BIO Ch1-3 PDF

Chapter 1: The Human Body:An Orientation and Chemistry comes to life Anatomy - the study of body parts Physiology - the study of the function of body parts Principle of complementary of structure and function - they are inseparable Structural Organization - smallest chemical level to the whole org...

Chapter 1: The Human Body:An Orientation and Chemistry comes to life Anatomy - the study of body parts Physiology - the study of the function of body parts Principle of complementary of structure and function - they are inseparable Structural Organization - smallest chemical level to the whole organism level: From smallest to biggest: Chemical level - organelles,molecules,atoms Cellular level - single cell Tissue level - group of similar cells Organ level - two or more types of tissues Organ system level - organic that work closely together Organism level - all organs systems combine to make the whole organism Requirements for life: Digestion Metabolism Reproduction Growth Excretion Responsiveness Movement Maintaining boundaries Body Organ Systems: Integumentary system - skin, hair, nails -forms external body covering -synthesizes vitamin D Skeletal system - joints,bones -blood cells are formed with bones -bones store mineral Muscular system - skeletal muscles -manipulation to the environment, locomotion -maintain posture -produces heat Nervous system - brain, nerves,spinal cord -respond to internal and external changes by activating muscles and glands Endocrine system - ovary, adrenal gland, pancreas, thymus, thyroid gland, pineal gland, pituitary gland, testis -secrete hormones that regulate processes such as growth, reproduction and nutrients Cardiovascular system - heart, blood vessels -blood vessels transport blood -carries oxygen,carbon dioxide,nutrients,waste -heart pumps the blood Lymphatic system - lymph nodes,lymphatic vessels,red bone marrow,thymus,thoracic duct, spleen -picks up fluid leaked from blood vessels and return it to the blood -disposes of debris in the lymphatic streams Respiratory system - nasal cavity,pharynx,larynx,trachea,lung,bronchus -keeps blood constantly supplied with oxygen and removes carbon dioxide -thee exchanges occur through the walls of the air sacs of the lungs Digestive system - organ cavity,esophagus,liver,stomach,small intestine,large intestine,rectum,anus -breaks down food into absorbable units that enter the blood for distribution to body cells -indigestible foodstuffs are eliminated as feces Urinary system - kidney,ureter,urinary bladder,urethra -eliminates nitrogenous wastes from the body -regulates water,electrolyte and acid base balance of the blood Male/female reproductive system - prostate,penis,testis,scrotum,ductus deferens,ovary,uterine tube,uterus,vagina,mammary glands -overall function is production of offspring -testes produces sperm and male sex hormone -male ducts and glands aids in delivery of sperm to the female reproductive tract -ovaries produces eggs and female sex hormones -the remaining structure serves as sites for fertilization and development of the fetus -mammary glands of female breasts produces milk to nourish the newborn Survival needs of organism: Nutrients - carbohydrates,proteins,fats,minerals Oxygen - essential for release of energy from foods Water - most abundant molecule in body, fluid base for secretions and excretions Normal body temperature - if body falls below or goes above 37 degrees, rates of chemical reactions are affected Appropriate atmospheric pressure - specific air pressure is needed for adequate breathing and gas exchange in lungs Homeostasis: The maintenance of relatively stable internal condition despite continuous changes in environment: -a dynamic state of equilibrium, always adjusting as needed -maintained by contribution of all organ systems Homeostasis Controls: Body must constantly be monitored and regulated to maintain homeostasis -nervous and endocrine systems play a major role in maintaining homeostasis -variables are factors that can change the blood sugar, body temperature,blood volume Homeostatic control of variables: Receptors - detects change Control center - determine the outcome Effector - response Homeostatic controls: Negative & Positive feedback Negative feedback: Example: regulation of blood glucose,body temperature -reduces or shut off original stimulus -variable changes in opposite direction Positive feedback: Example: enhancement of labor contractions by oxytocin -enhance the original stimulus -causes variable to continue the same direction Anatomical terms: Superior (cranial) - towards the upper part of the body Inferior (caudal) -towards the lower part of the body Anterior (ventral) - towards in front of the body Posterior (dorsal) - towards the back of the body Medial - towards the middle of the body Lateral - away from the midline of the body Intermediate - Both Proximal - closer to the origin of body Distal - farther from the origin of body Superficial (external) - at the body surface Deep (internal) - more internal of the body Body planes and sections: Sagittal plane - divide body vertically from left and right Frontal (coronal) plane - divides from front and back Transverse (horizontal) plane - divides body top and bottom Body Cavities: Dorsal: Cranial - brain Vertebral - spinal cord Ventral: Thoracic - heart,lungs Abdominal - digestive