General Biology PDF

INTRODUCTION TO BIOLOGY SCIENCE - From Latin “Scientia” meaning knowledge - A body of knowledge that delves into the natural wonders of the world by utilizing systematic processes (eg. scientific method) Basic Science...

INTRODUCTION TO BIOLOGY SCIENCE - From Latin “Scientia” meaning knowledge - A body of knowledge that delves into the natural wonders of the world by utilizing systematic processes (eg. scientific method) Basic Science Applied Science - Theories and knowledge fundamentals - Application of knowledge with scientific without application explanations - Solves practical problems - Branches of Science: 1. Natural Science a. Physical Science - Physics, chemistry b. Life Science - Anatomy, botany c. Earth Science - Astronomy, geology 2. Social Science - Psychology, anthropology, law, economics 3. Formal Science - Math, logic, statistics Biology - From Greek “Bios” (Life) and “Logos” (Study) - Study of living organisms and their interactions with one another and their environment - A science because it undergoes the Scientific Method - method of research with defined steps that include experiments and careful observation - testing of hypotheses by means of repeatable experiments - Hypothesis - suggested explanation for an event, which can be tested - Types of Scientific Reasoning 1. Inductive Reasoning - Specific to general - Bottom-up reasoning - Observing a pattern in a particular problem before drawing a conclusion 2. Deductive Reasoning - General to specific - Top-bottom reasoning - General ideas are drawn as a premise or grounds before drawing specific conclusions - Two main pathways of scientific study 1. Descriptive/Discovery science - Usually inductive, aims to observe, explore, and discover 2. Hypothesis-based science - Usually deductive, begins with a specific question or problem and a potential answer or solution that can be tested 1  *Null hypothesis - either two variables have no or the same effect *Alternative hypothesis - there is a difference in the result between variables Are viruses living things? - Viruses dont contain cell and organelles, but made up of genetic material within a protective shell “captids” - Incapable of homeostasis, temperature regulation - Needs a host to survive and replicate and as an energy source - Incapable of metabolic processes - As long as they dont posses all the core principles of life, they are nonliving things Properties of Life/Characteristics of Life Order / Composition - highly organized - coordinated structures that consist of one or more cells a. Unicellular - Asexual reproduction - Cannot be seen by the naked eye b. Multicellular - Organized into tissues - Made up of multiple cells Sensitivity or Response to Stimuli - Adapt to certain conditions/stimuli that leads to evolution - Eg. - plants can bend toward a source of light, climb on fences and walls, or respond to touch - tiny bacteria can move toward or away from chemicals (chemotaxis) or light (phototaxis). a. Positive Response - movement toward a stimulus b. Negative Response - movement away from a stimulus Reproduction - Process where organisms reproduce and release offspring - Ability to pass down genetic information - Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form two new cells. - Multicellular organisms often produce specialized reproductive germline cells that will form new individuals. - genes containing DNA are passed along to an organism’s offspring. - These genes ensure that the offspring will belong to the same species and will have similar characteristics, such as size and shape. a. Single-celled organisms 2  - Duplicates DNA and divides it equally to form two new cells b. Multicellular organisms - Produces gametes, oocytes, and sperm cells - Fertilization occurs and DNA genes are passed to the offspring 1. Asexual - One parent - Eg. cell division, fragmentation, budding, plant cutting 2. Sexual - Two parents - Eg. producing sperm and egg cells, fertilization Growth and Development - Organisms grow and develop following specific instructions coded for by their genes. - genes provide instructions that will direct cellular growth and development, ensuring that a species’ young will grow up to exhibit many of the same characteristics as its parents. Regulation - multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. - Eg. Nutrient transport and Blood flow. - Organs (groups of tissues working together) perform specific functions, such as carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body. Homeostasis - Maintenance of a stable internal environment - regulated through control systems which have receptors, a set point and effectors in common. - Requirements of Organisms for Maintenance of Life: 1. Water 2. Food 3. Oxygen 4. Heat 5. Pressure - Homeostasis Receptor - senses the change in environment different from the set point (36.6C) Control Center - generates the response Effector - the muscle (that contracts or relaxes) or gland that secretes - Kinds of Response: A. Positive Response Loop - feedback serves to intensify a response until an endpoint is reached B. Negative Response Loop - feedback serbes to reduce an excessive response and keep a variable within the normal range Energy Processing / Gathering and Using Energy 3  - The cellular “machinery” - Having a source of energy for metabolic activities - Metabolism - building and breaking down of chemical substances a. Catabolism (Cellular Respiration) - Reactions involved in breaking down of molecules into smaller substances - Produces energy - STEPS: Glycolysis, Intermediate Step, Krebs Cycle, Electron Transport Chain b. Anabolism (Photosynthesis) - Reactions involved in the synthesis or build-up of complex molecules from simple substances - Requires energy - STEPS: Light-dependent Reaction, Light-independent Reaction (Calvin Cycle) - All organisms use a source of energy for their metabolic activities. - Some organisms capture energy from the sun and convert it into chemical energy in food - others use chemical energy in molecules they take in as food 5 Core Principles of Life 1. Cell 2. Gene 3. Evolution by Natural Selection 4. Chemistry 5. Information Level of Organization of Living Things Cellular 1. Atom - smallest unit of matter; composed of protons, neutrons, and electrons 2. Molecule - a group made up of one or more atoms chemically bonded 3. Macromolecule - very large molecule for biological processes 4. Organelle - subcellular structure that has one or more specific jobs to perform in the cell 5. Cell - basic structural, functional, and biological unit of life, responsible for life’s processes Organismal 6. Tissue - group of cells that possess a similar structure and perform a specific function 7. Organ - made up of cells and tissues that perform specific functions 8. Organ System - a biological system consisting of a group of organs that work together to perform functions 9. Organism - an individual living thing that carries on the activities of life by means of organs Populational 10. Population - all organisms of the same group or speciesthat live in a specific area and capable of breeding among themselves 11. Species - a class of things of the same kind and with the same name 12. Community - an interacting group of various organisms in a common location 13. Ecosystem - community of living organisms and their physical environment (nonliving things) interacting together 14. Biome - community of plants and animals that occur naturally in an area, often sharing common characteristics specific to that area 15. Biosphere - a global ecosystem made up of living organisms (biota) and the nonliving (abiotic) factors that provide them with energy and nutrients 4 5 BIOLOGICAL MACROMOLECULES Organic Compounds - Compounds that contain carbon - Covalently bonded (sharing of electrons - does not lead to complete positivity/negativity) - Attraction depends on the valence electrons - Presented as Structural Formulas - Tells how they are arranged - Inorganic compounds are presented as molecular formulas - Tell only the number of atoms present in the molecule - Isomers - compounds that have the same formula but different arrangement - Eg. Fructose and Galactose are isomers of Glucose (C6H12O6) - Eg. Biological Macromolecules - Large molecules essential for life - Made up of Monomers - macromolecules are usually polymers - A building block; usually referring to the same type of “block” that makes up something larger - Eg. Carbohydrates, lipids, proteins, and nucleic acids - Form by Dehydration Synthesis Reaction - AKA Condensation Reaction and Dehydration Synthesis - monomers combine with each other using covalent bonds to form larger molecules known as polymers - In doing so, monomers release water molecules as byproducts. 