Introduction to Orgo

Organic chem – the study of C based
compounds (must have both C & H)

Why Carbon?




It’s versatile!
4 valence electrons (4 covalent bonds)
Form simple or complex compounds
C chains form backbone of most biological
molecules (straight, bent, double bond, rings)
Hydrocarbons

Hydrocarbons ONLY
consist of C & H

Importance – store
energy

Hydrophobic
Organic Shorthand
Isomers

Isomers – same number of atoms per
element, different arrangement

3 types:




Structural – differ in covalent
partners
Geometric – differ in arrangement
around a double bond
Enantiomers – mirror images of each
other
Different structure means different
function!
Functional Groups

Functional groups – parts of organic molecules that
are most commonly involved in chemical reactions

replace H in hydrocarbons

Most are hydrophilic

Variation of life is due to molecular variation
Functional Groups
Isomers
Geometric Isomers
Structural Isomers
cis
Enantiomers
trans
10/29 – Do Now

Draw the following compounds using organic shorthand.
1.

5.
2.
3.
C4H9OH
4.
C4H8
Draw out all hydrogens and carbons for the following
compounds. What is the chemical formula?
6.
7.
8.
Practice Problem

Draw the following compound (Retinol – Vitamin A) using
organic shorthand.
Isomers

Isomers – same number of atoms per
element, different arrangement

3 types:




Structural – differ in covalent
partners
Geometric – differ in arrangement
around a double bond
Enantiomers – mirror images of each
other
Different structure means different
function!
Cyanide is an organic compound.
1.
2.
True
False
0%
1
0%
2
What kind of isomers are these?
1.
2.
3.
Structural
Geometric
Enantiomers
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1
0%
2
0%
3
This is a fatty acid. What type of
isomer would you expect to see?
1.
2.
3.
Structural
Geometric
Enantiomers
0%
1
0%
2
0%
3
Functional Groups

Functional groups – parts of organic molecules that
are most commonly involved in chemical reactions

replace H in hydrocarbons

Most are hydrophilic

Variation of life is due to molecular variation
Functional Groups
Macromolecules

Huge biological
molecules!

4 classes:





Carbohydrates
Lipids
Proteins
Nucleic Acids
Polymers – long
molecule made of
monomers
Polymerization

Building dimers or polymers



Condensation rxn AKA dehydration synthesis:
Monomer-OH + monomer-H  dimer + H2O
Breaking down dimers or polymers


Reverse rxn called hydrolysis
Dimer + H2O  monomer-OH + monomer-H
The breaking down of foods during
digestion is an example of dehydration
synthesis.
1.
2.
True
False
0%
1
0%
2
The breaking down of foods during
digestion is an example of dehydration
synthesis.
1.
2.
True
*False
0%
1
0%
2
Amino acids (shown below) are linked
together to form proteins. This is an example
of dehydration synthesis.
1.
2.
True
False
0%
1
0%
2
Amino acids (shown below) are linked
together to form proteins. This is an example
of dehydration synthesis.
1.
2.
*True
False
0%
1
0%
2
Carbohydrates

Cells get most of their energy from carbs

Carbs are sugars, most end in “-ose”

Multiple of molecular formula: CH2O

Glucose: C6H12O6

Carbonyl group

Multiple hydroxyl groups
Carbohydrates

Monosaccharides


Monomers: simple sugars w/ 3-7 carbons
Ex. (C6H12O6): Glucose, Fructose, Galactose

Disaccharide – formed by 2 monosaccharides
forming a glycosidic linkage by dehydration
synthesis

Ex:



glucose + glucose  maltose + H2O
glucose + fructose  sucrose + H2O
glucose + galactose  lactose + H2O
Carbohydrates
Carbohydrates

Polysaccharides: 100’s – 1000’s of monosaccharides joined
by glycosidic linkages

Storage polysaccharides

Starch



Glycogen



Plants – stored in plastids
Made entirely of glucose - helical
Animals – stored in liver & muscle (in vertebrates)
Made entirely of glucose - branched
Structural polysaccharides

