Lesson 1 Biochemistry PDF

BIOCHEMISTRY… The Chemistry of Life Chapter 1: Introduction to Biochemistry Engr. Caryl A. Silang Bio Chemistry  Bio= life  Chemistry = how things interact  Biochemistry= the branch of science in which you study the chemical and physical processes that occur in a...

BIOCHEMISTRY… The Chemistry of Life Chapter 1: Introduction to Biochemistry Engr. Caryl A. Silang Bio Chemistry  Bio= life  Chemistry = how things interact  Biochemistry= the branch of science in which you study the chemical and physical processes that occur in an organism. Definition of Biochemistry:  According to the book Biochemistry by H. Stephen Stoker, biochemistry is the study of the chemical substances found in living organisms and the chemical interactions of these substances with each other. Definition of Biochemistry  Biochemistry is also called as biological chemistry or physiological chemistry which is the study of chemical processes in the living organisms.  It can also be defined as the study of molecular basis of life  Biochemistry teaches how the biological molecules like carbohydrates, proteins, lipids, nucleic acids gives rise to different chemical processes in the living cell which in turn gives rise to the complexity of life. Significance in Nursing  As the definition says that biochemistry is the study of chemical processes in the living cell, it is very essential that a nurse being a medical professional, study and understand biochemistry in order to care for their patients. Significance in Nursing Cases: some conditions thus, can be explained on the basis of biochemistry: 1. If an infant is always vomiting after giving milk, she or he probably has galactose intolerance. 2. If an infant is born with jaundice, her or his liver is not fully functional. 3. When color of infant’s urine turns dark, probably he/she suffers from amino acid metabolic disorder. A patient was admitted to the hospital and during the stay in the hospital he suddenly comes up with certain symptoms like confusion, dizziness, shaky feeling, pounding heart, racing pulse, sweating , trembling and weakness His medical history showed that he has diabetes mellitus and was taking insulin  Knowing the normal processes that occur within the body will help us to identify the alterations that can occur during disease conditions so that an effective medical treatment can be facilitated.  What Does Life Require? A Definition of Life  There is no simple definition of life.  But, all Earth organisms… require liquid water have a common set of biological molecules can maintain homeostasis can evolve  Homeostasis  Homeostasis – a dynamic state of equilibrium in which internal conditions remain relative stable (Steady State)  homeostasis maintains constant conditions in the internal environment  A homeostatic control system has  a receptor – can sense internal conditions  a set point – what conditions should be maintained at.  a control center – processes information & sends instructions to effectors  an effector – can make changes to internal conditions  Homeostasis refers to any automatic process that a living thing uses to keep its body steady on the inside while continuing to adjust to conditions outside of the body, or in its environment. The body makes these changes in order to work the right way and survive.  In other words, homeostasis is a mechanism that maintains a stable internal environment despite the changes present in the external environment.  The biochemistry teaches about the normal and abnormal metabolite levels and this knowledge helps the doctor and nurse to take special care of the patient by maintaining the fluid and electrolytes.  HOMEOSTATIS – the ability or tendency of a living organism, cell, or group to keep the conditions inside it the same despite any changes in the conditions around it, or this state of internal balance.  Examples of homeostasis in humans include the regulation of blood sugar via insulin, the regulation of body temperature by the hypothalamus, the constant surveillance and functioning of the immune system, regulation of blood pressure via sensors in the walls of arteries, the pH balance maintained by the lungs and kidneys and the regulation of breathing by the medulla oblongata and the pons in the brain. Internal body temperature  When the body monitors a parameter and elicits change to return a parameter to normal, the resulting state is termed homeostasis. A homeostasis example is internal body temperature. If the internal body temperature climbs too high, the body will respond by sweating to cool it off. Homeostasis  Biochemistry teaches about homeostasis and electrolyte balance and in medical field, it should understand the importance of it in the body.  All the organs and tissues in the body function to maintain this homeostasis.  