Basic Biochemistry Water, Carbon, and Functional Groups

Water Abundance of water makes Earth habitable Abundance of water makes Earth habitable Unique properties Unique properties

Water Molecules Polar due to differences in electronegativity Polar due to differences in electronegativity Hydrogen bonds form Hydrogen bonds form

Properties of Water Cohesion Cohesion Adhesion Adhesion Surface tension Surface tension

Properties of Water (What is temperature?) (What is temperature?) High specific heat High specific heat Evaporative cooling Evaporative cooling Good solvent Good solvent

Interactions with Water Hydrophilic vs. hydrophobic Hydrophilic vs. hydrophobic

Carbon Can bond to 4 other atoms Can bond to 4 other atoms Carbon chains can be long, be branched, or be circular Carbon chains can be long, be branched, or be circular Hydrocarbon chains Hydrocarbon chains

Functional Groups Most commonly involved in reactions Most commonly involved in reactions Types: Types: Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate Chart pg Chart pg

ATP Adenosine triphosphate used for energy transfer Adenosine triphosphate used for energy transfer ADP + P i ↔ ATP ADP + P i ↔ ATP

Macromolecules

Review What are the four essential macromolecules in the cell? What are the four essential macromolecules in the cell? What are their structures? What are their structures? What are their functions? What are their functions?

Macromolecules Can be 10,000s of atoms Can be 10,000s of atoms Polymers: linked chain of monomers Polymers: linked chain of monomers Variation in sequence is major difference Variation in sequence is major difference

Dehydration Synthesis Removal of water to link two monomers Removal of water to link two monomers Requires energy and help of enzymes Requires energy and help of enzymes Hydrolysis breaks bonds (ex. Digestion) Hydrolysis breaks bonds (ex. Digestion)

Carbohydrates Sugars and their polymers Sugars and their polymers Mono-, di-, and polysaccharides Mono-, di-, and polysaccharides Monosaccharides (-ose) can have three-seven carbons Monosaccharides (-ose) can have three-seven carbons Chain or ring forms Chain or ring forms

Carbohydrates Glucose (C 6 H 12 O 6 ) and Sucrose (C 12 H 22 O 11 ) are most common Glucose (C 6 H 12 O 6 ) and Sucrose (C 12 H 22 O 11 ) are most common Polysaccharide uses: storage or structure Polysaccharide uses: storage or structure

Carbohydrates Starch = helical polymer of glucose (in plants) Starch = helical polymer of glucose (in plants) Glycogen = more branched; stored in liver/muscle cells Glycogen = more branched; stored in liver/muscle cells Cellulose = most abundant organic compound Cellulose = most abundant organic compound Never branched. Hydrogen bonding to nearby cellulose molecules. Microfibrils are structurally strong. Never branched. Hydrogen bonding to nearby cellulose molecules. Microfibrils are structurally strong. Chitin = fungi structures; exoskeletons Chitin = fungi structures; exoskeletons

Lipids Fats, steroids, phospholipids Fats, steroids, phospholipids Hydrophobic Hydrophobic Fats = glycerol (3-C alcohol) and 3 fatty acids (hydrocarbons) Fats = glycerol (3-C alcohol) and 3 fatty acids (hydrocarbons) Saturated vs. unsaturated Saturated vs. unsaturated Primarily energy storage Primarily energy storage

Lipids Phospholipids = glycerol + 2 fatty acids + phosphate Phospholipids = glycerol + 2 fatty acids + phosphate Partially hydrophilic, partially hydrophobic Partially hydrophilic, partially hydrophobic Lipid bilayer membranes Lipid bilayer membranes

Lipids Steroids = four fused rings Steroids = four fused rings Cholesterol, many hormones Cholesterol, many hormones

Proteins Most structurally complex See chart pg. 78 for types Enzymes catalyze reactions 20 different amino acids combine to create a polypeptide

