Biology Notes PDF

  01 October 2024 11:41     Lab reports 02 October 2024 15:22   - Put     Atoms and molecules 10 October 2024 17:54     Atoms and componds 10 October 2024 17:57   Concept 1: Matter consists of chemical elements in pure form and in combinations called compounds   Living organ...

  01 October 2024 11:41     Lab reports 02 October 2024 15:22   - Put     Atoms and molecules 10 October 2024 17:54     Atoms and componds 10 October 2024 17:57   Concept 1: Matter consists of chemical elements in pure form and in combinations called compounds   Living organisms are composed of MATTER which is made up of elements   ELEMENT: a substance that cannot be broken down into another substance by a chemical reaction   COMPOUND: a substance consisting of two or more different elements combined in a fixed ratio   [Periodic table ]   Elements in the same GROUP have the same number of valence electrons. Outer most electrons on atoms   Elements in the same PERIOD have the same number of occupied electron shells.   [Concept 2] An element's properties depend on the atoms   ATOM: The smallest unit of an element that retains the chemical properties of the element. structure of its atoms.   Atomic mass is protons plus neutrons. [protons] [neutrons] [electrons]   All atoms of an element have the same number of protons but may differ in the number of neutrons Isotopes are two atoms of an element that differ in the number of neutrons   [Energy levels of electrons..]   ENERGY = capacity to cause change eg. "work".   [Electron distribution and chemical properties...]   The chemical behaviour of an atom is determined by the distribution of electrons in the atom's electron shells.   VALENCE ELECTRONS are the outermost electrons of an atom that participate in chemical interactions and determine the chemical properties of the element.   Valence electrons are located in the outermost energy level (VALENCE SHELL) and play a crucial role in the formation of chemical bonds and chemical reactions.   The configuration of these electrons influences an atoms ability to gain, lose or share electrons during chemical interactions.   [Electron orbitals...]   Electrons do NOT orbit the nucleus is concentric circles like shown in electron-shell diagrams! The space where electrons spend most of their time is 3-dimensional and are referred to as ORBITALS.   Each ELECTRON SHELL contains electrons at a particular energy level, distributed among a specific number of orbitals of distinctive shapes and orientations.   No more than 2 electrons can occupy a single orbital.      The reactivity of an atom arises from the presence of unpaired electrons in one or more orbitals of the atom's VALENCE SHELL......UNPAIRED ELECTRONS ALLOW INTERACTION WITH OTHER ATOMS IN ORDER TO COMPLETE THEIR VALENCE SHELLS   Example: Methane     [Covalent bonds...]   A hydrogen H2 molecule (H-H) contains a SINGLE BOND.        Oxygen - 6 electrons in its valence shell   Two oxygen atoms form a molecule of O2 by sharing TWO pairs of valence electrons forming a DOUBLE BOND (O=O).       Carbon dioxide (CO2) - formed by two double bonds sharing 4 pairs of valence electrons (C=O=O).   Bonds are represented by   MOLECULES are 2 or more atoms held together by chemical bonds, for example H2 and O2 are pure elements, H2O and CH4.   A COMPOUND is a combination of 2 or more DIFFERENT elements. For example H2O and CH4.   All compounds are molecules but not all molecules are compounds   [Come back to this ]     Chemistry of water Thursday 24 October 2024 12:03   - Carbonic acid dissociates into H^+^ and HCO~3~^-^. - The added H^+^ combines with carbonate ions forming more HCO~3~^-^. - Less CO~3~^2-^ is available for calcification -- the formation of calcium carbonate -- by marine organisms eg. coral, shellfish. Prediction that the carbonate concentration could decrease by 40% by 2100! Air will be between those spaces allowing water to float.   Water is a versatile solvent due to its polarity. The different charges.   At the equilibrium point water molecules hugely exceed H+ or OH- - so it is rare   WEAK ACIDS don't fully dissociate and are in an equilibrium     Carbon 24 October 2024 14:09   - [CARBON] is unparalleled in its ability to form large complex molecules making biological diversity possible. - The molecules of life that distinguish living matter from inanimate material are all made of carbon bonded to other elements. - eg. H, O, N, S and P. - The overall percentages of the major elements of life C, H, O, N, S and P are uniform from one organism to the next -- indicates a common evolutionary origin of all Life. - Because carbon can form 4 bonds, these building blocks can be used to make an inexhaustible variety of organic molecules. - Each carbon atom act as an intersection point in a molecule where 4 branches can occur in different directions. Hence the ability to form large complex molecules. - Carbon chains form the skeletons of most organic molecules. - They can vary in length and shape which is a source of molecular complexity and diversity that is seen in living matter. - Hydrocarbons are organic molecules that consist of only carbon and hydrogen. - [ISOMERS] -- compounds that have the same number of atoms of the same elements but different [STRUCTURES] and thus [PROPERTIES]. - Analogy -- right hand won't fit in a left-hand glove! So enantiomers are important in drugs because usually only one enantiomer is active and able to bind to a specific molecule. - Hydrocarbons are the most basic type of organic molecules, and they form the \"skeleton\" for other, more complex molecules. - Other chemical groups can replace hydrogen atoms in hydrocarbons, making the molecules more complex. - These new groups change the shape of the molecule, allowing it to react differently or have unique functions. - This adds variety to molecules, leading to more diversity and special properties in different molecules - - **[FUNCTIONAL GROUPS]** are the components of organic molecules that are most commonly involved in chemical reactions - Different [CHEMICAL GROUPS] are involved in [CHARACTERISTIC CHEMICAL REACTIONS] because they have unique [SHAPE] and [CHARGE]. - Hydroxyl - Carbonyl chemically reactive - Carboxyl - Amino all hydrophilic (except - Sulfhydryl sulfhydryl) so increase - Phosphate solubility -  - With ATP one phosphate may be removed in a reaction with water to form adenosine diphosphate (ADP). - This inorganic phosphate ion, HOPO~3~^-^ is often just shortened to P~i~. - This reaction releases [ENERGY] that is vital for cell function. Cabron can promote molecular bonding in dopamine.   vv        Carbohydrates and lipids 24 October 2024 14:56   - Of these 4: carbohydrates, proteins and nucleic acids are termed [MACROMOLECULES] because of their large size. Lipids are small molecule. - **Large carbohydrates, proteins and nucleic acids are [CHAIN-LIKE] molecules termed [POLYMERS].** Polymers means many - The **simplest carbohydrates** are **monosaccharides** (like glucose), which are basic building blocks for more complex carbohydrates. - Monosaccharides have a formula based on **CH₂O** (carbon, hydrogen, oxygen), and **glucose (C₆H₁₂O₆)** is an example that\'s important for energy in living organisms. - The molecule has a CARBONYL group (\>C=O) and multiple --OH groups. - Location of the carbonyl dictates whether an ALDOSE (aldehyde sugar) or KETOSE (ketone sugar). - Glucose = aldose; Fructose, an isomer of glucose = ketose.     