Unit 1 Introduction to Biochemistry PDF

Unit 1 Introduction to Biochemistry  What is Biochemistry Biochemistry is the study of the chemical substances found in living organisms and the and the chemical interactions of these substances with each other. Bio= life Chemistry= how things interact Biochemistry thr...

Unit 1 Introduction to Biochemistry  What is Biochemistry Biochemistry is the study of the chemical substances found in living organisms and the and the chemical interactions of these substances with each other. Bio= life Chemistry= how things interact Biochemistry through the years.. Biochemistry emerged in the late 18th and early 19th century. The term Biochemistry was first introduced by the German Chemist Carl Neuberg (Father of Modern Biochemistry) in 1903. In the 1940s Clinical Biochemistry evolved, as an autonomous field. Year Pioneer Workers Discovery/Work 1835 Berzilus Enzymes Catalysis 1897 Edward Buchner Enzyme Extraction 1857 Louis Pasteur Fermentation Process 1934 Lohmann Role of Creatine PO4 in muscles 1937 Hans Kreb TCA Cycle 1921 Banting and Macleod Insulin 1929 Fiske and Subbarow Role of ATPs Year Pioneer Worker Discovery/Work 1953 Watson and Crick Double Stranded DNA 1921 Karl Landsteiner Protein Structure 1967 Peter Mitchell Oxidative Phosphorylation 1967 Marshall Nirenberg Genetic Code on mRNA 1972 Paul Berg Recombinant DNA Technology 1985 Karry Mullis Polymerase Chain Reaction 1970 Har Gobind Khorana Synthesized Gene  The Chemical Elements of Life Scientists believe that about 25 of the known elements are essential to life. BIG 4: make up about 96% of the human body carbon (C), oxygen (O), hydrogen (H) and nitrogen (N) The Chemical Elements of Life  Chemical Composition of Living Organisms 30/92 elements create the living matter All elements contained in living matter are called biogenic elements  Chemical Composition of Living Organisms 1. Macrobiogenic elements – C, O, H, N, S, P, Na, K, Ca, Mg, Cl, Fe. They have a building function. 2. Microbiogenic elements – Cu, I, Mo, Mn, Zn, Co. The average content in living organisms is less than 0.1%. They have catalytic function. 3. Trace elements – Al, As, B, Br, F, Li, Ni, Se, Si, Ti, V. Their content in organisms is less than 0.001 %. Trace elements are parts of enzymes and their function is catalytic.  Chemical Composition of Living Organisms Living organisms are composed of several types of biomolecules. Low molecular substances (M r < 10 000) Water, inorganic (mineral) substances, intermediates of metabolic pathways (carboxylic acids etc.), final products of metabolic pathways (amino acids, monosaccharides, lipids, nucleotides) High molecular substances (M r > 10 000) Proteins, polysaccharides, nucleic acids The Cell  HISTORY OF CELL BIOLOGY Aristotle ( 384 —322 B.C.) and Paracelsus concluded that “all animals and plants, however, complicated, are constituted of a few elements which are repeated in each of them.” Da Vinci (1485) recommended the uses of lenses in viewing small objects. In 1558, Swiss biologist, Conrad Gesner published results of his studies on the structure of foraminifera, protists from pond scum.  Growth of Cell Biology during 16th and 18th Centuries first useful compound microscope was invented in 1590 by Francis Janssen and Zacharias Janssen In1610, an Italian Galileo Galilei invented a simple microscope having only one magnifying lens. This microscope was used to study the arrangement of the facets in the compound eye of insects.  Cells: Where the name came from? English microscopist Robert Hooke is credited with coining the term cell (Cella = hollow space) in 1665, because they looked like the small rooms that monks lived in called Cells He examined a thin slice cut from a piece of dried cork under the compound microscopes  Anton van Leeuwenhoek In 1670, he discovered “wee animalcules” in the water in a drop of pond water using a microscope. In 1673, Leeuwenhoek (a Dutch microscope maker), was first to view organism (living things) Leeuwenhoek used a simple, handheld microscope to view pond water & scrapings from his teeth 15 Beginning of the Cell Theory In 1838, a German botanist named Matthias Schleiden concluded that all plants were made of cells Schleiden is a cofounder of the cell theory  Beginning of the Cell Theory In 1839, a German zoologist named Theodore Schwann concluded that all animals were made of cells Schwann also cofounded the cell theory Beginning of the Cell Theory In 1855, a German medical doctor named Rudolph Virchow observed, under the microscope, cells dividing He reasoned that all cells come from other pre-existing cells by cell division  Modern Version of Cell Theory All living organisms (animals, plants and microbes) are made up of one or more cells and cell products. All metabolic reactions in unicellular and multicellular organisms take place in cells. Cells originate only from other cells, i.e., no cell can originate spontaneously but comes into being only by division and duplication of already existing cells. The smallest clearly defined unit of life is the cell.  