viscera Pelvic -urinary bladder,reproductive organs,rectum Body Quadrants: RUQ - indication of gallbladder issues LUQ - indication of stomach issues RLQ/LLQ - indication of intestine issues Chapter 2: Chemistry and Physiological Reactions Structure of Atoms: Protons - positive charge Neutrons - no electric charge Electrons - negative charge Chemical Bonds: energy relationships between of reacting atoms -Ionic bonds -Covalent Bonds -Hydrogen bonds Ionic Bonds - transfer of electrons Anion - negative charge Cation - positive charge Covalent Bond - sharing of electrons 2 electrons -single bond 4 elections - double bond 6 electrons - triple bond Two types of covalent bonds: Polar covalent bond Nonpolar covalent bond Hydrogen Bonds: attractive force between electropositive hydrogen of one molecule and electronegative atom of another molecule Biochemistry - study of chemical composition and reactions of living matter Inorganic compounds - water,salts, acids, bases (do not contain carbon) Organic compounds - carbohydrates,fats,proteins,nucleic acids (contain carbon) Inorganic compounds Water - 60-80% of the volume of living cells Salts - ionic compound (electrolytes) that separate ions in water Acids -protons donors, releases hydrogen ions Bases - proton acceptors, releases hydrogen ions pH Scale - measurement of concentration of hydrogen ions The more hydrogen the more acidic The less hydrogen the less acidic Buffers - resist abrupt and large swings in pH scale -Can release hydrogen ions if ph rises -Can bind hydrogen ions if pH falls -Converts strong acids and bases into weaker form -Carbonic acid- bicarbonate system Organic Compounds: Synthesis and Hydrolysis -Carbohydrates -Lipids -Proteins -Nucleic acids Dehydration synthesis - removal of water Synthesis - adding of water Carbohydrates - contain C,H,O Three classes: Monosaccharide - one single sugar Disaccharides - two sugars Polysaccharides - many sugars Monosaccharides -Glucose -Fructose -Galactose -Ribose -Deoxyribose Disaccharides -Glucose + Fructose = Sucrose -Glucose + Glucose = Maltose -Galactose + Glucose = Lactose Lipids - contain C,H,O,P, Insoluble in water Main types: Triglycerides Phospholipids Steroids Eicosanoids Triglycerides - 1 glycerol + 3 fatty acids + dehydration synthesis Saturated vs Unsaturated Saturated fat - solid at room temperature, no double bond Unsaturated fat - liquid at room temperature, double bond Phospholipids - 1 glycerol + 2 fatty acids + P -Glycerol + P (upper) = polar and hydrophilic -2 Fatty acids (lower) = nonpolar and hydrophobic Cholesterol and Steroid Synthesis -Cholesterol - 4 interlocking ring structure (made by liver and also found in animal fats e.g. cheese,eggs,meat) -Cholesterol is starting material for synthesis of VitaminD,steroid hormones and bile salts Eicosanoids -Derived from a fatty acid (arachidonic acid) found in cell membranes -Most important eicosanoids are prostaglandins which plays a role in blood clotting, control of blood pressure, inflammation, and labor contractions Proteins - 20-30% of cell mass, contain C,H,O,N,S,P -polymers of amino acids monomers held together by peptide bonds Level of Protein Structure 1.Primary structure - amino acid forms the polypeptide chain 2.Secondary structure - primary chain form spirals and sheets (a-helices,b-sheets) 3.Tertiary structure - folded up to from a compact globular molecule held together by intramolecular bonds 4.Quaternary structure - Two or more polypeptide chain each with its own tertiary structure, combine to form a functional protein Amino Acids and Peptide Bonds -All protein are made from 20 types of amino acids -Joined by covalent bonds called peptide bonds Contain both an amino group and acid group -Differ by which of 20 different “R groups” is present Fibrous and Globular Proteins Shapes of proteins fall into one of two categories: Fibrous or globular 1.Fibrous (structural) proteins -Strandlike, water-insoluble, and stable -Most have tertiary or quaternary structure (3-D) -Provide mechanical support and tensile strength Examples: keratin, elastin, collagen and contractile fibers 2.Globular (functional) proteins -Compact, spherical, water-soluble, and sensitive to environmental changes Tertiary or quaternary structure (3-D) Contain specific functional regions (active sites) Examples: antibodies, hormones and enzymes Enzymes - globular proteins that act biological catalysts -catalyst regular and increase speed of chemical reactions -act on very specific substrate -eg. Hydrolases,oxidases (ase) Nucleic Acids - C,H,O,N,P -made up of monomers called nucleotides (nitrogen base,pentose sugar, phosphate group) Two Major classes: Deoxyribonucleic acid (DNA) -hold genetic blueprint for the synthesis of all proteins -double helix -located in cell nucleus 4 nitrogen bases (Purines: adenine(A),guanine(G) Pyrimidines: cytosine(C) thymine(T)) Ribonucleic acid (RNA) -single stranded linear molecule outside of nucleus -contain ribose sugar -thymine is replaced with uracil 3 varieties of RNA (mRNA, tRNA,rRNA) -Chemical energy released when glucose is broken down is capture in ATP (adenosine triphosphate In DNA, the base pairs are: A (adenine) pairs with T (thymine) U(uracil). C (cytosine) pairs with G (guanine). G (guanine) pairs with C (cytosine). T (thymine) pairs with A (adenine). If adenine makes up 18% of the nucleotides of