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2. Cell structure and organelle function eukaryotes membrane enclosed organelles: nucleus, ER, mitochondria, Golgi apparatus hitchhiker: virus.

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Presentation on theme: "2. Cell structure and organelle function eukaryotes membrane enclosed organelles: nucleus, ER, mitochondria, Golgi apparatus hitchhiker: virus."— Presentation transcript:

1 2. Cell structure and organelle function eukaryotes membrane enclosed organelles: nucleus, ER, mitochondria, Golgi apparatus hitchhiker: virus

2 The minimal requirements for a cell appear to be Molecules to store information and a mechanism to copy it A way to find and extract energy A way to enclose the space where these process happen Bacterium---the very basic cell structure Figure 1-18 Molecular Biology of the Cell, 4 th edition The bacterium Vibrio cholerae, showing its simple internal organization. Like many other species, Vibrio has a helical appendage at one end—a flagellum—that rotates as a propeller to drive the cell forward.

3 As things get more complex additional machinery is needed To move when diffusion (thermal energy) is too slow or random cell motility, division (cytokineses), intracellular transport To bind and communicate with other cells To invade or prevent invasion by other cells The types of unique intracellular organelles appear to be limited and well conserved even in very different cell types The minimal requirements for a cell appear to be Molecules to store information and a mechanism to copy it A way to find and extract energy A way to enclose the space where these process happen

4 Figure 1-31 Molecular Biology of the Cell, 4 th edition Eukaryotic cell structure Animal cell

5 Plant cell

6 Figure 1-21 Molecular Biology of the Cell, 4 th edition The three major domains of the living world procaryotes Originally living organisms are classified as procaryotes and eucaryotes. Due to divergence in evolution, the two groups of procaryotes are further divided into eubacteria and archaea. The living organisms are classified into 3 major domains.

7 Basic terminology for part of (eukaryotic) cells Nucleus Cytoplasm Cytosol Endoplasmic reticulum (ER) Ribosomes Golgi apparatus Mitocondria; (chloroplasts in plants) Lysosomes Endosomes Peroxisomes Centrosome Cytoskeleton red = membrane bounded Figure 12-1 Structure of a highly specialized eukaryotic cell: the epithelial lining e.g. the gut or lung

8 Table 12.1 Relative volumes occupied by the major intracellular compartments in a liver cell (hepatocyte) Intracellular compartment % of total cell volume cytosol 54 mitocondria 22 rough ER cisternae 9 smooth ER cisternae + Golgi cisternae 6 nucleus 6 peroxisomes 1 lysosomes 1 endosomes 1

9 Figure 12-4 Molecular Biology of the Cell, 4 th edition Hypothetical model for the evolution of eukaryotic cells Internal membrane helps organelles to perform their specialized functions 1. nucleus

10 Figure 12-4 Molecular Biology of the Cell, 4 th edition 2. mitocondria Mitocondria have their own genomes independently from the nucleus. Their genomes share resemblance with those in bacteria. Internal membrane helps organelles to perform their specialized functions

11 Nucleus Figure 4-9 Molecular Biology of the Cell, 4 th edition Structure: double-membrane nuclear envelope, nuclear pores, nuclear lamina, contains DNA, DNA-associated proteins Functions: store and regulate genetic information. Also regulate all other cellular activities

12 Nucleus: nuclear pores Figure Molecular Biology of the Cell, 4 th edition  5 kDa freely diffuse Specialized proteins, nucleoporins, form octagonal-shape channels through the nuclear envelope that regulate passage of molecules. Open aqueous channels

13 How nucleus regulates cellular activities? Figure Molecular Biology of the Cell, 4 th edition Key: nuclear import receptor

14 Nucleus: nuclear membrane Figure Molecular Biology of the Cell, 4 th edition Figure 12-9 Molecular Biology of the Cell, 4 th edition The nuclear lamina gives shape and stability to the nuclear envelope.

15 DNA 2 m Nucleus: how DNA is packed inside the nucleus? 6  m nucleus human genome—approximately 3.2 × 10 9 nucleotides Specialized proteins bind to and fold the DNA, generating a series of coils and loops that prevens DNA from becoming an unmanageable tangle. nucleosome Figure 4-24 Molecular Biology of the Cell, 4 th edition chromosome Those 3.2 × 10 9 nucleotides are now packed and distributed over 24 different chromosome.

