Cell Composition and Structure Lecture Notes PDF

Cell composition and structure Lecturer: Dr. Michelle Kuzma Adapted from: Dept head, Dr. Danuta Mielżyńska- Švach Molecular biology 2024/2025  Areas of cell study Cytology Cytochemistry Cytopathology Cytophysiology Cytogenetics ...

Cell composition and structure Lecturer: Dr. Michelle Kuzma Adapted from: Dept head, Dr. Danuta Mielżyńska- Švach Molecular biology 2024/2025  Areas of cell study Cytology Cytochemistry Cytopathology Cytophysiology Cytogenetics  The cell Cells are the smallest living structural and functional unit that comprise all organisms All cells are formed by the division of other cells (i.e., cell division) Cells contain genetic information that is passed on to daughter cells during cell division. All cells are made up of the same chemical compounds. All metabolic processes necessary for life occur in cells.  Types of Cells Prokaryotic Eurkaryotic Types of Cells  Eukaryotic organisms Single-cell: protozoa, Multi-cell some algae and fungi Fungi Plants Animals  Prokaryotic cell components Cell surface: ❑ cell membrane ❑ cell wall ❑ capsule (mucus) ❑ flagella, cilia ❑ pili, fimbriae Cell interior: ❑ cytosol ❑ nucleoid (equivalent of cell nucleus) ❑ ribosomes ❑ plasmids  Eukaryotic animal cell A eukaryotic cell consists of the following components each responsible for specific functions: ❑ cytoplasm (cytoplasmic matrix) ❑ cytoskeleton ❑ nucleus ❑ endoplasmic reticulum ❑ mitochondria ❑ Golgi apparatus ❑ lysosomes ❑ peroxisomes  Cell components All organisms are composed of two types of chemicals: inorganic and organic. Inorganic compounds mainly constitute the inanimate part of nature. Organic compounds occur almost only in living organisms or their remains.  Inorganic components Inorganic components that build cells include: ❑ Chemical elements: ❑ Macroelements - at least 0.01% of cell mass (0.1mg/1g) ❑ Microelements - between 0.01 - 0.00001% of cell mass (0.1 mg/1g to 0.1 µg/g) ❑ Trace elements – occur in the µg/g range in cells but intake required is on the scale of mg/g ❑ Ultratrace elements - occur in the µg/g range and require µg/g of dietary intake ❑ Water (~70%)  Chemical elements Macroelements Microelements Carbon (C) Iron (Fe) Hydrogen (H) Silicon (Si) Oxygen (O) Copper (Cu) Nitrogen (N) Manganese (Mn) Phosphorus (P) Fluorine (F) Sulphur (S) Iodine (I) Potassium (K) Boron (B) Sodium (Na) Molybdenum (Ml) Magnesium (Mg) Zinc (Zn) Ultraelements: radium (Ra), silver (Ag) and gold (Au)  Water The main component of every organism (on average 70 - 80% of the content of a living cell) Essential for proper functioning of the body Solvent for many chemical compounds (solutes) and an environment for all reactions Substrate and product of many chemical reactions Biological functions of water are due to its chemical structure and properties The structure of a water molecule A water molecule consists of one oxygen atom and two hydrogen atoms. A specialized dipole-dipole force known as a hydrogen bond exists between the oxygen and hydrogen A hydrogen bond is inherently polarized due to the difference in electronegativity between the two atoms. The uneven distribution of charges causes the water molecule to be dipolar. The attraction of hydrogen atoms (∂+) by oxygen atoms (∂-) causes water molecules to combine into larger groups (i.e., association) The structure of a water molecule The structure of the carbon atom The nucleus of a carbon atom contains: ❑ 6 protons (red) ❑ 6 neutrons (blue) The carbon atom has two electron shells: ❑ I (K shell) – contains 2 electrons, ❑ II (L shell) – contains 4 electrons.  The structure of the carbon atom A carbon atom contains four valence electrons and four vacancies for electrons from other elements. Carbon has a unique role in the cell because of its ability to form strong covalent bonds with other carbon atoms: C-C. Thus carbon atoms can join to form: ❑ chains ❑ branched structures ❑ rings Organic compounds consist of carbon atoms bonded to at least one other element. Namely, hydrogen and oxygen, as well as, nitrogen, sulfur and phosphorus, among others.  Organic components Cells contain four major families of small organic (containing carbon and hydrogen) molecules: ❑ saccharides ❑ fatty acids ❑ amino acids ❑ nucleotides The small organic molecules of the cell are carbon compounds that contain up to 30 or so carbon atoms. They are usually found free in solution in the cytosol. Monomer subunits construct the cell’s macromolecules (polymers). Organic components  Carbohydrates Carbohydrates consist of saccharides of which mainly contain carbon, hydrogen and oxygen. ⚫ one molecule - monosaccharides (glucose, fructose) ⚫ two molecules - disaccharides (sucrose, lactose, maltose) ⚫ several (up to 10) molecules – oligosaccharides (raffinose) ⚫ many molecules – polysaccharides (cellulose, starch) The longer the carbon chain, the less soluble the carbohydrate is in water Sucrose Raffinose Glucose  Carbohydrate function Energy storage / production: ❑ glycogen in animals ❑ starch in plants Structure: ❑ cellulose in cell walls of plants ❑ chitin in the cell walls in fungi ❑ ribose and deoxyribose sugars of DNA and RNA ❑ modifiers of proteins Transport: ❑ glucose in animals and humans ❑ sucrose in plants  Fatty acids Fatty acids usually contain an even number of carbon atoms (14 to 24) Fatty acids have a carboxyl group (acid) connected to a hydrocarbon chain (fat) The shorter the chain, the more fluid the fatty acid Saturated fatty acids only have single bonds Unsaturated fatty acids have one or more double bonds Fatty acids  Lipids Lipids are esters of fatty acids bonded to alcohols. Examples include: ❑ glycerol ❑ sphingosine ❑ higher monohydric alcohols (>6 C atoms) Insoluble in water due to the low ability to polarize under the influence of water  Types of lipids Steroids, i.e. a fats composed of 4 rings (sterane) Simple lipids are esters formed from alcohols and fatty acids: ❑ Fats and oils (triglycerides) ❑ Waxes (esters with non-glycerol alcohols) Complex lipids are made of an alcohol, fatty acids and another molecule, such as: ❑ phosphoric acid - phospholipid ❑ carbohydrate - glycolipid  Lipid functions Structural: building blocks of biological membranes (e.g., phospholipid bilayer, rigidity of plasma membrane) Energy storage: Energy reserves: ❑ in animals - stored as subcutaneous tissue, mainly in hibernators (e.g., squirrel, bear and badger) ❑ in plants - in seeds (e.g., sunflower, soybean and rapeseed), fruits and roots Signaling: steroid hormones, vitamins A and D.  Lipid functions Protection - Fat reserves protect: ❑ the eyeballs, kidneys and other abdominal organs from mechanical injuries in animals​, ❑ leaves and fruits of many plants from excessive water loss, in the form of wax coverings, ❑ marine mammals (e.g., seals, whales and walruses) from low temperatures. Cell composition  Cell structure The internal cell environment is separated from the extrernal environment by a cell membrane (plasma membrane) or by an additional cell wall (e.g., some bacteria, plant cells) The internal environment of the cell is known as the cytoplasm containing cytosol and organelles Organelles (little organs) are either membrane bound or non- membrane bound  Cell structure: cell membrane Every cell and all of its organelles are surrounded by a cell / plasma membrane All cell membranes, both extracellular and intracellular, consist of the following components: ❑ lipids ❑ proteins ❑ sugars  Cell structure: cell membrane Functions of the cell membrane: ❑ protect from physical, chemical and biological factors ❑ react to chemical, thermal and mechanical stimuli ❑ enzymatic - catalysis of various metabolic reactions ❑ regulate transport of substances into and out of the cell ❑ maintain the balance of osmotic pressure between the inside and the outside of the cell  Cell structure: cytoplasm The cytoplasm is a colloidal solution (i.e., a solution in which the particles of dissolved substance are: ❑ too small to settle under the influence of gravity, ❑ too large to dissolve in water and form a proper solution.) There are two phases in cytoplasm: ❑ dispersive - water (90% of the volume of cytoplasm) ❑ dispersed - substances suspended in water (approx. 9% organic compounds, and approx. 