6  - Breaks down through Hydrolysis Synthesis - Polymers are broken down into monomers through the introduction of water molecules Biomolecules Carbohydrates - Purpose: a. Gives instant energy for the body through glucose - Glucose - a simple sugar that is a component of starch and an ingredient in many staple foods b. Forms the cell walls of plants (Cellulose) and fungi (Chitin) - Chitin also makes exoskeletons for insects and crabs - Provide ATP for most cell functions - Sources: rice, bread, pasta, wheat, GO foods - Made up of Monosaccharide monomers a. Monosaccharides - Simple sugars with 1 sugar unit - Gen. Formula: (CH2O)n or CnH2nOn - Most monosaccharide names end in “-ose” - Identified based on the number of Carbon atoms - Usually ranges from 3 to 7 - eg. Triose, Pentose, Hexose - Aldose - sugar with an aldehyde group (R-CHO), the carbonyl group is attached to a hydrogen atom (at the end) - Ketose - sugar with a ketone group [RC(=O)R’], the carbonyl group is attached to two carbon atoms (in the middle) - Can exist as linear chains or as ringed-shaped molecules - they are usually found in ring forms in aqueous solutions 7  - Common Monosaccharides a. Glucose (C6H12O6) - Aldose, forming a hexagon - used in cellular respiration to make ATP - During cellular respiration, energy is released from glucose, and that energy is used to make adenosine triphosphate (ATP) - Excess glucose is often stored as starch that is catabolized by herbivores/omnivores - In ring form, glucose can have 2 different arrangements of the hydroxyl group (OH) around the anomeric carbon (carbon 1 that becomes asymmetric in the process of ring formation) - Alpha Position (α) - hydroxyl group is below carbon 1 in the sugar - Beta Position (β) - hydroxyl group is above the plane - These dictate which polysaccharides can be broken down How Linear Glucose turns into rings - The ring form is formed by reacting the free aldehyde end of open-chain glucose with one of the hydroxyl groups attached to other carbon atoms of the chain. - The oxygen from the hydroxyl group bonds with the hydrogen of the aldehyde b. Galactose (C6H12O6) - part of lactose (milk sugar) - aldose, forming a hexagon c. Fructose (C6H12O6) - found in sucrose (in fruits) - ketose, making a pentagon d. Ribose (C5H10O5) 8 b. Disaccharides - form when two monosaccharides undergo dehydration reaction - Gen. Formula: C12H22O11 - During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another, releasing a molecule of water (H2O) and forming a covalent bond - Glycosidic Bond - a covalent bond formed between a carbohydrate molecule and another molecule - AKA glycosidic linkages, can be of the alpha or the beta type - Common Disaccharides: a. Lactose - Consists of glucose and galactose b. Maltose - or malt sugar, formed by a dehydration reaction between two glucose molecules c. Sucrose - most common disaccharide, or table sugar, composed of glucose and fructose c. Oligosaccharides - a saccharide polymer containing typically three to nine simple sugars. d. Polysaccharides - A long chain of monosaccharides linked by glycosidic bonds - Chains may be unbranched (amylose) or branched (amylopectin) - Gen. Formula: (C6H10O5)n - Common Polysaccharides ☘️ 1. Storage Polysaccharides a. Starch - Stored forms of sugars in plants - made up of a mixture of amylose and amylopectin (polymers of glucose) 🐽 - Has α glycosidic bonds, which can be digested by animals b. Glycogen - Storage form of sugars in humans and other vertebrates - Made up of monomers of glucose - Highly branched molecule usually stored in the liver and muscle cells - Stored form of sugars in plants - made up of a mixture of amylose and amylopectin (polymers of glucose) - Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process known as glycogenolysis. - Has α glycosidic bonds, which can be digested by animals ☘️ 2. Structural Polysaccharides a. Cellulose - Most abundant natural biopolymer - The cell wall of plants is mostly made of cellulose; provides structural support to the cell - Has rigidity and high tensile strength - Cellulase can break down cellulose into glucose monomers - Has β glycosidic bonds, making it indigestible for animals b. Chitin - A polysaccharide-containing nitrogen - made of repeating units of N-acetyl-β-d-glucosamine, a modified sugar. 9  - Make up the exoskeleton of arthropods (insects, crustaceans) - Major component of fungal cell walls - Has β glycosidic bonds, making it indigestible for animals c. Peptidoglycan - Or murein, provides rigidity to the cell - Found in the cell walls of bacteria - Consists of sugars and amino acids that form a mesh-like layer (sacculus) that surrounds the bacterial cytoplasmic membrane ★ Most sugars end in “-ose”, a carbohydrate clue ★ Carbohydrates contain soluble and insoluble elements; the insoluble part is known as fiber, which is mostly cellulose. Lipids - Largely nonpolar in nature - Hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds - Non-polar molecules are hydrophobic or insoluble in water - Functions: a. Long-term energy storage as fats b. Insulation from the environment c. Building blocks of hormones d. Constituents of cellular membranes - Common Lipids: a. Triglycerides - Contain glycerol and 3+ fatty acids, bonded by ester bonds through dehydration synthesis I. Fatty Acids - Has a hydrocarbon chain, methyl group, and an acid group 10 - Can either be saturated or unsaturated: i. Saturated (single bonds) - Solid at room temperature - Unhealthier because it has the ability to stack itselves on each other, forming blockages ii. Unsaturated (double bonds) - Double bonds result in kink/bending, which affects the melting point of the fat - Liquid at room temperature, most are called oils a. Trans Fats - Hydrophobic - Hydrogen in the double bond is opposite each other - Unhealthier because it has the ability to stack itselves on each other, forming blockages b. Cis Fats - Hydrophobic - Hydrogen in the double bond are on the same side - The cis double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature - Omega Fatty Acids - Essential fatty acids are fatty acids required but not synthesized by the human body. They have to be supplemented through ingestion via the diet. - Omega-3 fatty acids fall into this category and are one of only two known for humans (the other being omega-6 fatty acid). - These are polyunsaturated fatty acids and are called omega-3 because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by a double bond. - The farthest carbon away from the carboxyl group is numbered as the omega (ω) carbon - if the double bond is between the third and fourth carbon from that end, it is known as an omega-3 fatty acid. - Nutritionally important because the body does not make them, 11  - omega-3 fatty acids include alphalinoleic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), all of which are polyunsaturated. - For the elasticity of fish whose under colder conditions II. Glycerol - An organic compound (alcohol) with 3C, 5H, and 3OH b. Waxes - Non-polar; Made up of long fatty acid chains esterified to long-chain alcohols - Making them more hydrophobic - Found in the protective coating on leaves and other surfaces of animals c. Phospholipids - major constituents of the plasma membrane, the outermost layer of animal cells. - Contain glycerol, 2 fatty acids (forming a diacylglycerol), and a phosphate group (attached at the 3rd Carbon of glycerol) - The phosphate head is hydrophilic and Fatty acid tails are hydrophobic - Because of this, phospholipids arrange so that only the hydrophilic head interact with a watery environment; while the hydrophobic tails crowd inward - In water, phospholipids assemble into a bilayer structure or micelle; otherwise, it forms phospholipid bilayer when in a membrane 12  d. Steroids - Composed of four fused rings of carbon and several of them, like cholesterol, have a short tail - Many steroids also have the -OH group, putting the, in the alcohol classification (sterols) - Grouped with other lipids because they are also hydrophobic and insoluble in water - Present in the plasma membrane where it stabilizes the membrane - Eg. - Cholesterol - Most common steroid, mainly synthesized in the liver - Precursor to many steroid hormones like testosterone and estrogen, Vitamin D, and Bile salts (helps in the emulsification of fats and their subsequent absorption by cells - Component of the plasma membrane of animal cells and is found in within the phospholipid bilayer. Controls/contibutes for membrane fluidity e. Sphingolipids - Specifically found in the brain, lungs, nerve tissues - Serve as surfactants to reduce tension in the lungs, maintaining their shape Proteins - One of the most abundant organic molecule 13 - Proteins have different shapes and molecular weights; some are globular in shape whereas others are fibrous in nature - Hemoglobin is a globular protein - are long strands of polypeptide chains that have cross-linkages due to hydrogen bonds - They have little or no tertiary structure - Due to the large number of hydrophobic R groups fibrous proteins are insoluble in water - Collagen, found in our skin, is a fibrous protein - compact, roughly spherical (circular) in shape and soluble in water - Polymers of amino acids, arranged in a linear sequence - Made from long chains of amino acids - Amino Acid - All amino acids have similar structures: with a carboxyl (-COOH), an amino group (-NH2), and an R group (gives unique chemical properties) - Each polypeptide has a free amino group at one end (the N terminal, or the amino terminal) - the other end has a free carboxyl group, (the C or carboxyl terminal). 