16 Endoplasmic recticulum (ER) Function: synthesize proteins (RER) and lipids (SER). ER also sequester Ca ++ in the cytoplasm (Ca ++ storage) necessary for the rapid response to extracellular signals such as the contraction and relaxation of muscle. Structure: labyrinth (network) of continuous sheet enclosing a single internal space  ER lumen or ER cisternal space. ER membrane is selective for molecular transport between the ER lumen and the cytosol. media/79/ B7393C9.jpg

17 Two types of ER Figure Molecular Biology of the Cell, 4 th edition Ribosomes attach to the ER membrane Note: a few free ribosomes synthesize proteins in the cytosol RER SERSER is abundant in cells that specialize in lipid metabolism such as hormone- secreting cells and hepatocytes.

18 Figure Molecular Biology of the Cell, 4 th edition Ribosomes synthesize proteins

19 Addition of sugars to the newly synthesized and folded proteins in ER Figure Molecular Biology of the Cell, 4 th edition Most proteins synthesized in RER are glycosylated by N-linked oligosaccharides. Panel 3-1 Molecular Biology of the Cell, 4 th edition The added sugars can be further trimmed or processed in the Golgi apparatus. Proteins are synthesized and completely folded in the ER.

20 Golgi apparatus Function: major site for carbohydrate synthesis as well as modification of proteins and lipids. Structure: stack of membrane-enclosed cisternae (about 4-6 per stack). Each stack has two distinct faces: cis face (entry face) and trans face (exist face). Located close to the nucleus. Figure Molecular Biology of the Cell, 4 th edition

21 Oligosaccharide chains are processed in the Golgi apparatus N-linked oligosaccharides can be processed into complex oligosaccharides and high-mannose oligosaccharides. Figure Molecular Biology of the Cell, 4 th edition

22 Transport from ER to the Golgi apparatus is mediated by vesicular tubular clusters Figure Molecular Biology of the Cell, 4 th edition Figure Molecular Biology of the Cell, 4 th edition

23 Movie 13.2 intracellular protein traffic

24 Mitocondria Figure 1-34 Molecular Biology of the Cell, 4 th edition Function: generate energy in the form of ATP in eucaryotes. Most of a eukaryotic cell’s ATP is generated from oxidation reactions (fatty acid breakdown, Kreb’s cycle) in the mitocondrion using a proton gradient set up in the space between the two membranes (chemi- osmotic coupling). Structure: stiff, elongated cylinders with diameter of um. They are very mobile and plastic. Unique orientation and location in different cell types. One of the first organelles imaged by light microscope

25 The highly convoluted structure Figure 14-8 Molecular Biology of the Cell, 4 th edition Matrix: large internal space containing a mixture of enzymes for oxidation reaction, mitocondrial genome Outer membrane: contain a permeable membrane (molecules < 5 kDa) and enzymes for mitocondrial lipid synthesis Intermembrane space: contain enzymes that aid the outflow of ATP Inner membrane: folds into many infoldings (cristae) to carry out electron transport and ATP production

26 Energy generation in mitochondria Figure Molecular Biology of the Cell, 4 th edition Oxidation of pyruvate and fatty acids produce acetyl CoA NADH (nicotine adenine dinucleotide) carries electrons to the inner mitocondrial membrane Conversion of C atoms in acetyl CoA to CO 2 generate high energy electron NADH (nicotine adenine dinucleotide) carries electrons to a series of three H + pump the inner mitocondrial membrane Electron transfer release energy to drive proton gradient across the membrane. Proton is used to drive the conversion of ADP  ATP Oxidative phosphorylation ~ 30 ATP is produced, 15 times higher than glycolysis

27 Viruses---the hitchhikers Figure 1-27 Molecular Biology of the Cell, 4 th edition Bacteriophage (bacterial virus) T4

28 Genes Can Be Transferred Between Organisms Figure 1-27 Molecular Biology of the Cell, 4 th edition T4 infects host bacterium Inside the host cell, the virus may remain as separate fragments of DNA (plasmids) and replicate independently from the host genes OR insert their plasmids into the DNA of the host cell.