Proteins Amino acids linked through peptide bonds in unique sequence Amino acids linked through peptide bonds in unique sequence Proteins consist of multiple polypeptides Proteins consist of multiple polypeptides Function relies on proteins recognizing/bonding to other molecules Function relies on proteins recognizing/bonding to other molecules

Protein Structure PRIMARY: amino acid sequence SECONDARY: α helix or β pleated sheet due to hydrogen bonding of C- N backbone

Protein Structure TERTIARY: interactions between ‘R’ groups (ionic, hydrogen bonds, hydrophilic/phobic) TERTIARY: interactions between ‘R’ groups (ionic, hydrogen bonds, hydrophilic/phobic) QUATERNARY: multiple polypeptide chains overlapping QUATERNARY: multiple polypeptide chains overlapping Denaturing… Denaturing…

Nucleic Acids DNA/RNA Direct protein synthesis Nucleotides  polynucleotides Pyrimidines (T, U, G) vs. purines (C, A)

Nucleic Acids Antiparallel double helix Antiparallel double helix 5’: phosphate 5’: phosphate 3’: C-OH 3’: C-OH Replication, transcription, translation Replication, transcription, translation

Phosphodiester Bond

Overview Higher levels of organization result in new, more complex properties. The structure of each macromolecule relates specifically to its function.

Self-Quiz, Chapter 5 Macromolecules

1 Which term includes all others in the list? Which term includes all others in the list? 1. Monosaccharide 2. Disaccharide 3. Starch 4. Carbohydrate 5. Polysaccharide

2 Which of the following statements concerning unsaturated fats is true? Which of the following statements concerning unsaturated fats is true? 1. They are more common in animals than plants. 2. They have double bonds I the carbon chains of their fatty acids 3. They generally solidify at room temperature. 4. They contain more hydrogen than saturated fats having the same number of carbon atoms. 5. They have fewer fatty acid molecules per fat molecule.

3 The structural level of a protein least affected by a disruption in hydrogen bonding is the The structural level of a protein least affected by a disruption in hydrogen bonding is the 1. Primary level. 2. Secondary level. 3. Tertiary level. 4. Quaternary level. 5. All structural levels are equally affected.

4 Which of the following pairs of base sequences could form a short stretch of a normal helix DNA? Which of the following pairs of base sequences could form a short stretch of a normal helix DNA? 1. 5’-purine-pyrimidine-purine- pyrimidine-3’ with 5’-purine- pyrimidine-purine-pyrimidine- 5’ 2. 5’-A-G-C-T-3’ with 5’-T-C-G- A-3’ 3. 5’-G-C-G-C-3’ with 5’-T-A-T- A-3’ 4. 5’-A-T-G-C-3’ with 5’-G-C-A- T-3’ 5. 1, 2, and 4 are all correct.

5 Enzymes that break down DNA catalyze the hydrolysis of the covalent bonds that join nucleotides together. What would happen to DNA molecules treated with these enzymes? Enzymes that break down DNA catalyze the hydrolysis of the covalent bonds that join nucleotides together. What would happen to DNA molecules treated with these enzymes? 1. The two strands of DNA would separate. 2. The phosphodiester bonds between deoxyribose sugars would be broken. 3. The purines would be separated from the deoxyribose sugars. 4. The pyrimidines would be separated from the deoxyribose sugar. 5. All bases would be separated from the deoxyribose sugars.

6 Which of the following is not a protein? Which of the following is not a protein? 1. Hemoglobin 2. Cholesterol 3. An antibody 4. An enzyme 5. insulin

7 Which of the following statements about the 5’ end of a polynucleotide strand is correct? Which of the following statements about the 5’ end of a polynucleotide strand is correct? 1. The 5’ end had a hydroxyl group. 2. The 5’ end has a phosphate group. 3. The 5’ end is identical to the 3’ end. 4. The 5’ end is antiparallel to the 3’ end. 5. The 5’ end is in the fifth position on one of the nitrogenous bases.