Cell Structure and Function 2 - Lecture Notes PDF

Cellular & Molecular Biology MD105 Dr C. Michaeloudes Cell structure and function 2 Dr C. Michaeloudes Cellular & Molecular Biology MD105  Lecture Objectives To understand: The structural organization of eukaryotic cells The structure and function of...

Cellular & Molecular Biology MD105 Dr C. Michaeloudes Cell structure and function 2 Dr C. Michaeloudes Cellular & Molecular Biology MD105  Lecture Objectives To understand: The structural organization of eukaryotic cells The structure and function of the main intracellular organelles The intracellular transport of proteins from ribosomes to the endoplasmic reticulum and then to the Golgi apparatus The role of lysosomes in recycling damaged organelles and extracellular material The role of mitochondria in energy production Structural organization of eukaryotic cells Cells are microscopic factories  Cells are microscopic factories Exterior wall/Gate Materials Products Power plant Generates power Assembly line Product assembly Control centre Assembly instructions for machinery and products Packaging Packaging and Recycling dispatch  Cell structure/organelles Cell membrane Import/export of molecules Mitochondrion Nutrients Proteins Production of energy /Lipids from nutrients Ribosomes/Endoplasmic reticulum Assembly and transport of proteins/lipids Nucleus Golgi apparatus Instructions in the form Packaging and of the DNA code dispatch of Lysosomes protein/lipids Recycling damaged organelles Cell membrane and cytoplasm Cell membrane Structure: lipid molecules arranged in a double layer Semi-permeable – some molecules can go through and some not Contains proteins that act as channels, receptors or enzymes Protective layer around all cells Allows nutrients to pass inside the cell and waste products to exit the cell Acts as sensor, receiving information about changes in its environment Image from Essential Cell Biology, 5th Edition Phospholipids and cholesterol Phospholipids Cholesterol Hydrophilic head Hydrophobic tail Main constituents of cell membranes Image from Essential Cell Biology, 5th Edition  Cell membrane lipid bilayer Hydrophilic Water head Lipid bilayer Hydrophobic tail Water Membrane lipids are exposed to two opposite forces: ▪ The hydrophilic head is attracted to water ▪ The hydrophobic tails aggregate away from water Formation of bilayer: ▪ Hydrophilic heads face the water on both surfaces of the bilayer ▪ Hydrophobic tails stay within the bilayer interior  Cell membrane functions Lipid bilayer Protein molecule Lipid bilayer controls what enters and leaves the cell ▪ Small hydrophobic molecules (O2, CO2) cross the membrane rapidly ▪ Small hydrophilic molecules (H2O) cross very slowly ▪ Large hydrophilic molecules (glucose, amino acids) and ions cannot cross - require special transporter proteins Membrane proteins are embedded in the lipid bilayer and perform other functions ▪ Transporters – movement of ions and macromolecules in/out of the cells ▪ Receptors – cell signalling ▪ Enzymes – chemical reaction catalysts Cytoplasm The part of the cell inside the cell membrane is called the cytoplasm Cytoplasm = cytosol + intracellular organelles Cytosol is an aqueous (water) matrix containing high concentrations of salts and macromolecules (proteins, sugars, lipids) The majority of the cell’s metabolic reactions occur in the cytosol  Nucleus The control centre  Nucleus Nucleolus DNA The control center of the cell Information stored in DNA Separated from the cytoplasm by the nuclear envelope Consists of two lipid bilayer membranes with pores that allow movement of molecules in and out The primary site of DNA and RNA synthesis Nuclear envelope Nucleolus: structure inside the nucleus involved in ribosome production  Nucleus – DNA storage DNA is packaged in the nucleus, associated with proteins in a state called chromatin Chromatin is dispersed as fine threads throughout the nucleus As the cell prepares to divide chromatin condenses into worm-like structures called chromosomes  REMINDER - Flow of genetic information DNA Gene transcription DNA is divided into segments called genes, which encode for mRNA proteins mRNA translation For a gene to encoded into a protein it needs to be transcribed Protein into its complementary messenger RNA (mRNA) Protein activity mRNA is then translated into a Phenotype protein  Nucleus – DNA replication and transcription DNA DNA replication occurs in the DNA replication nucleus Transcription Genes are transcribed into messenger RNA (mRNA) in the mRNA mRNA nucleus mRNA exits the nucleus through the mRNA nuclear pores and becomes translated to protein in structures called ribosomes TRANSLATION IN RIBOSOMES  Nucleolus – Ribosome formation Nuclear compartment where ribosome formation occurs Formed transiently when the chromosomes carrying ribosomal genes come together before cell division It is not surrounded by a membrane ▪ Aggregate of RNAs and protein Nucleolus Contains genes encoding for ribosomal RNA – a major structural component of ribosomes  Ribosomes Protein synthesis Ribosomes Ribosomes Protein production sites of the cell mRNA code is translated into proteins Particles made up