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30 3. Protein Structure and Function

31 'Glowing' jellyfish grabs Nobel Jellyfish will glow under blue and ultraviolet light because of a protein in their tissues. Scientists refer to it as green fluorescent protein, or GFP. Fluorescence protein is part of the gene---cells constantly emits green fluorescence Fluorescence protein has been bounded to protein inside the cells--- fade within weeks in the absence of antifading mounting media

32 Brainbow re/ stm Glowing mouse

33 'Glowing' jellyfish grabs Nobel Jellyfish will glow under blue and ultraviolet light because of a protein in their tissues. Scientists refer to it as green fluorescent protein, or GFP. Fluorescence protein is part of the gene---cells constantly emits green fluorescence Fluorescence protein has been bounded to protein inside the cells--- fade within weeks in the absence of antifading mounting media

34 Brainbow Glowing mouse

35 There are 20 amino acids It is useful to remember their most important structural features. At a minimum, memorize their names and one letter codes. Know which one is acidic, basic, hydrophobic, polar, big, small, reactive, inert There are a few modifications done to amino acids as or immediately after the protein is made: e.g. phosphorylation, acetylation, acylation, glycosylation

36 Figure 3-3. Cell and Molecular Biology, 4 th edition Essential amino acids

37 The side chains Panel 3-1 Cell and Molecular Biology, 4 th edition

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39 Peptide sequence Figure 3-2. Cell and Molecular Biology, 4 th edition

40 Three types of noncovalent bonds that help proteins fold. Although a single one of these bonds is quite weak, many of them often form together to create a strong bonding arrangement. The final folded structure, or conformation, adopted by any polypeptide chains is the one with the lowest free energy. Non-covalent bonds in protein folding Figure 3-5. Cell and Molecular Biology, 4 th edition

41 Formation of hydrogen bonds Figure 3-7. Cell and Molecular Biology, 4 th edition Large numbers of hydrogen bonds form between adjacent regions of the folded polypeptide chain and help stabilize its three-dimensional shape. The protein depicted is a portion of the enzyme lysozyme, and the hydrogen bonds between the three possible pairs of partners have been differently colored, as indicated.

42 The polar amino acid side chains tend to gather on the outside of the protein, where they can interact with water; the nonpolar amino acid side chains are buried on the inside to form a tightly packed hydrophobic core of atoms that are hidden from water. In this schematic drawing, the protein contains only about 30 amino acids. Figure 3-6. Cell and Molecular Biology, 4 th edition Proteins have hydrophobic cores

43 Changes in protein conformation Figure 3-8. Cell and Molecular Biology, 4 th edition Some proteins, often small ones, reach their proper folded state spontaneously. Once unfolded, kT allows them to find their equilibrium structure when returned to physiological conditions. Other proteins are metastable: they are helped to fold to structures they would practically never find at random. Protein folding in a living cell is often assisted by special proteins call molecular chaperones. A protein can be unfolded, or denatured, by treatment with certain solvents to disrupt the non-covalent bonds or heat (heat denaturation) and cold (< 20  C for certain antibodies)

44 Disulfide bond covalently link polypeptide chains together, providing a major stabilizing effect on a protein. Disulfide bonds stabilize protein structure Figure Cell and Molecular Biology, 4 th edition Figure Cell and Molecular Biology, 4 th edition

45 Recap: Protein structure and protein function Hierarchy of protein structure Primary structure Secondary structure Tertiary structure Quaternary structure amino acids joined together in a linear polypeptide chain local folding through H-bonds into  -helix or  -pleated sheet full 3-D organization of a polypeptide chain multi-subunit complex consisting of multiple polypeptide chains

46 The regular conformation of the polypeptide backbone observed in the α helix and the β sheet. (A, B, and C) The α helix. The N–H of every peptide bond is hydrogen-bonded to the C=O of a neighboring peptide bond located four peptide bonds away in the same chain. Secondary structure: alpha helix Figure 3-9. Cell and Molecular Biology, 4 th edition

