organic molecules
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Organic Molecules
Six Functional Groups
Six Functional Groups
Early Origin-of-Life Experiments Could the first steps of chemical evolution have
occurred on ancient Earth? To find out, Stanley Miller combined methane (CH4),
ammonia (NH3), and hydrogen (H2) in a closed system with water, and applied heat and electricity as an energy source.
The products included hydrogen cyanide (HCN) and formaldehyde (H2CO), important precursors for more-complex organic molecules and amino acids.
In more recent experiments, amino acids and other organic molecules have been found to form easily under these conditions.
Figure 3-3Nonpolar side chains
Polar side chains
Electrically chargedside chains
Glycine (G) Gly
Alanine (A) Ala
Valine (V) Val Leucine (L) Leu
Isoleucine (I) Ile
Methionine (M)Met
Phenylalanine (F)Phe
Tryptophan (W)Trp
Proline (P)Pro
Serine (S)Ser
Threonine (T)Thr
Cysteine (C)Cys
Tyrosine (Y)Tyr
Asparagine (N) Asn
Glutamine (Q)Gln
Acidic Basic
Aspartate (D)Asp
Glutamate (E)Glu
Lysine (K)Lys
Arginine (R)Arg
Histidine (H)His
No charged or electronegative atoms to form hydrogen bonds; not soluble in water
Charged side chains form hydrogen bonds; highly soluble in water
Partial charges can form hydrogen bonds; soluble in water
The Nature of Side Chains The 21 amino acids differ only in the variable side chain
or R-group attached to the central carbon
R-groups differ in their size, shape, reactivity, and interactions with water. (1) Nonpolar R-groups: Do not form hydrogen bonds; coalesce in water(2) Polar R-groups: Form hydrogen bonds; readily dissolve in water
Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms.
Primary Structure
A protein’s primary structure is its unique sequence of amino acids.
Because the amino acid R-groups affect a polypeptide’s properties and function, just a single amino acid change can radically alter protein function.
Figure 3-11
Normal amino acid sequence Single change in amino acid sequence
4 5 6 7 4 5 6 7
Normal red blood
cells
Sickled red blood
cells
Secondary Structure
Secondary structure results in part from hydrogen bonding between the carboxyl oxygen of one amino acid residue and the amino hydrogen of another. A polypeptide must bend to allow this hydrogen bonding—thus, -helices or -pleated sheets are formed.
Secondary structure depends on the primary structure—some amino acids are more likely to be involved in α-helices; while others, in β-pleated sheets.
Secondary Structure increases stability by way of the large number of hydrogen bonds.
Hydrogen bonds form between peptide chains.
Secondary structures of proteins result.
-helix -pleated sheet
-helix -pleated sheet
Ribbon diagrams of secondary structure.
Hydrogen bonds
Arrowheads are at the carboxyl end of the arrows
Tertiary Structure
The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold, and contribute to the 3D shape of the polypeptide.
R-group interactions include hydrogen bonds, van der Waals interactions, covalent disulfide bonds, and ionic bonds.
Hydrogen bonds can form between hydrogen atoms and the carboxyl group in the peptide-bonded backbone, and between hydrogen atoms and atoms with partial negative charges in side chains.
Tertiary Structures of Proteins
Interactions that determine the tertiary structure of proteins
Hydrogen bond between side chain and carboxyl oxygen
Hydrogen bond between two side chains
Hydrophobic interactions (van der Waals interactions)
Ionic bond
Disulfide bond
Tertiary Structures of Proteins
Tertiary structures are diverse.
A tertiary structure composed mostly of -helices
A tertiary structure composed mostly of -pleated sheets
A tertiary structure rich in disulfide bonds
Van der Waals Interactions van der Waals interactions are electrical
interactions between hydrophobic side chains. Although these interactions are weak, the large number of van der Waals interactions in a polypeptide significantly increases stability.
Covalent disulfide bonds form between sulfur-containing R-groups.
Ionic bonds form between groups that have full and opposing charges.