Cellulose – plant cell walls


Made of glucose – linear
Chitin

Exoskeleton of arthropods & fungi cell walls
A compound has the molecular
formula C5H10O5. Is it a carbohydrate?
1.
2.
Yes
No
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1
0%
2
A compound has the molecular
formula C5H10O5. Is it a carbohydrate?
1.
2.
*Yes
No
0%
1
0%
2
Two monosaccharides are joined
together by hydrolysis to form a
disaccharide.
1.
2.
True
False
0%
1
0%
2
Two monosaccharides are joined
together by hydrolysis to form a
disaccharide.
1.
2.
True
*False
0%
1
0%
2
Which of the following is only made in
animals?
1.
2.
3.
Collagen
Glycogen
Starch
0%
1
0%
2
0%
3
Which of the following is only made in
animals?
1.
2.
3.
Collagen
*Glycogen
Starch
0%
1
0%
2
0%
3
Which of the following is only
made by fungi?
1.
2.
3.
4.
Collagen
Glycogen
Starch
Chitin
0%
1
0%
2
0%
3
0%
4
Which of the following is only
made by fungi?
1.
2.
3.
4.
Collagen
Glycogen
Starch
*Chitin
0%
1
0%
2
0%
3
0%
4
11/6 - Do Now

Grab your clickers!

Take out your carbohydrates lab.

Draw the dehydration synthesis reaction that joins the
following two molecules:
Lipids

No polymers!

Hydrophobic (mostly hydrocarbons)

Store energy efficiently (2x more than carbs!)

Types :




Fats & oils
Phospholipids
Steroids
Waxes
Fats & Oils

Fat = dehydration synthesis of:


Glycerol C3H5(OH)3
Fatty acid: 16 or 18 carbon hydrocarbon chain w/ carboxyl
group

Glycerol + 3 fatty acid chains = triglyceride + 3 H2O

Function:



Energy storage
Insulation
Protective cushioning around organs
Saturated Fats

No double bonds between carbons

Saturated with hydrogens

Solid at room temperature

Mostly animal fat

Ex: butter, lard, adipose
Unsaturated Fats

1 or more double bonds between carbons

Bent or kinked chains

Liquid at room temperature

Mostly plant or fish fat

Ex: olive oil, cod liver oil, corn oil
Phospholipids

Glycerol + 2 fatty acids + phosphate

Phosphate head = hydrophilic

Fatty acid tails = hydrophobic

Form a bilayer in water

Makes up cell membranes
Phospholipids
Steroids

4 fused carbon rings with
various functional groups

Ex: cholesterol
 Component of cell
membrane & many
hormones
11/12 – Do Now

Take out your lipids HW from the weekend.

Grab your clickers!