Proteins and Nucleic Acids 24 October 2024 14:57   ENZYMES regulate metabolism by acting as catalysts = chemical agents that selectively speed up chemical reactions without being consumed.     [Concept 1. Proteins include a diversity of structures, resulting in a wide range of functions] Proteins are constructed from a set of 20 AMINO ACIDS linked in unbranched POLYMERS.   The BOND between AMINO ACIDS is called the PEPTIDE BOND so a polymer of amino acids is called a POLYPEPTIDE. A protein is a biologically functional molecule made up of one or more polypeptides each folded and coiled into a specific structure.   All amino acids share a common structure. An AMINO ACID has an AMINO GROUP (N-terminus) and a CARBOXYL GROUP (C-terminus).      [Protein Structure]   20 different side chains, Each with distinct chemistry, Sum is greater than the parts. Side chains determine the intramolecular chemistry of the single macromolecule.   Determine the intermolecular interactions between other macromolecules              [Special Amino Acids]   Glycine has only a H- as a side chain Fits well in stretches of Polar and non-polar amino acids Often at sites of Protein-Protein interactions   Proline is a ringed structure-Introduces bends and kinks in a peptides 2^o^ structure   Cysteine has a sulfhydryl group Used to form disulfide bridges between two Cys residues Stabilization of 3o conformations or binding multiple chains together     [Polypeptides (Amino Acid Polymers)] Two amino acids with the carboxyl group of one adjacent to the amino group of the other are joined by a DEHYDRATION REACTION (removal of water).   This forms a covalent bond called the PEPTIDE BOND.   Repeated over and over this produces a POLYPEPTIDE. Can range from a few amino acids to 1000 or more.   The purple sequence is termed the polypeptide backbone with the different side chains (R groups) of the amino acids sticking out.   The nature of the polypeptide is determined by the type and sequence of the side chains which determine how the molecule folds and what its final shape is.   Diversity of form and function in proteins comes from linking a limited set of monomers into diverse sequences.   the peptide bonds form a backbone with three key characteristics: R-group orientation Directionality Flexibility   remember in your end of your polypeptide chain you will always have one free amino acids (n termianls ) and on the other end you will always free carboxyl group ( c terminal ).   [Protein Structure and Function]   The unparalleled diversity of proteins in size, shape, and other aspects of structure is important because Function follows from structure   Proteins can serve diverse functions in cells because they are; -Diverse in size and shape -Diverse in the chemical properties of their amino acids     A functional protein is not just a polypeptide chain but one or more polypeptides precisely twisted, folded and coiled into a molecule of unique shape. These can be depicted by models.      Globular model shows the atoms and lots of little circles. Ribbon model shows the secondary structure, the formations of the alpha and beta sheets   The function of a protein depends on its ability to RECOGNISE and BIND to some other molecule   Example: Endorphine and morphine both fit into brain receptor proteins. Morphine mimics endorphins because of SIMILAR SHAPE meaning they can fit into the SHAPE of the protein receptor : lock and key. FUNCTION comes from molecular order, structure and shape.     [Primary structure]   is its sequence of amino acids it determined from the dna [secondary structure ]   The coils and folds of SECONDARY STRUCTURE result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an α helix and a folded structure called a β pleated sheet.     Hydrogen bonding between sections of the same backbone Is possible only when a polypeptide bends in a way that puts C = O and N--H groups close together   From the bending you can create 2 different structures    [Tertiary structure]   Tertiary structure is additional bonding that can take place within the polypeptide, in addition to hydrogen bonding we also have. TERTIARY STRUCTURE, the overall shape of a polypeptide, results from interactions between R groups, rather than interactions between backbone constituents. These interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, and\ van der Waals interactions.   Strong covalent bonds called disulfide bridges may reinforce the protein's structure.       [Quaternary Structure ]   results when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: two α and two β subunits   [Sickle-Cell Disease: A Change in Primary Structure]   Even a slight change in primary structure can affect a protein's function. An inherited disorder caused by substitution of glutamic acid for valine at position 6.   [What Determines Protein Structure?]   protein structure also depends on the PHYSICAL and CHEMICAL ENVIRONMENT it is in. If the pH, salt concentration, temperature are altered the hydrogen bonds, Wan der Waals forces that hold the protein in its 3-D structure are destroyed the protein unravels, loses its shape and becomes DENATURED.   Denaturation can sometimes be reversed when the denaturing agent is removed. Diseases such as Alzheimer's, Parkinson's, and mad cow disease are associated with misfolded proteins.   [Concept 2. Nucleic acids store, transmit, and help express hereditary information]   The primary structure of a polypeptide determines a proteins shape -- BUT WHAT DETERMINES PRIMARY STRUCTURE?   The amino acid sequence of a polypeptide is encoded by a unit of inheritance termed a GENE. Genes consist of DNA, a NUCLEIC ACID. NUCLEIC ACIDS are polymers made from monomers called NUCLEOTIDES.   DNA = deoxyribonucleic acid RNA = ribonucleic acid   The primary structure of a polypeptide determines a proteins shape -- BUT WHAT DETERMINES PRIMARY STRUCTURE?   The amino acid sequence of a polypeptide is encoded by a unit of inheritance termed a GENE. Genes consist of DNA, a NUCLEIC ACID. NUCLEIC ACIDS are polymers made from monomers called NUCLEOTIDES.   DNA = deoxyribonucleic acid RNA = ribonucleic acid    [Nucleic Acids]     Responsible for the storage, expression, and transmission of genetic information Two classes Deoxyribonucleic acid (DNA) Stores genetic information encoded in the sequence of nucleotide monomers   Ribonucleic acid (RNA) Decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain   Nucleic acids are polynucleotides. A NUCLEOTIDE monomer is composed of 3 parts : a 5 carbon sugar (pentose) a nitrogen-containing base 1 to 3 phosphate groups.            Purines are double ring structure and pyrimidines are single ring structure   [Nucleotide Polymers]   The linkage of nucleotides into a polynucleotide involves a dehydration reaction. In the polynucleotide the adjacent nucleotides are joined by a phosphodiester link -- a phosphate group that links the sugars of two nucleotides -- creates a repeating pattern called the SUGAR-PHOSPHATE BACKBONE sugar is binding to the phosphate   The two ends of the polymer are different -- one end has a phosphate attached to a 5' carbon -- the other has a --OH group on a 3' carbon -- the 5' end and the 3' end.   