1% mineral compounds)  Cell structure: cytoplasm Cytoplasm functions: ❑ fill the cell and give it shape ❑ environment for suspending cell organelles ❑ site of metabolic reactions ❑ move organelles and transport substances in the cell thanks to movement of the cytoplasm  Cell structure: cytoplasm Cytoplasm is ductile and viscous (high protein content). Cytoplasm occurs in two states of aggregation: ❑ semi-liquid (sol), ❑ semi-solid (gel). Cytoplasm has the ability to move: ❑ rotationally - around a [usually] centrally located vacuole ❑ circulating - between organelles ❑ pulsating - in different directions ❑ fountaining - flows around two vacuoles in opposite directions  Cytoplasmic movement rotationally circulating pulsating fountaining vacuole cell membrane direction of cytoplasmic flow  Cell structure: cytoskeleton All cells have to be able to rearrange their internal components as they grow, divide, and adapt to changing circumstances. These spatial and mechanical functions depend on a system of filaments called the cytoskeleton. The three families of protein filaments are: ❑ intermediate filaments (diameter from 8 to 10 nm) ❑ microtubules (diameter of about 25 nm) ❑ actin filaments (diameter of about 7 nm) Cytoskeleton  Cytoskeleton actin filaments microtubules intermediate filaments  Cytoskeleton Intermediate filaments are made of tissue-specific proteins (keratin, vimentin, etc.) of which: ❑ give cells resistance to mechanical damage, stretching, and crushing ❑ help maintain a specific cell shape ❑ build the cell nuclear lamina  Cytoskeleton Microtubules are composed of tubulin (a globular protein). They: ❑ build centrioles and the mitotic spindle ❑ are responsible for transport within the cell ❑ form cilia and flagella (e.g. movement of microvilli) In cells that do not divide (i.e., neurons, myocytes, RBCs, WBCs), microtubules group together in a region called the centrosome  Cytoskeleton Actin filaments (microfilaments) are made up of actin. They: ❑ provide mechanical support for the cell and various cell organelles ❑ are involved in the movement of cytoplasm and organelles ❑ enable creeping movement and cell shape change ❑ participate in the contraction of muscle cells Cell organelles (eukaryotic, animal)  Cell structure: organelles Membrane-bound organelles are divided into: ❑ double membrane-bound ❑ single membrane-bound Organelles surrounded by a double membrane are the: ❑ nucleus - contains genetic information ❑ mitochondria - the site of cellular respiration ❑ chloroplasts - a group of organelles found in plant cells  Cell structure: organelles Organelles surrounded by a single cell membrane: ❑ Golgi apparatus – modifies proteins, secretes various substances ❑ lysosomes - contain digestive enzymes ❑ peroxisomes - vesicles containing various compounds to breakdown peroxides ❑ endoplasmic reticulum (ER) - consists of a network of channels and flattened cisternae site of protein production ❑ vacuoles ❑ in animal cells they sequester waste products ❑ in plant cells they are the "garbage bins and warehouses” of the cell and sustain water balance  Cell structure: organelles Non-membrane bound organelles: ❑ cell wall - outer covering of some non-animal cells ❑ cytoskeleton - provides cell structure ❑ ribosomes - location of protein synthesis ❑ centrosome / microtubule organizing center – contain centrioles and microtubules important in cell division ❑ centriole – cylindrical organelle involved in spindle fibers creation in cell division  Nucleus Amount in a human cell: ❑ monokaryocytes, bikaryocytes, polykaryocytes, ❑ zero: erythrocytes and cells of the stratum corneum of the epidermis Size and shape: ❑ depends on the type of cell, age and functional state ❑ spherical, ellipsoidal, fragmented ❑ ~10% of the cell volume of mammalian cells Position: ❑ in the middle of the cell ❑ along the cell membrane  States of the nucleus The cell nucleus can be in three different states: ❑ interphase – between/preparation of cell division ❑ mitotic - during cell division ❑ metabolic – present in cells in the resting or G0 phase; directs metabolic processes, maintenance functions  Nucleus structure during interphase Components of the nucleus in interphase: ❑ nuclear envelope (membrane), ❑ nuclear matrix (nucleoplasm), ❑ nucleolus ❑ chromatin: ❑ condensed chromatin (heterochromatin) ❑ dispersed chromatin (euchromatin) Structure nucleus during interphase  Nucleolus Nucleolus The nucleus usually contains one nucleolus, unseparated from the nucleoplasm (no membrane) It consists of fragments of five chromosomes, containing DNA responsible for the synthesis of ribosomal RNA (rRNA) and ribosomal subunits. These regions are called nucleolar organizers (NORs) In humans, there are 10 NORs, which are located on the short arms of chromosome pairs: 13, 14, 15, 21, and 22 Nucleolus in interphase  Functions of the nucleus Functions of the nucleus: ❑ site of DNA synthesis - replication of genetic information before nuclear division ❑ site of synthesis of RNA from DNA (transcription) ❑ site of formation of ribosomes – the structures responsible for protein synthesis (translation)  The endoplasmic reticulum The endoplasmic reticulum is a system of single-layer membranes that form a network of cisternae, channels and vesicles. It ensures: ❑ enlargement of the internal surface area of the cell ❑ division of the cytoplasm into compartments ❑ determines the route of transport of organelles, substrates and products  The endoplasmic reticulum Smooth endoplasmic reticulum (agranular endoplasmic reticulum): ❑ lacks ribosomes ❑ Place of synthesis of lipids and steroids, removal of toxic substances, internal transport Rough endoplasmic reticulum (granular endoplasmic reticulum): ❑ contains ribosomes for protein synthesis, modification, and quality control ❑ connects the outer nuclear membrane with the cell membrane and organelle membranes The endoplasmic reticulum Smooth endoplasmic reticulum Rough endoplasmic reticulum  Ribosomes Ribosomes are made up of ribosomal RNA (rRNA) and proteins. There are two types of ribosomes in eukaryotes: ❑ free ribosomes - freely float in the cytoplasm, which produce proteins that function in the cytosol ❑ ribosomes associated with the endoplasmic reticulum - produce proteins that undergo post-translational modification and are exported from the cell ❑ ribosomes found in the mitochondria and chloroplasts are smaller and similar to ribosomes found in bacteria  Ribosomes Each ribosome is made up of two subunits that fit together: ❑ small ❑ large Ribosomes are divided into: ❑ small - prokaryotic (70s) ❑ large - eukaryotic (80s) Ribosomes  Mitochondria ❑ the number of mitochondria in a single cell depends on the organism, type of cell and the energy requirements of a given cell ❑ vary in size (2 to 8 μm) ❑ they can quickly change shape and size (filamentous, granular and branched) ❑ new mitochondria are created by division of existing ones  Mitochondria The number of mitochondria in various cells: ❑ epidermal cells: 2 to 6 ❑ sperm cells: 20 to 50 ❑ liver cells: 1,000 to 2,500 ❑ skeletal muscle fibers: up to 1,600 ❑ skin cells: ~2,000 ❑ nerve cells: 10,000 ❑ ova: >100,000  Mitochondrial structure Mitochondrial structure: ❑ two-layer membrane ❑ the outer membrane is smooth and allows many substances to pass through on the basis of passive transport ❑ the inner membrane allows only selected compounds to pass through (facilitated diffusion) ❑ there is an intermembrane space between the outer and inner membranes ❑ the inner membrane separates the intermembrane space from the mitochondrial matrix and has many folds called cristae Mitochondrial structure Mitochondrial structure  Mitochondrial structure Inside a mitochondrion is the mitochondrial matrix, which contains: ❑ double-stranded, circular mitochondrial DNA (mtDNA) ❑ ribosomes (70S) ❑ enzymes necessary for the production of ATP A single human mitochondrion: ❑ contains four to ten mtDNA molecules ❑ a single mtDNA molecule is packed into mtDNA-protein complexes called nucleoids, which are ellipsoidal in shape Mitochondrial structure Green: nucleoids Gray-blue: inner membrane Gray: outer membrane  Mitochondrial functions Mitochondrial functions: ❑ aerobic respiration - the Krebs cycle and the electron transport chain ❑ production of adenosine-5′-triphosphate (ATP) - a carrier of chemical energy used in cell metabolism ❑ delivery of ATP to other parts of the cell (mitochondria can move in the cytoplasm) Mitochondrial functions  Mitochondrial division Mitochondria divide in a manner similar to that of bacteria cells mitochondrial Fragmentation  The Golgi apparatus The Golgi apparatus is composed of: ❑ highly flattened, arched cisternae (3 - 20) ❑ separating vesicles The Golgi apparatus is composed of: ❑ cis cisternae (beginning) ❑ medial cisternae ❑ trans cisternae (end)  The Golgi apparatus The cis cisterna face towards the nucleus/ER where vesicles with substrates intended for processing enter. The trans cisterna face the cell membrane where vesicles with the finished product are released to head towards organelles or the cell membrane The Golgi apparatus receives components from: ❑ the perinuclear endoplasmic reticulum ❑ the cell membrane ❑ endosomes The Golgi apparatus  The Golgi apparatus Golgi apparatus functions: ❑ post-translational modification of proteins and lipids for export ❑ linking