MC 2 - Biochemistry PDF

MC 2 - BIOCHEMISTRY 1ST Semester | BSN 1-02 ORGANIC CHEMISTRY atoms. In each covalent bond, Organic chemistry is the study of carbon shares one of its electrons carbon compounds. with another atom, and in re...

MC 2 - BIOCHEMISTRY 1ST Semester | BSN 1-02 ORGANIC CHEMISTRY atoms. In each covalent bond, Organic chemistry is the study of carbon shares one of its electrons carbon compounds. with another atom, and in return, it Consist of carbon and hydrogen. shares one of their electrons. This Examples: ethyl alcohol, oil, sharing allows carbon to fill its outer antiseptics, petroleum gas shell with eight electrons, making it stable. The versatility and stability of carbon’s molecular structures provides the Covalent compounds were mostly enormous range of properties of its liquid/gas at room temp compounds. This is primarily for binary compounds (2 Carbon atoms can form a variety of elements) stable structures, like chains, rings, Covalent compounds, particularly and networks. This flexibility allows binary compounds (those made up carbon to create many different of two different elements), are often types of compounds, each with its liquids or gases at room own unique properties. Because of temperature. This is because the this, carbon-based molecules can bonds between their atoms involve be found in everything from the sharing of electrons, which diamonds and graphite to the generally results in molecules with molecules that make up living lower melting and boiling points organisms. compared to ionic compounds. Most processes of living organisms require organic compound. HYDROCARBON All foods are considered organic. Compound with only carbon and hydrogen. PALYTOXIN - made by species of some They are considered HYDROPHOBIC species of seaweed and coral (Repel water; does not mix well with water) such as oil, petroleum gas Most hydrocarbons are flammable CARBON and combustible especially Four valence electrons exposed to heat and oxygen. VALENCE ELECTRON – outer shell electron that participate in chemical bond with ORGANIC CHEMISTRY IN DAILY LIVES another atom. SMELLS AND TASTES Fruits, fish, mint - Fruits contain 4 covalent bonds to fill its octet ETHYLENE which POLAR COVALENT – Unequal sharing of triggers cell to electrons degrade and ripen NON POLAR COVALENT – Carbon bonds fruits. Some with another carbon vegetables and Carbon has four electrons in its fruits are high in outermost shell, and it needs eight ethylene. electrons to be stable—this is known MEDICATION Aspirin, Tylenol, as the "octet rule." To achieve a full decongestants, set of eight electrons, carbon forms sedatives, insulin four covalent bonds with other TRANSCRIBED BY: MARIE TAN 1 LECTURE 1| BIOCHEMISTRY – REVIEW OF ORGANIC CHEMISTRY ADDICTIVE Caffeine, Nicotine, SATURATED SUBSTANCES alcohol, narcotics - a carbon chain contains as many HORMONES Adrenaline, hydrogens as possible. dopamine, - Contain only single C-H Bonds serotonin. - Alkanes are saturated. - Sex hormone is - Downside for saturating chain is the considered more saturated, the more it organic because it becomes compact together. The is made up of more tightly compact, the more it cholesterol. becomes solid. Cholesterol is a - If you take saturated foods high in type of lipid, and trans fat, there is a possibility that it lipid is part of can clog the heart which causes hydrocarbon. HEART ATTACK. FOOD Carbohydrates, protein, fats, UNSATURATED vitamins - a carbon chain contains at least GENETICS RNA, DNA one multiple (double or triple) bond. CONSUMER Plastics, nylon, - Relatively unstable because it PRODUCTS rayon, polyester contains multiple bond that are reactive GENERAL FORMULAS - ALKENE AND ALKYNE - Most fats came from plant ALKANES materials. Plant based oil are - Carbon with only one bond with unsaturated as long as not hydrogen hydrogenated. Non hydrogenated - Stable compared to others. plant oils are high in unsaturated - Cx H2x+2 fats which is easy to use and less likely to become solid. ALKENES - Double bond HYDROCARBONS - Less hydrogen - To break down one bond, one hydrogen will be given to be stable ALKYNES - Triple bond - Give at least two hydrogen ALKENES and ALKYNES have much higher energy and more reactive which easily cause them to break down and remain unstable than ALKANES. Some