a particular sample of DNA from an organism, approximately what percentage of the nucleotides in this sample will be guanine? -So, adenine + thymine = 18% + 18% = 36%. -100% - 36% = 64% guanine & cytosine -Guanine (G) = 64% ÷ 2 = 32% =32% ATP: -Directly powers chemical reactions in cell -offers immediate,usable energy needed by body cells -structure - Adenine containing RNA nucleotide with two additional phosphate groups Chapter 3 - Cells: The Living Units Cells theory: -Cell is the structural and function unit of life -How well the entire organism functions depends on individual and combined activities of cells Human cells have three basic parts: -Plasma membrane - flexible outer boundary -Cytoplasm - intracellular fluid containing organelles -Nucleus - DNA containing control center Plasma membrane -Acts as an active barrier separating intracellular and extracellular fluid -Plays dynamic role in cellular activity by controlling what enters and what leaves cells Structure of plasma membrane: Polar hydrophilic head Nonpolar hydrophobic tail Membrane Proteins perform many tasks: 1.Transport - help move substances in and out of the cells 2.Receptors - receive signals from outside the cell and send messages into the cell to trigger response 3.Enzymes - speed up chemical reactions 4.Structural support - help maintain the shape of the cell and attach to cytoskeleton or extracellular matrix 5.Cell recognition - help cells identify each other (glycoprotein) 6.Adhesion - enable cells to stick to each other and form tissues Cell Junctions - most are bound together to form tissues and organs Three ways cells can be bound to each other -Tight junctions - prevent leakage of fluids between cells -Desmosomes - hold cells together firmly -Gap junctions - allow cells to communicate directly Transports: Passive transport - no energy required Active transport - energy (ATP) required Passive Membrane transport - high to low, no energy Three types of passive transport: SImple diffusion - nonpolar substances go straight through membrane and small polar can sometimes pass Facilitated diffusion: Carrier-mediated- carrier proteins change shape and move the molecule across membrane then go back to its original shape Channel-mediated facilitated - certain size and charge (ions) Osmosis - movement of water from one side of the membrane to the other aquaporins: let water pass through more easily towards area with less water Osmolarity is a way to measure how many solute particles (like salt or sugar) are dissolved in a liquid (usually water). The more solute there is, the less water there is, because the solute takes up space. When there’s a lot of solute in one area, water moves toward that area to balance things out. Water always moves from places with more water and less solute to places with less water and more solute. Tonicity describes how a solution affects the size or shape of a cell by changing how much water is inside the cell: Isotonic solution: The solution has the same concentration of solutes as the inside of the cell. Water moves in and out of the cell equally, so the cell stays the same size. Hypertonic solution: The solution has more solutes than inside the cell, so water leaves the cell. This makes the cell shrink, which is called crenation. Hypotonic solution: The solution has fewer solutes than inside the cell, so water enters the cell. This makes the cell swell, and if too much water enters, the cell can burst, which is called lysis. Active Membrane Transport Active transport Vesicular transport Both active transport and vesicular transport need energy (ATP) to move things across the cell membrane because: The solute is too big to fit through the channels, The solute can't dissolve in fat, so it can't pass through the membrane, The solute needs to go "uphill", from a low concentration to a high concentration, which takes extra energy. ATP gives the power for these processes to happen. Active Transport Active transport uses special proteins called solute pumps to move things across the cell membrane. These proteins: Attach to specific substances and can release them to move them across. Some proteins move more than one thing at a time: ○ Antiporters move one substance in while moving another substance out. ○ Symporters move two substances in the same direction. This process moves substances from low concentration to high concentration, which requires energy (ATP). There are two types of active transport: 1. Primary active transport: This uses energy directly from breaking down ATP to move substances across the cell membrane. 2. Secondary active transport: This uses energy from ion gradients (like sodium) created by primary active transport. It moves other substances along with the ions without using ATP directly. Vesicular Transport Vesicular transport is how cells move big particles, large molecules, and liquids across their membranes using small sacs called vesicles. This process needs energy from the cell, usually from ATP. Vesicular transport includes: 1. Endocytosis: Moving substances into the cell. There are three types: ○ Phagocytosis: "Cell eating" large particles. ○ Pinocytosis: "Cell drinking" small amounts of liquid.  ○ Receptor-mediated endocytosis: Taking in specific molecules using receptors. 