carbohydrates to proteins, fats, and nucleosides ❑ sulfation of proteins and proteoglycans ❑ recycling of the cell membrane after endocytosis  The Golgi apparatus All secretory proteins, hydrolases and some integral membrane proteins are synthesized in their respective precursor forms The maturation of the precursor forms of proteins takes place in the Golgi apparatus coined controlled proteolysis The mechanism of proalbumin and preproinsulin maturation is well known The Golgi apparatus preproinsulin proinsulin insulin  Lysosomes Lysosomes have different shapes and sizes depending on cell type and function: ❑ macrophages - several microns ❑ hepatocytes and neurons - 0.5 to 1 μm Lysosomes are usually spherical or oval vesicles surrounded by a single membrane The number and location of lysosomes may differ even in cells of the same tissue. In hepatocytes and fibroblasts, lysosomes occupy up to ~0.5% of the cytoplasmic volume and up to 2.5% in macrophages  Lysosomes There are about 40 hydrolytic enzymes (acid hydrolases) in lysosomes, which catalyze intracellular digestion reactions Enzymes within lysosomes function in acidic environments (pH 5) A low pH environment is created by the transmembrane H + - ATPase / proton pump The lysosome membrane is resistant to acid hydrolases because it contains a range of unique proteins Structure of the lysosome  Types of lysosomes Lysosomes are categorized into: ❑ primary lysosomes: formed in the membranes of the rER and bud from the membrane of the Golgi apparatus ❑ secondary lysosomes: formed after the fusion of primary lysosomes with: ❑ endosomes ❑ autophagosomes  Types of lysosomes Secondary lysosomes are divided into: ❑ autolysosomes ❑ heterolysosomes Autolysosomes are formed by the fusion of a cell's own fragments (e.g., a damaged organelle) with a primary lysosome Autolysosomes participate in two processes: ❑ autophagy – destruction of damaged organelles ❑ autolysis – digestion of own dying or dead cells  Types of lysosomes Heterolysosomes (endosomes) are formed by the fusion of primary lysosomes with vesicles containing material taken in the cell by endocytosis (an endosome) Endosomes are subdivided depending on the type of material collected: ❑ phagosomes ❑ pinosomes In secondary lysosomes, decomposition byproducts are formed: simple sugars, amino acids, nucleotides of which can be used to synthesize other compounds in the cytosol Types of lysosomes  Perixosomes Peroxisomes are oval or spherical organelles surrounded by a single cell membrane Diameter ranges between 0.2 to 1.8 µm Number, morphology and physiological role depends on the type of cell, tissue and the stage of development, as well as, cellular stress Most abundant in liver, kidney and nervous tissue The granular matrix of peroxisomes may contain a crystalline core called the nucleoid, which may take on various forms depending on the species and type of tissue. Peroxisome structure matrix cell membrane nucleoid  Peroxisomes Peroxisomes are responsible for over 60 catabolic and anabolic processes and the enzymes enclosed in peroxisomes are responsible for: ❑ decomposition / reduction of toxic chemical compounds (detoxification) like ethanol to acetaldehyde ❑ β-oxidation reactions of fatty acids like oxidizing long- chain molecules (C22) to C8 molecules, ❑ α-oxidation reactions of branched fatty acids to create linear molecules composed of 8 carbon atoms  Peroxisomes ❑ cholesterol synthesis independent of the endoplasmic reticulum ❑ bile acid synthesis ❑ plasmalogen synthesis - part of the myelin sheath of neurons A byproduct of alcohol oxidation, β- and α-oxidation of fatty acids is hydrogen peroxide (H2O2), which is then broken down in peroxisomes by catalase or peroxidases.  Peroxisome formation Peroxisomes are formed: ❑ de novo from preperoxisomes ❑ as a result of division of pre-existing organelles De novo peroxisome formation involves the detachment of vesicles from the endoplasmic reticulum and mitochondria The resulting preperoxisomes recruit numerous enzymes, peroxins and integral membrane proteins The preperoxisomes fuse with each other and become a mature peroxisome  Peroxisome formation From pre-existing peroxisomes: ❑ the peroxisome takes the form of a tube ❑ a tightening ring is formed around the tube ❑ two daughter structures are created Peroxisome formation  Centrosome The centrosome (diplosome) is a structure found near the cell nucleus and the Golgi apparatus. It consists of two centrioles made of microtubules arranged in the form of cylinders. In the period preceding cell division, the centrosome duplicates itself and two centrosomes are formed (each with two centrioles), which move to opposite poles of the cell. Plant cells  Plant cells Compared to an animal cell, a plant cell contains additional components, such as: ❑ living (plasmic) components ❑ plastids ❑ dead (nonplasmic) components ❑ cell wall ❑ vacuole  Plastids Plastids are ovalur organelles surrounded by a double cell membrane They have plastid DNA and ribosomes All plastids arise from plastid precursors known as proplastids.  Types of plastids Chloroplasts contain the green pigment chlorophyll, which permits photosynthesis Chromoplasts contain xanthophyll and carotenoids Leucoplasts have an irregular shape and are colorless Leucoplasts perform storage functions and are divided into: ❑ proteinoplasts: contain proteins in the form of aleurone grains ❑ amyloplasts: contain carbohydrates - in the form of starch grains ❑ lipidoplasts: contain fats  Plastids Examples of plastids chromoplasts chloroplasts leucoplasts Chloroplast structure  Cell wall Plant eukaryotic organisms have a multi-layered cell wall made of cellulose or chitin Cellulose is a polymer of glucose composed of carbon, hydrogen and oxygen Chitin is a polymer of N-acetylglucosamine, which contains nitrogen in addition to carbon, hydrogen and oxygen There are two types of cell walls: ❑ Primary: made up of cellulose and pectin (a polysaccharide) that is formed during cell growth ❑ Secondary: made up of cellulose and lignin (a phenolic substance) that is produced after growth is completed  Functions of the cell wall Functions of the cell wall: ❑ gives shape and rigidity to the cell ❑ limits cell growth ❑ protects against: ❑ mechanical injuries ❑ bacterial, fungal and viral infections ❑ excessive evaporation  Plant vacuole The vacuole is surrounded by a single membrane, the tonoplast and the interior is filled with a solution called cell sap. Cell sap components: ❑ water (90%) ❑ ions (potassium, sodium, calcium, magnesium, zinc, sulfate, chloride) ❑ proteins (aleurone grains and amino acids) ❑ sugars (glucose, fructose in fruit, sucrose in sugar beets) ❑ organic acids  Vacuole functions Vacuole functions: ❑ maintain constant cell firmness (turgor pressure) ❑ store reserve materials ❑ gather unnecessary metabolic products Comparison  Endosymbiotic theory PROKARYOTIC cells (3.5 billion years ago) EUKARYOTIC cells (1.7 billion years ago) Explains the origin of mitochondria and chloroplasts in eukaryotic cells  Endosymbiotic theory The endosymbiotic theory assumes that eukaryotic organelles evolved from prokaryotic cells Evidence supporting the endosymbiotic theory: ❑ mitochondria and chloroplasts contain circular DNA molecules with a structure and size similar to that of bacterial DNA ❑ mitochondria and chloroplasts are formed by division; the cell does not create them de novo  Endosymbiotic theory ❑ mitochondrial and chloroplast ribosomes are similar to that of bacterial ribosomes, ❑ N-formylmethionine is the first amino acid in all proteins produced by the mitochondria and by chloroplasts like in bacteria Endosymbiotic theory Endosymbiotic theory  Cell metabolism Metabolism is the entirety of all biochemical reactions occurring in cells of living organisms It is the circulation of matter, energy and information that provides the organism reception of stimuli, growth, movement, reproduction, etc. There are two directions of metabolic changes: ❑ anabolic ❑ catabolic Directions of cell metabolism  Anabolism Anabolism involves the synthesis of complex organic compounds from simple compounds. Anabolic reactions require energy input More energy is stored in the products than in the respective substrates The energy is stored in the form of chemical bonds. energy substrate 1 + substrate 2 product  Catabolism Catabolism is the breakdown of complex organic compounds into simple products The products of catabolic reactions contain less energy than the respective substrates The energy released in catabolic processes is stored in bonds of energy carriers (e.g., adenosine triphosphate (ATP)) substrate product 1 + product 2 + ATP Cellular respiration  Cellular respiration Cellular respiration is the breakdown of organic compounds into inorganic compounds (i.e., CO2 