Lecture 1 - Final Review.docx

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Department
Biochem & Molecular Biology
Course
BIOC 2300
Professor
Dr.Carmichael Wallace
Semester
Winter

Description
LECTURE ONE 1.1- What is Life? All organisms obey the same chemical and physical laws that rule the universe. 1. Life is complex and dynamic. All organisms composed of the same elements (mainly carbon, nitrogen, oxygen, hydrogen, sulfur and phosphorus). Living processes are comprised of thousands of reactions where vast numbers of molecules interact. 2. Life is organized and self-sustaining. Living organisms are organized from smallest to largest (atom to organism). The functional capacity of each level depends on the structural/chemical properties of the one below it. Complex structures are made of biomolecules and macromolecules. Hundreds of biochemical reactions sustain life and are catalyzed by enzymes and organized into pathways. 3. Life is cellular. Cells are the basic unit of life, they differ greatly in structure in function but all have a membrane (to control transport). Cells can only arise from the division of existing cells. 4. Life is information based. Living organisms are information-processing systems. Maintenance of structural integrity and metabolic processes involves interaction of molecules between cells. Information is expressed in coded form inherent in the three dimensional structure of biomolecules. Protein synthesis is regulated by genes. Protein has a specific structure that allows it to interact with specific molecules with complementary shapes  information is transferred during this binding process. 5. Life adapts and evolves. All life has a common origin. New forms arise from older forms. Competitive advantage from organisms that may exploit a specific energy source within a habitat. Interplay between environmental change and genetic variation can lead to the accumulation of favorable traits and eventually to increasingly different forms of life. 1.2 – Biomolecules  - living organisms comprised of thousands of different organic and inorganic molecules - Water is 50-95% of a cell’s weight - sodium, potassium, magnesium, and calcium ions may all make up 1% of a cells weight - organic molecules make up the rest, comprised of six elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur. - trace amounts of metallic and non-metallic elements - structural complexity/diversity of organic molecules is thanks to the ability of carbon to form four strong, single covalent bonds to other carbon atoms or other atoms from other elements. Organic molecules with many carbons can form complicated structures. Functional Groups of Organic Biomolecules - Organization of the functional groups determine chemical properties of the molecule - Most biomolecules contain more than one functional group - Contribute to the behaviour of any molecule that contains it Alcohol R­OH Hydroxyl Polar (water­soluble).  Forms hydrogen  bonds. Aldehyde R­CO­H Carbonyl Polar, found in some  sugars Ketone R­CO­R’ Carbonyl Polar, found in some  sugars Acids R­CO­OH Carboxyl Weakly acidic. Has a  negative charge when  it donates a proton Amine R­NH 2 Amino Weakly basic. Has a  positive charge when  it accepts a proton Amide R­CO­NH 2 Amido Polar but does not  bear a charge Thiol R­SH Thiol  Easily oxidized. Can  form disulfide bonds  readily (­s­s­)  Ester R­CO­O­R’ Ester Found in some lipid  molecules Alkene RCH=CHR’ Double bond Important structural  component of many  biomolecules (found  in lipid molecules Major Classes of Small Biomolecules - Cells contain four families of small molecules = amino acids, sugars, fatty acids, and nucleotides. - They are used in the synthesis of larger molecules (many are polymers) - Some molecules have special biological functions. Ex: ATP = cellular reservoir for energy - Many small organic molecules involved in complex reaction pathways - Amino acids  proteins  catalysts & structural elements - Sugars carbohydrates  energy sources & structural elements - Fatty acids  energy sources & structural elements of complex lipid molecules - Nucleotides  DNA/RNA  Genetic information/Protein synthesis Amino Acids and Proteins Amino acids = amino group (NH ) and2carboxyl group (CO-OH). o Amino group can be alpha (attached to the carbon atom immediately nd adjacent to the carboxyl group. Most common), beta (attached to the 2 carbon), or gamma (attached to the 3 carbon).  Many naturally occurring amino acids are not alpha. Ex: beta- alanine, GABA o Side chain (R group) also attached to the alpha carbon. Determines the chemical properties of the amino acids once it has been incorporated into protein (like solubility) - Some standard amino acids have unique functions (ex: neurotransmitters glycine and glutamic acid) o Protein also has nonstandard amino acids that are modified versions of the standard amino acids o Structure and function of amino acids are often altered by conversion of certain amino acid residues to derivatives via phosphorylation, hydroxylation, and other chemical modifications - Amino acids primarily used in synthesis of polypeptides (which play a variety of roles in living organisms  transport proteins, structural proteins, enzymes[catalytic proteins]) - Individual amino acids are