1. Chapter 4 – Carbon and molecular basis of life

2. Friedrich Wöhler
He is best known for accidently discovering how to create urea. His experiment, now termed the Wohler synthesis, consists of creating urea. He was trying to make ammonium cyanate, by combining ammonium ions and cyanate ions, but instead found out how to make urea, which is ORGANIC. This occurred in This experiment is considered the starting point of organic chemistry.
The Wohler synthesis is of great historical significance because for the first time an organic compound was produced from inorganic reactants. This finding went against the mainstream theory of that time, called Vitalism, which stated that physical and chemical laws do not apply to living things. For this reason, a sharp boundary existed between organic and inorganic compounds. Urea was discovered in 1799 and could only be obtained from biological sources such as urine until Wohler came up with a way to synthesize it.

3. Stanley Miller
Stanley Lloyd Miller was an American chemist and biologist who is known for his studies into the origin of life, particularly the Miller-Urey experiment which demonstrated that organic compounds can be created by fairly simple physical processes from inorganic substances.
The Miller-Urey experiment was an experiment that simulated hypothetical conditions present on the early Earth and tested for the occurrence of chemical evolution. Specifically, the experiment tested that conditions on the primitive Earth favored chemical reactions that synthesized organic compounds from inorganic precursors. Considered to be the classic experiment on the origin of life, it was conducted in 1953 by Stanley L. Miller and Harold C. Urey at the University of Chicago.
It was later found that the mixture of gasses Miller used did not accurately reflect the early atmosphere. However, since then the experiment has been repeated with the more appropriate mixture of gasses and organic substances are still created.

4. Miller-Urey Experiment
The experiment used water (H2O), methane (CH4), ammonia (NH3) and hydrogen (H2). The chemicals were all sealed inside a sterile array of glass tubes and flasks connected together in a loop, with one flask half-full of liquid water and another flask containing a pair of electrodes.
The liquid water was heated to induce evaporation, sparks were fired between the electrodes to simulate lightning through the atmosphere and water vapor, and then the atmosphere was cooled again so that the water could condense and trickle back into the first flask in a continuous cycle.
At the end of one week of continuous operation Miller and Urey observed that as much as 10-15% of the carbon within the system was now in the form of organic compounds. Two percent of the carbon had formed amino acids, including 2-3 of the 22 that are used to make proteins in living cells, with glycine as the most abundant. Sugars, lipids, and some of the building blocks for nucleic acids were also formed. This helped disprove the vitalism theory. Instead, scientists embraced the idea of mechanism, the belief that the same physical and chemical laws govern all natural phenomena, including the processes of life.

5. Organic Molecules

6. Major Elements – Valence Electrons

7. Variations in Carbon Skeletons
The ability of carbon to form four covalent bonds makes large, complex molecules possible.

8. Fat Molecules - Hydrocarbons

9. Isomers
Isomers are compounds that have the same molecular formula but different structures, and therefore, different chemical properties.

10. Structural Isomers
Same molecular formula but differ in covalent arrangement of atoms
May also differ in the location of the double bond

11. Cis-trans Isomers
Have the same covalent partnership but differ in the spatial arrangement of atoms around a carbon=carbon DOUBLE BOND!
These are formerly called GEOMETRIC ISOMERS!
Subtle changes in shape can dramatically affect the function of the molecule. For example, the biochemistry of vision involves a light-induced change of retinal, a chemical compound in the eye, from the cis isomer to the trans isomer.

12. Enantiomers – Mirror Images
Molecules that are mirror images of each other. They are referred to as “left-handed” and “right-handed” versions. This is the case when 4 DIFFERENT molecules or groups of molecules are attached to an asymmetric carbon. (asymmetric carbon just means it is attached to 4 different things).
Even subtle structural differences in two enantiomers may have important functional significance because of emergent properties from specific arrangements of atoms.
For example, methamphetamine occurs in two enantiomers with very different effects. One is a highly addictive street drug called “crank”, while the other is sold for treatment of nasal congestion.