and H2O) for energy In the cytoplasm, glycolysis occurs where glucose molecules are broken down into pyruvic acid molecules (1:2 ratio) with no net production of ATP – oxygen is present, first step of aerobic respiration In the mitochondria, pyruvic acid and intermediate compounds are oxidized into end products (e.g., water, carbon dioxide) Intracellular respiration  References Fundamentals of Cell Biology, Volumes 1 and 2, B. Alberts, D. Bray, K. Hopkin et all. Lecture 2: The cell membrane Lecturer: Dr. Michelle Kuzma Adapted from: Dept. Head, Dr. Danuta Mielżyńska-Švach Molecular biology 2024/2025 Housekeeping ⚫ Slides will be shared ⚫ Please no recording o Video should be released online ⚫ Email contact regarding lectures: o [email protected] ⚫ Textbook: Essential Cell Biology, 6th ed. ▪ Bruce Alberts Cell membrane functions Membranes in the cell  Membrane structure All membranes in cells are built according to the same scheme. They always consist of the following compounds: ❑ lipids ❑ proteins ❑ sugars (carbohydrates) bound to: o lipids (glycolipids) o proteins (glycoproteins)  Membrane lipids Membrane lipids are divided into three groups based on their chemical structure: ❑ phospholipids ❑ sphingolipids ❑ sterols  Phospholipids Phospholipids are lipids composed of: ❑ two fatty acids, ❑ glycerol (an alcohol), ❑ phosphoric acid, ❑ a functional group attached to the phosphate that confers characteristic properties.  Phospholipids Common functional groups that are linked to the phosphate residue are: ❑ ethanolamine, ❑ choline, ❑ inositol, ❑ serine.  Sphingolipids Sphingolipids are lipids composed of: ❑ sphingosine (a long-chain amino alcohol), ❑ a fatty acid, ❑ phosphoric acid (optional), ❑ a functional group (i.e., ethanolamine, choline, serine, etc.). Sphingolipids are divided into two subgroups: ❑ sphingomyelins ❑ glycolipids  Sphingomyelin Sphingomyelin is made up of: ❑ sphingosine, ❑ a fatty acid, ❑ phosphoric acid, ❑ a functional group (i.e., serine, ethanolamine or choline). Critical in: ❑ brain matter ❑ neural tissue ❑ myelin sheath of nerve endings Sphingomyelin structure  Glycolipids Glycolipids are made up of: ❑ sphingosine, ❑ a fatty acid, ❑ one or more sugar molecules. The simplest glycolipids are cerebrosides that contain glucose or galactose. More complex glycolipids are gangliosides that contain up to seven sugar residues.  Glycolipid structure Ceramide  Sterols Sterols are alcohols belonging to the family of steroids. The most important representative of animal sterols is cholesterol. Cholesterol is a cyclic compound containing a branched side chain. sterol skeleton Cholesterol  Structure of membrane lipids Membrane lipids contain one or two fatty acid residues ❑ the fatty acid residues contain an even number of carbon atoms (usually 16 to 18) ❑ at least one bond in the fatty acid residue could be unsaturated The presence of unsaturated bonds causes the rest of the fatty acid to effectively take up more space. Structure of fatty acids  Structure of membrane lipids Membrane lipid molecules are amphiphilic meaning that they simultaneously exhibit: ❑ a hydrophilic (“water-loving”), polar end, ❑ a hydrophobic (“water-fearing”), nonpolar end. The hydrophilic part of the membrane phospholipid molecule, depending on its chemical structure, can: ❑ be electrically charged, ❑ have the polar character of an electric dipole.  Structure of membrane lipids Despite differences in structure, each of the various types of membrane lipids have a hydrophilic head and one to two hydrophobic tails. Structure of membrane lipids  Lipid bilayer The cell membrane is made up of a phospholipid bilayer, which is formed by two layers of phospholipids. They are arranged so that the: ❑ hydrophilic parts (polar heads) are on the surface of the bilayer, ❑ hydrophobic parts (hydrocarbon chains) face the interior of the bilayer. The escape of membrane lipids from the bilayer is prevented by the aqueous environment outside and inside of the cell. Lipid bilayer Lipid bilayer  Membrane proteins Membrane proteins are categorized by the degree of binding to the lipid bilayer: ❑ integral ❑ peripheral ❑ surface  Integral membrane proteins Integral membrane proteins are embedded within the plasma membrane and are divided into: ❑ monotopic membrane proteins that are attached to one side of the plasma membrane, ❑transmembrane proteins, which span across the entire thickness of the lipid bilayer, ❑ polytopic membrane proteins that span across the plasma membrane multiple times.  Integral membrane proteins The structure of integral membrane proteins is reinforced by the highly hydrophobic nature of the lipid component of the membrane. The hydrophobic amino acid side chains of integral membrane proteins interact with the hydrophobic hydrocarbon tails of the membrane lipids. The hydrophilic parts of integral membrane proteins face internally allowing passage of some polar molecules and water. Integral membrane proteins Non-penetrating integral membrane proteins Integral proteins that do not penetrate the plasma membrane are divided into: ❑ outer monolayer proteins (2), ❑ inner monolayer proteins (3), ❑ internal membrane proteins that are located between the two monolayers (i.e., in the hydrophobic part) (4).  Peripheral membrane proteins Peripheral membrane proteins are found on both the inner and outer surfaces of the cell membrane. Peripheral proteins can be bound to the cell membrane by: ❑ electrostatic/ionic bonding, ❑ hydrogen bonding, ❑ van der Waals forces.  Cell surface proteins Cell surface proteins occur only on the outer surface of the cell membrane. Surface proteins are connected to the cell membrane by an anchored element (anchor motif) (e.g., a protein loop or lipid). Types of membrane proteins  Functions of membrane proteins Transport membrane proteins enable the transport of substances across the membrane. Structural membrane proteins link cells together or to the extracellular matrix. Receptor membrane proteins are part of the body's signaling system. Enzymatic membrane proteins catalyze chemical reactions that occur on the surface or inside cells. Functions of membrane proteins  Glycolipids and glycoproteins Some proteins and lipids in the outer layer of the cell membrane covalently attach to sugars. Most membrane proteins attach to short sugar chains such as oligosaccharides to form glycoproteins. Some membrane proteins attach to long polysaccharide chain(s) to form proteoglycans. A single protein molecule can attach to multiple sugar chains. A single lipid molecule can attach to only one sugar chain to form a glycolipid.  Glycolipids and glycoproteins All the sugars (carbohydrates) that make up glycoproteins, proteoglycans and glycolipids are found only on the outer side of the cell membrane. These sugars form a sugar coating called the carbohydrate layer or glycocalyx. The glycocalyx is involved in: ❑ protecting the cell surface, ❑ recognizing other cells, ❑ forming contacts between cells, ❑ merging cells into larger groups. Structure of glycocalyx Cell membrane structure  Cell membrane properties Characteristic features of the cell membrane are: ❑ selective permeability, ❑ fluidity, ❑ asymmetry, ❑ heterogeneity.  Membrane permeability The primary function of the membrane is to create a barrier that controls the passage of molecules across the itself. Small nonpolar molecules (oxygen, carbon dioxide) diffuse passively through the lipid bilayer. Small uncharged polar molecules (water, ethanol) diffuse passively through the lipid bilayer. Larger uncharged molecules (amino acids, glucose) do not diffuse through the lipid bilayer. Ions and electrically charged molecules do not diffuse through the lipid bilayer. Membrane permeability  Membrane fluidity Fluidity is how well all components of the cell membrane can move. The cell membrane is an elastic, two-dimensional fluid. The fluidity of the membrane is influenced by its composition (i.e. the content of: ❑ cholesterol (-) ❑ unsaturated fatty acids (+)) The lipid bilayer is elastic meaning it can bend and return to its original conformation. Membrane fluidity  Membrane fluidity Membrane lipid molecules can perform various types of movements, such as: ❑ segmental movement (flexion) - changing the position of fatty acid chains in relation to the axis of the molecule ❑ rotational movement - around the axis of the molecule (frequent) ❑ translational movement: ❑ lateral movement - in the plane of the membrane (frequent), ❑ transverse movement ("flip-flop") - between membrane layers (rare).  