Introduction to Biochemistry PDF

Unit 1 Introduction to Biochemistry  BASIC CHEMISTRY Matter: anything that occupies space and has mass (solid, liquid, or gas) Mass: amount of matter in an object Weight: gravitational force acting on object (mass X gravitational force)  ENERGY...

Unit 1 Introduction to Biochemistry  BASIC CHEMISTRY Matter: anything that occupies space and has mass (solid, liquid, or gas) Mass: amount of matter in an object Weight: gravitational force acting on object (mass X gravitational force)  ENERGY Energy is the capacity to do work. Work is the moving of matter. Subdivided into: Kinetic energy is energy in motion; active energy Potential energy is stored energy; could do work but is not doing so  CHEMICAL ENERGY Chemical energy is a form of potential energy stored in chemical bonds. Chemical reactions may require or release energy. If the potential energy of the reactants is less than that of the products, energy input is needed. If the potential energy of the reactants is more than that of the products, energy is released.  CHEMICAL REACTION An example of a chemical reaction that uses energy is the production of ATP (adenosine triphosphate) from ADP (adenosine diphosphate), Pi (a phosphate group), and food molecules, such as glucose, which contain potential energy. ADP + Pi + energy from food → ATP  CHEMICAL REACTION An example of a reaction that releases energy is the breakdown of ATP (adenosine triphosphate) to ADP (adenosine diphosphate) and Pi (a phosphate group). ATP → ADP + Pi + energy used by cells Inorganic Chemistry VS Organic Chemistry Inorganic chemistry deals with those substances that do not contain carbon. Organic chemistry is the study of carbon-containing substances. Exception: some carbon containing compounds are not organic in that they do not also contain hydrogen, such as CO2 (carbon dioxide).  BIOCHEMISTRY: (biological chemistry, chemical biology, or chemistry of living systems). - Studies the chemical processes that take place in living organisms. History Biochemistry emerged in the late 18th and early 19th century. The term Biochemistry was first introduced by the German Chemist Carl Neuberg in 1903. In the 1940s Clinical Biochemistry evolved, as an autonomous field. Definition Biochemistry Greek = Bios means “Life” Simply define as the science that study the chemistry of a living cell Deals with the matter inside the living cell Human cell Cell Theory The cell theory (proposed independently in 1838 and 1839) is a cornerstone of biology. Matthias Schleiden Botanist 1. All organisms are made of cells. 2. The cell is the basic unit of life in all living things. 3. All cells come from existing cells. Theodor Schwann Physiologist Cells: the basic unit of life Cells Cells were discovered in 1665 by Robert Hooke. A person contains about 100 trillion cells. That’s 100,000,000,000,000 or 1 x 1014 cells. There are about 200 different cell Red and types in mammals (one of us). white blood cells above Cells are tiny, measuring on vessel- average about 0.002 cm (20 forming um) across. That’s about 1250 cells. cells, “shoulder-to-shoulder” per inch. nerve cell Cell size Cell size is limited -As cell size increases, it takes longer for material to diffuse from the cell membrane to the interior of the cell. Surface area-to- volume ratio: as a cell increases in size, the volume increases 10x faster than the surface area Cellular Anatomy  Cell Theory All cells have certain structures in common. 1. Nucleus/Nucleoid - contains Genetic material 1. Cytoplasm – a semifluid matrix 1. Cell membrane – a phospholipid bilayer Cytoplasm Semi-fluid matrix or jelly-like area between nucleus & cell membrane of a cell Surrounds organelles Organelles – tiny cell structure that performs a specialized function within the cell  Cytoplasm Cellular activities necessary for life include chemical reactions that facilitate: Acquiring energy Reproduction Adaptation Maintaining homeostasis  Cell (plasma) Membrane Cell structure that regulates passage of materials between cell & its environment; aid in protection & support of cell Semi-permeable membrane Hydrophilic head – part of the bilayer that contacts in the aqueous (watery) fluid both inside and outside the cell Hydrophobic tail – part of the bilayer that faces inward of the cell.  Cell (plasma) Membrane Organic molecule present in the membrane Lipids - double layer of lipid molecules (bilayer) Proteins - stick to surface of lipid bilayer. Others free to move around within layer. Some free- moving Carbohydrates - attached to proteins or lipids at membrane surface.  MOVEMENT THROUGH THE CELL MEMBRANE Cell Membrane are selectively permeable Some substances, like O2 and CO2, can pass directly through the cell membrane’s phospholipid bilayer. Some substances must pass through transmembrane protein channels, such as Na+ through its channels. The route of transport through the membrane depends on the size, shape, and charge of the substance. Some substances require carrier molecules to transport them across the cell membrane, such as glucose. Some substances require a vesicular transport across the membrane. The vesicle must fuse with the cell membrane for transport.  