13. Comparison of Male and Female Hormones Small differences in structure can make a huge difference!
The basic structure of testosterone (a male sex hormone) and estradiol (a female sex hormone) is the same. Both are steroids with four fused carbon rings, but the hormones differ in the chemical groups attached to the rings. As a result, testosterone and estradiol have different shapes, causing them to interact differently with many targets throughout the body.

14. Functional Groups – Memorize!!
Chemical groups known as functional groups affect molecular function through their direct involvement in chemical reactions.
All of the functional groups are HYDROPHILIC and INCREASE the SOLUBILITY of organic compounds in water.
There are seven that you need to know…see charts on the following slides…

15. ATP ATP is an important source of energy for cellular processes.
Adenosine triphosphate, or ATP, is the primary energy transfer molecule in living cells.
ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups.
When one inorganic phosphate ion is split off as a result of a reaction with water, ATP becomes adenosine diphosphate, or ADP.
In a sense, ATP “stores” the potential to react with water, releasing energy that can be used by the cell.

16. Functional Groups

18. CHAPTER 5 – THE STRUCTURE AND FUNCTION OF MACROMOLECULES

19. Dehydration Synthesis and Hydrolysis
Dehydration Reaction (Condensation Reaction)  Taking water OUT; FORMING a BOND; Builds Polymers from Monomers; Ex. Making a protein from amino acids
Hydrolysis  Putting water IN to BREAK a BOND; breaks down to form monomers from a larger polymer; Ex. Digestion and breaking down food
We take in food as organic polymers that are too large for our cells to absorb. In the digestive tract, enzymes direct the hydrolysis of specific polymers. The resulting monomers are absorbed by the cells lining the gut and transported to the bloodstream for distribution to body cells.
The cells of our body then use dehydration reactions to assemble the monomers into new and different polymers that carry out functions specific to the particular cell type.

20. Carbohydrates Main Function: Short term energy storage
Monomer: Monosaccharides
Bond Name: Glycosidic Linkage

21. Monosaccharides Monomer for Carbohydrates
Examples are Glucose, Fructose, Galactose
Can form in a ring or linear structure…usually a ring.

22. Disaccharides
Two monosaccharides together are called a DISACCHARIDE. This is formed by Dehydration Synthesis to make the bond and therefore you create a molecule of water.
Examples of Disaccharides are Maltose, Sucrose, and Lactose
The type of bond between two monosaccharides is called a glycosidic linkage (covalent).

23. Polysaccharides
Hundreds to thousands of monosaccharides linked together form polysaccharides
Formed by dehydration synthesis and use glycosidic linkages
Four polysaccharides you need to know:
Plant Storage = STARCH
Animal Storage = GLYCOGEN
Plant Structure = CELLULOSE
Animal Structure = CHITIN

24. Storage Polysaccharides – Starch and Glycogen
STARCH  PLANT STORAGE!
Animals that feed on plants, especially parts rich in starch, have digestive enzymes that can hydrolyze starch to glucose, making the glucose available as a nutrient for cells. Grains and potato tubers are the main sources of starch in the human diet.
GLYCOGEN  ANIMAL STORAGE!

25. Structure Polysaccharides – Cellulose and Chitin
CELLULOSE PLANT STRUCTURE!
Plants produce almost 1014 kg (100 billion tons) of cellulose per year. It is the most abundant organic compound on Earth.
CHITIN ANIMAL STRUCTURE!

26. Starch vs. Cellulose Structure
The linkages are different in starch vs. cellulose because glucose has two slightly different ring structures. These two ring forms differ in whether the hydroxyl group attached to the number 1 carbon is fixed above (beta) or below (alpha) the plane of the ring.

27. Alpha and Beta forms of Glucose

28. Lipids
Main Function: Long term energy storage, protection, insulation, component of cell membranes
Monomer: No real monomer!!

