Biochemistry Lecture Transcription PDF

DNA - stores genetic information, can explain diseases through hereditary RNA - delivers it in Ribosomes...

DNA - stores genetic information, can explain diseases through hereditary RNA - delivers it in Ribosomes CELL THEORY - Cell is the basic unit of life ENZYME - a type of protein (ex. Amylase, Kinase, Lipase) PCR - Polymerase Chain Reaction KARY MULLIS - discovered PCR AMINO ACID - Amine + Carboxylic Acid (COOH) NUCLEOTIDE - has a Phosphate group (Pentose) NUCLEOSIDE - has no Phosphate RIBONUCLEIC - with OH DEOXYRIBONUCLEIC - without OH MONOSACCHARIDE - an Exose (there are sugars that has 3, 4… carbons) Plants have starch, Humans have Glycogen BIOCHEMISTRY FATTY ACIDS - hydro chain, stored in adipose/adipocytes - “The study of biochemistry shows how the Cell is made of biomolecules collection of inanimate molecules that constitute living organisms interact to maintain TWO NOTABLE BREAKTHROUGHS IN THE and perpetuate life animated solely by the HISTORY OF BIOCHEMISTRY physical and chemical laws that govern the non living universe” - LEHNINGER, Principle of 1. Discovery of enzyme’s role as catalysts for Biochemistry biochemical reactions 2. Discovery of DNA as the carrier of genetic - “Biochemistry asks us how the remarkable information properties of living organisms arise from the thousands of different lifeless biomolecules” - LEHNINGER, Principle of biochemistry LIFE IS CHARACTERIZED BY: - The systematic study of the chemicals of living 1. BIOLOGICAL DIVERSITY systems, their organization into cells, and the principles of their chemical interactions as 2. CHEMICAL UNITY they participate in the process of life - Compounds that make up living system obey the fundamental laws of chemistry - THERE ARE - Humanity is continuously challenged to seek NO NEW PRINCIPLES understanding of the most fundamental processes of life at the molecular level - BIO: Life - CHEMISTRY: study of change in matter - BIOCHEMISTRY: Chemical reactions happening inside the body of a living organism BASIC SCOPE OF BIOCHEMISTRY PROTEINS (Amino Acids) - has ENZYMES 1. BIOCHEMICAL STRUCTURES which facilitates metabolic reactions in the body - Chemical and 3D structures - Physical and chemical properties LIPIDS (Fatty Acids) - if not present, there - Interaction, organization, and coordination will be no Phospholipids bilayer in cells - Synthesis and degradation DNA/RNA (Nucleic Acids) - involves in central dogma (DNA - RNA - PROTEINS)  - SI - VILLI - BLOODSTREAM - CELL GLUCOSE - CELL GLYCOLYSIS - ATP ANABOLISM - building up, like Photosynthesis (CO2 + H2O + SUNLIGHT = SUGAR) To have anabolism, there should be catabolism METABOLIC PATHWAYS - Series of chemical reactions occurring within a cell - Metabolic pathways are linked together by a common intermediate - Linked metabolic pathways = metabolic network 2. METABOLISM - Describes all chemical reactions by which complex molecules taken into an organism are broken down to produce energy and by which that energy is in turn used to build up complex molecules - Energy production, utilization, and conservation CATABOLISM - breaking down (Catabolic Reaction - bigger to smaller molecules)  - Transmission, expression, and storage of genetic information THE CELL - Cellular components are made up of biomolecules - The turnover (biosynthesis and degradation) of biomolecules happens inside the cell - Biochemical reactions are taking place inside the various cellular components - 1 cell organisms: Bacteria, Fungi, Protist (unicellular) - Human: Multicellular organism (cells inside coordinate to each other) - To observe bacteria, use OIO in microscope - Eukaryotic is bigger to see - Prokaryotic came to exist first - Organelles can have their own membrane (coating) - Plants have cell wall for protection - If humans have cell wall, we will be less flexible - Plants can do Krebs cycle, also animals because they have mitochondria - ETC: Electron-Transport Chain - PLASMID - transfers genetic information from 1 bacteria to another, this is where antibiotic resistance gene is present - gDNA: Genomic DNA, needed to live - DNA cannot go outside the nucleus so it created RNA to transfer informations - Ribosomes need RRNA - DNA can be vulnerable due to mitosis and meiosis, nucleus may disintegrate - RIBOSOME SMALL UNIT - came from RRNA - RER: Protein synthesis - SER: Lipid synthesis - ENDOCYTOSIS: enter of substance in cell - EXOCYTOSIS: exit of substance in cell WHAT IS A CELL? - Basic building block of life - Smallest living unit of an organism - Capable or growth, reproduction, energy adaptation, and response to the environment - A cell may be an entire organism or it may be one of billions of cells that make up an organism 3. GENETIC INFORMATION  MAJOR FUNCTIONS: TWO TYPES OF CELL Synthesis and degradation of biomolecules Selective transport of biochemical substances Metabolism Storage, transmission, and expression of genetic information PROKARYOTIC CELLS - The earliest and most primitive forms of life on Earth - Simple in structure Usually unicellular organisms No recognizable organelles Lack a nucleus Has its DNA concentrated in the nucleoid region of the cytoplasm