MOVEMENT THROUGH THE CELL MEMBRANE There are 2 ways substances move through the cell membrane. PASSIVE mechanisms ACTIVE mechanisms do not require energy. require cell energy Simple diffusion Active transport Facilitated diffusion Endocytosis Osmosis Exocytosis Filtration Transcytosis  Cell Wall The cell wall is the outer covering of a cell, present adjacent to the cell membrane. The cell wall is present in all plant cells. Nucleus Organelle that controls the cell’s activities & contains DNA Organelles are specialized structures that perform various jobs inside cells. Chromatin is a complex structure that forms in the chromosomes Chromosomes contains the DNA, or the genetic material. DNA, deoxyribonucleic acid, genetic material that is pass on from the parents to the offspring. Nucleus Nucleus Endomembrane System A series of membranes throughout the cytoplasm Divides cell into compartments where different cellular functions occur: 1. Endoplasmic reticulum 2. Golgi apparatus 3. Lysosomes Rough Endoplasmic Reticulum Contains ribosomes Ribosome is the site of protein synthesis (about half the cell’s proteins are made here). Protein movement (trafficking) Protein “proofreading” Endoplasmic Reticulum Smooth Endoplasmic Reticulum Called as smooth because it does not have the ribosome It synthesizes lipids, phospholipids as in plasma membranes, and steroids. Cells that secrete these products, such as cells of the testes, ovaries, and skin oil glands, have an excess of smooth endoplasmic reticulum. Golgi Apparatus  Lysosome Functions: Clean-up crew of the cell or the digestive enzyme of the cell Digesting food or cellular invaders Recycling cellular components Cell suicide (suicide is bad for cells, but good for us!) (The lysosome is not found in plant cells) This bacterium about to be eaten by an immune system cell will spend the last minutes of its existence within a lysosome. Energy Generating Part of the Cell “Power Stations” - change energy from 1 form to another Mitochondria – Organelle that changes chemical energy stored in food into compounds that can be used by the cell, called as adenosine triphosphate (ATP) Surrounded by 2 membranes -smooth outer membrane -folded inner membrane with layers called cristae Matrix is within the inner membrane Intermembrane space is located between the two membranes Think of the mitochondrion as the powerhouse of the cell. Both plant and animal cells contain many mitochondria. A class of diseases that causes muscle weakness and neurological disorders are due to malfunctioning mitochondria. Worn out mitochondria may be an important factor in aging. Energy Generating Part of the Cell Chloroplast – organelle that converts sunlight into chemical energy in plants & algae in the process of photosynthesis Starch is a primary product of photosynthesis in the chloroplasts of many higher plants. chlorophyll – green pigment that traps light energy. Can only be found in the plant cell Chloroplast Energy Generating Part of the Cell Storage Tank of the Cell Vacuole – organelle that stores materials such as water, salts, proteins, and carbohydrates. Stores food, fluid, waste products Plants have a large central vacuole for water storage Unicellular animals (i.e. bacteria) can use contractile vacuoles for movement Cytoskeleton Cytoskeleton Framework of the cell composed of a variety of filaments & fibers that support cell structure and drive cell movement Composed of a variety of filaments & fibers that support cell structure & drive cell movement: microtubules (hollow tubes made of proteins) – support, move organelles through cell, role in cell division by forming centrioles (animal & eukaryotic cells but not in plants) cilia & flagella – help move (i.e. sperm cell) microfilaments – (solid filaments of protein) movement & support of cell Cytoskeleton Microscopic Images Summary definition Animal v.s. Plant Cell Animal cell Plant cell Type of Cell Prokaryotic cells Unicellular organisms such as bacteria are examples of prokaryotes. Eukaryotic Cells All other cells are these. Prokaryote Eukaryote  Prokaryotic Cell Lack a membrane-bound nucleus Structurally smaller and simpler than eukaryotic cells (which have a nucleus). Most ancient and abundant type of cells Have circular DNA Prokaryotic cells are placed in two taxonomic domains: – Bacteria – Archaea Live in extreme habitats Structure of Bacteria Extremely small - 1–1.5 μm wide and 2–6 μm long Occur in three basic shapes: – Spherical coccus, – Rod-shaped bacillus, – Spiral spirillum (if rigid) or spirochete (if flexible). spirillum spirochete bacillus coccus Eukaryotic Cell Complex Have a nucleus Have a membrane - covered organelles Have linear DNA Are all other cells Comparison of prokaryotic and eukaryotic cell