14 - Combined through a condensation/dehydration synthesis reaction (removes water) - Linked through peptide bonds - Peptides - chain of amino acids linked by peptide bonds (can be dipeptide or polypeptide) - a polypeptide is a polymer of amino acids 15 - As these chains form, the polypeptide develops multiple levels of structures, which contributes to its overall shape 1. Primary Structure - The linear order of amino acids in a polypeptide chain - The sequence of every protein is determined by the gene encoding the protein - A change in nucleotide sequence of the gene’s coding region may lead to a different amino acid being added to the growing polypeptide chain, causing a change in protein structure and function 2. Secondary Structure - Refers to the beta-pleated sheet or alpha-helix that a protein chain can form due to hydrogen bonding and other chemical attractions between the R groups of nearby amino acids - Hydrogen bonds - bonding between hydrogen and oxygen atoms 16  3. Tertiary Structure - The overall structure of a polypeptide - Created when the secondary structure folds and twists upon itself held by a variety of bonds and interactions that form between the R groups - Commonly referred to as Proteins once they form the tertiary structure - R groups with like charges are repelled by each other; those with unlike charges are attracted to each other (ionic bonds) - When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein - Hydrophobic Interactions - interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding 4. Quaternary Structure - Some proteins can form quaternary structures - Formed by many polypeptide chains - Consists of interactions between multiple proteins - Often result in large protein complexes - Eg. Hemoglobin and Sodium channels in the cell membranes - Protein Denaturation - Protein shape is critical to its function, and this shape is maintained by many different types of chemical bonds. - Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, - changes in shape lead to loss of function, known as denaturation. - Often irreversible due ro the primary structure of the polypeptide is conserved during the process, leading to the loss of function - If the denaturing protein is removed, protein is allowed to resume its function - Factors: Temperature, Acid/pH level, 17 Nucleic Acids - An organic macromolecule - Most important macromolecules for the continuity of life - Carry the genetic blueprint of the cell - Carry instructions for the functioning of the cell - Responsible for storing genetic/hereditary information and protein synthesis - Nucleotide - The monomer building block for nucleic acids bound by phosphodiester bonds - Polynucleotides - monomers of nucleotides - Made up of 3 components i. 5C Sugar (Pentose) - RNA - Ribose - DNA - Deoxyribose (has 1 less oxygen) - The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. - The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). ii. Phosphate Group iii. Nitrogenous Base 18  - RNA - contain either Adenine, Uracil, Cytosine, or Guanine - DNA - contain either Adenine, Thymine, Cytosine, or Guanine - Purines VS. Pyrimidines - Purines - Adenine and Guanine, has 2 carbon-nitrogen rings - Pyrimidines - Cytosine, Thymine, Guanine, have single carbon-nitrogen ring - Linked together by dehydration synthesis, or polymerization reaction, of the sugar and phosphate group of another - A sugar-phosphate backbone is formed and the nitrogenous bases project to one side of the backbone - Structure: - RNA - single-stranded nucleic acid - DNA - double-stranded/helix nucleic acid - Types: a. Deoxyribonucleic Acid - The genetic material - Found in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria - DNA is not enclosed in a membranous envelope in prokaryotes - Main component of chromatin which will condense into the chromosome shape prior to cell division - The DNA in chromosomes is organized in a specific order that makes up a genes - Genes - contain the direction for every function, trait, and activity - Genome - the entire genetic content of a cell - The two strands in DNA are linked by hydrogen bonds that connects two nitrogenous bases - Structure: - Double-stranded helix molecule in opposite directions (anti-parallel) = 5’ to 3’ and 3’ to 5’ - Phosphodiester Linkage - The phosphodiester linkage is not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules - Complementary Base Pairings - DNA strands are complementary to each other. - During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand. 19 b. Ribonucleic Acid - Mostly involved in protein synthesis - Build specific proteins by assembling the amino acids in a particular order - Types of RNA i. Messenger RNA (mRNA) - carries the message from DNA, which controls all of the cellular activities in a cell. - In the cytoplasm, the mRNA interacts with ribosomes and other cellular machinery 20  - The mRNA is read in sets of three bases known as codons. - Each codon codes for a single amino acid. - In this way, the mRNA is read and the protein product is made. ii. RIbosomal RNA (rRNA) - major constituent of ribosomes on which the mRNA binds. - ensures the proper alignment of the mRNA and the ribosomes; - the rRNA of the ribosome also has an enzymatic activity (peptidyl transferase) and catalyzes the formation of the peptide bonds between two aligned amino acids. iii. Transport RNA (tRNA) - It carries the correct amino acid to the site of protein synthesis. - It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain iv. MicroRNA (miRNA) - smallest RNA molecules and their role involves the regulation of gene expression by interfering with the expression of certain mRNA messages. - Central Dogma of Life - information flow in an organism takes place from DNA to RNA to protein. - Functions as a way of producing proteins for gene expression 1. Replication - DNA is duplicated 2. Transcription - Process where RNA is produced/converted from DNA 3. Translation - RNA is translated into protein - Process of assembling a protein/polypeptide chain from amino acids/peptides dictated by mRNA - Codon - triplet of nucleobases determining sequence of amino acids - Start Codon - represented by AUG (methionine) - Stop Codon - ends the translation but does not produce an amino acid, represented by UAA, UAG, or UGA ENZYMES - most enzymes are Proteins (tertiary and quaternary structures), substances, or Ribonucleic acids - Act as a catalyst to accelerate a chemical reaction by lowering activation energy - Like in Respiration, Photosynthesis, Digestion, and Protein Synthesis - Not permanently changed in the chemical process 21 - Some Enzymes help to break down molecules, build up smaller molecules, or completely change them - Enzymes are selective to which they bind to, has specificity to certain substrates - Works with Substrate - The chemical reactants to which an enzyme binds at the Active Site - Examples: a. Catabolic Enzymes - break down i. Protease - breaks Proteins to Amino Acids ii. Carbohydrase - breaks Carbohydrates to Glucose iii. Lipase - breaks Fats/Lipids to Fatty Acids & Glycerols iv. Catalase - Breaks Hydrogen Peroxide to Water & Oxygen v. Pepsin - breaks down proteins to peptides vi. Amylase - assists in breaking down carbohydrates b. Anabolic Enzymes - build up c. Catalytic Enzymes - speed up rate of reaction - Parts of an Enzyme a. Active Site - The Active Site is the location within the enzyme where the substrate binds - where the “action” happens, - there is a unique combination of amino acid residues (also called side chains, or R groups) within the active site, making it unique to a specific substrate. b. Co-factor - Non-protein part - May be Cations (activators), bound temporarily to the active site to activate the enzyme - are inorganic ions such as iron (Fe++) and magnesium (Mg++) - the enzyme that builds DNA molecules, DNA polymerase, requires bound zinc ion (Zn++) to function. c. Coenzymes - Organic molecules like dietary vitamins 22  - are organic helper molecules, with a basic atomic structure made up of carbon and hydrogen, which are required for enzyme action. d. Prosthetic Groups - Permanently bound to the enzyme - Holoenzyme = Apoenzyme (Inactive Enzyme) + Coenzyme (Cofactor) - Models of Enzyme Action a. Collision theory states that for a chemical reaction to occur, the reacting particles must collide with one another. b. Lock and Key Hypothesis - The substrate fits into the active site where their shapes complement each other like puzzles c. Induced Fit Hypothesis - The enzyme, upon binding of a substrate, changes its shape and binds to the substrate more tightly - Environmental Effects of Enzyme Function a. Temperature - As temperature increases, the rate of reaction also increases due to higher kinetic energy - The suitable temperature for enzymes to function properly is 37C (not always) 23  - Increasing or decreasing the temperature affects the chemical bonds in the active site, making them less suited to bind with substrates - Extreme Temperatures can Denature Enzymes - Optimum temperature - temperature wherein there is the highest rate of reaction, differs for different enzymes b. pH Level - Measure of Acidity - Amino acids in the active sites are acidic or basic - Fluctuations in the pH can affect these amino acids, making it harder for substrates to bind - Extreme pH Levels can Denature Enzymes - Optimal pH - ph level where there is the highest rate of reaction, depending on where the enzymes work in (eg. enzymes in the stomach works best at pH level 2) c. Enzyme Concentration - Increasing enzyme concentration will increase the rate of reaction as more enzymes will be available to bind with substrates - However, after a certain concentration, any increase will not affect the rate of reaction d. Substrate Concentration - Increasing substrate concentration increases rate of reaction as more substrates will be colliding with enzymes, so more products will be produces - Only valid until certain concentration 24  - Saturation point - all enzymes are occupied by the amount of substrate present, meaning no more reactions - Inhibition of Enzyme Activity - Inhibitors reduce or stop the activity of enzymes by blocking or distorting the active site - Types of inhibitors: a. Competitive Inhibitors - Occupy the active site, which blocks substrates from