2. Exocytosis: Moving substances out of the cell. 3. Vesicular trafficking: Moving materials from one part of the cell or organelle to another. Exocytosis Exocytosis is the process where a cell moves substances out of itself using small sacs called vesicles. Function: It helps the cell release things like hormones, neurotransmitters, or waste products. By doing this, the cell can communicate with other cells or get rid of materials it doesn’t need anymore. Cytoplasm Cytoplasm is the material inside a cell, found between the plasma membrane and the nucleus. It includes: Cytosol: A gel-like fluid made mostly of water, along with dissolved substances like proteins, salts, and sugars. Organelles: The cell's "machines" that perform specific functions. These can be either surrounded by membranes (membranous) or not (nonmembranous). Cytoplasmic organelles can be classified as either membranous or nonmembranous: Membranous organelles: Mitochondria: Produce energy for the cell. Endoplasmic reticulum: Helps in protein and lipid synthesis. Golgi apparatus: Modifies and packages proteins for transport. Peroxisomes: Break down fatty acids and detoxify harmful substances. Lysosomes: Contain enzymes that digest waste materials. Nonmembranous organelles: Ribosomes: Make proteins. Cytoskeleton: Provides structure and support to the cell. Centrioles: Help with cell division. The membranes of these organelles create separate compartments, which is important for the cell to function properly. Mitochondira Mitochondria are often called the “power plants” of cells because they produce most of the cell's energy molecules, known as ATP, through a process called aerobic respiration, which requires oxygen. Key features: Double membranes: They have an outer and an inner membrane. The inner membrane is folded into structures called cristae, which contain proteins important for energy production. Own DNA and ribosomes: Mitochondria have their own DNA, RNA, and ribosomes, which is similar to bacteria. This unique structure and function support their role in energy production and suggest a close evolutionary relationship with bacteria. Endoplasmic Reticulum The endoplasmic reticulum (ER) is connected to the outer membrane of the nucleus and comes in two types: 1. Rough ER: Function: This is where proteins are made that will be secreted from the cell or incorporated into the cell's membrane. As proteins are made, they enter the ER's fluid-filled tubes (cisterns) and get modified. Once complete, these proteins are packaged in vesicles and sent to the Golgi apparatus for further processing. 2. Smooth ER: Function: This part doesn’t have ribosomes on its surface and is involved in several important processes: ○ Lipid metabolism: Helps make cholesterol, steroid hormones, and lipids for lipoproteins. ○ Glycogen conversion: Changes glycogen into free glucose. ○ Calcium storage: Stores and releases calcium ions, which are important for various cell functions. Golgi Apparatus The Golgi apparatus is made up of stacked, flattened sacs called cisternae. Its main job is to modify, concentrate, and package proteins and lipids received from the rough ER. Here’s how it works in three steps: 1. Receiving: Transport vesicles from the rough ER fuse with the cis (inner) face of the Golgi. 2. Processing: The proteins or lipids inside are modified, tagged, sorted, and packaged for their final destinations. 3. Shipping: The Golgi acts like a traffic director, deciding which of three pathways the final products will take as new transport vesicles pinch off from the trans (outer) face. Peroxisomes Peroxisomes are membranous sacs that contain powerful detoxifying substances to neutralize toxins in the cell. Key functions: Detoxification of free radicals: These are toxic and highly reactive molecules that can harm cells if not removed. They are natural by-products of cellular metabolism. Main detoxifying processes: ○ Oxidase enzymes use oxygen to convert toxins into hydrogen peroxide (H₂O₂), which is toxic. ○ Peroxisomes also contain catalase, an enzyme that converts hydrogen peroxide into harmless water, helping keep the cell safe from damage. Lysosomes Lysosomes are spherical membranous sacs filled with digestive enzymes called acid hydrolases. They serve as "safe" sites for digestion within the cell, isolating potentially harmful processes from the rest of the cell. Key functions: Digesting materials: Lysosomes break down ingested bacteria, viruses, and toxins. Degrading nonfunctional organelles: They help recycle parts of the cell by breaking down damaged or old organelles. Metabolic functions: Lysosomes also break down glycogen and release glucose when needed. Clinical -Homeostatic Imbalance Lysosomal storage diseases occur when one or more lysosomal digestive enzymes are mutated and do not work properly. Example: Tay-Sachs disease is a condition where the body lacks a specific lysosomal enzyme needed to break down glycolipids in brain cells. Because this enzyme is missing, glycolipids accumulate, which disrupts normal functioning of the nervous system and leads to serious health issues. Non-membranous Organelles: Ribosomes Ribosomes are nonmembranous organelles that serve as the sites of protein synthesis. They are made up of proteins and ribosomal RNA (rRNA). Two forms of ribosomes: 1. Free ribosomes: These float freely in the cytosol and synthesize soluble proteins that function within the cytosol or other organelles. 