The bases are attached along the sugar-phosphate backbone.   The sequence of bases along a DNA (or RNA polymer) is unique for each gene -- provide specific information.   The linear order of bases in a gene specifies the amino acid sequence of a protein -- the primary structure -- which in turn specifies the shape/structure of the protein and thus FUNCTION.     A pairs with T G pairs with C   It is this feature of DNA that makes it possible to make 2 identical copies of each DNA molecule in a cell that is preparing to divide.   Daughter cells are genetically identical to the parent -- so the nature of DNA structure allows the molecule to transmit genetic information.   [Structure ]   DNA molecules have 2 polynucleotides ('strands') that wind around an imaginary axis forming the DOUBLE HELIX. The 2 sugar-phosphate backbones run in opposite 5'-3' directions -- ANTIPARALLEL.   DNA is read in a 5' to 3' direction      [RNA Has a Sugar-Phosphate Backbone]   RNA exists as a SINGLE STRAND but base-pairing can occur between regions of the SAME molecule -- this allows TRANSFER RNA to take on a STRUCTURE that is essential for its function.   IN RNA A pairs with U. The sugar-phosphate backbone of a nucleic acid is directional One end has an unlinked 5′ carbon The other end has an unlinked 3′ carbon   Genomics and proteomics have transformed biological inquiry and applications. DNA sequencing has given rise to the science of GENOMICS and BIOINFORMATICS. Transformed evolutionary biology, medical science, forensics etc.         Fd 20 amino acids that are used to build proteins...   Amino acids differ in their properties due to differing side chains, called R groups   The physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid thus influencing its functional role in a protein.   Nonpolar side chain - Hydrophobic Polar side chain - Hydrophilic Acidic side chains (negative charge) or basic side chains (positive charge).       Hydrogen bonds occur between: The carbonyl group of one amino acid And the amino group of another           Cell structure and function 24 October 2024 12:21 Variation amongst cells   External morphology -- the size, shape, colour, pattern, and outward appearance of an organism Remember, E. coli and S. cerevisiae are Latin, so should be in italics Prokaryotic cells they lack an enclosed nucleus or membrane bound organelles Examples: Cocci, bacilli, vibrio     Eukaryotic cells plants, animals and fungi , Nucleus in an enclosed envelope and membrane bound organelles.   Plants cells Most plants are multicellular organisms and obtain their energy via photosynthesis Fungi cells Yeasts, moulds, and mushrooms, they have Heterotrophs with chitin in their cell walls and are Genetically more similar to animals than to plants Note: Heterotrophic -- an organism that eats other plants or animals for energy and nutrients Chitin -- a polysaccharide chain Animals cells Heterotrophic, motile or non-motile, and have a blastula stage of embryonic development Note: hollow sphere of cells Eukaryotic cells can also be rigid, like calcified bone, be fluid and flexible like neutrophil and be brick shaped and fixed shaped columnar like epithelial cells. Organelles Remember, eukaryotes have lots of membrane bound organelles, whereas prokaryotes have none Nucleus Nucleus has entry and out points called nuclear points Chromatins is a complex of DNA and protein because DNA wraps around the histones, this combination of dna and histones is what we call chromatins. Genes to proteins The central dogma refers to how genetic information can be stored (DNA), and turned into a product (protein) within a biological system Transcription \--DNA → messenger RNA Translation \--mRNA → protein Only 4 nucleotides, but 20 amino acids Ø        Going from the language of dna to the language of protein, 4 to 20 letters Note: Genotype -- the genes you have Phenotype -- your observable characteristics Translation Going from mRNA → Protein you only need 4 nucleotides, but 20 amino acids Its more complicated than going from DNA → RNA No equivalent of Watson-Crick base-pairing Genotype → Phenotype Ribosomes ribosome is like a molecular machine that helps the cell make proteins. It is made of two parts: 1.        Small subunit: This part reads the instructions (the mRNA) that tell the ribosome which amino acids to add to the growing protein. 2.        Large subunit: This part links the amino acids together, making a chain (a protein) by forming strong peptide bonds between them. The amino acids are brought to the ribosome by tRNA. Free ribosomes - float around freely in the cell's fluid (cytosol) and can work together in groups called polysomes to make proteins. All ribosomes in bacteria (prokaryotes) are free-floating. Membrane-bound ribosomes: These are attached to the surface of the endoplasmic reticulum (ER) in eukaryotic cells (like in humans) and help make proteins that are sent to specific places. Ø        Its going through the rough er because it has ribosomes attached to it. Mrna will go through it like a tunnel Endoplastic reticulum SER (smooth endoplastic reticulum) has far fewer ribosomes and is much smaller - lipid, phospholipid, and steroid synthesis. Golgi body Also called Golgi apparatus, Golgi complex, or just Golgi. Cisternae are the name of flat stacks found in certain cell structures like endoplasmic reticulum (ER) or Golgi apparatus. These help in the processing and transport of proteins and other molecules. Ø        Think of it like A stack of pancakes that made up the Golgi body Proteins arrive from the ER on the cis face and then Modified within the cisternae by enzymes. They are also sorted in the trans Golgi network then sent to the correct destination in the cell either to cell membrane for secretion(meaning to release substances from the cell outside, or to lysosomes for digestion because lysosomes digest or break down larger molecules, waste materials or harmful things like bacteria. the TGN helps direct these molecules by packaging them into small membrane-bound vesicles that are transported. Protein sorting the tgn packages the proteins into vesicles, For constitutive/exocytotic secretion, vesicles continuously transport proteins to the plasma membrane, where they release materials such as lipids and proteins and secretory proteins out the cell note: Constitutive means its occurring all the time The cell membrane is made up of lipids and proteins. By constantly releasing these components, the cell can repair or expand its membrane. Secretory proteins: These are proteins that the cell produces and needs to send outside. They might be hormones, enzymes, or other signaling molecules that help the cell communicate or perform its functions in the body. \--In regulated secretion, once the proteins are stored in vesicles they wait until a specific signal trigger their release. Once they receive that signal, they can rlease hormones, neurotransmitters and enzymes. Ø        Regulated secretion When something specific is happening   Proteins destined for lysosomes, such as digestive enzymes (lysozymes), are synthesized in the rough endoplasmic reticulum (RER). Lysosomal exocytosis (proteins to be digested can be sent to the lysosome to be destroyed by digestive lysozyme enzymes, or lysozymes are sent to digest something outside of the cell) Ø        Lysosomes are the vesicle that lysozymes lives in. Their job is to destroy proteins Ø        Remember, a lysoSOME and a lysoZYME are different terms. Lysosomes are a type of vesicle, lysozymes are a type of enzyme   How do things move inside the cell? nm -- nanometre (1 millimetre = 1,000 micrometres = 1,000,000 nanometres) Pseudopodia -- a temporary protrusion of the surface of a cell for movement and/or feeding.   