bonding to the active site - However, bonding of enzymes and substrates may still happen, leading to just lower rate of reaction - In some cases, substrates can remove competitive inhibitors b. Noncompetitive Inhibitors - Attach to parts of the enzyme other than the active site (allosteric site), which distorts the shape of the enzyme, - Substrates cant remove noncompetitive inhibitors - Allosteric Inhibition - inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the affinity of the enzyme for its substrate. - Allosteric Activation - inhibitor molecules bind to enzymes in a location which changes the activation site in a way that allows substrates to bind to it 25  - Feedback Inhibition - The end product attached itself to the enzyme as an allosteric inhibitor to change the active site, so the substrate cannot bind to it anymore - Too much product/substrates is bad CELL STRUCTURE AND FUNCTION Cell Theory - All living organisms are made up of cells - Principles of Cell Theory: - Old Cell Theory 1. Cells are the basic/smallest unit of life that carry out action a. Because they show all the processes of all living organisms - Eg. - Energy Processing in the Mitochondria and Chloroplast (the totality of all chemical reactions of the cell/body) - Homeostasis in the cell; Nucleus as the control center, Cell membrane that regulates which can enter the cell, lysosomes as the digestive system - Reproduction through Cell division - Cells have Order/Composition because it is made up of organelles that work together - Cells grow through accumulation of nutrients b. Individual organelles cant show these processes on their own (as well as viruses) 2. All living things are composed of cells 3. All cells come from pre-existing cells - Modern Cell Theory 1. Genetic information is passed down during cell division 26  2. Cells have the basic chemical composition 3. Energy flow happens in the cell - Timeline: 1. 1590 Zacharias - Invented the compound microscope Janssen 2. 1655 Robert Hooke - Coined the word “Cells ”using a light microscope to look at cork tissues in the publication Micrographia 3. 1674 Antonie van - Observed microscopic organisms in pond water Leeuwenhoek - terming them ‘animalcules’ 4. 1838 Matthias - realizes all plants are made up of cells. Schleiden - Is co-credited with developing the first two principles of cell theory 5. 1839 Theodor - realizes all animals are made up of cells. Schwann - Is co-credited with developing the principles of cell theory 6. 1855 Rudolf Virchow - says that cells come from other cells. - Is credited with the third principle of cell theory Components of All Cells - Organelle - “Little Organ” - A specialized cellular part that has a specific function 27 - All cells have: a. Plasma membrane - an outer covering that separates the cell’s interior from its surrounding environment b. Cytoplasm - consisting of a jelly-like cytosol within the cell in which other cellular components are found c. DNA - the genetic material of the cell d. Ribosomes - synthesize proteins 28 Categories of Cells Prokaryotic Cell (Before Nucleus) - Prokaryotes - the organsim - single-celled organisms of the domains Bacteria and Archaea - Smaller in size - Dont have membrane-bound organelles, but has cell membrane (ribosomes) - Has DNA and RNA but dont contain a nucleus - Prokaryotic DNA is found in a central part of the cell: the nucleoid - DNA is found in the cytoplasm or in a circular form called plasmid - Are simple unicellular organisms that allow them to duplicate quickly - Examples: a. Bacteria - can either be disease-causing pathogens to beneficial b. Archaea - not pathogenic and live in extreme environments - Cell Contents a. Peptidoglycan Cell Wall - Peptidoglycan or Murein - A polysaccharide with sacculus - acts as an extra layer of protection, - helps the cell maintain its shape, - prevents dehydration. b. Polysaccharide Capsule - enables the cell to attach to surfaces in its environment c. Flagella - Used for locomotion/movement d. Pili (singular = sex pilus) - In Sex Pilus - Used to exchange genetic material during a type of cell division (conjugation) - In Pili (many) - helps attach to surfaces e. Fimbriae - Used by bacteria to attach to a host cell - Cell Size - Prokaryotic cells (0.1 to 5.0 μm in diameter) are significantly smaller than eukaryotic cells (10 to 100 μm in diameter) - The small size of prokaryotes allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. 29  - Similarly, any wastes produced within a prokaryotic cell can quickly diffuse out. - Smaller cells have larger surface areas which allows them to disperse better - Larger cells can carry more nutrients and more organelles Eukaryotic Cells (True Nucleus) - cells of animals, plants, fungi, and protists - Eukaryotes - the organism - Components: - a membrane-bound nucleus (true nucleus) - numerous membrane-bound organelles (little organs) with specialized functions - several, rod-shaped chromosomes. - Plant and Animal Cell - - Parts of a Eukaryotic Cell 1. Plasma Membrane 30  - phospholipid bilayer with embedded proteins i. Glycoprotein - protein with carbohydrate attached ii. Glycolipid - lipid with carbohydrate attached - separates the internal contents of the cell from its surrounding environment. - controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. - Plasma Membrane Modifications - microvilli (singular = microvillus) - Increases the surface area for absorption of nutrients - fingerlike projections from folding of the plasma membranes of cells that specialize in absorption - found lining the small intestine, - Only appears in plasma membrane that faces cavity from which substances will be absorbed - Celiac Disease - genetic; immune response to gluten which also damages the Microvilli; leads to malnutrition, cramping, and diarrhea; makes it hard for the body to absorb nutrients - excellent example of form following function. 2. Cytoplasm - Gel-like compound where organelles float - the entire region of a cell between the plasma membrane and the nuclear envelope - Consists of: 31  - Organelles suspended in the gel-like cytosol (intercellular fluid) - Cytoskeleton - Various chemicals - 70 to 80 percent water, has a semi-solid consistency, from the proteins within it. - Where metabolic reactions (eg. protein synthesis) occur - Where sugars (eg. glucose) polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol can be found - Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm 3. Nucleus (plural = nuclei) - Prominent organelle in the cell - Houses the cell’s DNA and directs protein synthesis - DNA stays inside the nucleus, RNA goes outside the nucleus a. Nuclear Envelope - Boundary of the nucleus - Consists of two phospholipid bilayer - double-membrane structure that constitutes the outermost portion of the nucleus - inner and outer membranes of the nuclear envelope are phospholipid bilayers. - punctuated with Nuclear Pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. - Nucleoplasm - semi-solid fluid inside the nucleus, where we find the chromatin and the nucleolus b. Chromatin - Unwound protein chromosome complexes - Descirbes the material making up the chromosomes when condensed and decondensed c. Chromosomes - Made up of DNA, which is made of genes - series of triplet codes that correspond to an amino acid - In eukaryotic cells, chromosomes are linear in structure - Eukaryotes have a specific number of chromosomes (46 in humans) - Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. - When the cell is in the growth and maintenance phases of its life cycle, proteins are attached to chromosomes, and they resemble an unwound, jumbled bunch of threads. Order: 1. Nucleotides - basic building blocks of DNA 2. Deoxyribonucleic Acid - a long molecule made up of nucleotides arranged in a specific sequence 32  3. Gene - specific sequence of nucleotides within the DNA that codes for a particular protein or functional RNA. 4. Chromatin - DNA is packaged into a complex structure called chromatin 5. Chromosomes - are highly condensed and organized structures formed from chromatin. Nucleotides form DNA, which contains genes. DNA wraps around histones to form chromatin, which further condenses into chromosomes, the structures that organize and carry genetic information during cell division. d. Nucleolus (plural = nucleoli) - A darkly staining area within the nucleus - Some chromosomes have sections of DNA that encode ribosomal RNA - The nucleolus aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits - The subunits are then transported out through the pores in the nuclear envelope to the cytoplasm. - Where the ribosomes are made 4. Ribosomes - Responsible for protein synthesis - ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. (viewed in an electron microscope) - may be attached to the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum and the outer membrane of the nuclear envelope - large complexes of protein and ribosomal RNA, - consist of two subunits, called “large” and “small” - receive their “orders” for protein synthesis from the nucleus where the DNA is transcribed into messenger RNA (mRNA). - The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. - Found in every cell, abundant in cells that synthesis large amounts of protein 5. Mitochondria (singular = mitochondrion) - Powerhouses or energy factories of the cell - responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. - Cellular respiration is the process of making ATP using the chemical energy found in glucose and other nutrients. - Cellular respiration uses oxygen and produces carbon dioxide as a waste product. - oval-shaped, double membrane organelles that have their own ribosomes and DNA - Each membrane is a phospholipid bilayer embedded with proteins - Cristae - The inner layer that has folds called cristae for ATP synthesis and to increase surface area for cellular respiration. 