Certain disease conditions may create an imbalance of one or more electrolytes which is a serious condition. What Does Life Require? Additional Characteristics of Life  Cellular organization  Growth and metabolism  Reproduction  Heredity Characteristics of Living Systems 1. Living organisms are complicated and highly organized O composed of many cells O cells are highly structured into organelles; macromolecules within organelles take part in many chemical reactions Characteristics of Living Systems 2. Biological structures serve functional purposes Structures are specific The levels of organization observed by organelles and macromolecules allows them to perform specific functions  Characteristics of Living Systems 3. Energy transfomations occur within living systems OSolar energy is transformed into ATP (adenosine triphosphate) and NADPH (nicotinamide adenine dinucleotide phosphate) which are special biomolecules which provide energy to the cell OActivities of the cell which require energy include biosynthesis, movement and osmotic work against a concentration gradient Characteristics of Living Systems 4. Living systems are highly efficient at self-replication.  This is due to DNA (deoxyribonucleic acid) molecules which are able to reproduce into duplicate DNA strands from an original DNA strand.  What are living organisms made of?  Living organisms are composed of lifeless molecules  Isolated molecules conform to all the physical and chemical laws that describe the behavior of inanimate matter  In appropriate complexity and number, molecules compose living things  Living systems differ from inanimate matter because of these characteristics:  Grow, move, use energy through metabolism, respond to stimuli, reproduce and replicate themselves On Life and Chemistry...  “Living things are composed of lifeless molecules” (Albert Lehninger)  “Chemistry is the logic of biological phenomena” (Garrett and Grisham) Distinctive Properties of Living Systems  Organisms are complicated and highly organized  Biological structures serve functional purposes  Living systems are actively engaged in energy transformations  Living systems have a remarkable capacity for self-replication Matter…  All matter, whether living or nonliving, is made of the same type building blocks called atoms  An atom is the smallest basic unit of matter  All atoms have the same basic structure, composed of three smaller particles  Proton – a positively charged particle in an atom’s nucleus  Neutron – a neutral (no charge) particle which has about the same mass as a proton and is also in the nucleus  Electron – a negatively charged particle found outside the nucleus. Electrons are much, much smaller than proton and neutrons Physical Properties of Chemicals  Elements: fundamental forms of matter  examples: carbon, hydrogen, oxygen, etc  Atoms: the smallest units of an element  Atoms are composed of protons, neutrons, and electrons  Protons (positive charge) + neutrons form atomic nucleus  Electrons (negative charge) are outside the nucleus. Figure 2.3 Elements…  Different types of atoms are called elements, which cannot be broken down by ordinary chemical means  Which element an atom is depends on the number of protons in the atom’s nucleus  For example… all hydrogen atoms have 1proton and all oxygen atoms have 8 protons  Only about 25 different elements are found in organisms  However, atoms of different elements can “link” or bond together to form compounds 6 Elements of Organic Molecule  Carbon  Hydrogen  Oxygen  Nitrogen  Phosphorous  Sulfur Biomolecules: The Molecules of Life H, O, C and N make up 99+% of atoms in the human body ELEMENT PERCENTAGE Oxygen 63 Hydrogen 25.2 Carbon 9.5 Nitrogen 1.4 Biomolecules: The Molecules of Life  What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of life?  Answer: Their ability to form covalent bonds by electron-pair sharing.  I. Basics of Chemistry  A. The Atom  Copper, Zinc, Selenium, Elements in the body: Molybdenum, Fluorine,  Oxygen Chlorine, Iodine, Manganese, Cobalt, Iron (0.70%)  Carbon  Lithium, Strontium, Aluminum,  Hydrogen Silicon, Lead, Vanadium,  Nitrogen Arsenic, Bromine (trace  Calcium amounts)  Phosphorus  Reference: H. A. Harper, V. W.  Potassium Rodwell, P. A. Mayes, Review of  Sulfur Physiological Chemistry, 16th ed., Lange Medical Publications, Los  Sodium Altos, California 1977.  