein synthesis; in prokaryotic cells, both these processes occur together. Structure: RNA is also made of nucleotides, similar to DNA. DNA is “supercoiled” in prokaryotic cells, meaning that the DNA is o Each nucleotide has three parts: either under-wound or over-wound from its normal relaxed state. 1. Nitrogenous base: A molecule containing nitrogen. In eukaryotic cells, DNA is wrapped around proteins known as histones to form structures called nucleosomes. 2. Sugar: A five-carbon sugar called ribose.  3. Phosphate group: One or more phosphate groups Cell Structure attached to the sugar. Cells as building blocks: 1. Cells: The smallest unit of life. Everything living is made up of cells. RNA Structure and Function 2. Organisms: A living thing, whether it’s just one cell (like bacteria) or 1. DNA Stays in the Nucleus: DNA, which contains the instructions for many cells (like humans). making proteins, never leaves the nucleus of the cell. 3. Tissues: Groups of similar cells working together to perform a 2. mRNA as the Messenger: Instead, a molecule called messenger specific function. RNA (mRNA) is used to carry the instructions from the DNA to the 4. Organs: Made up of different tissues working together (like the heart, rest of the cell. This process is called transcription. stomach, or brain). 3. Transcription: During transcription, mRNA is made by copying the 5. Organ Systems: Groups of organs that work together to perform sequence of one strand of DNA. For example, if the DNA sequence complex functions (like the digestive system or nervous system). is TCCAAGTC, the mRNA sequence will be AGGUUCAG. 6. Types of Cells: 4. mRNA Travels to Ribosomes: The mRNA then leaves the nucleus and goes to the ribosomes, which are the cell’s protein-making o Prokaryotic Cells: Simple cells without a nucleus (like factories. bacteria). 5. Translation: At the ribosomes, another type of RNA called transfer o Eukaryotic Cells: More complex cells with a nucleus (like RNA (tRNA) helps translate the mRNA’s instructions into a protein. animal and plant cells). The tRNA reads the mRNA sequence in groups of three bases, Types of Specialized Cells called codons. Each codon corresponds to a specific amino acid, the 1. Different Cell Types: Your body has many different kinds of cells, building blocks of proteins. each with a specific job, just like different materials are used to build 6. Ribosomes and rRNA: Ribosomes, which contain ribosomal RNA a house. (rRNA), hold everything in place and help form the bonds between 2. Examples of Cell Types: amino acids to build the protein.  o Epithelial Cells: Protect the surface of your body and cover Image Orientation: When you look at a specimen through a organs and cavities. microscope: ▪ If the specimen is right-side up and facing right on the slide, it o Bone Cells: Support and protect your body. will look upside-down and facing left through the microscope. o Immune Cells: Fight off bacteria and other invaders. ▪ Moving the slide left makes the image appear to move right, o Blood Cells: Carry nutrients and oxygen around your body and moving it down makes the image appear to move up. and remove carbon dioxide. Why This Happens: This happens because microscopes use two sets of lenses to magnify the image, which flips the image. Some o Nasal Sinus Cells: Found in the nose, viewed with a light microscopes, like binocular or dissecting microscopes, have an extra microscope. lens system that makes the final image appear upright. o Onion Cells: Found in onions, also viewed with a light microscope. Types of Microscopes: o Vibrio tasmaniensis Bacterial Cells: A type of bacteria, seen through a scanning electron microscope. 1. Light Microscope – student microscopes are light microscopes. They use visible light to magnify the specimen. 3. Roles of Cells: Each type of cell is crucial for your body’s growth, ▪ How They Work: Light passes through the lenses and development, and daily maintenance. bends, allowing you to see the specimen. 4. Common Characteristics: Despite their variety, all cells share some ▪ Viewing Living Organisms: Light microscopes are great for basic features, whether they come from bacteria, onions, or humans. looking at living things. ▪ Transparency of Cells: Individual cells are usually clear, so you can’t see their parts unless they are stained. Microscopy ▪ Staining: Staining makes cell parts visible, but it usually kills the cells. Microscopes: Scientists use microscopes to see cells. A microscope ▪ Magnification is the process of enlarging an object in magnifies objects, making them look bigger. An instrument that can appearance. be used to observe small objects. Photos taken with a microscope ▪ Most light microscopes used in a college biology lab can are called micrographs. magnify cells up to approximately 400 times and have a resolution of about 200 nanometers.  2. Simple Microscope – using a single convex lense. Base: The bottom part of the microscope that provides 3. Compound Microscope – invented by: Zacharias Janssen and Hans stability and support. Janssen. Arm: The curved structure that connects the base to the ▪ Used multiple lenses. head of the microscope. It’s used to carry the microscope. 