33  - Mitochondrial Matrix - The area surrounded by the folds 6. Peroxisomes - small, round organelles enclosed by single membranes. - carry out oxidation reactions that break down fatty acids and amino acids. - detoxify many poisons that may enter the body (the liver has a lot of peroxisomes). - oxidation reactions release hydrogen peroxide, H2O2, which would be damaging to cells; reactions are confined to peroxisomes, - But enzymes (Catalase) safely break down the H2O2 into oxygen and water - alcohol is detoxified by peroxisomes in liver cells. - Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars. 7. Vesicles and Vacuoles - membrane-bound sacs that function in storage and transport. - vacuoles are somewhat larger than vesicles, - The membranes of vesicles can fuse with either the plasma membrane or other membrane systems within the cell. - some agents such as enzymes within plant vacuoles break down macromolecules. - The membrane of a vacuole does not fuse with the membranes of other cellular components. - In plant cells, vacuoles store water - They excrete water if the cell needs it - They absorb water from the cytoplasm or extracellular space when needed - More vesicles in plant cells - the digestive processes take place in vacuoles and lysosomes. 8. Centrosome - microtubule-organizing center (MTOC) found near the nuclei of animal cells. - Organizes interphase microtubules and mitotic spindles - During interphase, microtubules are organized in astral arrays that emanate from the centrosome and serve as a scaffold for organelle and vesicle trafficking - contains a pair of centrioles - two structures that lie perpendicular to each other - Each centriole is a cylinder of nine triplets of microtubules. - Spindle fibers provide the tract for the chromosomes to separate from each other during cell division - Held together by nontubulin proteins - No clear function, because cells that have had the centrosome removed can still divide, and plant cells, which lack centrosomes, are capable of cell division. - the organelle where all microtubules originate - replicates itself before a cell divides, 34. 9. Lysosomes - not found in plant cells but found in animal cells - the cell’s “garbage disposal.” - Modified and specialized vesicles which has digestive enzymes - Enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. - These enzymes are active at a much lower pH than that of the cytoplasm. - The pH within lysosomes is more acidic than the pH of the cytoplasm. - the digestive processes take place in vacuoles and lysosomes in plant cells - Like in the white blood cells, engulf - Pseudopods - are temporary, protruding extensions of the cell membrane used for movement and feeding. They are most commonly found in certain types of eukaryotic cells, such as amoebas and some white blood cells. They are the one that moves and pulls the cell 10. Cell Wall 35  - structure external to the plasma membrane - a rigid covering that protects the cell - provides structural support - gives shape to the cell. - Fungal and protistan cells also have cell walls. - Peptidoglycan - the chief component of prokaryotic cell walls, polysaccharides with polypeptides attached - Chitin - cell walls of fungi, polysaccharide with Nitrogen - Cellulose - the major organic molecule in the plant cell wall, a polysaccharide made up of glucose units. 11. Chloroplasts - plant cell organelles that carry out photosynthesis. - Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. - plants (autotrophs) are able to make their own food, like sugars, while animals (heterotrophs) must ingest their food. - have their own DNA and ribosomes - have outer and inner membranes - within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked fluid-filled membrane sacs called thylakoids - Each stack of thylakoids is called a granum (plural = grana). - Stroma - fluid enclosed by the inner membrane that surrounds the grana. - Contains Chlorophyll - green pigment that captures light energy to drive photosynthesis 36 12. Central Vacuole - plays a key role in regulating the cell’s concentration of water in changing environmental conditions. - if you forget to water a plant for a few days, it wilts - as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm. - As the central vacuole shrinks, it leaves the cell wall unsupported. - This loss of support to the cell walls of plant cells results in the wilted appearance of the plant. - The central vacuole also supports the expansion of the cell. - When the central vacuole holds more water, the cell gets larger without having to invest a lot of energy in synthesizing new cytoplasm. 13. The Endomembrane System - group of membranes and organelles in eukaryotic cells - work together to modify, package, and transport lipids and proteins. - nuclear envelope, lysosomes, and vesicles, the endoplasmic reticulum and Golgi apparatus, plasma membrane is included in the endomembrane system because it interacts with the other endomembranous organelles. - The endomembrane system does not include the membranes of either mitochondria or chloroplasts. 37 14. Endoplasmic Reticulum - a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. - Lumen or Cisternal Space - The hollow portion of the ER tubules. - The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope. - Proteins exit the ER using a vacuole to go towards the golgi body a. Rough Endoplasmic Reticulum (RER) 38  - named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope - Ribosomes transfer their newly synthesized proteins into the lumen of the RER where they undergo structural modifications, such as folding or the acquisition of side chains. - These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles— or secreted from the cell (such as protein hormones, enzymes). - Synthesizes proteins - The RER also makes phospholipids for cellular membranes. - If the phospholipids or modified proteins are not destined to stay in the RER, they will reach their destinations via transport vesicles that bud from the RER’s membrane - Since the RER is engaged in modifying proteins (such as enzymes, for example) that will be secreted from the cell, you would be correct in assuming that the RER is abundant in cells that secrete proteins. b. Smooth Endoplasmic Reticulum (SER) - continuous with the RER but has few or no ribosomes on its cytoplasmic surface - Functions of the SER include : - Metabolism - synthesis of carbohydrates, lipids, and steroid hormones; - detoxification of medications and poisons; - storage of calcium ions. - In muscle cells, a specialized SER called the sarcoplasmic reticulum is responsible for storage of the calcium ions that are needed to trigger the coordinated contractions of the muscle cells. 15. Golgi Apparatus - a series of flattened membrane-bound sacs called cisternae, stacked together - Sorting, tagging, packaging, and distribution of lipids and proteins - Cis Face - The receiving side of the Golgi apparatus - Trans Face - The opposite side is involved in shipping out the processed products. - Forms the tertiary and quaternary structures of proteins, primary and secondary in the Ribosomes and ER - Attaches other substances to the proteins - Exocytosis - process by which vesicles containing cellular products fuse with the plasma membrane, releasing their contents outside the cell. The Golgi apparatus plays a central role in preparing these vesicles for exocytosis. 39  - The transport vesicles that formed from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. - As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. - The most frequent modification is the addition of short chains of sugar molecules. - These newly modified proteins and lipids are then tagged with phosphate groups or other small molecules so that they can be routed to their proper destinations - the modified and tagged proteins are packaged into secretory vesicles that bud from the trans face of the Golgi. - some of these vesicles deposit their contents into other parts of the cell where they will be used - other secretory vesicles fuse with the plasma membrane and release their contents outside the cell. - In plant cells, the Golgi apparatus has the additional role of synthesizing polysaccharides, - some of which are incorporated into the cell wall, - some of which are used in other parts of the cell. 16. Cytoskeleton - network of protein fibers that - help maintain the shape of the cell, - secure some organelles in specific positions, - allow cytoplasm and vesicles to move within the cell, - enable cells within multicellular organisms to move 40 - three types of fibers within the cytoskeleton: a. Microfilaments - the narrowest - have a diameter of about 7 nm - function in cellular movement - made of two intertwined strands (like beads) of a globular protein called actin - also known as actin filaments. - Actin is powered by ATP to assemble its filamentous form, which serves as a track for the movement of a motor protein called myosin. - This enables actin to engage in cellular events requiring motion, such as cell division in animal cells - cytoplasmic streaming - the circular movement of the cell cytoplasm in plant cells. - Actin and myosin are plentiful in muscle cells. - When your actin and myosin filaments slide past each other, your muscles contract - also provide some rigidity and shape to the cell. - They can depolymerize (disassemble) and reform quickly, thus enabling a cell to change its shape and move. - White blood cells (your body’s infection-fighting cells) make good use of this ability. - They can move to the site of an infection and phagocytize the pathogen. 