Membrane fluidity Segmental movement is caused by the movement of the hydrocarbon chains of phospholipids. The more mobile the hydrocarbon chains are, the larger the effective volume the chains occupy (i.e., looser packing). Factors influencing the fluidity of the cell membrane: ❑ length of the hydrocarbon chains (14 - 24 C) ❑ number of unsaturated bonds ❑ amount of cholesterol ❑ temperature Lateral and rotational movements take place within the same layer, respectively. Membrane fluidity  Membrane fluidity Transverse movement of the "flip-flop" type occurs because of the passage of lipids from the outer layer to the inner layer of the membrane and vice versa. Transverse movement is classified as: ❑ uncatalyzed ❑ catalyzed by enzymes (flippases) Membrane fluidity  Membrane fluidity Membrane integral proteins can undergo: ❑ rotational movements - rotate around the axis of the molecule ❑ lateral movements - move in the plane of the membrane Due to size of the proteins, the rotational and lateral movements are slower than those of lipids. Membrane proteins do not exhibit transverse movement (i.e., the "flip-flop" type).  Restriction of lateral movement of proteins The lateral movement of proteins can be restricted due to attachment to: ❑ the cell cortex inside of the cell, ❑ extracellular matrix molecules outside of the cell, ❑ proteins on the surface of another cell.  Membrane asymmetry Membrane asymmetry means that respective layers (leaflets) of the cell membrane have a different composition of lipids and proteins. The outer layer of the cell membrane contains: ❑ mainly phosphatidylcholines and sphingomyelin, ❑ surface proteins, ❑ a large amount of glycolipids and glycoproteins. The inner layer of the cell membrane contains mainly: ❑ lipids with electrically charged polar heads like phosphatidylserine, ❑ lipids that easily form hydrogen bonds, like phosphatidylethanolamine. Membrane asymmetry Choline Serine Ethanolamine  Membrane heterogeneity The cell membrane is non-uniform or heterogeneous. Most of the cell membrane is made of a lipid bilayer. The main components of which are phospholipids, cholesterol, glycolipids and proteins. Additionly, there are independent structures: ❑ lipid rafts (rafts) ❑ caveolae  Membrane heterogeneity Lipid rafts are: ❑ flat and dynamic areas of the cell membrane, ❑ rich in cholesterol and sphingolipids, ❑ involved in signalling and transport. Caveolae are: ❑ bottle-shaped invaginations of the cell membrane, ❑ rich in cholesterol, sphingolipids and caveolin, ❑ involved in signalling, endocytosis and transcytosis. Rafts and caveolae are not found in the membranes of lymphocytes, erythrocytes and nerve cells.  Lipid raft Intercellular space 1.Non-raft membrane 2. Lipid raft 3. Raft-associated transmembrane protein 4. Nonraft-associated transmembrane protein 5. Glycosylation modifications (on glycoproteins and glycolipids) 6. GPI-anchored protein 7. Cholesterol 8. Glycolipid Caveola  Membrane transport small molecules large molecules passive active bulk transport transport transport osmosis ATPases simple diffusion Co-transporters endocytosis exocytosis facilitated diffusion phagocytosis pinocytosis receptor-mediated endocytosis  Passive transport Osmosis H2O molecules can diffuse directly through a lipid bilayer. The passage of water molecules from an area of h ​ igh H2O concentration to an area of ​low H2O concentration is called osmosis. The process of osmosis is relatively slow. That is why some cells contain specialized channels in their cell membrane called aquaporins to facilitate the transport of water molecules. Osmosis Aquaporin structure  Passive transport Does not require input of external energy Passive transport of a substance with an electrical charge depends on the: ❑ concentration gradient, ❑ membrane potential. The net force of ion movement is created by the electrochemical gradient, which determines the direction of passive transport. Always occurs in the direction of the concentration gradient (i.e., high to low) Passive transport  Passive transport Simple diffusion is the process by which solutes pass through a cell membrane along the concentration gradient of the solution. The rate of diffusion depends on: ❑ the difference in concentrations (directly proportional), ❑ the electric field across the membrane (charge equalization), ❑ the gradient of hydrostatic pressure across the membrane, ❑ the permeability coefficient of the given substance, ❑ the temperature.  Passive transport Facilitated diffusion (passive-mediated) does not require external energy input. Facilitated diffusion in cell membranes can occur by two means: ❑ a protein channel ❑ a protein transporter The entity facilitating transport is a membrane protein. Passive transport  Ion channels Facilitated diffusion can occur through ion channels. Protein ion channels: ❑ connect intracellular and extracellular spaces, ❑ are filled with water. Protein ion channels are selective depending on: ❑ the diameter and shape of the ion channel, ❑ the arrangement of charged amino acids lining the channel, ❑ the type of ion (i.e., anion, cation).  Ion channels The function of ion channels is to temporarily increase the permeability of the membrane to selected inorganic ions. An ion channel can be: ❑ open, which allows ions to pass through freely, ❑ closed, which allows ions to pass through periodically. Opening and closing of the channel is in response to external stimuli (i.e., temperature, electrochemical gradient, mechanical stimuli, concentration gradient). The concentration of the opening agent affects the number of open channels. This is the most efficient type of transport. Ion channels  Transporters Transporters (carrier proteins) are responsible for the movement across cell membranes of mostly: ❑ small water-soluble, organic molecules, ❑ some inorganic ions. Each transporter is highly selective (i.e., each often transports only one type of solute.) Transporters open only on one side of the cell membrane, but never on both sides at the same time. Transporters  Facilitated diffusion A carrier protein for facilitated diffusion undergoes different confirmational states. For the transport of glucose there is an: ❑ outward open state - binding sites for the solute are exposed to the outside of the cell membrane, ❑ closed state - binding sites are inaccessible from both sides of the cell membrane, ❑ inward open state - binding sites for the solute are exposed to the inside of the cell membrane. Facilitated diffusion  Facilitated diffusion Facilitated diffusion depends on: the concentration gradient around the transporter, the rate of interactions between the carrier protein and the transported substance, the rate of conformational changes of the protein, hormones. Insulin increases the transport of: glucose in adipose tissue and muscle cells, amino acids in the liver. Glucocorticoids increase the transport of amino acids into liver cells  Coupled transport Coupled transport is a type of carrier transport under facilitated diffusion. The characteristic feature is that the transporter has binding sites for two substances. Depending on the direction of transport of the substance in relation to the direction of flow of the accompanying substance, we distinguish the two types of transport: ❑ symport: when both substances flow in the same direction ❑ antiport: when the flow of the substances are in opposite directions Coupled transport  Active transport Active transport: ❑ occurs against the concentration gradient of the substance being transported, ❑ requires energy input, ❑ supplies the cell with substances, such as amino acids, sugars, sodium and potassium ions, etc., ❑ ensures an appropriate osmotic pressure. We distinguish two types of active transport: ❑ primary ❑ secondary  Active transport Primary (direct) active transport There is a direct relationship of transport with the process of energy release (e.g., through ATP hydrolysis). Secondary active transport A transported substance (e.g., Na+) is transported down its an electrochemical gradient, which determines the co-transport with a second substance (e.g., sugar, amino acid) against its gradient. The electrochemical gradient is the source of energy for secondary active transport.  