Unit 1 AP Exam Review

Water and Biological Macromolecules

Hydrogen Bonds

Water and DNA

The intermolecular attraction between a highly electronegative molecule and a hydrogen molecule attached to a highly electronegative molecule (FON)

In water, hydrogen bonds are between oxygen and hydrogen atoms.

In DNA, hydrogen bonds between the nitrogenous bases on each strand.

• There are 2 bonds between A and T/U and 3 bonds between C and G.

7 Properties of Water

Cohesion is the attraction between water molecules. It is responsible for surface tension and water’s high heat capacity(requires lots of energy to change temperature, making it an important regulator for ).

Adhesion is the attraction between water molecules and other molecules.

Capillary Action, which allows water to move up plant roots, is possible because of cohesion and adhesion.

Water molecules are polar, meaning they have slightly negative oxygen atoms and slightly positive hydrogen atoms, allowing for hydrogen bonds. Polarity makes water a universal solvent because it can dissolve a wide variety of substances.

4 Macromolecules: Monomers and Function

Carbohydrates: CHO(Carbon, Hydrogen, Oxygen)

• Monomer: Monosaccharide

• Short term energy storage, part of the cell membrane, contains elements for building macromolecules

Lipids: CHOP(Phosphorus)

• Monomer: Glycerol and fatty acids

• Long term energy storage, insulation, part of the cell membrane

Proteins: CHONS(Nitrogen, Sulfur)

• Monomer: Amino Acid

• Enzymatic function, structural support, transport, hormones

Nucleic Acids: CHONP

• Monomer: Nucleotides

• Storage for genetic information, directing protein synthesis, playing roles in cellular processes (cell signaling, energy transport)

Carbohydrate

Structure and Bonds

Simple sugars(CH_²O), hydroxyl

Carbohydrates are linked by glycosidic bonds, which are covalent bonds formed between the anomeric carbon of one monosaccharide and the hydroxyl group of another.

Protein

Structure and Bonds

In a protein, amino acid monomers are held together by covalent peptide bonds between the amino group of one monomer and the carboxylic acid group of the adjacent monomer.

Central carbon connected to a hydrogen atom, a carboxyl group(COOH), an amino group(NH_²), and an R group which determines the folding of the protein, its chemical properties, and its shape and function based on polarity and/or charge.

The two ends of a protein, or polypeptide chain, are called the N-terminus (amino terminus) with the free amino group and the C-terminus (carboxyl terminus) with free carboxyl group. The C-terminus is the location of the growing polypeptide strand.

Amino Acids: R Groups

Charged, Polar, Nonpolar

Polar R groups are hydrophilic and tend to appear on the surface of proteins. They contain highly electronegative atoms like nitrogen and oxygen.

• Charged Polar groups have full positive or negative charges making them highly hydrophilic and affecting their interactions with other molecules.

• Uncharged Polar R groups have only partial charges. In a diagram, they do not have a plus or minus charge.

Nonpolar R groups are hydrophobic and tend to cluster in the center of a protein.

Protein Folding

Primary, Secondary, Tertiary, Quaternary

Primary Level: A linear sequence of amino-acids held together by peptide bonds

Secondary Level: Hydrogen bonds fold the chains into alpha-helices and beta-sheets

Tertiary Level: Polar bonds and ionic bonds fold the helices and sheets into a 3-D structure, at which point the protein is usually functional

Quaternary Level: Hydrogen bonds and Van Der Waal forces bring multiple polypeptide units together

Nucleic Acid

Structure and Bonds

5-carbon sugar(pentose), nitrogenous base(AUTCG), phosphate group

A polymer has a sugar-phosphate backbone, nucleotide monomers, one 5’ end with a phosphate and one 3’ end with a hydroxyl group. The 3’ end is the location of the growing nucleic acid strand.

A phosphodiester bond forms the sugar-phosphate backbone of DNA and RNA by connecting the 3’ hydroxyl of one nucleotide to the 5' phosphate group of the next.

3 Different Types of Lipids

Structure

Steroids(cholesterol): 4 fused carbon rings

Triglycerides(fats and oils): Glycerol backbone with three fatty acids attached

• The primary form of fat storage in the body

Phospholipids: A phosphate group, a glycerol membrane, fatty acids

• A major component of cell membranes, acting as emulsifiers

Saturated and Unsaturated Lipids

The degree of saturation in lipids significantly impacts their function. Saturated lipids pack tightly and form solid structures while unsaturated lipids, containing double bonds, lead to more fluid and flexible structures. Saturated lipids are solid at room temperature while unsaturated lipids are liquid.

Dehydration Synthesis

Combines two molecules into one molecule, producing water as a byproduct

Ex. Glucose + Fructose = Sucrose +H₂O

Hydrolysis

Breaks a molecule into two molecules by using a water molecule

Ex. ATP + Water = ADP + Inorganic Phosphate

Starch vs Cellulose

Starch contains alpha-glycosidic bonds, which can be broken down by animals, while cellulose contains beta-glycosidic bonds, which cannot be broken down by animals.

Both are polysaccharides(carbohydrates).

DNA vs RNA

4 Differences, 1 Similarity

DNA uses the pentose sugar deoxyribose while RNA uses the pentose sugar ribose.

DNA uses the nitrogenous base thymine while RNA uses the nitrogenous base uracil.

DNA is traditionally double-stranded while RNA is single-stranded.

Both are synthesized in a 5’ to 3’ direction but DNA is read in the 3’ to 5’ while RNA is read in the 5’ to 3’ direction.

Substitution of a Nonpolar R Group with a Polar R Group in a Protein

Significantly alters a protein's structure during folding.

The polar R group gravitates towards the exterior of the protein, causing a structural shift and thus changing the protein’s function.

Substitution of a Cytosine with a Thymine in DNA

A transitional mutation where one pyrimidine is replaced with another, potentially resulting in a missense, nonsense or silent mutation

• Missense mutation: The altered codon codes for a different amino acid, changing the protein's structure and function.

• Nonsense mutation: The altered codon becomes a stop codon, prematurely ending protein synthesis and creating a truncated, non-functional protein.

• Silent mutation: The amino acid sequence is unchanged due to redundancy in the genetic code, resulting in no functional change.

Substitution of a Cytosine with a Guanine in DNA

Results in the pairing of two purines, which is biochemically unstable, as well as potentially changing protein structure and function

Substitution of a Deoxyribose with a Ribose in a Nucleic Acid

Alters stability and reactivity, with ribose making RNA more reactive and less stable than DNA

Rosalind Franklin’s X-Ray

Shows that DNA has a double-helix structure