29. Structure of Fat Molecules
No technical monomer for fats
Fats are constructed from two smaller kinds of molecules: glycerol and fatty acids
Many NON-POLAR bonds in fatty acid chains, so fats are hydrophobic and do not dissolve in water
When 3 fatty acid chains bond with one glycerol (via dehydration synthesis) a TRIGLYCERIDE is created using 3 ESTER LINKAGES

30. Saturated vs. Unsaturated Fats
Because plants are immobile, they can function with bulky energy storage in the form of starch. Plants use oils when dispersal and compact storage are important, as in seeds. Animals must carry their energy stores with them, so they benefit from having a more compact fuel reservoir of fat.
Saturated Fats  all single bonds; straight chain; animal fats; solid at room temperature
**A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis) through plaque deposits. The process of hydrogenating vegetable oils produces saturated fats and also unsaturated fats with trans double bonds. These trans fat molecules contribute more than saturated fats to atherosclerosis.
Unsaturated Fats  at least one C =C double bond; kinks in chain; plant and fish fats; liquid at room temperature

31. Phospholipids
Structure: Two fatty acid chains attached to a phosphate and glycerol molecule
Head: Phosphate and hydrophilic
Tail: FA chains and hydrophobic
Major component of cell membrane; arranged in bilayer so heads can come into contact with water and tails are protected from it in the interior
Amphipathic is the term used when something has both hydrophobic and hydrophilic regions

32. Structures formed by phospholipids in aqueous solutions

33. Steroids
Steroids are lipids with a carbon skeleton consisting of four fused rings.
Different steroids are created by varying the functional groups attached to the rings. Cholesterol, an important steroid, is a component in animal cell membranes. Cholesterol is the precursor from which all other steroids are synthesized. Many of these other steroids are hormones, including the vertebrate sex hormones.

34. Proteins Main Function: Everything! Monomer: Amino Acids
Bond Name: Peptide Bonds

35. Functions of Proteins
Proteins are instrumental in almost everything an organism does (structural support, storage, transport, cellular communication, movement, and defense). ENZYMES are also proteins and function as catalysts in chemical reactions.

36. Structure of Amino Acids
Carboxyl Group (-COOH)
Amino Group (-NH2)
Central Carbon
Hydrogen
“R” group

37. Charged form of Amino Acids
This is a “charged” amino acid, overall it is neutral, but it affects the bonds it will make. You need to be able to recognize that this is an amino acid if you see it.

38. The “R” groups are all different
The “R” groups are all different. There are 4 different categories that they fall into:
Nonpolar
Polar Neutral
Polar Acidic
Polar Basic
20 Amino Acids
These make up proteins – they are the monomers…link them together to form a polymer  a PROTEIN!

39. Dipeptides – formed by peptide bonds
A PEPTIDE BOND is formed between the H of one amino acid (amino group) and the OH of another AA (carboxyl group). A molecule of water is produced. This process is done by dehydration synthesis.

40. Making Polypeptide Chains
PEPTIDE BONDS – bonds between one amino acid and the next; these are created by dehydration synthesis (condensation)
In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule.
For example, an antibody binds to a particular foreign substance. Natural signal molecules called endorphins bind to specific receptor proteins on the surface of brain cells in humans, producing euphoria and relieving pain. Morphine, heroin, and other opiate drugs mimic endorphins because they are similar in shape and can bind to the brain’s endorphin receptors.

41. Primary Structure of a Protein
The primary structure of a protein is the order of the amino acids. This is coded for by DNA in the cell.

42. Sickle-Cell Disease
This disease is caused by a substitution in ONE amino acid. It affects the primary structure of the protein hemoglobin causing this disorder.
Even a slight change in the primary structure can affect a protein’s conformation and ability to function. The substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin, the protein that carries oxygen in red blood cells, can cause sickle-cell disease, an inherited blood disorder. The abnormal hemoglobin molecules crystallize, deforming some of the red blood cells into a sickle shape and clogging capillaries.