Primary active transport Sodium-potassium pump The pump uses the energy released during ATP hydrolysis to move Na+ ions out of the cell and K+ ions into the cell. During this process, a phosphate group released from ATP is attached to the transporter. The Na+/K+ pump helps maintain a low concentration of Na+ and a high concentration of K+ inside the cell. The ATP-driven Na+/K+ pump occupies a central position in the energy management of animal cells. Sodium-potassium pump  Secondary active transport Glucose transport The transport protein simultaneously: ❑ allows sodium ions to move along their concentration gradient, ❑ transports a glucose molecule into the cell against its concentration gradient, ❑ uses the electrochemical gradient of Na+ to drive active glucose import. Glucose transport  Bulk transport Bulk transport is used to transport large molecules (i.e., amino acids, proteins and others) that cannot pass directly through the cell membrane barrier. Transport of large molecules requires disruption of the cell membrane. This process is completed via vesicles. Types of bulk transport: ❑ endocytosis ❑ exocytosis  Bulk transport Endocytosis is the uptake of substances into the cell including viruses, bacteria and other cells (or cell fragments) by enclosing them in a membrane-bound vesicle formed by the outer cell membrane. Exocytosis is the removal of undigested waste or secretion of compounds (e.g., hormones) from the cell exported via a membrane-bound vesicle, which then fuses with the outer cell membrane. Transmembrane transport  Transmembrane transport Types of endocytosis: ❑ phagocytosis ❑ pinocytosis ❑ receptor-mediated endocytosis Stages of phagocytosis: ❑ uptake of macromolecules or bacteria ❑ formation of a phagosome ❑ transport of substances enclosed within the phagosome to a primary lysosomes ❑ formation of a secondary lysosomes as a result of the fusion between a phagosome with a primary lysosome  Transmembrane transport Stages of pinocytosis: ❑ uptake of fluids and substances dissolved within them ❑ formation of a pinosome ❑ transport of substances enclosed within the pinosome to a primary lysosome ❑ formation of a secondary lysosome as a result of the fusion between a pinosome with a primary lysosome  Transmembrane transport Stages of receptor-mediated endocytosis Membrane stage: ❑ receptor located on the surface of the cell membrane called the pit ❑ binding of a specific molecule (i.e., ligand to the respective receptor) Intracellular stage: ❑ formation of an endosome, which progresses from an early to a late stage ❑ movement of the endosome to specific cellular compartments or to a lysosome Types of endocytosis Bulk transport  Lysosomal degradation The degradation of macromolecules takes place in lysosomes, which contain numerous specific hydrolases.  Protein degradation In a healthy organism, 3 - 5% of proteins are degraded; in a sick organism much more are broken down. Therefore, protein metabolism must be under constant and strict control. In cells of a healthy organism, proteins are degraded if: ❑ the lifespan has ended, ❑ the structure is improper, ❑ the protein is damaged, ❑ there is an excessive amount of that kind of protein.  Protein degradation Protein degradation in eukaryotic cells occurs in two ways: Lysosomal proteolysis, referred to as non-selective degradation In lysosomes, exogenous proteins and old endogenous proteins (e.g., structural proteins) are degraded. Proteasomal proteolysis, referred to as selective degradation, which is associated with the ubiquination.  Ubiquination The ubiquitin system consists of the following elements: ❑ ubiquitin - made of 76 amino acid residues, ❑ ubiquitin-activating enzyme (E 1), ❑ ubiquitin-conjugating enzyme (E 2), ❑ ubiquitin ligase (E 3), ❑ proteasome, ❑ ubiquitin-detaching enzyme - deubiquitinase (DUB).  Ubiquitin Ubiquitin (a globular protein, Ub) attaches to the protein that is to be degraded in order for the proteasome enzyme complex to recognize it. Ubiquitin is composed of: ❑ alpha-helix segments (marked in blue), ❑ beta-sheets (marked in green).  Proteasomes Proteasomes are found in all eukaryotic cells and breakdown proteins bound to ubiquitin. Proteasomes are present in the cytoplasm and in the nucleus. The number of proteosomes varies and depends on the cell's need for protein breakdown. On average, there are about 30,000 proteasomes in a single eukaryotic cell.  Structure of the proteasome Proteasomes are large, high-molecular-weight enzyme complexes. Proteasome structure: ❑ cylindrical made of 28 proteases (central part) ❑ the active sites of the proteases are directed towards the interior of the proteosome ❑ the ends of the cylinder are closed by large protein complexes that resemble plugs. Structure of the proteasome  Proteasome functions Proteasome functions: ❑ bind to proteins to be degraded ❑ unfold a protein and bring it into the "cylinder" ❑ cut (lyse) proteins into short peptides ❑ release the peptides from either end of the cylinder Energy (from ATP hydrolysis) is required to carry out this process Degradation via proteosomes Organelle degradation (autophagy) Dying organelles, such as mitochondria, endoplasmic reticulum membranes, nuclei and peroxisomes send signals to form autophagosome membranes. Autophagosomes: ❑ enclose the damaged organelles, ❑ isolate the organelles from the cytosol, ❑ degrade the organelles after joining with a primary lysosomes within the secondary lysosomes (autolysosome).  Organelle degradation Degradation of the nucleus (nucleophagy): Fragments of the nucleus are subject to degradation in the event of damage to DNA and/or improper separation of chromosomes during cell division. Nucleophagy causes the formation of structures in the cell called micronuclei that contain: ❑ parts of chromosomes, ❑ whole chromosomes, ❑ fragments of the nuclear envelope.  Organelle degradation Mitochondrial degradation (mitophagy): One of the main signals for mitophagy is oxygen deprivation (hypoxia). Lysosome degradation (lysophagy): The signal for lysophagy is: ❑ increased permeability of lysosomal membranes, ❑ appearance of proteins typical of lysosomal membranes in the cytoplasm, ❑ ubiquitination of lysosomal surface proteins.  Organelle degradation Ribosome degradation (ribophagy): The signal for ribophagy is the demand for nitrogen, specifically, for amino acids, such as arginine (Arg) and leucine (Leu), and nucleotides. Proteasome degradation (proteaphagy): Proteaphagy occurs through the binding of appropriate receptors to autophagosome proteins.  Literature Essential Cell Biology, B. Alberts, D. Bray, K. Hopkin Volume 2: Chapter 11. Membrane Structure Chapter 12. Transport Across Membranes Chapter 15. Intracellular Compartments and Protein Transport (Endocytosis Pathways Only)  Cell signaling Lecturer: Dr. Michelle Kuzma Adapted from: Dept. Head, Dr. Danuta Mielżyńska-Švach Molecular biology 2024/2025  Homeostasis Organisms cope with the variability of their external environment by maintaining a relatively stable internal environment. The process by which this is done is called homeostasis (homeo - similar, stasis - state). When homeostasis is disrupted, the organism attempts to compensate. If compensation is successful, homeostasis is restored. If compensation is unsuccessful, homeostasis is disrupted, which can result in disease. Homeostasis  Homeostasis Homeostasis is associated with concepts, such as: ❑ extracellular fluid (ECF), which serves as a link between the external environment and cells, ❑ intracellular fluid (ICF), which is located inside cells.  Homeostasis In homeostasis, the composition of both compartments are relatively stable. Since substances are constantly moving between the two compartments, there is a dynamic steady state. A dynamic steady state does not equate to equilibrium because the concentrations of many substances in the ECF and ICF differ; there is rather an established state of imbalance. Established state of imbalance  The role of homeostasis In the case of multicellular organisms, coordination of activities must be ensured on the following levels: ❑ cells within tissues, ❑ tissues within organs and systems, ❑ systems within the entire organism. To maintain homeostasis, cells must cooperate with each other. The cooperation of individual cells and tissues requires the exchange of information carried out through intercellular communication (i.e., cell signaling).  Intercellular communication Intercellular communication is essential for: ❑ cell survival, ❑ cell division, ❑ cell differentiation, ❑ cell death.  Intercellular signaling Coordination between cells involves the transmission of signals. There are two basic types of signals: ❑ electrical - related to changes of the cell's membrane potential ❑ chemical - chemical compounds (i.e., molecules) secreted by cells into the extracellular space Cells that respond to electrical or chemical signals are called the target cells.  Methods of communication There are two types of communication depending on the distance the signal travels to reach a target cell: ❑ local ❑ distant Types of local communication: ❑ juxtacrine (contact-dependent) ❑ paracrine ❑ autocrine Types of distant communication: ❑ endocrine (hormonal) ❑ neuronal communication  Types of cell communication Juxtacrine/contact-dependent cell-cell communication requires direct contact between cells Direct transfer of molecules occurs via gap junctions between adjacent cells.  Types of cell communication Juxtacrine communication (direct contact) A signaling molecule on the surface of the cell membrane of one cell binds to a receptor on the cell membrane surface of another cell. Cellular receptors: specialized proteins capable of receiving, transforming and transmitting information from the external environment to effectors in the cell.  