2. Membrane-bound ribosomes: These are attached to the membrane of the endoplasmic reticulum (ER). They synthesize proteins that are either incorporated into membranes, sent to lysosomes, or exported from the cell. Cytoskeleton The cytoskeleton is an elaborate network of protein rods and tubules that runs throughout the cytosol. It provides structural support and helps with the movement of cell components. It acts like the cell's "bones, ligaments, and muscles." Key features: It consists of hundreds of different proteins that link the rods to other structures within the cell. It plays a crucial role in maintaining the cell's shape and facilitating cellular movement. Three types of cytoskeletal elements: 1. Microfilaments: These are the thinnest filaments made of actin. They are involved in muscle contraction, cell division, and the movement of cell components. 2. Intermediate filaments: These provide tensile strength to the cell and help maintain its shape. They are made of various proteins, including keratin and vimentin.  3. Microtubules: These are hollow tubes made of tubulin. They help with maintaining cell shape, providing tracks for the movement of organelles, and are crucial in cell division (forming the mitotic spindle). Example of cytoskeleton The spindle apparatus plays a crucial role during cell division. At the center of this process is the centrosome, which serves as a microtubule organizing center. It consists of two structures called centrioles, which are barrel-shaped organelles positioned at right angles to each other. Key functions: During cell division, microtubules are assembled and radiate from the centrosome toward the opposite poles of the cell, forming the spindle. This spindle is essential for accurately separating chromosomes into the two daughter cells. Centrioles also serve as the foundation for the formation of cilia and flagella, which are structures that help with cell movement and fluid movement across cell surfaces. Microvilli Microvilli are tiny, finger-like projections that extend from the surface of certain cells, particularly epithelial cells. They significantly increase the surface area of the cell, which enhances its ability to absorb substances, such as nutrients in the intestines. Key features: Structure: Microvilli are composed of a core of actin filaments, which help maintain their shape and support. Function: They are mainly involved in absorption, secretion, and sensing the environment. In the intestines, for example, microvilli increase the surface area available for nutrient absorption. Location: They are commonly found in cells lining the small intestine and kidney tubules, where efficient absorption is critical. Nucleus The nucleus contains the genetic material of the cell, which serves as the blueprint for synthesizing nearly all cellular proteins. It responds to various signals that determine the types and amounts of proteins the cell needs to produce. Key points: Most cells have one nucleus (uninucleate), but some, like skeletal muscle cells, certain bone cells, and some liver cells, can have multiple nuclei (multinucleate). Red blood cells are unique in that they are anucleate, meaning they lack a nucleus entirely, which allows more space for hemoglobin, the protein that carries oxygen. Structure of the Nucleus The nucleus has three main structures: 1. Nuclear envelope: This is a double membrane that surrounds the nucleus, separating its contents from the cytoplasm. It has pores that allow for the exchange of materials between the nucleus and the rest of the cell. 2. Nucleoli: These are dark-staining spherical bodies within the nucleus, usually one or two per nucleus. They are involved in synthesizing ribosomal RNA (rRNA) and assembling ribosome subunits, which are essential for protein synthesis. 3. Chromatin: This is the complex of DNA and proteins found in the nucleus. Chromatin exists in a relaxed state during interphase and condenses into chromosomes during cell division. It contains the genetic information necessary for the synthesis of proteins and the regulation of cellular activities. Chromatin Chromatin consists of about 30% threadlike strands of DNA, 60% histone proteins, and 10% RNA. Key features: Nucleosomes: Chromatin is organized into fundamental units called nucleosomes, which consist of DNA wrapped around histone proteins. This structure helps regulate gene expression by controlling how tightly or loosely DNA is packaged. Chromosomes: When the cell prepares to divide, chromatin condenses into chromosomes. This condensed state protects the fragile strands of DNA during cell division, ensuring that genetic material is accurately distributed to daughter cells. Cell Cycle The cell cycle is the series of changes a cell undergoes from the time it is formed until it reproduces. It consists of two major periods: 1. Interphase: This is the phase where the cell grows and carries out its normal functions. During interphase, the cell prepares for division by replicating its DNA and organelles. 2. Cell division (mitotic phase): This is the phase where the cell divides into two daughter cells. It involves processes like mitosis, where the nucleus divides, followed by cytokinesis, which divides the cytoplasm. Interphase 1. Unwind the DNA: The DNA strands open up like a zipper. 