1. Building Blocks of Life
Chemistry of Carbon
Building Blocks of Life

2. Why study Carbon? All of life is built on carbon Cells ~72% H2O
~25% carbon compounds
carbohydrates
lipids
proteins
nucleic acids
~3% salts
Na, Cl, K…
Why do we study carbon -- is it the most abundant element in living organisms?
H & O most abundant
C is the next most abundant

3. Chemistry of Life Organic chemistry is the study of carbon compounds
C atoms are versatile building blocks
bonding properties
4 stable covalent bonds
Carbon chemistry = organic chemistry
Why is it a foundational atom?
What makes it so important?
Can’t be a good building block if you only form 1 or 2 bonds. H C H H H

4. Macromolecules
Smaller organic molecules join together to form larger molecules
macromolecules
4 major classes of macromolecules:
carbohydrates
lipids
proteins
nucleic acids

5. Dehydration synthesis
Polymers
Most macromolecules are also polymers.( carbs, proteins, & nucleic acid) (Lipids are not!)
Long molecules built by linking repeating building blocks in a chain
monomers
building blocks
repeated subunits
covalent bonds
H2O HO H
• great variety of polymers can be built from a small set of monomers
• monomers can be connected in many combinations like the 26 letters in the alphabet can be used to create a great diversity of words
• each cell has millions of different macromolecules
Dehydration synthesis

6. You gotta be open to “bonding!
How to build a polymer
You gotta be open to “bonding!
Synthesis
joins monomers by “taking” H2O out
one monomer donates OH–
other monomer donates H+
together these form H2O
requires energy & enzymes
H2O HO H
enzyme
Dehydration synthesis
Condensation reaction

7. How to break down a polymer
Breaking up is hard to do!
Digestion
use H2O to breakdown polymers
reverse of dehydration synthesis
cleave off one monomer at a time
H2O is split into H+ and OH–
H+ & OH– attach to ends
requires enzymes
releases energy
H2O HO H
enzyme
Most macromolecules are polymers
• build:
condensation (dehydration) reaction
• breakdown:
hydrolysis
An immense variety of polymers can be built from a small set of monomers
Hydrolysis
Digestion

8. Carbohydrates

9. OH H HO
CH2OH O
Carbohydrates
energy molecules

10. Carbohydrates are composed of C, H, O
(CH2O)x C6H12O6
Function:
energy u energy storage
raw materials u structural materials
Monomer: monosaccharides (sugars)
ex: sugars, starches, cellulose
(CH2O)x
C6H12O6
carb = carbon
hydr = hydrogen
ate = oxygen compound
sugar

11. Sugars 6 5 3 Most names for sugars end in -ose
Classified by number of carbons
6C = hexose (glucose)
5C = pentose (ribose)
3C = triose (glyceraldehyde)
Glyceraldehyde H OH O C OH H HO
CH2OH O
Glucose H OH HO O
Ribose
CH2OH 6 5 3

12. Building sugars Dehydration synthesis monosaccharides disaccharide |
H2O
maltose |
glucose |
glucose |
maltose
glycosidic linkage

13. Building sugars Dehydration synthesis monosaccharides disaccharide |
H2O |
glucose |
fructose |
sucrose
(table sugar)
sucrose = table sugar
Let’s go to the videotape!

14. Polysaccharides Polymers of sugars Function:
costs little energy to build
easily reversible = release energy
Function:
energy storage
starch (plants)
glycogen (animals)
in liver & muscles
structure
cellulose (plants)
chitin (arthropods & fungi)
Polysaccharides are polymers of hundreds to thousands of monosaccharides

15. Proteins

16. Proteins Most diverse group of macromolecules
Elements: Carbon, Hydrogen, Oxygen, Nitrogen
Monomer: Amino Acids
Function: involved in almost everything
enzymes (speed up chemical reactions)
structure (keratin, collagen)
carriers & transport (hemoglobin, aquaporin)
cell communication (signals and receptors)
defense (antibodies)
movement (actin & myosin)
storage (seed proteins)
Storage: beans (seed proteins)
Movement: muscle fibers
Cell surface proteins: labels that ID cell as self vs. foreign
Antibodies: recognize the labels
ENZYMES!!!!

