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Lecture #1: Melchor L. Cerdania Department of Chemistry Silliman University

This document summarizes key concepts from Lecture #1 on biochemistry and organic chemistry. It defines biochemistry as the study of molecules involved in biological processes and their reactions. Organic chemistry is defined as the study of organic compounds containing carbon, along with their reactions. The document discusses atoms and chemical bonds, including ionic and covalent bonds. It also covers Lewis structures, functional groups, isomerism, acids and bases, and intermolecular forces in organic chemistry.

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Glayzell Altrinna
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101 views44 pages

Lecture #1: Melchor L. Cerdania Department of Chemistry Silliman University

This document summarizes key concepts from Lecture #1 on biochemistry and organic chemistry. It defines biochemistry as the study of molecules involved in biological processes and their reactions. Organic chemistry is defined as the study of organic compounds containing carbon, along with their reactions. The document discusses atoms and chemical bonds, including ionic and covalent bonds. It also covers Lewis structures, functional groups, isomerism, acids and bases, and intermolecular forces in organic chemistry.

Uploaded by

Glayzell Altrinna
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Lecture #1

Melchor L. Cerdania
Department of Chemistry
Silliman University
 Biochemistry
 study of molecules involved in biological processes
 study of reactions these molecules undergo
 molecules in biochemistry are considered as organic compounds
 Organic Chemistry
 study of organic compounds
 compounds containing carbon atoms except those of carbonates,
bicarbonates, and cyanide
 reactions of organic compounds
https://www.thoughtco.com/difference-between-organic-and-inorganic-603912
https://www.slideshare.net/obanbrahma/organic-chem-29156459
https://byjus.com/biology/biomolecules/
https://www.compoundchem.com/2014/01/24/functional-groups-in-organic-compounds/
 Atoms have electrons
 # of e- = 8  stable atom (octet rule)
 Atoms want to have 8 valence electrons
 Chemical bonds (bonding)
 Types of bonds  ionic and covalent
 Ionic – transfer of e- (involves a metal and a non-metal)
 Covalent – sharing of e- (involves 2 non-metals)
 Ionic bonds – strong type of bonds; present in inorganic
compounds; reason of high boiling and melting points of
inorganic compounds, electrical conductivity (physical
properties); ions
 Covalent bonds – weaker type of bonds; present in organic
compounds; imparts low boiling and melting points of organic
compounds; molecules

 Note: physical properties mentioned could be use to differentiate


inorganic from organic compounds
 also known as electron dot structures
 a simple way of showing the covalent bonds in a molecule
 electrons are represented as dots
 For
 Hydrogen – 1 dot  1s2 e-
 Carbon – 4 dots  2s22p2
 Oxygen – 6 dots  2s22p4
 Alternative to Lewis structure is the line-bond structure
(Kekule Structure)
 The number of bonds the atom will make
depends on the needed number of additional
valence electrons to reach the noble gas
configuration
 Bonding and non-bonding e-
 How many hydrogen atoms does phosphorus bond to in
forming a molecule of phosphine, PH??
 Determine to what group P belongs to.
 Determine the number of e- needed to have an octet.
 Number needed means number of hydrogen
 Phosphine is PH3.
 Draw the Lewis and Kekule Structures of a molecule of
chloroform, CHCl3.

:
Cl : Cl :
:

:
H C Cl H C Cl :

:
:
:
:
Cl : Cl :

:
 What are likely the formulas for the following compounds?
 GeCl?
 AlH?
 CH?Cl2
 SiF?
 CH3NH?
 Write line-bond structures for the following substances. Show
all non-bonding electrons.
 H2S, hydrogen sulfide
 CH3Li, methyllithium
 CH3NH2, methylamine
 Why can’t an organic compound have the formula C2H7?
 Four bonds due to hybridization
 Different orbitals used in bonding means different types of
covalent bond
 For carbon, 2 orbitals  2 types of bond
 Not the case due to hybridization
 Due to hybridization different orbitals becomes the same
 For methane (CH4), not four different types of bond but only
one
 For carbon  sp3, sp2, sp
 sp3- methane and ethane
 sp2- ethylene
 sp2- ethylene
 sp- acetylene
 sp- acetylene
 Like ionic compounds, organic molecules are also represented
by formulas (structures)
 Structural formula, condensed formula, line formula (skeletal
formula)
 Carvone, a substance responsible for the odor of spearmint,
has the following structure. Tell how many hydrogens are
bonded to each carbon and give the molecular formula of
carvone.
 Proposed the structural, condensed and line formulas for the
following compound.
 C5H12
 C2H7N
 C3H6O
 C4H9Cl
 Covalent bond  sharing of e-
 Different types of covalent bonds
 Polar and non-polar covalent bonds
 electronegativity
 Proton donor – acid; proton acceptor - base
 Strength of acid depends on their ability to give proton; base
ability to accept proton
 Strong acids like HCl react completely with water while weak
acids, acetic acid, react slightly
 Strength is described by its Ka value often converted to pKa
 pKa low – strong; pKa high - weak
 Organic acids
 Polar organic compounds
 Hydrogen bonded to a an electronegative atom
and to a carbon next to a polar bond like C = C
 Lost of H results to a stable anion.
 Organic bases
 Characterized by the presence of an atom with lone pair of electrons
like nitrogen
 Interaction of molecule between one another
 Interactions affect the properties of compounds like organic
compound
 Also known as intermolecular forces or van der Waals forces
 Several types:
 Dipole – dipole forces
 Dispersion forces
 Hydrogen bonds
 Dipole – dipole forces
 Polar molecules
 Electrostatic interaction among dipoles
 Dispersion forces
 Neighboring molecules
 Constant change of charges in a molecule
 Temporary dipoles
 Hydrogen bond
 Most important interaction in biological systems
 Occurs when H is bonded to a very electronegative atom (F,O, N)
 Hydrophilic
 hydrophobic

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