Topic 2 Flashcards
What are organic molecules?
- are the building blocks of living things
- contain carbon and hydrogen
What is organic chemistry?
The study of the chemistry of carbon compounds
What does the synthesis of urea show in 1828?
- demonstrated that organic compounds can be prepared in the laboratory from non-living material
DNA
Deoxyribonucleic acid
RNA
Ribonucleic acid
Trends for electronegativity
Increasing towards the right and going upwards
Electronegativity
- tend to accept electrons
Electropositive
Tend to give up electrons
How do ionic bonds form?
Elements near the edges of the periodic table give or accept electrons causing them to become charged. Then they form ionic bonds with each other due to their opposite charges
How do covalent bonds form?
Elements near the middle that do no give up or accept electrons easily tend to share electrons forming covalent bonds
Polar covalent bond
Electrons are shared but not equally
Nonpolar covalent bond
Electrons shared equally
What makes carbon the central component of all molecules that form living organisms?
Carbon’s ability to form 4 covalent bonds with as many as 4 different atoms
Carbon hybridization
-two non bonding electrons fill the 1s orbital
- 4 valence or bonding electrons are distributed in 4 orbitals in second energy level; one in the 2s orbital, one in each 2px, 2py, and 2pz orbital.
- four orbitals can hybridize to generate 4 sp3 orbitals of equal energy
Carbon sp3 hybridization geometry
- adopts a tetrahedral geometry
- forms 4 single bonds, each with one electron from each of its sp3 orbitals
- the angle between the C-H bonds are 109.5
What are the simplest organic compounds?
Hydrocarbons, compounds of carbon and hydrogen
The simplest organic compound
- methane, the major component of natural gas
What is methane comprised of?
- a single C atom covalently bonded to 4 H atoms in a tetrahedral manner
- angle is 109.5
How are C-H bonds formed?
- formed by overlap between the sp3 orbitals of C and the s orbitals of the Hs.
- the single e- in each of these orbitals is shared between the two atoms
What do shared orbitals produce?
- produce a new sigma orbital, the covalent bond formed by the shared electrons
Some simple hydrocarbons - alkanes
Methane - 1 group
Ethane - 2 groups
Propane - 3 groups
Butane - 4 groups
Alkanes
Only contain single bonds
- both C-H and C-C bonds are sigma bonds
- the C-C bonds are between sp3 orbitals
What are aliphatic compounds?
-linear, branched or cyclic hydrocarbons that are not aromatic
- can have double and triple bonds
Sp2 hybridization
Carbon—carbon double bonds
- the sp2 orbitals between 2sp2 hybridized carbons overlap to form a sigma bond
- the second bond is formed by overlap between p bonds to to create a pi bond
- the two bonds of this double bond are non equivalent
So hybridization
Carbon-carbon triple bonds
- two p orbitals overlap between 2 sp hybridized carbons forming 2 pi bonds
- the sigma bonds between the sp orbitals make a third bond
Where can rotation occur?
Only across a single bond, not across a double or triple bond
What does removing a hydrogen from an alkane result in?
In alkyl group or substituent which can bond to other atoms/molecules/groups
OH
Alcohol
NH2
Amine
F, Cl, Br, I
Alkyl halide
OR
Ether
Polarity
The asymmetric distribution of e- results in polarity
When there is a partial positive charge on one end, and a partial negative charge on the other end
Polar molecules
Asymmetric charge distribution due to unequal sharing of bonding electrons
Polar covalent bond
When an electronegative atom will haver a greater share of the bonding electrons than the electropositive atom, a polar covalent bond forms
Permanent dipole
When electrons on an atom results in having the molecule having a partial negative charge while another part of the molecule has a partial positive charge
Non-polar molecules
- symmetric charge distribution for their bonding electrons
- also when the bounded atoms are identical or of similar electronegativity
What do function groups of simple organic compounds have?
- have specific properties and reactivities based on their polarity, electronegativity
- more reactive than their alkyl substituents
Thiol
Functional group is sulfhydryl -SH
Acids
The function groups is a carboxyl, COOH, comprised of a carbonyl group (carbon with double to oxygen) bonded to a hydroxyl group via the carbon
Amines
A nitrogen
- is basic (can be protonated, becoming positively charged
Phosphate
Can be pronated
- acidic
Amides
Hydroxyl group of a carboxyl if acid is replaced by an amino acid
Localized electrons
- when the molecules have discrete single and double bonds
- electrons stay on their atom
Delocalized electrons
- molecule does not have discrete single and double C-O bonds
- electrons do not stay on their atom
Resonance
The delocalization of electrons across bonds
- results in a more stable molecule
What are amino acid in proteins joined by?
By peptide bonds with delocalized electrons
What is a important property of peptides/proteins?
Delocalization
How does delocalization of electrons limit rotation?
- it imposes partial double bond character on the bonds and limits rotation about those bonds
What does limited for rotation affect?
- influences the folding of that polypeptide
Aromatic compounds
- cyclic ring-shaped molecules that have alternating single and double bonds that result in the delocalization of their electrons to form a pi (p) electron cloud
What is the simplest aromatic compound?
Benzene (C6H6)
Compare and contrast an aromatic molecule and an aliphatic molecule
Aromatic:
- cyclized 6 carbon ring with sp2 carbons linked by alternating single and double bonds
- each C has one H
- rigid, planar structure,
- electrons are delocalized in a pi bond
- unique properties due to resonance
- very stable (not reactive)
Aliphatic:
- cyclized 6 carbon ring with sp3 carbons linked by single bonds
- each C has two Hs
- flexible, non-planar structure
Benzene
- a planar molecule
- six identical carbon carbond bonds
- each pi electron is shared by all six carbons
- pi electrons are delocalized
What cyclic molecules are aromatic?
Only the ones that form a closed loop of overlapping pi orbitals
What physical properties affect aromatic compounds interactions with other molecules?
- flat molecular structures
- a tendency to stack upon one another, especially in water (Electrostatic attraction)
Can 5-membered rings also be aromatic compounds?
Yes
What 4 of the 20 naturally occurring amino acids in proteins contain aromatic side chains?
- histidine (contains an imidazole group)
- phenylalanine (contains an phenyl [=benzene] group)
- tyrosine (contains a phenol [a phenyl ring with a hydroxyl])
- tryptophan (contains an indol group)
What are aromatic bases?
Components of nucleotides which form DNA
- the bases get stacked in the DNA which contributes to the stability of the DNA
Isomers
Non-identical compounds having the same molecular formula
constitutional isomers
Have the same molecular formula bit their atoms are linked differently
Stereoisomers
- have the same molecular formula and the same linkage between the atoms, but differ in the 30 dimensional orientation of the atoms in space
- cis-trans isomers
- isomers that contain asymmetric centers
Cis-trans stereoisomers in alkenes
- rotation can occur across a single bond
- cis: R groups on the same side
- trans: R groups on opposite sides
Chiral objects
- chiral objects are not symmetrical.
- the mirror image of a chiral object can not be superimposed on the object
- do not have a plane of symmetry
This is caused by an asymmetric carbon center
Achiral objects
- these objects are symmetrical
- can be superimposed upon their mirror images
Enantiomers
- chiral molecules that are mirror images one another
- distinct compounds with different properties