oils are hydrogenated which causes STRUCTURE AND PHYSICAL PROPERTIES them to become less reactive. They also last long and known for SHELL STABLE. SATURATION TRANSCRIBED BY: 2 LECTURE 1| BIOCHEMISTRY – REVIEW OF ORGANIC CHEMISTRY Larger molar mass = Higher boiling point FUNCTIONAL GROUP WITH COMMON - Molecules with a larger molar mass COMPOUND typically have more atoms, leading to more significant van der Waals OH Alcohol forces (dispersion forces) between Carboxylic acid molecules. These intermolecular O (OXYGEN) Esters forces require more energy to Ethers break, resulting in a higher boiling NH2 Amines point. Amides Bigger compound – higher boiling point POLYMERS - Larger compounds (in terms of size and surface area) usually have - Large molecules with many stronger intermolecular forces repeating units made from smaller because of increased surface molecules contact between molecules, - Consist of large molecules called leading to a higher boiling point. MACROMOLECULES and composed of subunits called PETROCHEMICALS MONOMERS - Simple small hydrocarbons - Isolated from oils. OCTANE Used in gasoline PROPANE Used in grills, heater MANMADE POLYMERS BUTANE Lighter fluid NYLON FUNCTIONAL GROUPS - Group of atoms which control how the molecule reacts. KEVLAR - Usually interact with other elements such as oxygen, nitrogen, and sulfur CARBONYL GROUP – One carbon that contains double bond with one oxygen. PVC NATURAL POLYMERS PROTEINS TRANSCRIBED BY: 3 LECTURE 1| BIOCHEMISTRY – REVIEW OF ORGANIC CHEMISTRY RNA 2. Number the Carbon Atoms in the Parent Chain 3. Identify and Name the Substituents - Identify the side chains or substituents attached to the parent DNA chain. These could be alkyl groups (e.g., methyl, ethyl) or other functional groups. 4. Determine the Suffix - Identify the primary functional group in the molecule and add the POLYSSACHARIDE appropriate suffix to the base name of the parent chain. The suffix indicates the type of compound: o -ane: Alkane (single bonds) o -ene: Alkene (double bonds) o -yne: Alkyne (triple bonds) PHARMACEUTICALS o -ol: Alcohol o -al: Aldehyde - Most pharmaceuticals are o -one: Ketone complex, organic molecules o -oic acid: Carboxylic acid, - Can be natural or manmade etc. For example, let's name CH₃CH₂CH(OH)CH₃: 1. Identify the longest chain: The longest chain is 4 carbons, so the IUPAC base name is "butane." 2. Number the chain: Number from the INTERNATIONAL UNION OF PURE AND end closest to the hydroxyl group, APPLIED CHEMISTRY giving the hydroxyl group the lowest possible number. 3. Identify the substituents: There's an - OH group on carbon 2. 4. Assign locants: The hydroxyl group is on carbon 2. 5. Determine the suffix: The suffix is -ol because it's an alcohol. 6. Combine the elements: The IUPAC 1. Identify the Longest Carbon name is butan-2-ol. Chain (Parent Chain) - Find the longest continuous chain of CHIRALITY carbon atoms in the molecule. This chain determines the base name of - Chiral molecule cannot be the compound. superimposed on its mirror image - If there are multiple chains of equal ENANTIOMERS – Relationship between length, choose the one with the non- super imposable mirror images. most substituents (side groups). TRANSCRIBED BY: 4 LECTURE 1| BIOCHEMISTRY – REVIEW OF ORGANIC CHEMISTRY - Achiral molecule can be - Same connectivity (Order of atoms superimposed on its mirror image. but different in their specific orientation and space) 2-BROMO-3-CHLOROPENTANE There are 2 chiral centers which can draw potentially up to 4 stereoisomers The easiest way to tell if its CHIRAL or ACHIRAL is to look for plane of symmetry. Any molecule with plane or center of symmetry is ACHIRAL. Compound 1 and 2 are called DIASTEOMERS because only one chiral center has changed. CHIRALITY CENTER Compound 2 and 3 are ENANTIOMERS because both When a sp3 hybridized atom is chiral center has changed. connected to four different group Chirality center can be seen in implicit hydrogen Heteroatoms (Atoms that aren’t carbon) can also be a chirality center Molecules with one chirality center will be chiral. Molecules with more than one may or may not be chiral. Molecule can have zero chirality center and still be chiral, as long as it has no planes or center of symmetry STEREOISOMERS - Same molecular formula TRANSCRIBED BY: 5