Cell Biology; BIO 116 PDF

Cell Biology; BIO 116 How big are living organisms Living Organisms Originated from a Common Ancestral Cell ❑All cells are thought to have evolved from a common ancestor because the structures and molecules in all cells have so many similarities. ❑Two distinct types of primitive organisms: th...

Cell Biology; BIO 116 How big are living organisms Living Organisms Originated from a Common Ancestral Cell ❑All cells are thought to have evolved from a common ancestor because the structures and molecules in all cells have so many similarities. ❑Two distinct types of primitive organisms: the bacteria and the archaea. ❑According to the evolutionary tree, the archaea and the eukaryotes diverged from bacteria billions of years ago before they diverged from each other. ❑Gene duplications and mutations gave rise to new organisms during evolution. ❑Tree branches/relationships are assigned due to morphological and DNA and protein sequences similarities between organisms. Living Organisms Originated from a Common Ancestral Cell Living Organisms Originated from a Common Ancestral Cell Living Organisms Originated from a Common Ancestral Cell  Characteristics of Living Organisms What characterize living things?  Characteristics of Living Organisms Are organized Acquire materials and energy Reproduce Respond to stimuli Are homeostatic Grow and develop Have the capacity to adapt What is Adaptation? Long term / evolution / natural selection Short term Give example  Cells Are Prokaryotic or Eukaryotic The biological universe consists of two types of cells-prokaryotic and eukaryotic. Eukaryotes include four kingdoms: plants, animals, fungi, and protists. Fungi, exist in both multicellular forms (molds) and unicellular forms (yeasts), and the protozoans (proto, primitive; zaan, animal) are exclusively unicellular. Prokaryotes include bacteria and archaea. Prokaryotic cells consist of a single closed compartment that is surrounded by the plasma membrane, lacks a defined nucleus, and has a relatively simple internal organization. All prokaryotes consist of cells of this type.  Domains Domains are the highest level of classification. Three domains Based on biochemical and genetic criteria.  Domain Bacteria Bacteria are single- celled organisms that lack a membrane-bound nucleus. Bacteria are found almost everywhere on the planet Earth.  Domain Archaea Archaea are single- celled organisms that lack a membrane-bound nucleus. Archaea can be found in environments that are too hostile for other life forms. Archaea + Bacteria = Prokaryotes  Domain Eukarya The cells of all eukaryotes have a membrane- bound nucleus. Members of the Domain Eukarya are further categorized into one of four Kingdoms. Domain Eukarya  Scientific Names Binomial (two names) – Genus name, species name –Examples: »Homo sapiens (human) »Felis domesticus (domestic cat) Carl Linnaeus; The father of modern taxonomy, he was a Swedish botanist, physician, and zoologist who formalised binomial nomenclature. Systema Naturae, published 1735; 10th ed.1758.  Categories of Classification Domain Kingdom Phylum Class Order Family Genus species  Categories of Classification Domain Most inclusive Kingdom Phylum Class Order Family Genus species Least inclusive Systematic position of Humans Domain? Kingdom? Systematic position of Humans What is the cell  Prokaryotic Cell Structure and Function Bacteria, a numerous type of prokaryote, are single celled organisms; the cyanobacteria, or blue-green algae, can be unicellular or be filamentous chains of cells. Although bacterial cells do not have membrane-bounded compartments, many proteins are precisely localized in their aqueous interior (cytosol). Although prokaryotes are microscopic in size, but they make up a huge part of the earth's biomass. A single Escherichia coli bacterium has a dry weight for an estimated 1-1.5 kg of the average human's weight. The estimated number of bacteria on earth is weighing a total of about 1012 kg. Prokaryotic Cell s of Prokaryotic cell; cell structures: 1. Cell wall Prokaryotic cell; Cell Structures: 1. Cell wall MurNAc GlcNAc m-DAP meso-Diaminopimelic acid Prokaryotic cell; Cell Structures: 1. Cell wall; Gram Staining Prokaryotic cell; Cell Structures: 1. Cell wall; Gram Staining Gram-positive & Gram-negative bacilli Prokaryotic cell; cell structures: 1. Cell wall; beta-lactam antibiotics Penicillin, core structure Ampicillin Cephalosporins  Elements that make up 95% of living organisms (by weight) –C Carbon –H Hydrogen –N Nitrogen –O Oxygen –P Phosphorus –S Sulfur Other elements: Na, Ca, Fe, Mg, etc.  