43. Secondary Structure of a Protein
The secondary structure of a protein is due to HYDROGEN BONDS within the polypeptide chain.
It can form either an Alpha Helix or Beta Pleated Sheets depending on whether it folds or coils…different parts of the protein can do different things.

44. Tertiary Structure of a Protein
Tertiary Structure is determined by interactions of the “R” groups of the amino acids.
Interactions include clustering of hydrophobic groups, hydrogen bonds, van der waals interactions, disulfide bridges, and ionic bonds.

45. Quaternary Structure of a Protein
Hemoglobin is a globular protein with quaternary structure.
Hemoglobin consists of four polypeptide subunits: two  and two  chains. Both types of subunits consist of primarily -helical secondary structure.
Each subunit has a nonpeptide heme component with an iron atom that binds oxygen
**Only occurs if there is more than one polypeptide chain!

46. Four levels of Protein Folding
Accumulation of incorrectly folded polypeptides is associated with many diseases, including Alzheimer's, Parkinson’s, and mad cow disease.

47. Denaturation
Denaturation occurs when a protein comes unraveled and it loses its form, and therefore its function. Some can renature, others cannot. Several factors cause denaturation: pH, temperature, salt concentration
An example how denaturation can occur in humans is when you get a fever. The extreme heat can denature the proteins in the blood and thus they become non-functional. This is why high fevers can be fatal.

48. Chaperonin Proteins
These proteins help protect developing proteins while they are folding up and forming. They act as chaperones. Chaperonins do not specify the final structure of a polypeptide but rather work to segregate and protect the polypeptide while it folds spontaneously.

49. Nucleic Acids Main Function: Storing genetic information
Monomer: Nucleotides
Bond Name: Phosphodiester Linkages and Hydrogen Bonds

50. DNA & RNA Two main types of nucleic acids
DNA controls gene expression, in which RNA has a vital role in synthesizing proteins
Organisms inherit their DNA from their parents
Although DNA is the genetic code, it is not involved in the day-to-day operations of the cell (that is the role of the proteins)
DNA and RNA are made up of nucleotides

51. DNA → RNA → Protein DNA carries the genetic code
RNA carries out protein synthesis in the ribosomes. This process includes mRNA, rRNA, and tRNA. We will learn more about these in another unit.

52. Nucleotides – Monomers of Nucleic Acids
- Pentose Sugar
- Nitrogen bases
-Phosphate Groups

53. Nitrogen Bases Two Types of Bases: -Purines – two rings
- Pyrimidines – one ring
DNA: A, T, C, G
RNA: A, U, C, G

54. Bases and Sugars of Nucleotides
A sugar and a nitrogen base are called a nucleoside.
When you add the phosphate group, it becomes a nucleotide.

55. Structure of DNA – Double Helix
Strands in DNA run antiparallel!
Structure of DNA – Double Helix
Bonding in DNA 
Bonds in the sugar/phosphate backbone are called phosphodiester linkages. These are covalent bonds between the sugar of one nucleotide and the phosphate of the next.
There are also hydrogen bonds in DNA between the nitrogen bases. These hold the two strands together.

56. Genomics vs. Proteomics
Genomics is an approach of addressing problems by analyzing large sets of genes or comparing whole genomes of different species.
Similar to genomics, proteomic is the approach that analyzes large sets of protein sequences.
We will learn much more about this, and these specific processes, in the biotechnology unit.

57. Differences in Hemoglobin between Humans and Other Animals
Two species that appear to be closely related based on fossil and molecular evidence should also be more similar in DNA and protein sequences than are more distantly related species.
Scientists can compare the sequence of 146 amino acids in the polypeptide chain of human hemoglobin to the sequences in five other vertebrates. Humans and gorillas differ in just 1 amino acid, while humans and frogs differ in 67 amino acids. Despite these differences, all the species have functional hemoglobin.