from RNA (produced in the nucleolus) and proteins (ribonucleoproteins) Not surrounded by a membrane Ribosomes found in two sites: 1. the cytoplasm (free ribosomes) 2. Attached to the endoplasmic reticulum  Ribosome function DNA mRNA is released from the nucleus into DNA replication the cytoplasm through nuclear pores mRNA is attached to ribosomes, which Transcription translate it into proteins mRNA mRNA Free ribosomes translate proteins that remain in the cytoplasm mRNA are incorporated in mitochondria and nucleus Ribosome Endoplasmic reticulum ribosomes translate proteins that Polypeptide are incorporated in the cell membrane are destined to be released by the cell  Endoplasmic Reticulum Protein and lipid synthesis  Endoplasmic reticulum Endoplasmic reticulum Assembly site of the cell Assembly and transport of proteins and lipids A continuous network of membranes that form a series of flattened sacs and tubes Attached to the nuclear membrane and spreads into the cytoplasm 2 types of endoplasmic reticulum Rough 1. Rough - ribosomes attached to it 2. Smooth - no ribosomes Smooth Smooth endoplasmic reticulum function Synthesis of lipids Cholesterol Steroid hormones Storage of glucose in the form of glycogen Liver, kidney and muscle Detoxification enzymes Lipid-soluble drugs and toxins Cytochrome P450 enzymes – convert lipid- soluble drugs to water-soluble for excretion in urine Regulation of calcium levels Stores and releases calcium Bone structure, muscle/nerve function  Rough endoplasmic reticulum function Ribosomes attach to the endoplasmic reticulum if the polypeptide they synthesize contains a specific amino acid sequence ER signal sequence Inside the rough ER lumen: The synthesis of the polypeptide is completed The polypeptide is folded into its 3D form (protein) – if its is incorrectly folded it is discarded (quality control) Proteins are packaged in vesicles (bubbles of liquid surrounded by lipid membrane) and sent to the Golgi apparatus for sorting  Protein synthesis and folding in the endoplasmic reticulum 1. Ribosome translating 2. A signal-recognition 3. The SRP is recognized 4. The polypeptide polypeptide chain particle (SRP) in the by an SRP receptor in the chain is folded into its containing a specific cytoplasm binds to the ER ER membrane and the 3D structure. amino acid sequence signal sequence and the synthesis of the called the ER signal ribosome polypeptide chain is sequence completed inside the ER lumen  Folded proteins are packaged in vesicles and released from the endoplasmic reticulum Vesicle Protein Liquid Lipid bilayer Folded proteins are packaged in vesicles and released from the endoplasmic reticulum Vesicles = small structures consisting of fluid enclosed by a lipid bilayer Vesicles fuse with lipid membranes and release their contents  Vesicle formation in the ER 3 2 1 Cargo Coat proteins receptors Protein ER lumen 1. The protein to be exported 2. Coat proteins assemble 3. The cargo protein is (cargo) is recognised by cargo into spherical structures packaged into the formed receptor proteins in the ER which pull the attached ER vesicle, which is released membrane. The receptors membrane into a spherical from the ER recruit coat proteins which shape also bind to the ER membrane  Golgi Apparatus Protein/lipid modification and sorting  Golgi apparatus Sorting office of the cell Receives proteins and lipids from the ER, modifies them, and then dispatches them to other destinations in the cell. Near the nucleus and endoplasmic reticulum Collection of 3-20 flattened, Golgi membrane-enclosed sacs called cisternae stacked on top of each other Resemble a stack of pita breads  Golgi apparatus cis face (entry) Cisternae Lumen trans face (exit) cis face – vesicles from ER transport proteins/lipids to the Golgi Cisternae – contains enzymes that chemically modify proteins/lipids i.e addition of sugars (glycosylation) or phosphate (phosphorylation) trans-face – dispatches proteins/lipids to their final destination (lysosomes, cell membrane, secretion)  Golgi apparatus Lysosomes Cell membrane Secretion cis-face trans-face (entry) Cisternae (entry) 1. Vesicles released by the ER 2. Proteins/lipids are transported 3. Proteins/lipids are transfer lipids and proteins to through the cisternae via vesicles and dispatched to their final the cis-face of the Golgi are chemically modified – modification destination in vesicles apparatus determines their destination  Vesicle fusion with Golgi Receptor 1. Tethering proteins on the target membrane surface make Cargo initial contact with the incoming vesicle pulling it near 2. SNARE proteins on the vesicle (vSNARE) specifically interact with matching SNARE proteins on the target membrane (tSNARE) docking the vesicle to the target membrane vSNARE 3. Vesicle and target membranes fuse and the cargo proteins is delivered into the Golgi apparatus Tethering protein CYTOSOL Target membrane tSNARE  Lysosomes Recycling centre  Lysosomes Lysosome Recycling site of the cell Contains enzymes that break down extracellular materials or damaged organelles The resulting components are re-used (recycled) or excreted by the cell Lysosome  Lysosomes Membrane-enclosed organelles filled