Quaternary Structure
Some proteins contain several distinct polypeptide subunits that interact to form a single structure; the bonding of two or more subunits produces quaternary structure.
The combined effects of primary, secondary, tertiary, and sometimes quaternary structure allow for amazing diversity in protein form and function.
Quaternary Structures of Proteins
Cro protein, a dimer Hemoglobin, a tetramer
Figure 3-14-Table 3-3
Carbohydrates
Simple Sugars
Monosaccharide Single sugar Ex. Glucose (blood
sugar)
Disaccharide Two sugars Ex. Sucrose, Lactose, Fructose
Linear and Ring Forms
Linear form of glucose Ring forms of glucose
-Glucose
-Glucose
Oxygen from the5-carbon bonds to the1-carbon, resulting in a ring structure
Figure 5-4
Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…
-Glucose -Glucose
…between various carbons and with various geometries.
-Galactose -Glucose Lactose (a disaccharide)
Maltose (a disaccharide)
In this case, the hydroxyl groups fromthe 1-carbon and 4-carbon react toproduct a -1,4-glycosidic linkageand water
The hydroxyl groups from the1-carbon and 4-carbon reactto produce an -1,4-glycosidiclinkage and water
Figure 5-4a
Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…
-Glucose -Glucose Maltose (a disaccharide)
The hydroxyl groups from the1-carbon and 4-carbon reactto produce an -1,4-glycosidiclinkage and water
Figure 5-4b
…between various carbons and with various geometries.
-Galactose -Glucose Lactose (a disaccharide)
In this case, the hydroxyl groups fromthe 1-carbon and 4-carbon react toproduct a -1,4-glycosidic linkageand water
Polysaccharide
Complex Carbohydrate ( Starch) Ex. Starch, Cellulose, Chitin More than one ring structure
Cellulose, Chitin, Peptidoglycan
Cellulose in plant cell wall Chitin in insect exoskeleton
Peptidoglycan in bacterial cell wall
Figure 5-5a-Table 5-1
Figure 5-5b-Table 5-1
Figure 5-5c-Table 5-1
Glycoproteins: Identification Badge for Cells
Outsideof cell
Insideof cell
Glycoprotein
Lipids
Lipids –Fats, Oils, Waxes, Steroids (cholesterol)
Unsaturated Comes from plants and is liquid at room
temperature Ex. Corn oil, Olive oil, Sunflower oil Better for you
Saturated Comes from animals and is solid at room
temperature Ex. Bacon, animal fat Bad for you
Nucleic Acids
Nucleic Acids
DNA Deoxyribonucleic
Acid Phosphate,
Deoxyribose sugar, Nitrogen Base
Double sided Helical Structure Found in nucleus
RNA Ribonucleic Acid
Phosphate, Ribose sugar, Nitrogen Base
Single sided Can be various
places in the cell depending on type
Figure 4-1
Nucleotide
Sugars
Nitrogen-containing bases
Phosphate group
5-carbon sugar
Nitrogenous base
Ribose Deoxyribose
Cytosine (C) Uracil (U)Pyrimidines
Thymine (T)
Guanine (G) Adenine (A)Purines
Only in RNA Only in DNA
Figure 4-2
Phosphodiester linkage
Condensation reaction
Figure 4-3 The sugar-phosphatespine of RNA
The sequence of bases found in an RNA strandis written in the 5´ 3´direction
Nitrogenousbases
3´ and 5´ carbonsjoined byphosphodiesterlinkage
Unlinked 3´ carbon:New nucleotidesare added here
Figure 4-6bHydrogen bonds form between G-C pairs and A-T pairs.
Guanine Cytosine
ThymineAdenine
Su
gar
-ph
osp
hat
e b
ackb
on
e
Hydrogen bonds
DNA contains thymine,whereas RNA contains uracil
5
53
3
Majorgroove
Minorgroove
Length of onecompleteturn of helix(10 rungs perturn) 3.4 nm
Distancebetweenbases 0.34nm
Width of thehelix 2.0 nm