41 b. Intermediate Filaments - made of several strands of fibrous proteins that are wound together - diameter, 8 to 10 nm, is between those of microfilaments and microtubules. - have no role in cell movement; function is purely structural. - bear tension, thus maintaining the shape of the cell, and anchor the nucleus and other organelles in place. - create a supportive scaffolding inside the cell. - the most diverse group of cytoskeletal elements. - Several types of fibrous proteins are found in the intermediate filaments including keratin - create a supportive scaffolding inside the cell. c. Microtubules - small hollow tubes - The walls of the microtubule are made of polymerized dimers of α-tubulin and β-tubulin, two globular proteins - diameter of about 25 nm the widest components of the cytoskeleton - help the cell resist compression - provide a track along which vesicles move through the cell - pull replicated chromosomes to opposite ends of a dividing cell. - Like microfilaments, microtubules can dissolve and reform quickly. - also the structural elements of flagella, cilia, and centrioles in animal cells, the centrosome is the microtubule organizing center 42 17. Flagella and Cilia - Flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell (for example, sperm, Euglena). - When present, the cell has just one flagellum or a few flagella - When cilia (singular = cilium) are present many of them extend along the entire surface of the plasma membrane. - They are short, hair-like structures that are used to move entire cells (such as paramecia) or substances along the outer surface of the cell (for example, the cilia of cells lining the Fallopian tubes or cilia lining the cells of the respiratory tract - In animals, they move particles along the cells - In protists, they move the entire cell - share a common structural arrangement of microtubules called a “9 + 2 array.” - a single flagellum or cilium is made of a ring of nine microtubule doublets, surrounding a single microtubule doublet in the center 43 CONNECTION BETWEEN CELLS - Tissue - group of similar cells working together - If cells work together, they must communicate with each other - Extracellular Matrix of Animal Cells - Most animal cells release materials into the extracellular space. - The primary components of these materials are proteins, and the most abundant protein is collagen. - Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. - These materials are called the extracellular matrix - the extracellular matrix holds the cells together to form a tissue, - it also allows the cells within the tissue to communicate with each other. - Cells have protein receptors on the extracellular surfaces of their plasma membranes. - Cell Communication: 44 - Plasmodesmata - In plant cells - numerous channels that - pass between cell walls of adjacent plant cells, - connect their cytoplasm, - enable materials to be transported from cell to cell, and thus throughout the plant - Tight Junctions - watertight seal between two adjacent animal cells - The cells are held tightly against each other by proteins (predominantly claudins and occludins) - tight adherence prevents materials from leaking between the cells; - typically found in epithelial tissues that line internal organs and cavities, and comprise most of the skin. - the tight junctions of the epithelial cells lining your urinary bladder prevent urine from leaking out into the extracellular space. - Desmosome - found only in animal cells - act like spot welds between adjacent epithelial cells - Short proteins called cadherins in the plasma membrane connect to intermediate filaments to create desmosomes. - The cadherins join two adjacent cells together and maintain the cells in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles. 45  - Gap Junctions - in animal cells, like plasmodesmata in plant cells - channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate - develop when a set of six proteins (called connexins) in the plasma membrane arrange themselves in an elongated donut-like configuration called a connexon. - When the pores (“doughnut holes”) of connexons in adjacent animal cells align, a channel between the two cells forms. - Gap junctions are particularly important in cardiac muscle: - The electrical signal for the muscle to contract is passed - efficiently through gap junctions, allowing the heart muscle cells to contract in tandem. CELL MODIFICATION AND ADAPTION Cell Specialization and Differentiation - Specialized Cells - Have a specific role in the body - They have a specific shape or structure to help them fulfill the role - Have specific amounts of different organelles - Differentiation - Process by which cell changes to become specialized - Changes the shape, structure, and organization of organelles - Stem Cells - Has the ability to divide through Mitosis and to Differentiate 46  - Zygote - a fertilized egg single-cell - Became a ball of cells through cell division - Embryonic Stem Cells - identical unspecialized cells - Able to become every cell in the body - When the zygote becomes about 8 cells big, then it starts differentiation. The embryonic stem cells begin to specialize - Differentiation happens because genes in the DNA are switched on/off and the cells start making different proteins - The set of genes set on in a cell is different from another, which results in different functions and looks - Cells adopt/specialize according to their functions based on their surrounding cells (cell to cell recognition) - Ectoderm - cells specialize to skin cells - Mesoderm - - Adult Stem Cells - Found in infants, children, and adults - can only differentiate into a few types of cells - Forms the type of tissue in which they are found in - Maintain the tissues and organs; can divide and reproduce indefinitely - Mainly used for Repair and Replacement - In Plant Cells - Retains the ability of stem cells to form all types of specialized cells - Stem cells are found in regions called meristems, located in the growing roots and shoots of plants - Stem cells can form to any type of specialized plant cell like xylem (carries water and minerals from the roots to the leaves) or phloem (carries the food prepared by the leaves to different parts of the plant) - A single cell from a meristem tissue can grow into a new plant - Basis for Tissue Culture - used for cloning plants Cell Modification and Adaptation a. Microvilli: - Increases the surface area for increased absorption 47 b. Nerve cells: - Dont divide and replicate like other cells - Nerve cells have neuronal extensions - Axons - send electrical signals - Dendrites - receive electrical signals c. Red Blood cells: - No nucleus → increases the area available inside the cell for the hemoglobin - Flattened surface → increases the surface area for oxygen diffusion - Flexibility → allows for the cell to squeeze through the tiny capillaries of the circulatory system d. Tracheal Cells: - Have cilia that moves rhythmically so that we can cough out foreign substances Cillia in the fallopian tube helps the egg cell travel 48  e. Sperm Cells: - Delivers genetic material to an egg cell for fertilization - Has a number of adaptations: - In the nucleus, it only has half as much genetic material as a normal adult cell to combine with an egg cell - Flagellum allows to swim through the uterus and fallopian tube to reach the cell - Cell is streamlined which helps it swim along - The MidPiece has lots of mitochondria provides the energy for swimming - The Crown/Acrosome has digestive enzymes to break a hole into the egg when it reaches the ovum CELL TRANSPORT MECHANISMS Cell Membrane - Functions: - outline the borders of the cell - determines the nature of its interaction with its environment - selectively permeable - some molecules can pass through while others cant, so waste materials can leave and harmful materials cant enter - flexible - markers for recognition between cells - transmit signals by means of integral proteins known as receptors. - receivers of extracellular inputs - activators of intracellular processes 49 - Structures: - A fluid mosaic that controls what goes in or out of the cell - Fluid because it is flexible - Made up of phospholipids, proteins, and cholesterol a. Has two layers of phospholipids (lipid bilayer) - molecules can pass through pag non-polar siya kasi need ng protein channels if polar sya - Hydrophobic molecules (eg, Alcohol) pass quicker into the layer, than hydropholic - Proteins move slower as they are the largest molecule; Oxygen is the fastest - Backbone - Not rigid and can move in a flexible wave-like motion - The hydrophilic layers will be oriented towards the extracellular fluid (outside) and the cytoplasm (inside the cell) - Has scattered proteins embedded in the phospholipid layers; some with carbohydrates attached - Some small molecules seep in between the lipid bilayers, which make up the majority of the semipermeable cell membranes, but some molecules are too big to get in - Larger molecules move through protein channels embedded in the bilayer b. Cholesterol - Made in the liver - Regulates the fluidity and permeability of the cell membrane as it causes the phospholipids to stay together - Found