with hydrolytic enzymes that digest macromolecules (proteases, nucleases, lipases etc) Digestion products (amino acids, fatty acids, nucleotides) are released to the cytoplasm through transporter proteins and are re-used or secreted Hydrolases work best at acidic pH Lysosomes have a pH of 4.5-5 H+ pump moves H+ into the lysosome maintaining low pH Material destined to be degraded are transported to the lysosomes in vesicles Vesicles fuse with lysosomes to allow degradation  Lysosome function Three types of materials are degraded in lysosomes: 1. Extracellular large particles (e.g bacteria, dead cells) Cells engulf particles through the process of phagocytosis (”cell eating”) and transport them to lysosomes in vesicles called phagosomes 2. Extracellular macromolecules (e.g proteins, lipids) Cells take up macromolecules through the process of endocytosis (“inside the cell”) and transport them to lysosomes in vesicles called endosomes 3. Damaged organelles (e.g mitochondria) Organelles are enclosed in vesicles called autophagosomes and transported to the lysosomes – autophagy (“self eating”)  Lysosome function Bacterium Phagocytosis Phagosome Extracellular Endosome Hydrolases macromolecules e.g proteins, lipids Endocytosis Lysosomes Autophagosome Damaged Autophagy organelle  Summary video https://www.youtube.com/watch?v=Fcxc8Gv7NiU  Mitochondria The power generator  Mitochondria The power generators of the cell Mitochondria Release energy from nutrients i.e glucose, fatty acids Number of mitochondria varies between different ▪ Cells with high-energy needs (e.g skeletal muscle cells) have more mitochondria than cells with lower energy needs (e.g immune cells) Mitochondria numbers increase when energy is needed ▪ Marathon runners have more mitochondria in their leg muscles  Outer membrane Mitochondria Cristae Surrounded by two highly-specialized membranes; outer membrane and inner membrane Outer membrane – contains pores (porins) that allow small molecules and inorganic ions to enter the mitochondria from the cytoplasm Matrix – similar composition to cytoplasm; site of many metabolic reactions Inner membrane – contains multiple infoldings called cristae, which increase surface area Matrix ▪ site where the majority of the cell’s energy is Inner membrane produced in the form of ATP - oxidative phosphorylation (Biochemistry course)  Mitochondria contain their own DNA and ribosomes Mitochondria contain DNA and ribosomes in the matrix Evolved from aerobic bacteria that were engulfed by anaerobic archaeal cells billions of years ago and established a symbiotic relationship ▪ Integrated into eukaryotic cells as organelles Mitochondrial DNA is circular ▪ Encodes for some of the proteins involved in oxidative phosphorylation (energy production) DNA Mitochondrial DNA transcribed into mRNA which is Ribosomes translated into proteins by the ribosomes  Cell structure and function Mitochondrion Nucleus Energy production DNA storage/replication Gene transcription Ribosomes Protein synthesis Rough ER Completion of protein synthesis and protein folding Lysosome Recycling of Smooth ER extracellular Lipid materials and Golgi apparatus synthesis/detoxification/ damaged Protein/lipid modification calcium storage organelles and distribution Organelle dysfunction causes disease  Lysosomal storage diseases Diseases caused by mutations in genes encoding proteins involved in lysosome function (e.g hydrolases) The lysosome does not function properly so proteins, lipids and damaged organelles do not become degraded ▪ Accumulation of macromolecules (e.g proteins and lipids) that become toxic ▪ Cell dysfunction and death ▪ Pathology Lysosomal storage diseases Platt, F.M., d’Azzo, A., Davidson, B.L. et al. Lysosomal storage diseases. Nat Rev Dis Primers 4, 27 (2018)  Tay Sachs disease The best-studied lysosomal storage disease Rare neurodegenerative disorder ▪ Incidence of 1 in 3600 in the Ashkenazi Jewish population ▪ Much lower in individuals from other ethnicities Mutations in the HEXA gene causes deficiency of the lysosomal beta-hexosaminidase A enzyme beta-hexosaminidase A breaks down the fatty acid GM2 ganglioside, which is important for nerve cell function Accumulation of GM2 ganglioside at pathogenic levels leads to nerve cell death and progressive neuronal degeneration in the brain and spinal cord  Mitochondrial diseases Genetic diseases characterized by dysfunctional mitochondria Gene mutations in mitochondrial and nuclear DNA Insufficient ATP (energy) production Cell dysfunction and death Involve a range of clinical symptoms and involve multiple tissues ▪ Particularly nervous system and skeletal muscle Mitochondrial diseases Gorman, G., Chinnery, P., DiMauro, S. et al. Mitochondrial diseases. Nat Rev Dis Primers 2, 16080 (2016)  Mitochondrial diseases Leber hereditary optic neuropathy (LHON) ▪ Visual loss, dystonia, cardiac pre-excitation syndromes, associated with multiple sclerosis-like symptoms (Harding syndrome) Mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome ▪ Stroke-like episodes, deafness, diabetes mellitus, pigmented retinopathy, cardiomyopathy, cerebellar ataxia, seizures, encephalopathy, lactic acidosis and myopathy