4. Electron Microscopes: Use a beam of electrons instead of light to Stage: The flat platform where you place the slides for see specimens. viewing. ▪ Higher Magnification and Detail: They can magnify more Stage Clips: Clips on the stage that hold the slide securely. and show more detail than light microscopes. Mechanical Stage: A stage that can be moved precisely ▪ Preparation Kills Specimens: Preparing samples for using knobs. electron microscopes kills them because electrons need a Coarse Adjustment Knob: The larger knob used for vacuum to work best. focusing the microscope by moving the stage up and down. ▪ Electron microscopes provide a much higher magnification, Fine Adjustment Knob: The smaller knob used for fine- 100,000x, and a have a resolution of 50 picometers. tuning the focus after using the coarse adjustment knob. Types of Electron Microscopes: Pillar: The vertical part that supports the stage and connects it to the base. ▪ Scanning Electron Microscope (SEM): Scans the surface Body Tube: The tube that connects the eyepiece to the of a cell, showing surface details. objective lenses. ▪ Transmission Electron Microscope (TEM): Penetrates the Nosepiece (Revolving Turret): The rotating part that holds cell, showing internal structures. the objective lenses and allows you to switch between them. ▪ Size and Cost: Electron microscopes are larger and more 2. Magnifying parts of a microscope are the components that enlarge expensive than light microscopes. the image of the specimen. ▪ Objective Lenses: These lenses are closest to the specimen Parts of Microscope: and provide the primary magnification. Examples: 1. Mechanical parts of a microscope are the components that support a) Low Power Objective: Typically 4x or 10x magnification. and adjust the microscope, allowing you to view specimens b) High Power Objective: Usually 40x or 60x magnification. effectively. c) Oil Immersion Objective: Often 100x magnification, used with a special oil to improve clarity.  ▪ Eyepiece (Ocular Lens): The lens you look through, which Mirror: In microscopes without built-in light sources, a mirror is used further magnifies the image produced by the objective lens. to reflect external light (like sunlight or a lamp) onto the specimen. Examples: The mirror can be adjusted to direct light precisely. a) Standard Eyepiece: Usually provides 10x magnification. Filters: These are used to modify the light’s color or intensity. For b) High-Power Eyepiece: Can provide 15x or 20x example, blue filters are often used to improve resolution by magnification. providing shorter wavelength light. ▪ Condenser Lens: Focuses light onto the specimen, enhancing Field Diaphragm: This component controls the diameter of the light the illumination and contrast. beam entering the condenser, helping to reduce stray light and improve image quality. How They Work Together: 2 Types of Microscopic Slides: Objective Lens: Magnifies the specimen first. Eyepiece: Further magnifies the image created by the objective 1. Flat Slide lens. 2. Concave Slide Condenser Lens: Improves the lighting and clarity of the image. 3. The illuminating parts of a microscope are essential for providing the MICROSCOPE SLIDE PRESENTATION – thought-out methodology that light needed to view specimens clearly. allows your samples to explain clearly. Illuminator: This is the primary light source, which can be a built-in Step 1. SLIDE MOUNT - refers to the way a specimen is placed on a electric lamp or an external light source. Common types include microscope slide for observation. tungsten-halogen lamps, LED lights, and xenon lamps. Condenser Lens: This lens focuses the light from the illuminator Dry Mount – simplest way to mount a slide onto the specimen. It helps to concentrate the light into a cone, Wet Mount – useful for the observation of motile specimens capable improving the clarity and brightness of the image. of motions. Smear Mount – AKA temporary mount – examine samples of blood. Iris Diaphragm: Located within or below the condenser, this adjustable aperture controls the amount of light reaching the specimen. It helps to enhance contrast and resolution. COMMONLY STAINING MEDIA - Staining is a technique used in biology to Function: The intracellular matrix supports internal cellular enhance the contrast of specimens under a microscope, making it easier to processes, while the extracellular matrix provides external support observe and identify specific structures within cells and tissues. and facilitates cell-to-cell communication 1. Iodine – stain starch; black – blue color CELL THEORY 2. Methylene Blue – stains nuclei; blue color ▪ Antoine Van Leeuwenhoek: A Dutch shopkeeper who was very 3. Crystal Violet – gram staining; deep violet or purple skilled at making lenses. He used his simple microscopes to observe 4. Eosin Y – cytoplasm staining; bright pink – red color tiny organisms like protista and sperm, which he called 5. Toluidine Blue – stain acidic tissue like nucleic acid; blue “animalcules.” PREPARATION OF TISSUES FOR STUDY ▪ Robert Hooke: In 1665, he published a book called Micrographia. He 1. Fixation – prevent putrefaction/degradation used a lens to look at cork tissue and coined the term “cell” for the 2. Dehydration – removal of water box-like structures he saw. 3. Clearing – alcohol is removed (miscible – homogenous solution) ▪ Discoveries: In the 1670s, van Leeuwenhoek discovered bacteria 4. Infiltration and Embedding – Infiltration means tissue is being placed and protozoa. in paraffin wax while embedding means, to provide solid support for the tissue during sectioning. 