Microfilaments (actin) Actin filaments, also known as microfilaments, are the smallest elements of the cytoskeleton and are among the most common proteins found in eukaryotic cells.     They are made up of globular actin proteins (G-actin)(monomers) that polymerize to form long, thin strands called filamentous actin (F-actin)(polymer). These actin filaments play several important roles in the cell, including changing the cell\'s shape and length, which is particularly crucial for muscle contraction. They help extend the cell membrane to form structures like pseudopodia for movement, assist in dividing the cell during the process of cytokinesis, and contribute to cell adhesion by connecting neighbouring cells. Overall, actin filaments are essential for maintaining the structure and function of cells. Note: Pseudopodia -- a temporary protrusion of the surface of a cell for movement and/or feeding Look over this again   Cytoskeletal elements are protein-based structures within cells that provide support, shape, and organization. They play crucial roles in various cellular functions, including movement, division, and maintaining the integrity of the cell. The three main types of cytoskeletal elements are: Microtubules (made from tubulin, hollow tubes, 25 nm Ø) Intermediate filaments (8 -- 12 nm Ø) Microfilaments Microtubules help move organelles and vesicles inside the cell. Motor proteins (kinesin and dynein) attach the cargo to the outside of the microtubule. Kinesin moves towards the cell\'s edge (+ end), while dynein moves towards the nucleus (-- end). Ø        Remember kinesin to Dundee, moving away and dynein To Edinburgh moving to the nucleus Ø        Cargo refers to various materials, such as organelles, vesicles, proteins, or other cellular components, that are transported within the cell by motor proteins like kinesin and dynein Note: Kinesin and dynein are examples of mechanoenzymes, which can convert chemical energy (ATP) into kinetic energy (movement)   Mitochondria Mitochondria are bacilli-shaped, divide by binary fission, produce ATP, and have two membranes. The inner membrane forms cristae, creating two compartments (intermembrane space and matrix), and they contain their own DNA. Binary fission---they get longer then divide in half Cristae, the folds of the inner mitochondrial membrane, create two compartments by dividing the space within the mitochondrion: 1.        Intermembrane space: The area between the outer and inner membranes. 2.        Mitochondrial matrix: The space inside the inner membrane, where metabolic reactions occur. The cristae increase the surface area of the inner membrane, enhancing the mitochondrion\'s ability to produce ATP. Ø        Mitochondrion -- singular for mitochondria Ø        They have their own Dan separate from rest of the DNA Chloroplast chloroplast Shaped like a bacilli and divide by binary fission Synthesise ATP (energy) through a photosynthetic pigment called chlorophyll Two membranes with an intermembrane space Has its own DNA Cell junctions         Help hold cells together and Allow communication between neighbouring cells         Permit movement of water and solutes between cells (osmotic regulation)   Gap junctions Are Chemical communication between cells and Connexon cylinder made from 6 connexin proteins Ø        Moving much smaller structures within cells because of Very smaller middle Adheren and desmosome   Several different methods to anchor cells to each other ◉        Adherens junctions -- cells linked actin-to-actin via cadherin or integrins ◉        Desmosomes -- cells linked keratin-to-keratin via cadherin ◉        Hemidesmosomes -- cytoskeleton of cells linked to extracellular matrix via integrins Tight juctions Tight junctions control water and solute movement between epithelial cells. They line organs and blood vessels. More tight junctions mean tighter barriers, while fewer create leakier barriers. Examples: Tight epithelia like kidneys, don't want everything to leak out so you might have more tj         Your gut you will have more tj so you don't want all the water to be trapped there             Moving much smaller structures within cells         Very smaller middle     Plasma membrane 24 October 2024 22:03   Plasma membrane = cell membrane = cytoplasmic membrane (NOT THE SAME as the cell wall -- do not confuse!)     membrane Green hexagons = sugars Lipid = a class of fatty acids, inclusing oils, waxes and steroids. In this context, mostly fatty phospholipids        ECM -- extra cellular matrix - this has 2 forms, the interstitial ecm which is connecting cells that are close together but the cells aren\'t physically attached to each other. And the basement membrane it's a matrix that you build cells on top off   [How the ecm is involved with tissue healing, wound healing after a burn ]       [The Fluid Mosaic Model]   Viscosity -- how much a fluid will resist deformation (water has a very low viscosity, honey has a very high viscosity) [ ]   Tails affect how fluid the membrane is          Unsaturated makes the membrane more viscous, viscosity can affect membrane fusing and membrane diving, it will take longer to do these things if the lipids are getting cold and had no way to regulate their viscosity the membrane will crystallise and break. The lipids in the membrane have become solid   The plasma membrane is NOT a solid object Proteins and lipids are floating in the membrane and can move around to make microdomains   [Crossing the membrane ]   Hydrophobic -- soluble in lipid so can cross the lipid membrane Hydrophilic -- soluble in water, so cannot cross the lipid membrane   Small hydrophobic molecules (e.g. steroid hormones) can cross the membrane on their own Most small hydrophilic molecules and ions need to use protein channels to cross (e.g. glucose, sodium ions, hydrogen ions) Very large molecules generally can't pass the membrane at all Very small non-ionic molecules (e.g. O2) can cross the membrane on their own   [Different processes of transport]   Diffusion Facilitated diffusion Active transport   [Diffusion ] Small hydrophobic molecules (soluble in lipids, not soluble in water) and small non-ionic molecules (e.g. CO2, O2) can cross on their own Not specialised transport mechanisms by diffusion.   [Diffusion -- osmosis ]   Water can cross the membrane by diffusion the specific type of diff.usion is osmosis. H2O crosses by passive diffusion BUT very slowly, so needs a specific channel to move through (aquaporins).   