What is a Cell The word cell comes from the Latin word "cella", meaning "small room“ A cell is the smallest unit that is capable of performing life functions.  Cell Size and Types Cells, the basic units of organisms, can only be observed under microscope Three Basic types of cells include: Animal Cell Plant Cell Bacterial Cell  Number of Cells Although ALL living things are made of cells, organisms may be: Unicellular – composed of one cell Multicellular- composed of many cells that may organize into tissues, etc.  CELL SIZE Typical cells range from 5 – 50 micrometers (microns) in diameter  Which Cell Type is Larger? Plant cell > _____________ _________ Animal cell > ___________ bacteria  Multicellular Organisms Cells in multicellular organisms often specialize (take on different shapes & functions)  Two Types of Cells Prokaryotic Eukaryotic  Prokaryotes – The first Cells Simplest type of cell Do not have structures surrounded by membranes Few internal structures One-celled organisms, Bacteria  Prokaryotes Nucleoid region (center) contains the DNA Surrounded by cell membrane & cell wall (peptidoglycan) Contain ribosomes (no membrane) in their cytoplasm to make proteins  Eukaryotes Cells that HAVE a nucleus and membrane-bound organelles Includes protists, fungi, plants, and animals More complex type of cells  Eukaryotic Cell Contain 3 basic cell structures: Nucleus Cell Membrane Cytoplasm with organelles Prokaryotes vs Eukaryotes  Two Main Types of Eukaryotic Cells Animal Cell Plant Cell “Typical” Animal Cell “Typical” Plant Cell Plant vs Animal Cell Cell Parts: The Organelles Very small (Microscopic) Perform various functions for a cell Found in the cytoplasm May or may not be membrane- bound  Cell or Plasma Membrane Composed of double layer of phospholipids and proteins Surrounds outside of ALL cells Controls what enters or leaves the cell Living layer Outside of cell Carbohydrate Proteins chains Cell membrane Inside of cell Protein channel Lipid bilayer (cytoplasm)  Phospholipids Heads contain glycerol & phosphate and are hydrophilic (attract water) Tails are made of fatty acids and are hydrophobic (repel water) Make up a bilayer where tails point inward toward each other Can move laterally to allow small molecules (O2, CO2, & H2O to enter) The Cell Membrane is Fluid Molecules in cell membranes are constantly moving and changing  Cell Membrane Proteins Proteins help move large molecules or aid in cell recognition Peripheral proteins are attached on the surface (inner or outer) Integral proteins are embedded completely through the membrane GLYCOPROTEINS Recognize “self” Glycoproteins have carbohydrate tails to act as markers for cell recognition  Cell Membrane in Plants Lies immediately against Cell membrane the cell wall in plant cells Pushes out against the cell wall to maintain cell shape Nonliving layer Found in plants, fungi, & bacteria Made of cellulose in plants Made of peptidoglycan in bacteria Made of chitin in Fungi  Cell Wall the rigid, semi-permeable protective layer in some cell types. This outer covering is positioned next to the cell membrane (plasma membrane) in most plant cells, fungi, bacteria, algae, and some archaea. Animal cells do not have a cell wall.  Cytoplasm of a Cell Jelly-like substance cytoplasm enclosed by cell membrane Provides a medium for chemical reactions to take place Contains organelles to carry out specific jobs Found in ALL cells  Mitochondrion “Powerhouse” of the cell Generate cellular energy (ATP) More active cells like muscle cells have MORE mitochondria Both plants & animal cells have mitochondria Site of CELLULAR RESPIRATION (burning glucose) MITOCHONDRIA Surrounded by a DOUBLE membrane Has its own DNA Folded inner membrane called CRISTAE (increases surface area for more chemical Reactions) Interesting Fact --- Mitochondria Come from cytoplasm in the EGG cell during fertilization Therefore … You inherit your mitochondria from your mother!  Endoplasmic Reticulum - ER Network of hollow membrane tubules Connects to nuclear envelope & cell membrane Functions in Synthesis of cell products & Transport Two kinds of ER ---ROUGH & SMOOTH Rough Endoplasmic Reticulum (Rough ER) Has ribosomes on its surface Makes membrane proteins and proteins for EXPORT out of cell Rough Endoplasmic Reticulum (Rough ER) Proteins are made by ribosomes on ER surface They are then threaded into the interior of the Rough ER to be modified and transported  Smooth Endoplasmic Reticulum Smooth ER lacks ribosomes on its surface Is attached to the ends of rough ER Makes cell products that are USED INSIDE the cell Functions of the Smooth ER Makes membrane lipids (steroids) Regulates calcium (muscle cells) Destroys toxic substances (Liver)  Ribosomes Made of PROTEINS and rRNA “Protein factories” for cell Join amino acids to make proteins Process called protein synthesis   Golgi Bodies Stacks of flattened sacs Have a shipping side CIS (trans face) and receiving side (cis face) Receive proteins made by ER Transport vesicles with modified proteins pinch TRANS off the ends Transport vesicle  Golgi Bodies Look like a stack of pancakes Modify, sort, & package molecules from ER for storage OR transport out of cell  Lysosomes Contain digestive enzymes Break down food, bacteria, and worn out cell parts for cells Programmed for cell death (AUTOLYSIS) Lyse (break open) & release enzymes to break down & recycle cell parts)  Cytoskeleton a system of criss-cross filaments or fibres that is present in the cytoplasm of eukaryotic cells (cells containing a nucleus). The cytoskeleton organizes other constituents of the cell, maintains the cell’s shape, and is responsible for the locomotion of the cell itself and the movement of the various organelles within it.  