BIOL 200 Lectures 1-3 (Intro stuff)

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Amino Acid Structure

Amine (N) Terminus, Carboxylic (C) Terminus, with defining R sidechain.

How are amino acids formed?

C terminus of one bonds to N terminus of another, creating a peptide bond (polymerization).

How many amino acids are there? How many are essential?

20 of them. 9 cannot be made by the body (essential).

Hydrophobic amino acid characteristics

• Hydrocarbon chains

• Aromatic rings

• Nonpolar

Hydrophillic amino acid characteristics

• either charged, or polar and uncharged

Special amino acids and their characteristics

1.) Cysteine - contains SH side group that can form disulfide bonds. plays a role in enzyme catalysis

2.) Proline - ring structure that creates a kink in polypeptide chain

3.) Glycine - smallest amino acid (side chain is just H)

What are nucleotides? Describe their structure.

• Monomers of DNA and RNA

• Made of pentose (5 Carbon sugar), negatively charged phosphate group and nitrogeneous base.

What makes Nucleotides polar?

Negatively charged phosphate group.

Different between ribose and deoxyribose?

deoxyribose is missing an oxygen on the second carbon.

Uracil

Pyrimidine used instead of thymine in RNA.

What connects nucleotides?

• 5’ carbon bonds to to phosphate before

• 3’ carbon on sugar has another OH group, bonding to the following phosphate.

• Called a phosphodiester bond (think P-O-C followed by C-O-P)

Why is RNA prone to breaking?

Added hydroxyl at 2’ C spontaneously reacts with phosphate group, breaking DNA.

Why is DNA the genetic material over RNA?

Missing OH group on 2’ C prevents spontaneous reaction with phosphate group.

Describe double helix DNA structure (left or right-handed helix, how far apart bases are, how often turns are made).

• Right handed double helix

• Bases spaced 0.34nm apart

• Turn completed every 3.4-3.6nm (every 10ish bases)

• Forms major and minor grooves

Major groove of DNA

Bigger, where most protein interaction occurs.

Minor groove of DNA

Smaller, cannot distinguish all bases (less interaction)

Amino evidence of common ancestry

• Shared use of amino acids and nucleotides across organisms

• Shared use of codons across all organisms

• Only L amino acid stereoisomers form proteins

• Catalytic site sequence of rRNA very similar across organisms

Primary structure of proteins

Linear, directional polypeptide chains (N to C terminus)

Daltons

Unit of measurement for polypeptide chains (1Da = 1 atomic mass unit)

Secondary structure

• local conformations of peptoide chain backbone that generate stability

• 2 major conformations based on hydrogen bonding between backbone amides: alpha-helices and beta-sheets.

Alpha helices

• periodic secondary structure, with 3.6 amino acids per turn

• Properties depend on side chains

• Do NOT have proline

Beta pleated sheets

• Short segments of 5-8 amino acids

• Hydrogen bonds form between two adjacent strands

• Can run parallel or antiparallel.

Motifs

• Combination of secondary structures that form distinct 3D structures

• Have specific functions, such as alpha helix coiled coil which is in fibrous proteins and transcription factors.

Alipathic residues

• Hydrophobic amino acid side chains that consist of linear or branched hydrocarbon structures.

• Buried between helices motifs (hydrophobic interactions)

PET synthesis

• most common type of polyester

• contains ester group and aromatic ring

• Input heat energy

• Introduce molecule that gets rid of byproducts