These are essential for the regulation of the cell as we want the cell to be isotonic   Hypertonic solution -- higher extracellular solute concentration than inside the cell, so water is lost from the cell Hypotonic solution -- lower extracellular solute concentration than inside the cell, so water is gained by the cell Isotonic solution -- same extracellular solute concentration as inside the cell, so no water is lost or gained   Solute -- a liquid with something dissolved into it      [Channel proteins]   Facilitated diffusion For example, aquaporins for H2O Some are always open (like a tunnel) Some require a signal to open (like a tunnel with a gate) For example, Na+ or K+ ion channels   [Regulation of transport]   Gated proteins -- gate is open or shut Can be controlled by: Voltage across the membrane (e.g. in nerve cells) = voltage gated Contact with an extracellular or intracellular signalling molecule (usually a short-term effect) = ligand gated Chemical changes to the protein (e.g. phosphorylation, can have long-term effects)   [Carrier proteins]     The thing that wants to go through the plasma membrane has to interact with the carrier protein, used for larger molecules, For example, glucose transporters and neurotransmitters (dopamine, serotonin) Each carrier is specific to a family of molecules Requires energy input (ATP) [Types of carrier proteins ]    Uniporter --allows 1 substance, 1 way (e.g. voltage-gated potassium channels) Symporter -- 2 or more substances, 1 way (e.g. Na-K-Cl cotransporter) Antiporter -- 1 substance leaves while a 2nd substance enters (e.g. Na+/K+ pump)   Remember correct notation for ions -- Na^+^ and K^+^,   [Using Energy To Go Against The Gradient]   Diffusion cant work If you\'re are forcing the concentration to go up even though the con is already high, the energy that will allow the cell to defeat this gradient is atp   ATP -- adenosine triphosphate Energy source inside the cell       You break the bond to form adiene dis the to form the 2 phospahte groups that's how it formed tohether thrn thr world will be a better place to live in amen thank you god Cell wall is found in plant cells   g      Plasma 2 02 November 2024 05:47   The cell membrane is essential as it forms the boundary of the cell, controlling entry and exit of substances, and maintaining the internal conditions of the cell.   \- Cells are physically connected to neighboring cells through membrane systems, forming a network.   \- The fluid mosaic model is a more detailed representation of the cell membrane, which is sometimes also referred to as the plasma membrane or occasionally the plastic membrane. It is important to distinguish the cell membrane from the cell wall, which is a different structure found in plant cells. The fluid mosaic model describes the cell membrane as a complex and dynamic structure.   \- The cell membrane is a complex and dynamic structure composed of phospholipids, proteins, sugars, and carbohydrates, forming a fluid mosaic model. The phospholipids have a hydrophilic (water-loving) edge facing the outside and a hydrophobic (water-repelling) tail pointing inwards, which is an efficient way of forming a membrane.     \- Cholesterol is used by eukaryotes to stabilize their cell membranes, but prokaryotes and plants use other sterols instead.   \- Transmembrane proteins cross both sides of the lipid bilayer, while peripheral proteins only interact with one side of the membrane. Integral proteins are transmembrane proteins that are permanently associated with a membrane.   \- Peripheral proteins can have a temporary relationship with the cell membrane, associating and dissociating, while integral proteins are permanently embedded in the membrane. Examples of these will be discussed in the upcoming signalling topic.   \- Sugars (carbohydrates) are attached to lipids as glycolipids or to proteins as glycoproteins, and these are always found on the extracellular side of the cell membrane, never on the inside.   \- The cell matrix has two forms: the interstitial ECM (extracellular matrix) that connects nearby cells, and the interstitial matrix that plays important roles in cell structure and communication. - The cell skeleton within the cell and the network of fibers outside the cell (matrix) both have important roles. - The immune system can recognize foreign cells based on different carbohydrates on their surface, such as those found on red blood cells (A, B, or O types).   \- The extracellular matrix (ECM) acts as a foundation or basement membrane that cells are built upon, similar to the foundation of a house. The ECM plays an important role in tissue healing and wound repair.   \- Skin grafts in pigs: Pigs with burns received skin grafts using the same protocol as in humans. Pressure garments were used for the first 17 weeks to help the skin graft heal and look as normal as possible. The pigs on the left side healed in open air for 29 weeks without pressure, while the others wore pressure garments for a shorter duration than recommended.   \- The extracellular matrix (ECM) plays a crucial role in skin graft healing and appearance. Pressure garments applied for 17 weeks helped the skin graft heal with a smoother, more web-like ECM structure, compared to the \"rail-like\" ECM in the groups without pressure garments for the full duration. \- Pressure garments applied for 17 weeks help skin grafts heal with a smoother, more web-like extracellular matrix (ECM) structure, compared to a \"rail-like\" ECM in groups without pressure garments for the full duration. - The fluidity of the cell membrane is controlled by the hydrophilic heads and hydrophobic tails of the phospholipids.   \- Unsaturated fatty acid tails in cell membranes create a \"kick\" or leg in the chain, preventing the lipids from packing together tightly. This makes the membrane more fluid and less viscous. Saturated fatty acid tails, on the other hand, allow the lipids to pack together more closely, resulting in a more viscous membrane.   \- Fluid cell membranes have more unsaturated phospholipids, making them more fluid and able to change shape easily, while viscous membranes have fewer unsaturated lipids, making them more resistant to shape changes, similar to the difference between water and honey.   \- Viscous cell membranes with fewer unsaturated lipids can affect the movement and interaction of signalling proteins within the membrane, as they will move more slowly and take longer to come together and interact, as well as to move apart and stop interacting.   \- Cell membrane fluidity affects the movement and interaction of signalling proteins within the membrane, as well as the ease of membrane fusion.     Phospholipids in aqueous solution automatically form a bilayer structure, which is energetically favorable and an efficient way of forming a membrane. Cholesterol is also present in various locations within the cell and will be discussed in the context of membrane fluidity.     Plants use other sterols instead of cholesterol in their cell membranes Proteins in cell membranes can be transmembrane (crossing both sides), peripheral (interacting with one side), or integral (fully inserted through the membrane).   Membranes are essential for cell division and survival, as they can change viscosity (thickness) based on temperature e.g. coconut oil is solid at cold temperatures but liquid when warm.       Membranes are fluid and dynamic, not solid structures, and their viscosity (thickness) changes with temperature to maintain cell function and survival. Extreme temperatures can cause membranes to crystallize or become too fluid, leading to cell damage.       