2. Make Copies: Each open strand acts as a template to create a new matching strand. 3. Start the Process: A short RNA piece is added first to help kick things off. 4. Build the New Strands: An enzyme called DNA polymerase adds the building blocks (nucleotides) to form the new strands. 5. Connect the Pieces: Another enzyme, DNA ligase, glues together any small gaps on the new strands. Cell Division 1. Continuous Replication: Most cells need to divide regularly for growth and repair. However, some cells, like skeletal, cardiac, and nerve cells, don’t divide well. When they get damaged, they’re often replaced by scar tissue instead of new cells. 2. M Phase of Cell Cycle: This is when the cell actually divides, and it has two main parts: ○ Mitosis: The process where the cell's nucleus divides. ○ Cytokinesis: The process that divides the rest of the cell, creating two separate cells. 3. Control of Division: It's important for cells to divide only when needed. They shouldn’t divide too much, as that can lead to issues like tumors. Cell division is the process by which a parent cell divides into two or more daughter cells. It's essential for growth, development, and repair in multicellular organisms. There are two main types of cell division: 1. Mitosis: This process results in two genetically identical daughter cells. It's used for growth and tissue repair. Mitosis involves several stages: ○ Prophase: Chromosomes condense and become visible. The nuclear envelope breaks down. ○ Metaphase: Chromosomes line up in the middle of the cell. ○ Anaphase: Chromosomes are pulled apart to opposite sides of the cell.  ○ Telophase: The nuclear envelope re-forms around each set of chromosomes, and they begin to uncoil. 2. Cytokinesis: This is the final step of cell division, where the cytoplasm divides, creating two separate cells. In animal cells, this often occurs through a pinching process, while in plant cells, a cell plate forms. Control of Cell Division 1. Go Signals: These trigger the cell to divide: ○ Surface-to-Volume Ratio: When a cell grows too large and its membrane can’t support the needs of its volume, it gets a signal to divide. ○ Chemicals: Certain substances, like growth factors and hormones, can also stimulate cell division. 2. Stop Signals: These tell the cell to stop dividing: ○ Availability of Space: Cells usually stop dividing when they touch other cells. This is called contact inhibition. These signals help maintain proper cell growth and prevent issues like overcrowding or tumors. 1. Key Proteins: ○ Cyclins: These are regulatory proteins that build up during interphase, helping the cell get ready for division. ○ Cyclin-dependent Kinases (Cdks): These enzymes bind to cyclins and become activated. The cyclin-Cdk complex then triggers a series of events that prepare the cell for mitosis. ○ Destruction of Cyclins: After the cell divides, cyclins are broken down, allowing the process to start over. 2. Checkpoints: ○ Purpose: Checkpoints are critical points in the cell cycle where the cell checks for errors. If any issues are found, division is paused until repairs are made. ○ G1 Checkpoint: This is the most crucial checkpoint. If the cell doesn’t pass this checkpoint, it enters a resting state called G0, where it won’t divide further. These regulatory mechanisms ensure that cells divide correctly and maintain proper function. Protein Synthesis 1. Master Blueprint: DNA is like a master blueprint that contains the instructions for making proteins. 2. Genes: A gene is a specific segment of DNA that codes for one polypeptide (a chain of amino acids that forms a protein). 3. Nitrogen Bases: The code in DNA is determined by the order of four nitrogen bases: Adenine (A), Guanine (G), Thymine (T), and Cytosine (C).  4. Triplet Code: The genetic code is read in groups of three bases, known as a triplet code. Each triplet specifies a particular amino acid. ○ For example, the triplet GGC codes for the amino acid glycine, while GCC codes for arginine. 5. Exons and Introns: ○ Exons: These are the parts of the gene that actually code for amino acids. ○ Introns: These are noncoding segments that are found between the exons. They are not used in the final protein. This organization allows cells to create a wide variety of proteins based on the sequences of their genes. The Role of RNA 1. Messenger RNA (mRNA): ○ Single-Stranded: mRNA is a single strand of nucleotides. ○ Transcription: The code from the DNA template strand is copied into mRNA using complementary base pairing (A pairs with U, and C pairs with G). This process is called transcription. ○ Codons: mRNA maintains the triplet code from DNA, known as codons, which specify which amino acids will be added during protein synthesis. 2. Ribosomal RNA (rRNA): ○ Structural Component: rRNA is a key part of ribosomes, which are the organelles where proteins are made. ○ Translation: rRNA works with tRNA to help translate the message from mRNA into a polypeptide (a chain of amino acids). 