UNIQUE ORGANELLES ANIMAL CELLS: Lysosomes Flagella EUKARYOTIC CELLS PLANT CELLS: Chloroplasts (Plastids) - Have more complex structures and intracellular Central Vacuole and Tonoplast processes Cell Wall - Structural features: Plasmodesmata With distinct membrane-bound organelles Compartmentalization allows two incompatible reactions to occur in a single cell at the same time Commonly 1000-fold greater in volume than Prokaryotic cells ORGANELLES - Specialized subunits within a eukaryotic cell - Has its own specific function - Usually separately enclosed within its own membrane - Suspended in thick intracellular fluid (Cytosol) BIOMOLECULES  FUNCTIONS OF CARBOHYDRATES Stores and provides energy (glycogen, starch, monosaccharides) Structural integrity (cellulose in plant cell walls) As conjugates to other macromolecules (glycoproteins) Component of nucleic acids (ribose in RNA and deoxyribose in DNA) NUCLEIC ACIDS PROTEINS - Chemical carriers of genetic information - Most abundant biomolecule in the cell (15%) - Biopolymers of nucleotides linked by - Most varied and most diverse in terms of Phosphodiester bond structure and function - TWO FORMS: DNA (2-deoxyribonucleic acid) FUNCTIONS OF PROTEINS RNA (ribonucleic acid) Establishment and maintenance of structure (collagen, histones in DNA) Transport (hemoglobin, transferrin) Control and regulation (hormones like insulin and somatotropin) Defense and immunity (immunoglobulin) FUNCTIONS OF PROTEINS Catalysis (enzymes) Movement (myosin in muscles) Storage (ferritin) CARBOHYDRATES - most abundant biomolecule on Earth  AMINO ACIDS GENERAL STRUCTURE FUNCTIONS OF NUCLEOTIDES Energy currency in metabolic processes (ATP, ADP) Structural components of cofactors and coenzymes (NADH, FADH2) As building blocks for molecular repositories of genetic information (DNA and RNA) LIPIDS At neutral pH (pH = 7) - Heterogenous in structure Predominantly dipolar or Zwitterions - Exhibits low solubility/insolubility in water and solubility in organic solvents - Have very large hydrophobic (non-polar) portions FUNCTIONS OF LIPIDS As fuel for metabolic processes (fats and oils) Building block and nutrients/vitamins (phospholipids, glycolipids, cholesterol, Vitamins A, D, E, K) Insulation (fats and oils) Protective coverings (cutin and suberin) ZWITTERIONIC FORM Explains the physical properties of amino acids - Crystalline solid - Very high melting point - High solubility in water  Except for glycine, amino acids have an BASED ON STRUCTURE (functional groups in the asymmetric carbon side chain) - Four different groups of atoms bonded to the a-carbon Alkyl/Aliphatic - Chiral molecule Sulfur-containing - Optically active Alcohols Aromatics STEREOCHEMISTRY Acidic Basic Amino acids can exist as a pair of Enantiomers Amides ALKYL/ALIPHATIC Stabilize proteins through hydrophobic interaction D- and L- are absolute configurations around the chiral carbon D and L configuration: Amino acids residues naturally occurring protein molecules are exclusively L-isomers Proline limits structural flexibility because of D-amino acids are found only in a few peptides its rigid ring (eg. bacteria cell wall and some antibiotics) SULFUR-CONTAINING CLASSIFYING STD. AMINO ACIDS BASED ON NUTRITIONAL REQUIREMENT ESSENTIAL AMINO ACIDS - Must be supplied in the diet since they cannot Methionine is very hydrophobic be synthesized by the human body Cysteine is responsible for disulfide bridges in - Tryptophan, Valine, Threonine, Isoleucine, proteins Leucine, Lysine, Phenylalanine, Methionine, Histidine, Arginine ALCOHOLS NON-ESSENTIAL AMINO ACIDS - Can be synthesized by the body  ACIDIC Have -COOH side chains which are ionized at pH 7 Negatively charged Stabilize protein and interact with the aqueous environment through hydrogen bonding AROMATICS BASIC Stabilize protein through hydrophobic Have -NH2 side chains which are protonated at interaction pH 7; positively charged Tyr (-OH) can participate in H-bonding Trp and Tyr account for absorbance of light exhibited by most proteins at 280 nm AMIDES Absorbance at 280 nm is used for spectrophotometric determination of protein concentration Amide counterparts of acidic amino acids Can stabilize protein by hydrogen bonding SOME UNCOMMON AMINO ACIDS  PEPTIDES FORMATION OF A PEPTIDE BOND Peptide bonds are formed by condensation reaction of amino acids SOME TERMINOLOGIES PEPTIDES/OLIGOPEPTIDES - Continuous chains of a few amino acids usually not more than 50 residues POLYPEPTIDES - Amino acid chains with MW molecule becomes more stable - Accumulation of misfolded proteins are the causes of some diseases: 1. Alzheimer’s 2. Parkinson’s 3. Mad Cow 4. Senile Dementia PROTEIN DENATURATION - Alteration of the secondary, tertiary, and quaternary structure of proteins - The primary structure of the protein is preserved (peptide bond is not easily disrupted) - May result into reduction or complete loss of biological activity of the protein - Accomplished by the following agents of denaturation Physical Agents: heat, extremes of pH Chemical Agents: 1. Strong acids and bases 2. Heavy metal cations (Pb2+ , Hg2+) 3. Alkaloidal reagents (trichloroacetic acid) 4. Organic solvents (ethanol, acetone)