AP BIO 1.6 - 1.7

Nucleic acids

• constitute the genetic material of living organisms

• DNA and RNA

• store and transmit genetic information, regulatory functions

• No Sulfur

• Covalent bonds, called phosphodiester bonds, are formed between the 3’ Carbon of the terminal sugar and the phosphate group of the nucleotide

Nucleotides

• monomers for nucleic acids

• consists of: phosphate, nitrogen base, sugar (ribose or deoxyribose)

• joined by condensation synthesis

Nitrogen bases

1. Thymine = Adenine (ONLY DNA)

2. Uracil = Adenine (ONLY RNA)

3. Guanine ≡ Cytosine

Purines (2 rings): Adenine and Guanina

Pyramadines (1 ring): Thymine Cytosine Uracil

DNA

• deoxyribose nucelic acid

• has deoxyribose

• sugar lost the O in the prime carbon

• the bases are joined via hydrogen bonds

• one strand runs 5′ to 3′ 

• the other 3′ to 5′

RNA

• ribose nucleic acid

• has ribose

• sugar has not lost the O

• usually single-stranded, but may be folded into 3-D structures via H-Bonds

Nucleic acid structure

• The sugar and phosphate lie on outside of helix

• Nitrogenous bases are stacked in the interior

• The strands of the helix run in opposite directions (antiparralel orientation)

• Each base from one strand interacts via hydrogen bonding with a base from the opposing strand

proteins

Major functions of proteins:

• Enzymes—catalytic proteins 

• Defensive proteins (e.g., antibodies) 

• Hormonal and regulatory proteins—control physiological processes

• Receptor proteins—receive and respond to molecular signals 

• Storage proteins store amino acids

• Structural proteins—physical stability and movement

• Transport proteins carry substances (e.g., hemoglobin) 

• Genetic regulatory proteins regulate when, how, and to what extent a gene is expressed

Amino Acids

• monomes that makes porteins

• tRNA grabs amino acids to create proteins

• Amino group on the left connected to an alpha carbon atom that is connected to carboxyl group on the right and a H atom above the carbon

How are amino acids linked?

• via peptide bond/linkage, a dehydration synthesis reaction

• Carboxyl group of one amino acid is linked to the amino group of the incoming amino acid

• A molecule of water is released as part of the reaction

polypeptide

a chain of amino acids joined together by peptide linkages

primary protein structure

• sequence of amino acids in a polypeptide

• Determined by the message encoded in the nucleotide sequence in DNA.

secondary protein structure

• polar amino acids create H Bonds, resulting in repeated spatial patterns in different regions

• form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone

  • alpha helix: right-handed coil

  • pleated sheet

• interaction of peptide backbone

Tertiary

• side chain interactions

• polypeptide chain is bent and folded

• 3D shape

• outer groups are functional groups that can interact

• single polypeptide is formed

quaternary protein structure interations

• Disulfide bridges hold a folded polypeptide together

• Hydrogen bonds stabilize folds 

• Hydrophobic side chains can aggregate

• van der Waals interactions between hydrophobic side chains

• Ionic interactions form salt bridges 

quaternary protein structure

• Two or more polypeptide chains (subunits) bind together by hydrophobic and ionic interactions, and hydrogen bonds.

• involves more than 1 polypeptide

Denaturation

• destroying secondary and tertiary structure by disrupting weaker interactions

• caused by

  • High temperature 

  • Change in pH

  • Change in solvent – polar to nonpolar or nonpolar to polar

Enzymes

catalysts in biochemical reactions

• No catalyst makes a reaction occur that cannot otherwise occur

• The enzyme is not changed at the end of the reaction.

3 types of enzymes

• Catabolic – breakdown substrates

• Anabolic – build more complex molecules

• Catalytic – affects the rate of reaction

Enzyme effect on activation energy

substrates

• Reactants are substrates: they bind to a specific site on the enzyme—the active site.

• The enzyme–substrate complex (ES) is held together by hydrogen bonding, electrical attraction, or temporary covalent bonding.

Enzyme mechanisms

1. Inducing strain: causing stress and an increase in potential energy within a molecule, material, or biological tissue, often to create a more reactive or useful state, or to study its properties

ions and other molecules required for some enzyme ot function

• Cofactors—inorganic ions 

• Coenzymes add or remove chemical groups from the substrate. They can participate in many different reactions.

• Prosthetic groups (non-amino acid groups) permanently bound to their enzymes. 

Enzyme effect on rate of reaction

enzyme and homeostasis

Controlling the action of enzymes is an important in metabolic pathways and in homeostasis