5. Sectioning or Trimming – trimmed to expose the tissue; obtain thin ❖ Unified Cell Theory: Proposed in the late 1830s by botanist Matthias slices Schleiden and zoologist Theodor Schwann. It states: 6. Cryostat – to store the tissue for long – term storage. o All living things are made of one or more cells. INTRACELLULAR AND EXTRACELLULAR MATRIX o The cell is the basic unit of life. Key Differences o New cells come from existing cells. Location: The intracellular matrix is inside the cell, while the ❖ Spontaneous Generation: Schleiden and Schwann initially thought extracellular matrix is outside the cell. cells could arise spontaneously (abiogenesis), but this idea was later Composition: The intracellular matrix includes organelles and disproven. cytosol, whereas the extracellular matrix consists of proteins and ❖ Rudolf Virchow: Later added to this theory, famously saying, “All other macromolecules secreted by cells. cells come from pre-existing cells.”  ❖ Modern Cell Theory: The accepted parts of the theory today are: Prokaryotic Cells - Characteristics of Prokaryotic Cells o The cell is the fundamental unit of structure and function in All cells share four common components: living things. 1. a plasma membrane: an outer covering that separates the cell’s o All organisms are made up of one or more cells. interior from its surrounding environment. o Cells arise from other cells through cell division. 2. cytoplasm: a jelly-like cytosol within the cell in which other cellular components are found CELL SIZE 3. DNA: the genetic material of the cell 1. Size Difference: 4. ribosomes: where protein synthesis occurs o Prokaryotic Cells: Very small, about 0.1 to 5.0 micrometers (μm) in diameter. o Eukaryotic Cells: Larger, about 10 to 100 micrometers (μm) in ❖ Prokaryotes vs. Eukaryotes: diameter. o Prokaryotes: Simple, single-celled organisms without a 2. Advantages of Small Size: nucleus or other membrane-bound organelles. o In prokaryotic cells, small size means that substances like o Eukaryotes: More complex cells with a nucleus and ions and molecules can quickly spread throughout the cell. membrane-bound organelles. o Waste products can also quickly leave the cell. Prokaryotic DNA: Found in a central part of the cell called the nucleoid, not enclosed in a nucleus. 3. Eukaryotic Cells: Cell Wall and Capsule: o Because they are larger, eukaryotic cells have developed o Cell Wall: Made of peptidoglycan, provides protection, special structures to help move substances around inside the shape, and prevents dehydration. cell. o Capsule: Made of polysaccharides, helps the cell stick to surfaces. o  Structures for Movement and Attachment: 3. Nuclear Envelope: The outer part of the nucleus, made of two layers of phospholipids. It has pores that let ions, molecules, and RNA o Flagella: Used for movement. move in and out. o Pili: Used to exchange genetic material during reproduction 4. Nucleoplasm: The semi-solid fluid inside the nucleus, containing (conjugation). chromatin (DNA and proteins) and the nucleolus (where ribosomes o Fimbriae: Help bacteria attach to host cells. are made). 5. Chromosomes: Structures made of DNA inside the nucleus. In Eukaryotic Cells - Characteristics of Eukaryotic Cells prokaryotes, DNA is a single circular chromosome. In eukaryotes, DNA is in linear chromosomes. Eukaryotic cells have: So, the nucleus is the control center of the cell, storing DNA and managing 1. a membrane-bound nucleus the production of proteins and ribosomes. 2. numerous membrane-bound organelles (including the endoplasmic Other Membrane-bound organelles: reticulum, Golgi apparatus, chloroplasts, and mitochondria) 1. Mitochondria: Oval-shaped organelles with two membranes, their 3. several rod-shaped chromosomes own ribosomes, and DNA. They are the cell’s “energy factories” Eukaryotic cells have a true nucleus and specialized organelles that help because they make ATP, the main energy molecule, through cellular them perform various functions efficiently. respiration. 2. Endoplasmic Reticulum (ER): Modifies proteins and makes lipids. There are two types: The Nucleus and It’s Structures: o Rough ER: Has ribosomes on its surface and helps in protein 1. Nucleus: The most noticeable part of a eukaryotic cell. It has a synthesis. membrane around it, so it’s called a “true nucleus.” o Smooth ER: Lacks ribosomes and is involved in lipid 2. DNA Storage: The nucleus holds the cell’s DNA and controls the synthesis. making of proteins and ribosomes (which make proteins). 3. Golgi Apparatus: Sorts, tags, packages, and distributes lipids and proteins.  4. Peroxisomes: Small, round organelles with a single membrane. They 2. Cell Wall: Provides protection, structural support, and shape to the break down fatty acids and amino acids and detoxify poisons. plant cell. 5. Vesicles and Vacuoles: Membrane-bound sacs for storage and 3. Large Central Vacuole: Helps regulate the cell’s water content, transport. Vacuoles are larger than vesicles. Vesicles can fuse with especially in different environmental conditions. the plasma membrane or other membranes within the cell. 4. Chloroplasts: Organelles that carry out photosynthesis, converting Animal Cells Vs. Plants Cells sunlight into energy for the plant. 1. Common Organelles: Both animal and plant cells have organelles like the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, and more. 2. Differences: o Animal Cells: Have centrosomes and lysosomes. ▪ Centrosome: Helps organize microtubules near the nucleus. ▪ Lysosomes: Handle the cell’s digestion and waste removal. o Plant Cells: Do not have centrosomes and lysosomes. 1. Plant Cells vs. Animal Cells: o Plant Cells: Have a cell wall, large central vacuole, chloroplasts, and other specialized plastids. o Animal Cells: Do not have these structures.