inside the spaces of the bilayer c. Proteins - can be found in or through the membrane - may serve as enzymes, - as structural attachments for the fibers of the cytoskeleton, - as part of the cell’s recognition sites (“cell-specific”) proteins. - The body recognizes its own proteins and attacks foreign proteins associated with invasive pathogens. - Comes in different types: i. Integral Proteins (transmembrane) - Exposed to an aqueous environment on both sides of the membrane - transport large molecules across the cell membrane - integrated completely into the membrane structure, - hydrophobic membrane-spanning regions interact with the hydrophobic region of the phospholipid bilayer 50  ii. Peripheral Proteins - Located on the surface of a membrane (eg. external - cytoskeleton, enzymes; internal - protein receptors) - found on the exterior or interior surfaces of membranes, but only one side of the layer - attached either to integral proteins or to phospholipids. - involved in communication and some transport iii. Membrane Carbohydrates - Always found on the exterior surface of cells - bound to proteins (glycoproteins) or bound to lipids (glycolipids) - with peripheral proteins, form specialized sites on the cell surface that allow cells to recognize each other (i.e., self vs. non-self) - Glycocalyx important for - cell identification, - self/non-self determination, - embryonic development, - used in cell-cell attachments to form tissues. 1. Glycoproteins - plays a role in cell recognition by the immune system Why is it important for the cell membrane to be selective in allowing materials into and out of the cell? 1. Maintaining Homeostasis: The cell membrane regulates the internal environment of the cell by controlling which substances can enter and exit. This helps maintain a stable internal environment, essential for the cell's survival and function. 2. Nutrient Uptake: The membrane allows essential nutrients, such as glucose, amino acids, and ions, to enter the cell while preventing harmful substances from entering. This ensures that the cell receives the necessary materials for energy production, growth, and repair. 3. Waste Removal: The membrane selectively allows waste products to leave the cell, preventing the accumulation of toxic substances that could harm the cell. 4. Protection: By being selective, the cell membrane protects the cell from potentially harmful substances, such as toxins or pathogens, which could disrupt cellular processes or cause damage. 5. Communication and Signaling: The selective permeability of the cell membrane plays a role in cell communication and signaling. It 51  controls the entry and exit of signaling molecules, such as hormones and neurotransmitters, which are essential for coordinating cellular activities. 6. Energy Efficiency: The membrane's selectivity contributes to efficient energy use within the cell. For instance, it controls the movement of ions to maintain the proper balance of electrochemical gradients, which are essential for processes like ATP production. - How Viruses Infect Specific Organs - Membrane Fluidity - The freedom of movement of the cell membrane - integral proteins and lipids separate but loosely attached molecules. resemble the separate, multicolored tiles of a mosaic picture, float, moving somewhat with respect to one another. not like a balloon that can expand and contract - fairly rigid - can burst if penetrated, or if it takes in too much water. - a very fine needle can easily penetrate without causing it to burst, will flow and self-seal when the needle is extracted. 52  - Movement in the lipid layer include: Swinging Movement, Transversal Diffusion, Rotation, Lateral Diffusion - Factors That Maintain Fluidity - Temperature, Mosaic Characteristics, Cholesterol, Nature of Phospholipids - In temperature: - Colder Temps = more solid-like - Hotter Temps = more fluid and flexible Nature of Phospholipids Saturated Fatty Acids Unsaturated Fatty Acids - saturated fatty acids: no double bonds between - unsaturated fatty acids: double bonds between adjacent carbon atoms -->tails that are relatively adjacent carbon atoms --> a bend in the string of straight. carbons of approximately 30 degrees - saturated fatty acids with straight tails compressed - unsaturated fatty acids compressed --> maintain by decreasing temperatures ---> they press in on some space between the phospholipid molecules 53  each other --> dense and fairly rigid membrane. --> “elbow room” -->maintain fluidity in the membrane - compress membranes composed largely of saturated fatty acids --> less fluid and more susceptible to rupturing. - Fish adapt to cold environments by changing the proportion of unsaturated fatty acids in their membranes - In Animals, - Cholesterol alongside the phospholipids in the membrane → dampens the effects of temperature on the membrane. - Cholesterol as buffer - prevents lower temperatures from inhibiting fluidity - prevents increased temperatures from increasing fluidity too much. - Cholesterol has other functions: - organizing clusters of transmembrane proteins into lipid rafts. How Molecules Cross the Cell Membrane - Types of Passive Transport - Movement form High to Low concentration without using Energy (ATP) 54 a. Diffusion - Passive movement of transport → expends no energy - For small molecular weight material - particles move from an area of high concentration to low concentration until the concentration is equal across a space - Molecules move along the concentration gradient of the lipid bilayer - Concentration Gradient - a range of concentrations of a single substance in a physical space - a form of potential energy, dissipated as the gradient is eliminated. - Each separate substance in a medium, has its own concentration gradient, - Each substance will diffuse according to that gradient. - different rates of diffusion of the different substances in the medium. - Dynamic Equilibrium - substance is evenly distributed in the space - no more concentration gradient - molecules still move around in the space, without net movement of the number of molecules from one area to another. - Factors that Affect Diffusion: a. Pressure - higher pressure → increase rate of diffusion b. Extent of the Concentration Gradient - The greater the difference in concentration, the more rapid the diffusion. - The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes. c. Mass of the Molecules Diffusing - Heavier molecules move more slowly; therefore, they diffuse more slowly. - The reverse is true for lighter molecules. d. Temperature 55  - Higher temperatures → higher energy → faster movement of molecules → increased rate of diffusion. - Lower temperatures → lower energy of the molecules → decreased rate of diffusion. e. Solvent Density - Denser solvents will slow down diffusion - Increase in solvent density → decrease in rate of diffusion - less dense medium → diffusion increases. f. Solubility - nonpolar or lipid-soluble materials pass through plasma membranes → polar materials → faster rate of diffusion. - Substances that are soluble in alcohol and lipids diffuse faster - Water-soluble materials will only diffuse quickly if they go through channels g. Surface Area and Thickness of the Plasma Membrane - Increased surface area increases the rate of diffusion, - A thicker membrane reduces it. - Eg. Microvilli Eg. Thickness of Plasma Membrane - a normal lung has two membranes, the alveoli and capillaries - Alveoli diffuses O2 to the Capillary - Capillary diffuses CO2 to the Alveoli - In pneumonia, there will be a thickening of the membranes due to fluids and inflammation - This slows down the rate of diffusion h. Distance Traveled - The greater the distance that a substance must travel, the slower the rate of diffusion. - Factors that Affect the Rate of Diffusion: a. Molecule size - smaller molecules yield to higher rate of diffusion b. Molecule polarity - The hydrophobic region of the lipid bilayer repels polar molecules. So, nonpolar molecules will be able to diffuse across the plasma membrane, while polar molecules cant unless they use protein channels c. Charge on particle - charged particles/ions cant diffuse across the cell membrane d. Temperature - higher molecules mean faster movement and diffusion; lower temperatures mean slower diffusion rates If the body’s cells lose water, the rate of diffusion decreases in the cytoplasm Blood will be viscous There will be problems of delivery of material, leads to fatigue i. Filtration - material moves according to its concentration gradient through a membrane - involves the movement of water and solutes across a membrane due to hydrostatic pressure (pressure exerted by a fluid) rather than concentration gradient - rate of diffusion is enhanced by pressure → the substances filter more rapidly. - rate of diffusion almost totally dependent on pressure 56 b. Facilitated Diffusion/Transport - For Sodium, Potassium, Calcium, Glucose - Larger and polar materials diffuse across the plasma membrane with the help of membrane proteins. - concentration gradient exists - polar molecules that are repelled by the hydrophobic parts of the cell membrane. - Transport proteins: - integral proteins - transmembrane proteins. - channels or carriers - Allows only specific molecules to enter the cell a. Channel Proteins - specific for the substance that is being transported - hydrophilic domains exposed to the intracellular and extracellular fluids - hydrophilic channel through their core - Like tubes that allow molecules to pass through - Aquaporins - channel proteins that allow water to pass through the membrane at a very high rate. - may be always open or “gated” - Faster 57  b. Carrier Proteins - proteins that bind substances, change their shape, and move the bound molecule to the opposite side of the cell membrane - typically specific for a single substance. - finite number of carrier proteins → may be saturated with ligands c. Osmosis - diffusion of water 58 - movement of water through a semipermeable membrane according to the concentration gradient of water across the membrane - inversely proportional to the concentration of solutes. - transports only water across a membrane - What will limit the movement of water across a semipermeable membrane: Tonicity - the capability of a solution to modify the volume of cells by altering their water content - how an extracellular solution can change the volume of a cell by affecting osmosis. - directly correlates with the osmolarity of the solution. - Tonicity in Living Organisms - hypotonic environment: water enters a cell --> the cell swells. - isotonic condition: no net water movement--> no change in the size of the cell. - hypertonic solution: water leaves a cell --> the cell shrinks. 