Atomic Symbol Atomic Mass = Number of Protons + Number of Neutrons Atomic Number = The Number of Protons in the Nucleus  Isotopes 12 13 14 C 6 6 C C 6 * *radioactive Atoms of the same element with varying number of neutrons  Periodic Table number of electrons in outermost shell I VIII 1 2 1 H II III IV V VI VII He 1.008 4.003 3 4 5 6 7 8 9 10 number 2 Li Be B C N O F Ne 6.941 9.012 10.81 12.01 14.01 16.00 19.00 20.18 of electron 11 12 13 14 15 16 17 18 shells 3 Na Mg Al Si P S Cl Ar 22.99 24.31 26.98 28.09 30.97 32.07 35.45 39.95 19 20 21 22 23 24 25 26 4 K Ca Ga Ge As Se Br Kr 39.10 40.08 69.72 72.59 74.92 78.96 79.90 83.60  Covalent Bonds If the two bonded atoms share equal number of electrons.  Nonpolar Covalent Bonds If the sharing between two atoms is relatively equal, the covalent bond is described as nonpolar.  Polar Covalent Bonds If the sharing between two atoms is unequal, the covalent bond is described as polar.  Non-Covalent Bonding No electrons are involved in bonding the two structures such as: Ionic bonds: Bonds formed between metals and non- metals, e.g., sodium chloride salt (NaCl). Hydrogen bonds: Hydrogen bonds are formed between hydrogen and a more electronegative element such as oxygen, fluorine and nitrogen, e.g., water molecules. Van der Waals interactions: Non-specific and weak interactions between two atoms when they are in the Hydrogen Bonding  The Molecules of Cell Cells are composed of water (75% of cell volume), small molecules (e.g., simple sugars, amino acids, vitamins) and ions (e.g., sodium, chloride, calcium ions). The locations and concentrations of small molecules and ions within the cell are controlled by numerous proteins inserted in cellular membranes (pumps, transporters, and ion channels).  The Molecules of Cell A common theme in biology is the construction of large molecules (macromolecules) and structures by the covalent or noncovalent association of many similar or identical smaller molecules. The three most abundant classes of the biological macromolecules: 1) Proteins are linear polymers containing 10 to several thousand amino acids linked by peptide bonds. 2) Nucleic acids are linear polymers containing hundreds to millions of nucleotides linked by phosphodiester bonds. 3) Polysaccharides are linear or branched polymers of monosaccharides (sugars) such as glucose linked by glycosidic bonds. In addition to the above classes of biological macromolecules; lipids constitutes a 4th class of biomolecules that participates in energy production and compartmentalization (making divisions and partitions; membrane structures) inside the cell. Examples of Biomolecules Synthesis/Degradation of Polymers  Monosaccharides and Polysaccharides The building blocks of the polysaccharides are the simple sugars, or monosaccharides. Monosaccharides are carbohydrates (CH2O)n, where n equals 3, 4, 5, 6, or 7. Hexoses (n = 6) and pentoses (n = 5) are the most common monosaccharides. All monosaccharides contain hydroxyl (-OH) groups (a minimum of two groups) and either an aldehyde or a keto group (i.e., poly-hydroxy aldehydes or ketones).  Lipids and membrane structure In order for the cell to make membrane structures, it uses lipids as a water – insoluble material (immiscible with water) to separate the inside environment from the outside one. However, since the membrane resides in a water environment, lipid structures that is used in membrane architectures must adopt specific configuration of hydrophilic surfaces along with a hydrophobic core. Such a structure can be fulfilled by phospholipids (a structure made of phosphate, which is polar, and lipid, a non-polar, with or without additional substances.  Amino Acids Differing Only in Their Side Chains Compose Proteins The monomeric building blocks of proteins are 20 amino acids. All amino acids have a characteristic structure consisting of a central alpha carbon atom bonded to four different chemical groups: an amino (NH2) group, a carboxylic acid or carboxyl (COOH) group, a hydrogen (H) atom, and one variable group, called a side chain or R group. The "essential" amino acids, from a dietary standpoint, are the eight that we cannot synthesize and must obtain from food.  Nucleotides Are Used to Build Nucleic Acids Two types of chemically similar nucleic acids, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are the principal genetic- information-carrying molecules of the cell. The monomers from which DNA and RNA polymers are built, called nucleotides, all have a common structure: a phosphate group linked by a phospho-di-ester bond to a 5-carbon sugar (pentose) that holds a nitrogenous base. In RNA, the sugar is ribose, while in DNA, it is deoxyribose, in which carbon 2 does not have the (–OH) group. Nucleotides Are Used to Build Nucleic Acids Nucleotides Are Used to Build Nucleic Acids Plasma membrane Plasma membrane and the lipid bilayer The lipid bilayer; phospholipids, sphingolipids, and sterols