Types of cell communication Paracrine communication Molecules released by a cell into the extracellular fluid act on neighboring cells  Types of cell communication Autocrine communication Molecules released into the intercellular fluid act on the same cell that secreted them.  Types of cell communication Endocrine communication The endocrine system communicates through hormones (hormone - to stimulate), which are chemical compounds secreted into the blood and distributed throughout the body by the circulatory system. Hormones contact most of the body's cells, but only some are target cells. Types of cell communication  Types of cell communication Neuronal (synaptic) communication The nervous system uses a combination of electrical and chemical signals to communicate over long distances. The electrical signal travels along the neuron to its end where it is converted into a chemical signal. Neurons communicate with each other via synapses. Neuronal communication  Neuronal communication Chemicals secreted by neurons are called neurocrine molecules. Types of neurocrine molecules are: ❑ neurotransmitters that only diffuse across the synaptic cleft and therefore, have a fast effect, ❑ neurohormones that diffuse into the bloodstream and are distributed throughout the body thereby, having a relatively slower effect. Neuronal communication Examples of signaling molecules Also a neurotransmitter  Cells communication principles Only cells that have receptors for signaling molecules respond to a given signal (selective response). The response of a cell to a signal depends on the functional specialization of the cell and on receptor type (NOT the signaling molecule itself): ❑ there may be different receptors for one signaling molecule, ❑ one signaling molecule may induce different changes in different target cells, respectively, ❑ one signaling molecule may be able to induce many different changes in a given target cell. Cells communication principles Acetylcholine can cause a variety of reactions.  Intercellular communication Signaling molecules that bind to receptors are known as ligands and are categorized by how they interact with a given receptor: ❑ agonists: stimulate the receptor ❑ antagonists: inhibit the receptor  Intercellular communication Ligands are also called extracellular signaling molecules because they deliver information to a target cell. Binding of the ligand to the receptor upregulates, downregulates, partially activates the receptor. The receptor, in turn, activates one or more intercellular signaling molecules. The final signaling molecule triggers the final response, which may be protein modification or synthesis.  Types of signaling molecules Signaling molecules are divided into: ❑ those that pass through the cell membrane because they are small enough and/or hydrophobic; they require the presence of an intracellular receptor in the target cell, ❑ those that do not pass through the cell membrane because they are large and/or too hydrophilic; they require the presence of cell-surface receptors on the surface of the target cell.  Types of receptors Intracellular receptors are divided into: ❑ cytoplasmic receptors (Type I NR) ❑ nuclear receptors (Type II NR) Cell-surface receptors are divided into: ❑ ion channel-linked receptors, ❑ G protein-coupled receptors, ❑ enzyme-linked receptors. Types of receptors  Intracellular receptors Intracellular receptors are transcription factors located in the cytoplasm as well as in the nucleus. Respective ligands are small and hydrophobic molecules that can diffuse through the cell membrane, such as: ❑ steroid hormones, ❑ thyroid hormones, ❑ vitamin D, ❑ retinoic acid.  Intracellular receptors In the active state (ligand bound to receptor), intracellular receptors are only in the nucleus and participate in the regulation of gene expression (i.e., transcription)  Intracellular receptors Nuclear receptors are composed of several elements, such as: ❑ a ligand binding domain (LBD), ❑ a DNA binding domain (DBD), ❑ a hinge region that controls the movement of the activated receptor into the nucleus, ❑ a transcription-activating domain.  Intracellular receptors Intracellular receptors bind to the HRE (hormone response element) sequence in target genes. The HRE sequence consists of 15 nucleotides. These sequences are usually located within the promoter, but sometimes they are located at a distance from it.  Intracellular receptors Some nuclear receptors are monomeric. Most nuclear receptors are dimeric. The dimers can be either homodimers or heterodimers. Monomer Homodimer Hetreodimer  Intracellular receptors Intracellular receptor families include receptors: ❑ for lipophilic hormones, ❑ for active vitamin A (retinol), ❑ for active vitamin D3 (1,25-dihydroxycholecalciferol), ❑ for ligands that have yet to be identified ("orphan" receptors)  Steroid hormones The steroid hormone cortisol (involved in stress response) activates a target gene transcription regulator.  Cell-surface receptors Cell-surface receptors are proteins located on/within the membrane of the target cell. The ligands are large, hydrophilic and/or charged molecules that cannot diffuse through the cell membrane. All cell-surface receptor proteins bind to an extracellular signal molecule and transduce its message into one or more intracellular signaling molecules that alter the cell’s behavior. Cell-surface receptors Types of cell-surface receptors  Ion channel-linked receptors The binding of a ligand to a receptor causes a change in the conformation of the proteins that make up the ion channel. The membrane potential changes, which affects the permeability of the cell membrane to specific ions. Ions pass through the open channel according to the concentration gradient (Na+, K+, Ca2+, Cl-). Most receptors for neurotransmitters have this characteristic (fast response).  Mechanism of action Binding of a ligand to a cell-surface receptor Change in receptor conformation Depolarization or hyperpolarization of the cell membrane Creation of an action potential Channel opens and ion flow occurs with the concentration gradient Na+ K+ Na+ K+  Ion channel-coupled receptors The type of ion channel depends on the type of stimuli: ❑ voltage-gated ❑ ligand-gated by an extracellular ligand ❑ ligand-gated by an intracellular ligand ❑ mechanically gated An important feature of ion channels is selectivity (i.e., the ability to pass strictly defined types of ions through): ❑ cationic or anionic ❑ "specialized" - sodium, potassium, calcium, etc. Ion channel-coupled receptors  Ion channel-coupled receptors A voltage-gated ion channel changes conformation depending on the membrane potential: ❑ the channel is closed when the cell is at rest and the cell membrane is polarized, ❑ the channel is open when the cell membrane is depolarized, ❑ after a period of opening, the channel is temporarily inactivated and cannot open (refractory period), ❑ after repolarization of the cell membrane, the channel returns to its initial conformation, closed. Ion channel-coupled receptors  Ion channel-coupled receptors Ligand-gated ion channels activated by neurotransmitters convert chemical signals in the target cell into electrical signals. The ion channels open after binding a neurotransmitter, which causes a change in the permeability of the cell membrane to ions. As a result, the following occurs: ❑ a change in membrane potential, ❑ depolarization of the cell membrane, ❑ generation of an action potential. Ion channel-coupled receptors Ion channel-coupled receptors  G protein-coupled receptors G protein-coupled receptors (GPCRs) are receptors that combine with ligands to transmit a signal to secondary signaling molecules – signal transduction. Such signal transmission is usually much slower and more complex than via ion-channel-coupled receptors. GPCR effects last longer. GPCRs constitute the largest group of receptors.  Signal transduction Signal transduction consists of: ❑ the signaling cell sending a so-called ligand (i.e. an extracellular signaling molecule like a hormone or neurotransmitter), ❑ the ligand binds to a specific receptor present in the target cell membrane, ❑ intracellular signaling molecules are produced inside the cell. This initiates a series or cascade of reactions in which the final signal is transmitted to the effector protein. Signal transduction Cascade and amplification Cascade Amplification  Molecular relay race The signaling process inside a cell is often referred to as "a molecular relay race". Information is passed from one signaling molecule to another. These successive steps continues until: ❑ an enzyme involved in metabolism is activated or inactivated, ❑ the cytoskeleton acquires a new configuration, ❑ a specific gene is transcribed or turned off.  