Fill out the the Venn Diagram comparing carbs
and lipids.
Carbs
Lipid
s
Which of the following is a class of
molecules that encompasses all of the other
molecules listed?
1.
2.
3.
4.
5.
6.
Triglycerides
Waxes
Lipids
Fatty acids
Sterols
Phospholipids
0%
0%
1
2
0%
0%
0%
0%
3
4
5
6
Which of the following is a class of
molecules that encompasses all of the other
molecules listed?
1.
2.
3.
4.
5.
6.
*Triglycerides
Waxes
Lipids
Fatty acids
Sterols
Phospholipids
0%
0%
1
2
0%
0%
0%
0%
3
4
5
6
One molecule of fat is made by joining
three molecules of _________ to one molecule
of _________ .
1.
2.
3.
4.
Glycerol, fatty acid
Sterols, phosphate
Phosphate, sterols
Fatty acid, glycerol
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1
0%
2
0%
3
0%
4
One molecule of fat is made by joining
three molecules of _________ to one molecule
of _________ .
1.
2.
3.
4.
Glycerol, fatty acid
Sterols, phosphate
Phosphate, sterols
*Fatty acid,
glycerol
0%
1
0%
2
0%
3
0%
4
Which of the following is most likely to
have all single bonds in its fatty acid chain?
1.
2.
3.
4.
Coconut oil
Sunflower oil
Canola oil
Olive oil
0%
1
0%
2
0%
3
0%
4
Which of the following is most likely to
have all single bonds in its fatty acid chain?
1.
2.
3.
4.
*Coconut oil
Sunflower oil
Canola oil
Olive oil
0%
1
0%
2
0%
3
0%
4
Which of the following statements
about saturated fats is true?
1.
2.
3.
4.
They contain 1+ double
bonds in the hydrocarbon
tail.
They contain the maximum
number of hydrogens in
the hydrocarbon tail
They make up the majority
of plant oils.
They are healthier for you
then unsaturated fats.
0%
1
0%
2
0%
3
0%
4
Which of the following statements
about saturated fats is true?
1.
2.
3.
4.
They contain 1+ double
bonds in the hydrocarbon
tail.
*They contain the maximum
number of hydrogens in the
hydrocarbon tail
They make up the majority
of plant oils.
They are healthier for you
then unsaturated fats.
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2
0%
3
0%
4
Little Debbie Swiss Rolls
Hostess Cupcakes
11/14 – Do Now

Get your clickers!

Answer the following questions:
+
1.
2.
3.
4.
5.
Which two amino acids are shown as the reactants?
Draw the product.
What type of reaction is this?
What is the name of the newly formed bond?
Predict the following: The long chain made by the joining of MANY
amino acids using the newly formed BONDS is called a _____________.
Proteins

Functions: enzymes, structural support, storage, transport,
cellular communication, movement, defense

Monomer = amino acid




Short C chain
Amino group
Carboxylic acid group
“R” group determines type

Cells use 20 different amino acids to build 1000’s of different
proteins

Amino acids linked by peptide bonds via dehydration
synthesis to form polymers – polypeptides

Chaperonins assist in protein folding
Protein Structure

10 Structure
- Sequence of amino acids (length vary)
- Determined by genes

20 Structure




30 Structure - 3D (fold onto itself)




How polypeptide folds or coils
Α helix
β pleats
H bonds
Hydrophobic interaction
Disulfide bridges
40 Structure – bonds to other polypeptides

2 or more polypeptide chains bonded together
Protein Conformation

Structure of a protein is directly related to function

Protein conformation is determined when it is synthesized,
and it is maintained by chemical interactions

Protein conformation also depends on environmental
factors: pH, salt concentration, temp…etc

Protein can be denatured – unravel and lose conformation,
therefore biologically inactive.

When conditions change again, protein can be renatured
(restored to normal)
http://highered.mcgrawhill.com/sites/9834092339/student
_view0/chapter3/protein_denatura
tion.html
11/18 – Do Now

Happy Monday!

Please get your clickers!

Take out your lipids & proteins lab.