17. Amino acids H O | H || —C— C—OH —N— R Structure central carbon
amino group
carboxyl group (acid)
R group (side chain)
variable group
different for each amino acid
confers unique chemical properties to each amino acid
like 20 different letters of an alphabet
can make many words (proteins)
—N— H R
Oh, I get it!
amino = NH2
acid = COOH

18. Protein structure & function
Amino Acids bind together through dehydration synthesis with PEPTIDE bonds.
Function depends on structure
3-D structure
twisted, folded, coiled into unique shape
Hemoglobin
Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood.
Pepsin
Pepsin is the first in a series of enzymes in our digestive system that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins.
Collagen– Your Most Plentiful Protein
About one quarter of all of the protein in your body is collagen. Collagen is a major structural protein, forming molecular cables that strengthen the tendons and vast, resilient sheets that support the skin and internal organs. Bones and teeth are made by adding mineral crystals to collagen. Collagen provides structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton. But, in spite of its critical function in the body, collagen is a relatively simple protein.
collagen
hemoglobin
pepsin

19. Protein structure (review)
R groups
hydrophobic interactions
disulfide bridges
(H & ionic bonds) 3°
multiple polypeptides
hydrophobic interactions 1°
sequence determines structure and…
structure determines function.
Change the sequence & that changes the structure which changes the function.
amino acid sequence
peptide bonds 4° 2°
determined by DNA
R groups
H bonds

20. In Biology, size doesn’t matter,
SHAPE matters!
Protein denaturation
Unfolding a protein
conditions that disrupt bonds
pH changes
Temperature changes
alter 3-D shape
destroys functionality
some proteins can return to their functional shape after denaturation, many cannot

21. Lipids: Fats & Oils

22. Lipids Lipids are composed of C, H, O “Family groups”
long hydrocarbon chains (H-C)
“Family groups”
fats
phospholipids
steroids
Do not form polymers
not a continuing chain
Made of same elements as carbohydrates but very different structure/ proportions & therefore very different biological properties

23. dehydration synthesis
Fats
Structure:
glycerol (3C alcohol) + fatty acid
enzyme
Look at structure… What makes them hydrophobic?
Note functional group = carboxyl
H2O
dehydration synthesis

24. Building Fats Triacylglycerol 3 fatty acids linked to glycerol
hydroxyl
carboxyl
BIG FAT molecule!!

25. Why do humans like fatty foods?
Fats store energy
Function:
energy storage
concentrated
all H-C!
2x carbohydrates
cushion organs
insulates body
think whale blubber!
structure of cell membranes
What happens when you add oil to water
Why is there a lot of energy stored in fats?
• big molecule
• lots of bonds of stored energy
So why are we attracted to eating fat?
Think about our ancestors on the Serengeti Plain & during the Ice Age. Was eating fat an advantage?

26. Saturated fats All C bonded to H No C=C double bonds
long, straight chain
most animal fats
solid at room temp.
contributes to cardiovascular disease (atherosclerosis) = plaque deposits
Mostly animal fats

27. Unsaturated fats C=C double bonds in the fatty acids plant & fish fats
vegetable oils
liquid at room temperature
the kinks made by double bonded C prevent the molecules from packing tightly together
Mostly plant lipids
Think about “natural” peanut butter:
Lots of unsaturated fats Oil separates out
Companies want to make their product easier to use:
Stop the oil from separating Keep oil solid at room temp.
Hydrogenate it = chemically alter to saturate it
Affect nutrition?
mono-unsaturated?
poly-unsaturated?

28. Saturated vs. unsaturated

29. Steroids Structure: 4 fused C rings + ??
different steroids created by attaching different functional groups to rings
different structure creates different function
examples: cholesterol, sex hormones
cholesterol

30. Nucleic acids

31. Nucleic Acids Examples: DNA and RNA Function: genetic material
stores information
genes
blueprint for building proteins
DNA  RNA  proteins
transfers information
blueprint for new cells
blueprint for next generation
DNA
proteins

32. Nucleic Acids Examples: Structure: RNA (ribonucleic acid)
single helix
DNA (deoxyribonucleic acid)
double helix
Structure:
monomers = nucleotides
DNA
RNA

33. Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C)
ribose in RNA
deoxyribose in DNA
phosphate (PO4) group
Nitrogen base I’m the A,T,C,G or U part!
Are nucleic acids charged molecules?
DNA & RNA are negatively charged:
Don’t cross membranes.
Contain DNA within nucleus
Need help transporting mRNA across nuclear envelope.
Also use this property in gel electrophoresis.

34. Macromolecule Review

35. Carbohydrates Structure / monomer Function Examples monosaccharide
energy
raw materials
energy storage
structural compounds
Examples
glucose, starch, cellulose, glycogen
glycosidic bond

36. Lipids Structure / building block Function Examples
glycerol, fatty acid, cholesterol, H-C chains
Function
energy storage
membranes
hormones
Examples
fat, phospholipids, steroids
ester bond (in a fat)

37. Proteins Structure / monomer Function Examples amino acids
levels of structure
Function
enzymes u defense
transport u structure
signals u receptors
Examples
digestive enzymes, membrane channels, insulin hormone, actin
peptide bond

38. Nucleic acids Structure / monomer Function Examples nucleotide
information storage & transfer
Examples
DNA, RNA
phosphodiester bond