3. Transfer RNA (tRNA): ○ Amino Acid Carrier: tRNA carries specific amino acids to the ribosome. ○ Anticodon: Each tRNA has an area with a triplet code (anticodon) that matches a codon on the mRNA. This allows tRNA to deliver the correct amino acid to the growing polypeptide chain. ○ Translation: The process where tRNA pairs its anticodon with the mRNA codon at the ribosome is called translation, adding the specific amino acid to the polypeptide chain. Together, these types of RNA work in harmony to translate the genetic code into functional proteins. Protein Synthesis 1. Transcription: ○ This is the first step where the information in DNA is copied into messenger RNA (mRNA). The DNA strand serves as a template, and complementary base pairing creates an mRNA strand that carries the genetic code. 2. Translation: ○ In this second step, the mRNA is decoded to assemble polypeptides (chains of amino acids). Ribosomes read the mRNA codons, and transfer RNA (tRNA) brings the corresponding amino acids to form a polypeptide chain. These two processes work together to turn genetic information into functional proteins. Transcription 1. Initiation: ○ RNA polymerase, the enzyme responsible for transcription, attaches to the DNA and separates the two strands to start the process. 2. Elongation: ○ RNA polymerase adds complementary nucleotides to the growing mRNA strand. It matches the sequence based on the DNA template strand. ○ A short segment, about 12 base pairs long, where the DNA and mRNA are temporarily bonded, is called the DNA-RNA hybrid. 3. Termination: ○ Transcription ends when RNA polymerase encounters a specific termination signal in the DNA. This signals the end of the mRNA synthesis. These phases ensure that the genetic information is accurately copied from DNA to mRNA. Translation 1. Amino Acid Binding: ○ tRNA has a structure that allows it to bind a specific amino acid at one end (the stem). When the amino acid is attached, the tRNA is referred to as aminoacyl-tRNA. 2. Anticodon: ○ At the other end of the tRNA (the head) is an anticodon, which is a triplet code that determines which amino acid can be loaded onto the stem. The anticodon pairs with the corresponding codon on the mRNA during translation. ○ For example, tRNA with the anticodon UAU will carry the amino acid methionine to the ribosome. This process ensures that the correct amino acids are added in the proper sequence to build proteins based on the mRNA template.  1. Initiation: ○ The small ribosomal subunit binds to the mRNA at the start codon (usually AUG). ○ A specific tRNA carrying the corresponding amino acid (methionine) pairs with the start codon. ○ The large ribosomal subunit then joins to form a complete ribosome. 2. Elongation: ○ The ribosome moves along the mRNA, and tRNAs bring the appropriate amino acids to the ribosome based on the codons in the mRNA. ○ Each tRNA's anticodon pairs with the mRNA codon, and the ribosome catalyzes the formation of peptide bonds between amino acids, creating a growing polypeptide chain. 3. Termination: ○ Translation ends when the ribosome reaches a stop codon (like UAA, UAG, or UGA). ○ Release factors bind to the stop codon, prompting the ribosome to release the completed polypeptide and disassemble. These phases work together to translate the mRNA code into a functional protein. Initiation 1. Binding of the Small Ribosomal Subunit: ○ The small ribosomal subunit attaches to a special initiator tRNA carrying methionine. ○ This complex then binds to the mRNA that will be translated. 2. Scanning for the Start Codon: ○ The ribosome scans along the mRNA until it finds the first methionine codon, known as the start codon (AUG). 3. Formation of the Functional Ribosome: ○ When the anticodon of the initiator tRNA pairs with the start codon on the mRNA, the large ribosomal subunit attaches to the small subunit. ○ This creates a functional ribosome, with the initiator tRNA positioned in the P site (the peptidyl site) of the ribosome. 4. Empty Sites: ○ At the end of initiation, the A site (aminoacyl site) and the E site (exit site) of the ribosome are empty and ready for the next tRNA to enter. This sets the stage for the elongation phase, where the polypeptide chain will begin to grow. Elongation 1. Codon Recognition: ○ A tRNA with an anticodon complementary to the codon in the A site of the ribosome binds to that codon, bringing a specific amino acid into position. 2. Peptide Bond Formation: ○ Ribosomal enzymes facilitate the transfer of the growing polypeptide chain from the tRNA in the P site to the amino acid on the tRNA in the A site. This forms a new peptide bond, linking the amino acids together. 3. Translocation: ○ The ribosome moves down the mRNA by three bases (one codon), shifting the tRNAs: The tRNA in the A site moves to the P site. The tRNA in the P site moves to the E site (exit site). The tRNA in the E site is ejected from the ribosome. ○ Once the A site is empty, a new tRNA can enter, bringing its amino acid, and the process repeats. This cycle continues, adding amino acids to the growing polypeptide chain until a stop codon is reached. Termination Stop Codons: Translation ends when one of the three stop codons (UGA, UAA, or UAG) enters the A site of the ribosome. Release Factors: Instead of a tRNA, a protein called a release factor binds to the stop codon. This signals the ribosome to stop adding amino acids. Polypeptide Release: The completed polypeptide chain is released from the ribosome. Ribosome Disassembly: The ribosomal subunits disassemble, and the mRNA is freed for potential reuse or degradation. This marks the end of protein synthesis, resulting in a newly formed polypeptide ready for folding and further modifications. Rough ER Processing