Cells become homogeneous within 40 minutes, where proteins from different origins (human and mouse) mix and can no longer be distinguished. Biology is a relatively young field, with the fluid mosaic model being discovered in the 1970s. Humans are chimeras, meaning they have cells from different origins within their body.       Cells interact with their environment by taking in and expelling substances, which is essential for cell survival and function. Cells cannot exist in isolation and must exchange materials with their surroundings to avoid accumulating toxic waste products and obtain necessary nutrients and energy.       Small hydrophobic molecules like steroid hormones (e.g. testosterone, cortisol, estradiol) can diffuse across the cell membrane without any assistance, as they are able to move across the membrane freely.       Cells require protein channels to help transport substances across the cell membrane, as the fossil lipids alone do not allow for this. The professor will provide an example of how this works for water transport.       Different mechanisms of transport across the cell membrane: Small nonionic molecules can cross the membrane on their own (e.g. steroid hormones) Small hydrophilic molecules use channel or carrier proteins to enter the cell Larger molecules that cannot use channels or carriers must use a different process called endocytosis to enter the cell       Diffusion is the simplest way for molecules to cross the cell membrane, as hydrophobic molecules and small ionic molecules like oxygen and carbon dioxide can freely move across the membrane to reach equilibrium without any specialized transport mechanisms.       Osmosis is the specific type of diffusion where water molecules move across the cell membrane to reach equilibrium, but this process is too slow for the cell\'s needs. Cells use specialized channel proteins called aquaporins to efficiently transport water in and out of the cell, which is essential for regulating cell function.       Cells maintain structural stability and function by regulating water movement across the cell membrane. In a hypotonic solution, water will flow into the cell, causing it to swell and potentially burst. Conversely, in a hypertonic solution, water will flow out of the cell, causing it to lose structural integrity and collapse. The ideal situation is for the cell to maintain a balance, where no net water is gained or lost, allowing the cell to function properly.       Excessive water intake can cause cell walls to rupture and lead to cell death, similar to how water intoxication can cause the brain to swell. Dehydration does not cause headaches by the brain pulling away from the meninges, as this is not the actual cause of dehydrationrelated headaches.       Aquaporins are channel proteins that allow water to pass through the cell membrane. They are associated with various diseases.     Ion channels, such as sodium and potassium channels, are kept closed until a signal arrives to open them, allowing a rapid influx of ions through the channel protein. The signals that can open these channels including voltage changes, binding of signaling molecules (ligands), or chemical modifications like phosphorylation that change the shape of the channel protein.       Carrier proteins are not like open/closed channels, but require the substance to interact closely with the protein to cross the membrane. They are used for slightly larger molecules like glucose and neurotransmitters. Carrier proteins are specific to certain families of molecules and must change shape to transport them, which requires energy input.       Channel proteins can be opened or closed by various signals, such as voltage changes, binding of signaling molecules, or chemical modifications. They allow rapid influx of ions like sodium and potassium. Carrier proteins require the substance to interact closely with the protein to cross the membrane, and they must change shape to transport the substance, which requires energy input. Carrier proteins can transport more than one substance at a time, and they can be classified as uniported (single substance in one direction) or symported (two or more substances in one direction).       Sodiumcalcium pumps are examples of antiporter proteins that exchange sodium and calcium ions across the cell membrane. Antiporters are slower and less efficient than ion channels, as they require a significant change in shape to transport substances.       Cells use ATPpowered carrier proteins to transport substances against concentration gradients, as diffusion alone is not enough to bring in or expel substances when the concentrations are already high inside or outside the cell.       Adenine, a nucleotide used in DNA and RNA, has a similar structure to the righthand side of the blue molecule, which has a triphosphate with 3 phosphates.       ATP is the primary energy currency of cells, generated through various processes like the citric acid cycle and oxidation in mitochondria (for eukaryotes). The energy is released when the bond between the third and second phosphates of ATP is broken, providing a \"bump of energy\" that powers many cellular processes.   Sodiumpotassium pump is an ATPase that uses energy from ATP breakdown to transport sodium and potassium ions across the cell membrane. It is important to use the correct notation for ions, with superscript for charges (e.g., Na           Sodiumpotassium pumps in animal cells actively transport 3 sodium ions out and 2 potassium ions into the cell, creating a charge differential across the cell membrane that goes against the diffusion gradient.       Sodiumpotassium pumps are essential for maintaining low sodium and high potassium concentrations inside the cell, which is crucial for processes like action potentials in neurons. This cannot be achieved through diffusion alone.       Endocytosis and exocytosis are processes that allow large molecules to enter or exit the cell, as they cannot pass through the cell membrane directly. Endocytosis involves the cell membrane engulfing and bringing in large molecules, while exocytosis is the process of the cell expelling large molecules.       Endocytosis is a process where the cell membrane forms a vesicle to bring in specific proteins and other substances from the extracellular environment. The receptor on the cell membrane binds to the target protein, and the membrane then pinches off to form a vesicle that transports the protein into the cell.       The lecture discussed the process of \"imagination\" where a vehicle is formed within the cell and fuses with the plasma membrane to release substances into the extracellular fluid. However, this diagram does not fully represent the potential presence of proteins within the membrane around these vesicles.       Cells use membranebound vehicles to transport and insert new proteins, like sodiumpotassium pumps, into the cell membrane to maintain proper cell function and signaling.                   Cell signalling 02 November 2024 14:04   Humans have around 200 different cell types, which can be further divided into 10s of thousands of different cell types. All these cells need to communicate with each other, which is the focus of cell signaling something we have some control over, like controlling the muscles in our arm, but not the muscles that dilate our pupils or the functions of our kidneys.     