Molecular switches Many signaling molecules act as molecular switches because receiving a signal switches them from an inactive to an active state. When activated, they can turn on or inhibit other proteins in the signaling pathway. These proteins remain active until another process turns them off.  Molecular switches Molecular switches are divided into two classes: ❑ proteins whose activity are turned on or turned off by adding or removing phosphate groups (i.e., phosphorylation or dephosphorylation, respectively) ❑ proteins whose activity depends on the exchange of bound GDP (guanosine-5′-diphosphate) for GTP (guanosine-5′- triphosphate) and vice versa Types of molecular switches G protein-coupled receptors  7TM proteins GPCRs are the largest family of cell-surface receptors (there are over 700 in humans). Despite the diversity of signaling molecules that bind to them, all GPCRs have the structure of 7TM receptors. 7TM receptors consist of seven subunits (α-helices) that span the lipid bilayer of the cell membrane. 7TM receptors have: ❑ an extracellular ligand-binding domain, ❑ an intracellular G protein-binding domain. When a ligand binds to a 7TM receptor, a conformational change is induced.  7TM protein N C  G proteins G proteins are a group of proteins bound to guanosine-5′- diphosphate, known as GDP. G proteins are located on the cytoplasmic side of the cell membrane. G proteins are composed of three protein subunits (domains): ❑ alpha (α) ❑ beta (β) ❑ gamma (γ)  Protein kinase Protein kinases are a group of enzymes that phosphorylate proteins specific to a given kinase. Phosphorylation leads to a change in the conformation of the target protein, and therefore, can: ❑ change its activity, ❑ change its ability to bind to other proteins, ❑ cause the molecule to move within the cell. ~30% of proteins are regulated in this way. Most metabolic pathways of the cell, especially in cell signaling, involve enzymes from the protein kinase group.  G proteins There are different types of G proteins that are specific for different receptors and target proteins. They act as intermediaries and carry the signal from the modified 7TM receptor to the effector. The type of α-subunit present is most important for the specificity of signal transduction. G proteins based on the α subunit are divided into: ❑ stimulating (Gs) ❑ inhibitory (Gi)  Mechanism of action In the resting state, 7TM receptors and G proteins are inactive. Binding of a ligand to the membrane receptor causes a change in the conformation of the: ❑ 7TM receptor on the extracellular side of the membrane, ❑ G protein on the cytoplasmic side of the membrane. In the inactive G protein, GDP is linked to the alpha (α) subunit.  Mechanism of action Activation of the G protein involves the exchange of GDP for GTP in the α-subunit. This breaks up the G protein into two molecules: ❑ the α-subunit linked to GTP, ❑ The G βγ complex. The active α-subunit and the G βγ complex can interact with a specific target protein in the plasma membrane. Mechanism of action Mechanism of action α-subunit Mechanism of action βγ complex  Second messenger molecules The targets of G proteins are most often proteins that are located within the cell membrane. Examples include: ❑ adenylyl cyclase ❑ phospholipase These proteins catalyze the formation of second messenger molecules that are located inside of the cell. Adenylyl cyclase is responsible for the formation of cyclic adenosine-3′,5′-monophosphate (cAMP). Phospholipase C is responsible for the formation of molecules: ❑ inositol trisphosphate (IP3), ❑ diacylglycerol (DAG).  Adenylyl cyclase Ligands that cause activation of adenylyl cyclase are adrenaline, acetylcholine, and glucagon. Stages of adenylyl cyclase action are: ❑ the ligand binds to the 7TM receptor, ❑ the G protein is activated, ❑ the α-subunit of the G protein binds to adenylyl cyclase, ❑ the active adenylyl cyclase synthesizes cyclic adenosine- 3′,5′-monophosphate (cAMP). Adenylyl cyclase Adenylyl cyclase  Cyclic AMP Stages of cyclic AMP activity: ❑ activation of protein kinase A (PKA) ❑ activation of other proteins responsible for: ❑ glycogen breakdown (e.g., in muscle cells), ❑ regulation of gene expression (e.g., in endocrine cells of the hypothalamus), ❑ others. Protein kinase A Protein kinase A  Phospholipase C Ligands that cause activation of phospholipase C are acetylcholine, vasopressin and thrombin. Stages of phospholipase C activity: ❑ a ligand binds to the 7TM receptor ❑ the G protein is activated ❑ the α-subunit binds to phospholipase C ❑ activation of phospholipase C and breakdown of phosphatidylinositol (inner part of the cell membrane) ❑ formation of second messenger molecules: ❑ inositol triphosphate (IP3) -> diffuses into cytosol ❑ diacylglycerol (DAG) -> remains membrane-bound  Phospholipase C Action of inositol triphosphate (IP3): ❑ binds to the Ca2+ channel in the ER membrane and opens it ❑ an electrochemical gradient causes an efflux of Ca2+ ions from the ER to the cytosol Action of diacylglycerol (DAG): ❑ together with Ca2+ ions, participates in the activation of protein kinase C (PKC) in the cytosol ❑ PKC moves from the cytosol to the cytoplasmic side of the cell membrane ❑ active PKC participates in the phosphorylation of other proteins inside the cell. Phospholipase C  Enzyme-linked receptors Enzyme-linked receptors are receptors that act as enzymes or bind to proteins that become enzymes. Enzyme-linked receptors usually have only one transmembrane segment, which spans the lipid bilayer as a single α-helix that: ❑ binds to a ligand on the outside of the cell membrane, ❑ has a catalytic center or an enzyme- binding site on the inside of the cell membrane. Enzyme-linked receptors  Enzyme-limkedreceptors Enzyme-linked receptors: ❑ are active at low ligand concentrations, ❑ have slow subsequent responses (on the order of hours), ❑ have effects that may require many intracellular transduction steps that usually lead to a change in gene expression.  Enzyme-linked receptors Enzyme-linked receptors are divided into receptors with the following functions: ❑ tyrosine kinase ❑ serine-threonine kinase ❑ guanylate cyclase  Tyrosine kinase Growth factors (i.e., FGF, EGF, PDGF, VEGF) are the ligands that cause activation of tyrosine kinases. Stages of tyrosine kinase action: ❑ a ligand binds to a receptor (active site), ❑ connection of the membrane of two receptor molecules to form a dimer, ❑ stimulation of kinase activity - a mutual phosphorylation of tyrosine residues, ❑ binding of signaling proteins, ❑ phosphorylation of subsequent signaling proteins - transmission and/or amplification of a signal in the cell. Activation of tyrosine kinase  Ras protein Most tyrosine kinases activate Ras proteins. The Ras protein is: ❑ a monomeric G protein (GTPase), ❑ bound to the cell membrane by a membrane lipid, ❑ occurs in the following states: ❑ inactive (bound to GDP) ❑ active (bound to GTP) Ras protein activation  Ras protein activation An adaptor protein is attached to a specific phosphorylated tyrosine residue. The adaptor protein then binds to the GEF protein, forming a Ras-GEF complex. The Ras-GEF complex forces the Ras protein to convert GDP to GTP (i.e., causing its activation). Tyrosine kinase - Ras protein  The phosphorylation cascade The activated Ras protein triggers a phosphorylation cascade of three serine-threonine kinases that carry a signal further. Individual kinases in the cascade are phosphorylated and activated by enzymes called kinase kinases. The final kinase in the cascade is called the MAP kinase (mitogen-activated protein kinase) and is involved in the phosphorylation of further signaling or target proteins. The Ras protein - MAPK pathway  PI3K/Akt pathway Stages of growth and survival signaling (e.g., IGF): ❑ activation of tyrosine kinase, ❑ binding and activation of PI3K, ❑ PI3K phosphorylates phosphatidylinositol, ❑ binding of phosphatidylinositol to protein kinase B (PKB/Akt), ❑ Akt is phosphorylated by protein kinase 1 and protein kinase 2, ❑ release of active Akt from the cell membrane, ❑ active Akt then participates in the phosphorylation of other proteins inside the cell. PI3K/Akt pathway PI3K/Akt/mTor pathway Signal transduction  Cell signal response Extracellular signals can trigger fast or slow responses. Motility changes, secretion and metabolism require changes in protein function and therefore, occur rapidly. Cell growth, differentiation, or division require the synthesis of new proteins and changes in gene expression and therefore, occur relatively slowly. Signal integration Cell signal response  Literature Essential of Cell Biology B. Alberts, D. Bray, K. Hopkin. Volume 2:Chapter 16. Cell Signaling