Magnesium Compounds…  Atoms form compounds in two ways 1. Ionic bonds – consists of ions and forms through the electrical force between oppositely charged ions ◼ An ion is an atom that has lost or gained electrons ◼ Cation – an ion that loses electrons so becomes positively charged ◼ Anion – an ion that gains electrons so becomes negatively charged 2. Covalent bonds – forms when atoms share one or more pairs of electrons ◼ A molecule consists of two or more atoms held together by covalent bonds Molecules ⚫ 1. When two or more atoms join molecule together, they form a ___________. chemical bonds ⚫ 2. These are called _______________, and are based on interactions between electrons the _________. ⚫ 3. If a bond joins different elements, compound the new substance is a __________. Types of Bonds Ionic bonds ⚫ 1. _____________ ⚫a. Electrons move from one atom to the other. ⚫b. Atoms become positively or negatively charged; called ____. ions ⚫c. Charges attract or repel. conducting electricity ⚫d. Good for __________________. Types of Bonds Covalent bonds ⚫ 2. _______________ ⚫a. Electrons are shared between two atoms. ⚫b. Atoms must remain together ⚫c. Bonds are flexible large structures ⚫d. Good for ________________. Types of Bonds Hydrogen bonds ⚫ 3. _______________ ⚫a. Hydrogen holds electrons weakly ⚫b. Has a slightly positive charge, attracted to anything negative. ⚫c. Creates weak bonds that help hold structures but can be broken easily. DNA, hair, water ⚫d. Examples: _________________ Molecules and Energy ⚫ 1. Energy is stored in the bonds between atoms. Energy is required to make or break bonds. ______________ ⚫ 2. The amount of energy varies with the type of bond. Some bonds (hydrogen) are easily broken while others (triple covalent) are very hard. Why elements bond the way they do…  All atoms want 8 electrons in their outer most energy level (shell) This is called the octet rule.  That is why they do what they do  Ionic bonds – gain or lose electrons  Covalent share electrons  How do we identify each type  Ionic compound – metal + non-metal  Covalent compound – non-metal + non-metal Try These…  Identify the type of bond… 1. MgF2 2. S3O2 3. RbCl 4. PCl4 5. N2O  Organic Chemistry = The Chemistry of Carbon Copyright © 2010 Pearson Education, Inc.  Organic Chemistry ▪ All life on Earth is based on organic chemistry: the chemistry of the element carbon. ▪ Carbon makes up most of the mass of living organisms. ▪ Why? Copyright © 2010 Pearson Education, Inc.  Nonpolar & Hydrophobic Molecules ▪ Nonpolar molecules, such as oil, do not contain charged atoms. ▪ These atoms are called hydrophobic (water–hating). Copyright © 2010 Pearson Education, Inc. What elements are biomolecules composed of? O Biomolecules are composed mainly of six nonmetallic elements: carbon, oxygen, hydrogen, nitrogen, phosphorous, and sulfur O These atoms make up >97% of the weight of most organisms O These elements can form stable covalent bonds Points to note: O Water is a major component of cells O Carbon is more abundant in living organisms than it is in the rest of the universe  Periodic Table showing the elements present in biomolecules Important elements found in living cells are shown in color The six abundant elements are in red (CHNOPS) Five essential ions are in purple Trace elements are in dark blue (more common) and light blue (less common) Biomolecules are essentially organic compounds Common functional groups present in biomolecules Common linkages present in biomolecules  Why is carbon so predominant in living systems? O This is because of the ability of carbon atoms to bond together to form long chains and rings. Carbon Carbon can covalently bond with up to four other atoms. Carbon can form immensely diverse compounds, from simple to complex. Methane with 1 Carbon DNA with tens of Billions of atom Carbon atoms  Examples of Carbon Biomolecules LINEAR ALIPHATIC CYCLIC BRANCHED Carbon based molecules  Carbon based molecules are the foundation for life  Many of these molecules are large and called polymers. Poly- many A repeating unit of the same small molecule (monomer)  There are four main types of carbon-based molecules in living things 1. Carbohydrates 2. Proteins 3. Lipids 4. Nucleic acids Overview: The Molecules of Life  All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids  Macromolecules are large molecules composed of thousands of covalently connected atoms  Molecular structure and function are inseparable  Macromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks These small building-block molecules are called monomers Four classes of life’s organic molecules are polymers  Carbohydrates  Proteins  Nucleic acids  Lipids Structure and Function of Macromolecules Types of Macromolecules 1. Carbohydrates 2. Proteins 3. Lipids 4. Nucleic Acids Figure 2.12 Structure and Function of Macromolecules  Carbohydrates: molecules of carbon, oxygen, and hydrogen  Major source of energy for cells Figure 2.12 Carbohydrates…  Known as sugars and starches  Also include cellulose and glycogen  Made up of monosaccharides (monomer) which can be put together to form disaccharides and polysaccharides  Disaccharides – sucrose (table sugar)  Polysaccharides – starch, cellulose (cell wall component), and glycogen (storage of carbs in the liver and muscle) ◼ Glycogen is important for insulin in humans Why carbs are important to living organisms…  Short-term storage energy storage  Plant cell wall components – strength  Component of cell membranes – glycogen  It helps identify the type of cell Structure and Function of Macromolecules Proteins: polymers of amino acids; joined by peptide bonds Figure 2.13 Proteins…  Known as meat to us  Made up of amino acids (monomer) which can be put together to form polypeptides (50-300 a.a.)  20 different amino acids are found in human proteins Structure and Function of Macromolecules Proteins  There are 20 different common amino acids, with different chemical properties.  