47 (D, E, and F) The β sheet. In this example, adjacent peptide chains run in opposite (antiparallel) directions. The individual polypeptide chains (strands) in a β sheet are held together by hydrogen-bonding between peptide bonds in different strands, and the amino acid side chains in each strand alternately project above and below the plane of the sheet Figure 3-9. Cell and Molecular Biology, 4 th edition Secondary structure: beta sheet

48 Figure Cell and Molecular Biology, 4 th edition Beta sheets can have parallel or antiparallel strands

49 Protein domains, e.g. Src protein Protein domains have a unit of organization distinct from the four levels of protein structure. Any part of the polypeptide chain can fold independently into a compact, stable structure (folded domains). In Src protein, SH2 and SH3 domains perform regulatory functions and the other two domains from a protein kinase enzyme—notice the ATP binding cleft within the unit.

50 Only a very small fraction of random sequences of amino acids make polymers with a unique or stable structure. Nature has selected those sequences with specific folded shapes. The shapes and therefore functions can be very fragile to even tiny changes in atomic structure (mutation). A single protein can have separate sections each with its own folded domain, and linked by spacers. Figure Cell and Molecular Biology, 4 th edition

51 Two identical subunits bind head-to-head, held together by a combination of hydrophobic forces (blue) and a set of hydrogen bonds (yellow region). Large protein molecules contain more than one polypeptide chain protein subunit binding site Weak noncovalent bond allows protein chain to fold into a specific conformation and bind to each other to produce a larger structure.

52 Protein: classified by functions Enzymes  catalytic activity and function (-ase) Structural  collagen of tendons and cartilage, keratin of hair and nails Transport proteins  bind and carry ligand Motor proteins  can contract and change the shape of cytoskeleton Defensive  antibodies, thrombin Regulatory  growth factors, hormones, transcription factors Receptor  cell surface receptors

53 Protein Function: How shape determines function? The specific binding of protein molecules determines their activity and function--- 3-D shape/conformation matters. Binding always shows great specificity. A protein to bind tightly to a second molecule, which is called a ligand for that protein, through many weak non-covalent bonds. A ligand must fit precisely into a protein's binding site. Figure Cell and Molecular Biology, 4 th edition receptor enzyme transport protein

54 Allosteric enzymes: feedback mechanism Many enzyme has at least two different binding sites: active site--- recognizes the substrate regulatory site--- recognizes regulartory molecule Interaction depends on a conformational change in the protein: binding at one of the sites causes a shift from one folded shape to a slightly different folded shape. Figure Cell and Molecular Biology, 4 th edition Figure Cell and Molecular Biology, 4 th edition positive regulation negative regulation

55 Many protein functions are driven by phosphorylation Phosphorylation regulates thousands of protein functions in a typical eukaryotic cells. Phosphorylation occus by the addition of a phosphate group to amino acid side chains, usually the OH- terminal of serine, threonine and tyrosine. Figure Cell and Molecular Biology, 4 th edition

56 Protein kinases: catalyze phosphorylation (addition of phosphate) Proten phosphatases: catalyze dephosphorylation (removal of phosphate) Figure Cell and Molecular Biology, 4 th edition Individual protein kinases serve as microchips. Cyclin-dependent protein kinase (Cdk) regulates the cell cycle. Cdk becomes active when: 1.Cyclin is present 2.Pi added to specific threonine side chain 3.Pi removed from tyrosine side chain When all 3 requirements are met, Cdk is turned on.

57 GTP binding proteins as molecular switches Figure Cell and Molecular Biology, 4 th edition The activity of a GTP-binding protein (also called a GTPase) generally requires the presence of a tightly bound GTP molecule (switch “on”). Hydrolysis of this GTP molecule produces GDP and inorganic phosphate (P i ), and it causes the protein to convert to a different, usually inactive, conformation (switch “off”). Resetting the switch requires the tightly bound GDP to dissociate, a slow step that is greatly accelerated by specific signals; once the GDP has dissociated, a molecule of GTP is quickly rebound.

58 Phosphorylation in cell signaling Many signaling pathways important for the cell survival involve GTP-binding proteins (GTPases). The phosphate group is part of GTP that binds very tightly to the protein it regulates. When the tightly bound GTP is hydrolyzed to GDP, this domain undergoes a conformational change that inactivate it. Figure Cell and Molecular Biology, 4 th edition GTP = molecular switch


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