Add proteins to your Venn Diagram! Draw & fill in the
following:
Carbs
Lipids
Proteins
All of the following are true about both amino
acids and monosaccharides EXCEPT:
1.
2.
3.
4.
They are monomers.
The are linked to other
amino acids &
monosaccharides
(respectively) by
dehydration synthesis.
They are organic
molecules.
They are always
arranged in a ring.
0%
1
0%
2
0%
3
0%
4
All of the following are true about both amino
acids and monosaccharides EXCEPT:
1.
2.
3.
4.
They are monomers.
The are linked to other
amino acids &
monosaccharides
(respectively) by
dehydration synthesis.
They are organic
molecules.
*They are always
arranged in a ring.
0%
1
0%
2
0%
3
0%
4
All amino acids contain all of the
following groups EXCEPT:
1.
2.
3.
4.
amino
hydroxyl
carboxyl
central carbon
between 2
functional groups
0%
1
0%
2
0%
3
0%
4
All amino acids contain all of the
following groups EXCEPT:
1.
2.
3.
4.
amino
*hydroxyl
carboxyl
central carbon
between 2
functional groups
0%
1
0%
2
0%
3
0%
4
All proteins have a primary
structure.
1.
2.
True
False
0%
1
0%
2
All proteins have a primary
structure.
1.
2.
*True
False
0%
1
0%
2
The helix that forms in a protein chain as a
result of hydrogen bonds & other weak
forces is an example of:
1.
2.
3.
4.
Primary structure
Secondary
structure
Tertiary structure
Nonlinear
structure
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1
0%
2
0%
3
0%
4
The helix that forms in a protein chain as a
result of hydrogen bonds & other weak
forces is an example of:
1.
2.
3.
4.
Primary structure
*Secondary
structure
Tertiary structure
Nonlinear
structure
0%
1
0%
2
0%
3
0%
4
In the stable form of a protein, what is
generally oriented to the interior of the
protein molecule?
1.
2.
3.
4.
Hydrophilic
portions
Hydrophobic
portions
Large portions
Random portions
0%
1
0%
2
0%
3
0%
4
In the stable form of a protein, what is
generally oriented to the interior of the
protein molecule?
1.
2.
3.
4.
Hydrophilic
portions
*Hydrophobic
portions
Large portions
Random portions
0%
1
0%
2
0%
3
0%
4
Nucleic Acids

2 types:

DNA (deoxyribonucleic acid)





Found in nucleus of eukarya
Double stranded helix
Provides directions for its own replication
Also directs RNA synthesis

Though RNA controls 10 structure of proteins
RNA (ribonucleic acid)


Single stranded, variety of shapes
Transfers information from nucleus to cytoplasm (where
proteins are made)
DNA RNA Proteins
Structure of Nucleic Acids

Monomers – nucleotides composed of 3 parts:



Pentose (ribose or deoxyribose)
Phosphate group
Nitrogenous base

Pyrimidines – 6 membered rings of C & N




Cytosine (C)
Thymine (T)….DNA only
Uracil (U)… RNA only
Purines – 6 membered ring fused to 5 membered ring of C
&N


Adenine (A)
Guanine (G)
Nucleotide Structure
Bonding of Nucleotides
Bonding of Nucleotides
Write the complementary DNA
strand for the following:
1.
CGTAAGCGCTAATTA
2.
TCTTAAATGATCGATC
3.
AATGAATAGCTAGCTT
4.
GGCATTCGCGATCATG
5.
CGTTAGCATGCTTCAT
Write the complementary DNA
strand for the following:
1.
CGTAAGCGCTAATTA
GCATTCGCGATTAAT
2.
TCTTAAATGATCGATC
AGAATTTACTAGCTAG
3.
AATGAATAGCTAGCTT
TTACTTATCGATCGAA
4.
GGCATTCGCGATCATG
CCGTAAGCGCTAGTAC
5.
CGTTAGCATGCTTCAT
GCAATCGTACGAAGTA
Write the complementary RNA
strand for the following:
1.
CGTAAGCGCTAATTA
2.
TCTTAAATGATCGATC
3.
AATGAATAGCTAGCTT
4.
GGCATTCGCGATCATG
5.
CGTTAGCATGCTTCAT
Write the complementary RNA
strand for the following:
1.
CGTAAGCGCTAATTA
GCAUUCGCGAUUAAU
2.
TCTTAAATGATCGATC
AGAAUUUACUAGCUAG
3.
AATGAATAGCTAGCTT
UUACUUAUCGAUCGAA
4.
GGCATTCGCGATCATG
CCGUAAGCGCUAGUAC
5.
CGTTAGCATGCTTCAT
GCAAUCGUACGAAGUA
ATP

Not a macromolecule, but still important for
life!

Adenosine Triphosphate (ATP) – primary
energy transferring molecule in the cell

ATP   ADP + Pi + Energy