59  Osmolarity - the number of particles of solute per liter of solution - total solute concentration of the solution - low osmolarity = greater number of water molecules relative to the number of solute particles - high osmolarity = fewer water molecules with respect to solute particles - measures the number of particles (which may be molecules) in a solution. Hypotonic Solutions - Concentration of water is higher outside the cell, there are more salt solute inside the cell - the extracellular fluid has lower osmolarity than the fluid inside the cell - water enters the cell, making it swell and can burst if too much - Cytolysis - bursting of the cell; Hemolysis - bursting if the red blood cell - Plant cells dont burst because of the rigid cellulose/cell wall Hypertonic Solutions - the extracellular fluid has a higher osmolarity than the cell’s cytoplasm - the fluid contains less water than the cell does. - the cell has a relatively higher concentration of water vs salt - water will leave the cell, and cell will shrivel (plasmolysis, also how pickles are made) - Plasmolysis - the process of contraction or shrinkage of the protoplasm of a plant cell due to the lack of water - Preservation of food: water inside bacterial cells will diffuse out as it gets dehydrated from the salt-rich environment Isotonic Solutions - the extracellular fluid has the same osmolarity as the cell - no net movement of water into or out of the cell, but still has movement - The concentration of the cell is the same outside the cell - There is equal movement of water and solutes outside and inside the cell; water diffuse inside the cell, then the water inside the cell will diffuse out as it will get replaced by the extracellular water 60  Osmoregulation - In the urinary system of animals - process by which living organisms regulate the balance of water and electrolytes (salts) within their bodies to maintain homeostasis. - ways of controlling the effects of osmosis - cell walls prevent cell lysis in a hypotonic solution - the cytoplasm in plants always slightly hypertonic to the cellular environment 61  - turgor pressure - support of nonwoody plants - In dry soil: extracellular fluid hypertonic - Water leaves the cell because of the lack of water in the soil - Cell does not shrink because the cell wall is not flexible - Cell membrane detaches from the cell wall and constricts the cytoplasm (plasmolysis) Osmosis and Water Potential - Water potential (Ψ) is a measure of the potential energy of water in a system, influenced by solute concentration and pressure. It's expressed in units of pressure (Pascals or bars) and can be thought of as a way to predict the direction of water movement. - Water moves from areas of higher (less negative) water potential to areas of lower (more negative) water potential - Higher Water Potential - Hypotonic - Lower Water Potential - Hypertonic 62  In the context of Paramcia (Isotonic Process) - The vesicle collects water from the cell - The contractile vacuoles will pump out water out of the cell Salt water fishes produce concentrated urine - Types of Active Transport - Require the use of the cell’s energy (Adenosine triphosphate) - Can move substances against the concentration gradient - Electrochemical Gradient - combined gradient of concentration and electrical charge that affects an ion for muscle contraction 63 - How to move against the gradient: - Pumps - Active transport mechanisms that work against electrochemical gradients - maintains concentrations of ions and other substances needed by living cells in the face of these passive movements 64  - Carrier Proteins for Active Transport - Transporters - specific carrier proteins or pumps to facilitate movement - can also transport small, uncharged organic molecules like glucose - also found in facilitated diffusion - Kinds of Transporters: a. uniporter - carries one specific ion or molecule. - Ca2+ ATPase and H+ ATPase) b. symporter - carries two different ions or molecules, both in the same direction. c. antiporter - also carries two different ions or molecules, but in different directions. (sodium-potassium pump) - -Na+-K+ ATPase carries sodium and potassium ions - -H+-K+ ATPase carries hydrogen and potassium ions. a. Primary Active Transport - moves ions across a membrane and creates a difference in charge across that membrane - For Sodium, Potassium, Calcium 65  - directly dependent on ATP. - A phosphate attaches itself to the antiporter - active transport of 3 sodium out and 2 potassium in b. Secondary Active Transport - For Amino acids, lactose - movement of material that is due to the electrochemical gradient established by primary active transport - does not directly require ATP, but dependent on the electrochemical gradient from the primary active transport made by the ATP - still considered active because it depends on the use of energy as does primary transport 66  - electrogenic pump - creates a charge imbalance - creates an electrical imbalance across the membrane and contributes to the membrane potential - Secondary Active transport as Co-transport: - sodium ion concentrations build outside of the plasma membrane → electrochemical gradient - If channel protein exists and is open → sodium ions pulled through the membrane → - movement used to transport other substances that can attach themselves to the transport protein through the membrane → amino acids and glucose enter a cell - also used to store high-energy hydrogen ions in the mitochondria of plant and animal cells for the production of ATP. - potential energy that accumulates → kinetic energy as the ions surge through the channel protein ATP synthase → used to convert ADP into ATP. c. Bulk Transport - remove and take in larger molecules and particles - engulf entire unicellular microorganisms. - requires energy. i. Endocytosis (Going In) - moves particles, such as large molecules, parts of cells, even whole cells, into a cell. - The plasma membrane of the cell invaginates, forming a pocket around the target particle. - The pocket pinches off --> particle contained in a newly created intracellular vesicle formed from the plasma membrane. 1. Phagocytosis - “cell eating” - for Large macromolecules, whole cells, or cellular structures - large particles, such as cells or relatively large particles, are taken in by a cell. - Cell surrounds materials with its plasma membrane and forming a vesicle (called a phagosome). This process is essential for immune defense and cellular cleanup. - Neutrophils taking up pathogens 67  - clathrin - a coating protein, stabilizes the section of the membrane. → disengages from the membrane once the vesicle containing the particle is enclosed within the cell 2. Pinocytosis - “cell drinking” - For small molecules (liquid/water) - takes in small molecules and fluids, including water, which the cell needs from the extracellular fluid. - results in a much smaller vesicle than does phagocytosis - the vesicle does not need to merge with a lysosome 3. Potocytosis - For small molecules (liquids/water) - Involves the use of caveolin - a coating protein on the cytoplasmic side of the plasma membrane - similar function to clathrin. - vacuoles or vesicles formed in caveolae (singular caveola) smaller than those in pinocytosis. 68  - used to bring small molecules into the cell - transport these molecules through the cell for their release on the other side of the cell - a process called transcytosis. 4. Receptor-Mediated Endocytosis - For large quantities of macromolecules - employs receptor proteins in the plasma membrane that have a specific binding affinity for certain substances - Transports large quantities of macromolecules - clathrin is attached to the cytoplasmic side of the plasma membrane. - LDL removed from the blood - Some viruses, bacteria, and antigens enter the cells through receptor cross-reaction ii. Exocytosis (Going Out) - expel material from the cell into the extracellular fluid. - Waste material enveloped in a membrane --> fuses with the interior of the plasma membrane - → opens the membranous envelope on the exterior of the cell - → waste material is expelled into the extracellular space - secretion of proteins of the extracellular matrix - Secretion of hormones from the endocrine cells to the blood stream - secretion of neurotransmitters into the synaptic cleft by synaptic vesicles. (in ends of nerve cells, axioms) 69 70