Chloroplast structure within the cells of plants and green algae that is the site of photosynthesis, the process by which light energy is converted to chemical energy, resulting in the production of oxygen and energy-rich organic compounds.  Centrioles Centrioles are tubelike structures that aid in cell division. They generally are found close to the nucleus and are made up of nine tube-like structures that each have three tubules. 1. Cell division help with cell division in animal cells. The centrioles help in the formation of the spindle fibers that separate the chromosomes during cell division (mitosis). 2. Celiogenesis the formation of cilia and flagella on the surface of cells. Cilia and flagella help the cell move. The Control Organelle - Nucleus Controls the normal activities of the cell Contains the DNA in chromosomes Bounded by a nuclear envelope (membrane) with pores Usually the largest organelle  More on the Nucleus Nucleus Each cell has fixed number of chromosomes that carry genes Genes control cell characteristics  Nuclear Envelope Double membrane surrounding nucleus Also called nuclear membrane Contains nuclear pores for materials to enter & leave nucleus Connected to the rough ER Nuclear pores copyright cmassengale 62  Inside the Nucleus - The genetic material (DNA) is found DNA is spread out DNA is condensed & And appears as wrapped around proteins CHROMATIN forming in non-dividing cells as CHROMOSOMES in dividing cells Characteristic Bio-membranes and Organelles Plasma Membrane A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems. Nucleus Double membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome Mitochondrion Surrounded by a double membrane with a series of folds called cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium. Chloroplasts (plastids) Surrounded by a double membrane, containing stacked thylakoid membranes. Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars. Contains DNA, and like mitochondria is believed to have originated as a captured bacterium.. Rough endoplasmic reticulum (RER) A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes. Ribosomes Protein and RNA complex responsible for protein synthesis Smooth endoplasmic reticulum (SER) A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides. Golgi apparatus A series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization. Lysosymes A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials ingested by the cell. Vacuoles Membrane surrounded "bags" that contain water and storage materials in plants. Peroxisomes or Microbodies Produce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism. Cell wall Plants have a rigid cell wall in addition to their cell membranes Cytoplasm enclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles. Cytoskeleton Arrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments.  Organic Reactions Relevant to Biological Systems Oxidation-reduction reactions Hydrolytic reactions Condensation reactions Transamination and Deamination reactions Dehydration –Hydration reactions Esterification and Amidation reactions Decarboxylation  Oxidation-reduction Reactions Electrons in an organic redox reaction often are transferred. Oxidation: carbon atom in an organic compound loses a bond to hydrogen and gains a new bond to a heteroatom (or to another carbon) Reduction: carbon atom in an organic compound gains a bond to hydrogen and loses a bond to a heteroatom Hydrolysis and Condensation Reactions Hydrolysis: larger molecule forms two (or more) smaller molecules and water is consumed as a reactant. Hydrolysis ("hydro" = water and "lysis" = break) involves adding water to one large molecule to break it into multiple smaller molecules. Condensation: reaction is a reaction in which two molecules combine to form a single molecule.  Hydration and Dehydration Reactions Dehydration: chemical reaction that involves the loss of water from the reacting molecule or ion. Hydration: hydrogen and hydroxyl ion is attached to a carbon in a carbon double bond Esterification and Amidation Reactions Esterification: of combining an organic acid (RCOOH) with an alcohol (ROH) to form an ester (RCOOR) and water; or a chemical reaction resulting in the formation of at least one ester product. Amidation: reaction or formation of an amine  Decarboxylation Reactions Decarboxylation: chemical reaction that eliminates a carboxyl group and liberates carbon dioxide (CO2). Do Exercise 1