Local signaling is a type of cell to cell communication where cells are either in direct contact through gap junctions or in close proximity and use secreted messenger molecules to communicate.       Long distance signaling in the body is essential for large multicellular organisms like humans, and is facilitated by the endocrine system and hormones like adrenaline, which can travel through the bloodstream to trigger responses in various organs and cell types.       Adrenaline (also called epinephrine) is a hormone that can travel through the bloodstream to trigger responses in various organs and cell types, such as increasing heart rate, pupil dilation, and other physiological changes, even in distant parts of the body.       Neurotransmitters play a role in shaping the synaptic structure.       Key stages of cell signaling: Ligand/signaling molecule binds to receptor protein Transduction process of converting the signal into a cellular response Relay proteins pass the signal through a series of steps       Effector protein leads to cellular response Emphasize difference between \"affect\" and \"effect\"   Relay proteins activate effector proteins, which can result in cxertain shorterm changes (e.g., switching on/off enzymes, metabolism) or longterm changes (e.g., alteration of gene expression, such as in stem cells differentiating into muscle cells).       Longterm changes in cell signaling can lead to serious problems, such as the formation of cancerous cells, if the pathway is mistaken (e.g., a muscle cell turning into a bone cell by accident). Managing these longterm changes is crucial, as mistakes in the process can be disastrous. Additionally, cell signaling can also result in shortterm or longterm changes in the shape or movement of the cell.       GTP is similar in structure to ATP, but the difference is that GTP is used to carry signals in cell signaling pathways, in ( they help relay messages inside the cells) addition to ATP\'s role as an energy carrier. Proteins that can hydrolyze GTP into GDP are called GTPases. and the active GTP state is important for controlling signal cascades in cell signaling.   \--\"Signal cascades\" are chains of events inside a cell where one signal activates a series of molecules, leading to a specific response, like cell growth or movement.       GTPases are proteins that can hydrolyze GTP into GDP, but they are slow at this process. To have efficient switching on/off of GTP, two other protein families are introduced: GAP (GTPase Activating Protein) proteins, which make GTPases much better at hydrolyzing GTP into GDP, effectively switching them off.   In contrast, GEF (Guanine nucleotide Exchange Factor) proteins physically remove GDP and replace it with new GTP, switching the GTPase into an active state.     GTPases are proteins that can hydrolyze GTP into GDP, but this process is slow. GAP (GTPase Activating Protein) proteins make GTPases much better at hydrolyzing GTP into GDP, effectively switching them off quickly. In contrast, GEF (Guanine nucleotide Exchange Factor) proteins physically remove GDP and replace it with new GTP, switching the GTPase into an active state.       SOS1 is a Guanine nucleotide Exchange Factor (GEF) protein that specifically switches on the GTPase Ras by replacing GDP with GTP, activating it. Ras A1 is a GTPase Activating Protein (GAP) that specifically switches off the GTPase Ras by hydrolyzing GTP into GDP, inactivating it.   Ras is a type of protein (GTPase) that helps control cell growth and division       Transduction stage of cell signaling involves a series of relay events between signaling molecules, where protein phosphorylation is a common mechanism to pass the signal. Phosphorylation is a reversible process, allowing the activation and deactivation of proteins as needed in response to specific signals.       Phosphorylation is a common mechanism in the transduction stage of cell signaling, where a phosphate group is added to one of four amino acids (serine, threonine, tyrosine, or histidine) on the target protein, changing its shape and activating or deactivating it. This is a reversible process that allows for the activation and deactivation of proteins as needed in response to specific signals. Around 13,000 human proteins have phosphorylation sites.       Protein kinases add phosphate groups to proteins, activating or deactivating them as part of the transduction stage in cell signaling. Protein phosphatases remove these phosphate groups, reversing the effects. Specific protein kinases and phosphatases have more descriptive names.       Protein phosphorylation cascades: Activation of one protein (e.g., Protein A) leads to a series of phosphorylation events, where the activated protein phosphorylates and activates the next protein (Protein B), which then phosphorylates and activates the next (Protein C), and so on, resulting in a large signaling event. This is an important mechanism in cell signaling pathways.       Phosphorylation cascades in cell signaling can become extremely complex, with a single protein (e.g., Protein A) potentially able to phosphorylate and activate many other proteins (e.g., 6 Protein B and 100 Protein C), leading to a rapid and exponential increase in signaling activity within the cell. This complexity highlights the challenges in fully understanding cell signaling pathways, even after years of study.       Adrenaline (epinephrine) signaling cascade: Epinephrine activates adenylyl cyclase enzymes Adenylyl cyclase converts ATP to cyclic AMP (a second messenger) Cyclic AMP activates protein kinase A (PKA), which can trigger various cellular responses This signaling cascade allows rapid and efficient amplification of the adrenaline signal within the cell       Adrenaline (epinephrine) signaling cascade: Epinephrine activates adenylyl cyclase enzymes Adenylyl cyclase converts ATP to cyclic AMP (a second messenger) Cyclic AMP activates protein kinase A (PKA), which can trigger various cellular responses This signaling cascade allows rapid and efficient amplification of the adrenaline signal within the cell The production of cyclic AMP is a massive amplification event, with 10,000 times more cyclic AMP being produced than was initially triggered Protein kinase A (PKA) adds phosphorus (phosphorylates) to target proteins, activating them and producing a cellular response       Adrenaline (epinephrine) signaling cascade: Adrenaline activates adenylyl cyclase enzymes Adenylyl cyclase converts ATP to cyclic AMP (a second messenger) Cyclic AMP activates protein kinase A (PKA), which can trigger various cellular responses This signaling cascade allows rapid and efficient amplification of the adrenaline signal within the cell The production of cyclic AMP is a massive amplification event, with 10,000 times more cyclic AMP being produced than was initially triggered Protein kinase A (PKA) adds phosphorus (phosphorylates) to target proteins, activating them and producing a cellular response Adrenaline also liberates glucose molecules from glycogen, providing energy for cells to respond (e.g., to run away)   Adrenaline binds to a G proteincoupled receptor on the cell surface, which initiates a signaling cascade leading to an end product inside the cell. Steroid hormones can cross the plasma membrane directly to affect the cell.     [Next part ]   G protein coupled receptors are a major drug target, with 4 of the 10 topselling medications targeting them 8 Nobel Prizes have been awarded for work on G protein coupled receptors They are only found in eukaryotes, but there are over 800 different types in humans alone They control a wide variety of functions within the body       G proteincoupled receptors are highly associated with disease due to their varied and important roles, particularly in taste and smell. The tertiary structure of these receptors consists of 7 alpha helices, which is determined by the primary structure of the protein.       G proteincoupled receptors are transmembrane proteins that are integral to the cell membrane and cannot be removed from it once inserted. They initiate signaling cascades within the cell upon binding of ligands.       G proteincoupled receptors and G proteins are separate proteins G proteins act as messengers, relaying information from the activated receptor to other parts of the cell       G proteins are attached to the cell membrane and are initially inactive when bound to GDP. This inactive state is shown in the diagram.        G proteincoupled receptors undergo a conformational change when a ligand binds, allowing the G protein to interact with the receptor and replace GDP with GTP, activating the G protein and initiating a signaling cascade within the cell.       The thing that is activating the G protein is the ligand binding to the G proteincoupled receptor on the cell surface.       Activated G protein travels across the cell membrane and phosphorylates a membranebound enzyme, activating it. The GTP on the G protein is then hydrolyzed to GDP, inactivating the G protein and the enzyme.       The enzyme has allowed the G protein to hydrolyze GTP to GDP, deactivating the G protein and making it ready to be activated by the receptor again.       The ligand binds to the G proteincoupled receptor, causing a conformational change that allows the G protein to interact with the receptor and replace GDP with GTP, activating the G protein. The active G protein then moves along the plasma membrane to activate a target enzyme, revealing its active site to react with a substrate and produce a product.       Adrenaline binds to a G proteincoupled receptor called the adrenergic or adrenal receptor, which initiates a signaling cascade within the cell.     Epinephrine (a signaling molecule) binds to a G proteincoupled receptor, activating the G protein which then activates the enzyme adenyl cyclase. Adenyl cyclase converts ATP into cyclic AMP, which then activates protein kinase A.       The diagram shows the amplification cascade of G proteincoupled receptor signaling, where ligand binding to the receptor on the cell surface leads to the activation of G proteins, which then initiate a signaling cascade within the cell, ultimately resulting in the production of cyclic AMP and further downstream effects.         Tyrosine kinase receptors are highly conserved in eukaryotes, with at least 90 different types in humans. They are structured with a plasma membrane component.       The G proteincoupled receptor has important domains that extend into the cell, in addition to the portion that sticks out of the cell.       Tyrosine kinase receptors respond to various ligands by binding to them on the outside of the cell. This binding causes a conformational change in the receptor, activating its kinase domain on the inside of the cell. The activated kinase then phosphorylates specific tyrosine residues on target proteins, initiating signaling cascades within the cell.   \-\--\"Phosphorylates\" means adding a phosphate group to a molecule, usually a protein, to change its activity, often turning it on or off.   Ligands, such as growth factors and insulin, can bind to G proteincoupled receptors and initiate signaling cascades within the cell. Growth factors often lead to more permanent changes, while insulinmediated responses are more temporary. Thyroid hormones can also bind to receptors and cause permanent changes in the cell, but this is not always the case.       When a ligand is not bound, the G proteincoupled receptor monomers are separate within the plasma membrane and cannot interact to initiate signaling. The ligandbinding site is on the extracellular side of the receptor, and this represents the inactive state of the receptor.       Ligands bind to two monomers of a receptor, causing them to come together and activate their kinase activities, allowing the receptor to function.       Membrane fluidity is crucial for cell signaling as it allows the G proteincoupled receptor and G protein to come into contact with each other. If the membrane is too viscous, this interaction will be hindered, highlighting the importance of membrane fluidity in cell signaling processes.       The G proteincoupled receptor has 6 domains that need to be phosphorylated for the receptor to be fully active. The two monomers of the receptor come together and crossphosphorylate each other, using 6 ATP molecules that are converted to ADP in the process.       The lecture discussed how the activated G proteincoupled receptor undergoes a conformational change, allowing it to interact with and phosphorylate relay proteins, initiating a signaling cascade within the cell. The activated receptor is now ready to carry on the signaling process.       Relay proteins can leave the activated tyrosine kinase receptor and carry on the signaling process, either by continuing the signaling cascade or by diffusing away and interacting with other targets within the cell. Tyrosine kinase receptors have the ability to interact with many different types of relay proteins, allowing them to control a wide range of cellular effects from the binding of a single ligand.       The lecture discussed how a single G proteincoupled receptor can bind to one ligand type but then control a wide range of different cell responses. The professor mentioned that they will talk about these cell responses in more detail on Monday. The student was encouraged to take another attempt at the quiz, which will be properly recorded.     Cell signalling part 2 02 November 2024 16:28     Glossary 24 October 2024 12:26   A covalent bond is a chemical bond where two atoms share electrons to achieve stability. This type of bond usually forms between non-metal atoms, like in a water molecule (H₂O), where oxygen and hydrogen share electrons   Think of monomers like little building blocks, like Lego pieces. When you put a lot of these little blocks together, they form a long chain called a polymer. So, monomers are the small pieces, and polymers are the long chains made from those pieces all stuck together. For example, if you have a lot of little sugar blocks (monomers), they can connect to make a long chain of sugars (a polymer), like starch!       Intramolecular chemistry refers to the interactions and bonds that occur within a single molecule. These bonds hold the atoms of the molecule together. For example, in a water molecule (H₂O), the bonds between hydrogen and oxygen are intramolecular bonds because they happen within the same molecule.     Active transport Diffsuion -     Exam questions 24 October 2024 14:07   a. 1 × 10^--6^ M b. 1 × 10^6^ M c. 1 × 10^8^ M d. 1 × 10^--8^ M e. 1 × 10^--2^ M