Amino Acids are made up of carbon, oxygen, hydrogen, and nitrogen.  Different combinations of amino acids give proteins different properties. Why proteins are important to living organism…  Form body tissue  Skin, hair, muscles  Important for immune response  Antibodies – fight off foreign invaders  All enzymes in the body  Biological catalysts – they speed chemical reactions inside the body Structure and Function of Macromolecules  Lipids:hydrophobic; composed mostly of carbon and hydrogen  Three important types: Lipids…  Known as fats, oils and waxes  Made up of glycerol and fatty acids  Saturated fatty acids ◼ Single bonds join carbon (carbon – carbon) together ◼ Are oils at room temperatures  Unsaturated fatty acids ◼ Has at least one carbon = carbon (joined by double bonds)  3 fatty acids + 1 glycerol = triglyceride Why lipids are important to living organisms…  Long term storage of energy  Fat is the storage mechanism  Formation of cell membranes  Nerves and brain tissue  Phospholipids and cholesterol ◼ Phospholipids have hydrophobic heads and hydrophilic tails  Hormones  Made of steroids Structure and Function of Macromolecules  Nucleic acids = polymers of nucleotides  Nucleotide = a phosphate + sugar + a nitrogenous base Figure 2.15c Structure and Function of Macromolecules  Nucleotides are of two types, depending on the sugar  RNA = ribonucleic acid  DNA = deoxyribonucleic acid ◼ DNA is the hereditary material in nearly all organisms. Nucleic Acids…  Known as DNA and RNA  Made up of nucleotides A nucleotide consists of ◼ Phosphate group ◼ Pentose sugar (5-carbon sugar) ◼ Nitrogen base (A, T, C, G, or U) Why nucleic acids are important to living things…  DNA  Blueprint for life  Our genes  RNA  Translates DNA to make PROTEINS Structure and Function of Macromolecules  The structure of a DNA molecule is a double helix made up of nucleotides. Figure 2.15a Structure and Function of Macromolecules  Bonding between bases on opposite strands follows strict base- pairing rules: A with T  G with C  Macromolecules ⚫ A. What are they? Very large molecules that make ⚫ 1. __________________________________ most of the structure of the body _______________________________________ ⚫ 2. Made of smaller pieces called monomers that can be assembled like __________ legos to form a variety of structures. A large chain of monomers is called a polymer _________.  Macromolecules ⚫ B. Carbohydrates monosaccharide (sugar) ⚫ 1. Monomer: ____________________ polysaccharide (starch) ⚫ 2. Polymer: _____________________ rings of carbon with ⚫ 3. Structure:______________________ oxygen and hydrogen attached; CH2O ________________________________ energy, plant structure ⚫ 4. Uses: ___________________ sucrose, cellullose ⚫ 5. Examples: ________________ Examples of Carbohydrates  Macromolecules ⚫ C. Lipids Glycerol and fatty acid ⚫ 1. Monomer: __________ lipid or fat ⚫ 2. Polymer: ___________ 3 long chains of carbon ⚫ 3. Structure:______________________ hydrogen on a glycerol molecule ________________________________ energy, structure, warmth ⚫ 4. Uses: ________________________ fat, oil, cholesterol ⚫ 5. Examples: ____________________ Examples of Lipids  Macromolecules ⚫ D. Protein amino acid (20) ⚫ 1. Monomer: _______________ protein or polypeptide ⚫ 2. Polymer: _____________________ central carbon atom with ⚫ 3. Structure:______________________ ________________________________ hydrogen, amine, carboxyl, & R groups structure, emergency energy ⚫ 4. Uses: ________________________ skin, insulin, enzymes ⚫ 5. Examples: ____________________ Examples of Proteins  III. Macromolecules ⚫ E. Nucleic Acids nucleotide (5) ⚫ 1. Monomer: _______________ nucleic acid ⚫ 2. Polymer: ___________ 5-carbon sugar attached ⚫ 3. Structure:______________________ to nitrogen base and phosphate group ________________________________ stores genetic code ⚫ 4. Uses: ___________________ DNA and RNA ⚫ 5. Examples: _______________ Examples of Nucleic Acids Concept Check  What is the main element in an “organic” molecule?  How are monomers related to polymers?  What are the four main “organic” molecules living organisms need?