of Proteins 1. ER Signal Sequence: ○ A short segment of amino acids, called the ER signal sequence, is present on the growing polypeptide chain. This sequence signals the associated ribosome to attach to the surface of the rough ER. 2. Signal-Recognition Particle (SRP): ○ A signal-recognition particle (SRP) recognizes the ER signal sequence and directs the mRNA-ribosome complex to dock on the rough ER.  3. Docking on the ER: ○ Once the ribosome is docked on the rough ER, the forming polypeptide chain enters the lumen of the ER. 4. Vesicle Formation: ○ After the protein is synthesized, it is enclosed in a vesicle, which transports it to the Golgi apparatus for further processing, sorting, and packaging. This pathway ensures that proteins are properly processed and directed to their intended destinations within the cell. Summary: From DNA to Proteins 1. DNA to mRNA: ○ DNA triplets (sets of three bases) are transcribed into mRNA codons. Each codon corresponds to a specific amino acid. 2. mRNA to tRNA: ○ During translation, the mRNA codons are matched with tRNA anticodons. This ensures that the correct amino acids are added in the right order to form the protein. ○ The anticodon sequence of tRNA is similar to the DNA sequence, but with uracil (U) replacing thymine (T). This precise pairing ensures that the genetic code is accurately translated into the amino acid sequence of a protein, allowing for proper protein function. Cell Membrane Composition Phospholipid Bilayer: The cell membrane consists of a double layer of phospholipids, with hydrophilic (water-attracting) heads facing outward and hydrophobic (water-repelling) tails facing inward. Membrane Proteins: These proteins can be integral (spanning the membrane) or peripheral (attached to the surface). They play key roles in transport, communication, and structural support. Role of Membrane Proteins Membrane Transport: ○ Passive Transport: Movement of substances across the membrane without energy expenditure. Types include: Diffusion: Movement of small, nonpolar molecules (e.g., oxygen, carbon dioxide) through the lipid bilayer. Facilitated Diffusion: Movement of larger or polar molecules (e.g., glucose) through protein channels. Osmosis: Diffusion of water through a selectively permeable membrane. ○ Active Transport: Requires energy (usually ATP) to move substances against their concentration gradient. Examples include: Pump Proteins: Transport ions like Na⁺ and K⁺ across the membrane. Endocytosis: Process of engulfing substances into the cell. Exocytosis: Release of substances from the cell. Cell-to-Cell Adhesion: ○ Tight Junctions: Seal neighboring cells together to prevent leakage of molecules. ○ Desmosomes: Provide structural support and resistance to mechanical stress by anchoring adjacent cells. ○ Gap Junctions: Allow direct communication between cells by forming channels for the exchange of ions and small molecules. Organelles Membranous Organelles Nucleus: Contains DNA and controls cellular activities. Endoplasmic Reticulum (ER): ○ Rough ER: Studded with ribosomes; synthesizes proteins. ○ Smooth ER: Synthesizes lipids and detoxifies harmful substances. Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for transport. Mitochondria: Powerhouse of the cell; produces ATP through cellular respiration. Lysosomes: Contain digestive enzymes to break down waste. Non-Membranous Organelles Ribosomes: Sites of protein synthesis. Cytoskeleton: Provides structure and support, facilitates movement. Centrioles: Involved in cell division and formation of spindle fibers. The Nucleus and Cell Cycle 1. G1 Phase: ○ DNA exists as chromatin (uncondensed form). ○ The cell grows and synthesizes proteins. ○ Transcription: Initiation: RNA polymerase binds to DNA. Elongation: RNA polymerase synthesizes mRNA. Termination: RNA polymerase reaches the termination signal. ○ Translation: Initiation: Ribosome assembles on mRNA. Elongation: tRNA brings amino acids, forming a polypeptide chain. Termination: Stop codon is reached, and the polypeptide is released. 2. S Phase: ○ DNA replication occurs, converting chromatin into sister chromatids (each consisting of identical DNA strands). 3. G2 Phase: ○ Further growth and preparation for division occur, with checks for DNA integrity. 4. M Phase (Mitotic Phase): ○ Prophase: Chromatin condenses into chromosomes; the nuclear envelope breaks down. ○ Metaphase: Chromosomes line up at the cell's equator. ○ Anaphase: Sister chromatids are pulled apart to opposite poles. ○ Telophase: Nuclear envelopes reform around each set of chromosomes. ○ Cytokinesis: Cytoplasm divides, forming two distinct daughter cells. Control of the Cell Cycle Cyclins and Cyclin-Dependent Kinases (Cdks): Cyclins accumulate during the cell cycle and activate Cdks, which regulate progression through the cell cycle. Checkpoints: Critical points (G1, G2, and M checkpoints) ensure that the cell is ready to proceed to the next phase. If errors are detected, the cycle is halted for repairs. Complementary Base Pairing DNA: Composed of triplets (codons) made of adenine (A), guanine (G), thymine (T), and cytosine (C).  mRNA: Transcribed from DNA, replacing thymine (T) with uracil (U). Codons in mRNA correspond to specific amino acids. tRNA: Has anticodons that pair with mRNA codons, ensuring the correct amino acids are added during translation.