connected in peptides and polypeptides with a peptide bond Alpha amino acids Beta amino acids Gamma amino acids Sugars and Carbohydrates Sugar = has alcohol and carbonyl functional groups. Basic unit of carbohydrates (the most abundant organic molecules found in nature). - ketoses and aldoses. Ex: glucose is an aldohexose (six-carbon ending with an aldehyde), fructose is a ketohexose (six-carbonending with a ketone) Carbohydrates = monosaccharides (glucose & fructose) or polysaccharides (starch & cellulose, glycogen) Some biomolecules contain carbohydrate components: nucleotides (contains ribose or deoxyribose), proteins, lipids, glycoproteins/glycolipids appear on the external surface of cell membranes in multicellular organisms (important for cell interactions). Fatty Acids Fatty acids = monocarboxylic acids usually having an even number of carbon atoms. Formula is R-COOH. Can be saturated or unsaturated - Under physiological conditions the carboxyl group exists in the ionized state (R— COO) - o Charged carbonyl group has an affinity for water but the long nonpolar hydrocarbon chain usually renders most fatty acids insoluble in water - Don’t usually appear as independent/free molecules  usually components of lipid molecules Nucleotides and Nucleic Acids Nucleotides have three components: five-carbon sugar (ribose or deoxyribose), a nitrogenous base, and one or more phosphate groups. - Nitrogenous bases are heterocyclic aromatic rings with a variety of substituents o Either a bicyclic purine, or a monocyclic pyrimidine  Purines = Adenine (A), Guanine (G)  Pyrimidines = Thymine (T), Cytosine (C), Uracil (U) Nucleotides participate in many biosynthetic/energy-generating reactions. Also are the building blocks for nucleic acids Nucleic acid = DNA and RNA - DNA  deoxyribonucleic acid. Repository of genetic information. Structure involves two anti-parallel polynucleotide strands wound around eachother to form a right-handed double helix. o Contains purines (A/G) and pyrimidines (T/C)  pair A—T and G—C o Double helix forms due to complementary pairing b/w bases due to formation of hydrogen bonds o DNA is made up of coding and noncoding sequences  Coding sequences = genes. Specify the structure of functional gene products like polypeptides and RNA molecules.  Some noncoding sequences have regulatory functions (controlling the synthesis of certain proteins), while some have undetermined functions. - RNA = ribonucleic acid. Contains ribose instead of deoxyribose and uracil instead of thymine. Single stranded. Fold into complex three-dimensional structures created by local regions of complementary base pairing. Strand can serve as a template when the DNA double helix unwinds. o RNA molecules synthesized via transcription.  Complementary base pairing specifies the nucleotide base sequence of RNA o Three types: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (rRNA)  mRNA  each sequence possesses information that codes directly for the amino acid sequence of a polypeptide.  rRNA  makes up ribosomes which convert the mRNA base sequence into the amino acid sequence for the polypeptide.  tRNA  transfer RNA molecules to the ribosome during protein synthesis. o Also noncoding RNA (ncRNA) was discovered and is not involved in protein synthesis. Have roles in other cell functions.  Short interfering RNA (siRNA)  important in RNA interference, an antiviral defense mechanism  Micro RNA (miRNA)  regulate the timing of mRNA synthesis  Small nuclear RNA (snRNA)  facilitate the process by which mRNA precursor molecules are transformed into functional mRNA  Small nucleolar RNA (snoRNA)  assist with maturation of ribosomal RNA during ribosome formation Gene expression controls when/if the information encoded in a gene will be accessed. - Begins with transcription where a base sequence of a DNA segment is used to synthesize a gene product. - Transcription factors regulate the expression of protein-coding genes when they bind to specific regulatory DNA sequences referred to as response elements. o Transcription factors are synthesized and/or regulated by an information- processing mechanism initiated by a signal molecule (ex: insulin) or an abiotic factor like light. 1.3 – Is the Living Cell a Chemical Factory? Autopoiesis is used to describe living organisms. Life emerges from thousands of self- regulating biochemical reactions. - Metabolism is made possible via the constant flow of energy and nutrients and functionality of enzymes. o Functions of metabolism  Acquisition and utilization of energy  Synthesis of molecules needed for cell structure and functioning (proteins, carbs, lipids, nucleic acids…)  Growth and development  Removal of waste products o Metabolism requires lots of useful energy! Biochemical Reactions 1) Nucleophilic Substitution Reactions = one atom/group is substituted for another Attacking species = nucleophile  anions/neutral species w/ non-bonding electron paires Electrophiles = deficient in electron density, so are easily attacked by the nucleophile Outgoing nucleophile = leaving group Ex: reaction of glucose with ATP, hydrolysis reactions 2) Elimination Reactions = double bond is formed when atoms in a molecule are removed ex: removal of water from biom
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