1.4.2 Proteins & Nucleic Acids

Protein

M: amino acids
P: polypeptide
B: peptide bond
E: CHON (S)

• “protein” refers to the final functional structure & may be composed of multiple polypeptides (subunits)

Protein function

• structure

• transport

• enzymes

• communication

• storage

• movement

• defense

Amino Acids

• Carboxyl Group

• Amino Group

  • carboxyl + amino = peptide bond

• Variable R-group

  • determines the 20(21) amino acids

  • aka “side chains”

• α-Carbon

Amino Acid Groups

1. Positively Charged (Basic) Group

2. Negatively Charged (Acidic) Group

3. Uncharged Polar Group

4. Uncharged Nonpolar Group

   a. Aliphatic (linear)

   b. Aromatic (ring)

(only uncharged nonpolar grp has aliphatic/aromatic AAs)

Protein Mutation

• switching amino acids within groups

  • likely benign

• switching amino acids between groups

  • likely pathogenic

  • changes protein’s properties & can affect the protein’s structure and therefore its function

Cysteine

• sulfhydryl group

• can form covalent bonds w/ another cysteine

  • Disulfide Bonds

only protein with a sulfhydryl group

Protein Structure

Primary, Secondary, Tertiary, Quaternary

Primary Structure

• order of amino acids in a polypeptide

  • N-terminal (amino end)

  • C-terminal (carboxyl end)

• linked by peptide bonds

Secondary Structure

• local folding in regions of the polypeptide

• α-helix and β-pleated sheet

• Held tgt by hydrogen bonds b/w carbonyl & amino groups

No R-groups are bonded yet

Tertiary Structure

• the unique three-dimensional structure of a polypeptide

  • determined mostly by interactions of R-groups

Bonds

1. Covalent Disulfide Bonds

2. Ionic Bonds

3. Hydrogen Bonds

4. Van Der Waals Forces

Tertiary Structure Bonds

always between R-groups

1. Covalent Disulfide Bonds

   • b/w 2 Cysteine

2. Ionic

   • b/w pos. & neg. charged R group

3. Hydrogen Bonds

   • b/w the uncharged polar R groups

4. Van Der Waals Forces (hydrophobic interactions)

   • b/w the uncharged nonpolar R groups

Van Der Waals Forces

(hydrophobic interactions)

b/w the uncharged nonpolar R groups

tertiary structure bond

Covalent Disulfide Bonds

between 2 cysteine

tertiary structure bond

Ionic Bonds

between pos. & neg. charged R groups

tertiary structure bond

Hydrogen Bonds

between uncharged polar R groups

tertiary structure bond

BPQ Cysteine and Serine switching is pathogenic b/c…

Only cysteines can form disulfide bonds, so turning into a serine loses that bond b/w two cysteines

Quaternary Structure

• Formed from the combination of multiple polypeptides (subunits)

• same bonds as in tertiary structure

BPQ Guess the Amino Acid

Left - is nonpolar & hydrophobic b/c it’s in the cell membrance (???)
Right - the inside amino acid is hydrophobic and the outside amino acid is hydrophilic

Nucleic Acids

M: nucleotides

P: DNA & RNA

• Deoxyribonucleic Acid

• Ribonucleic Acid

B: Phosphodiester Bond

E: CHONP

• only macromolecule with both N & P

Nucleic Acid Function

• Information

• Protein Synthesis

• Regulation

• Energy

• Structure

Nucleotide

1. Nitrogen Base

   • Pyrimidines

     • Cytosine

     • Thymine

     • Uracil

   • Purine

     • Adenine

     • Guanine

2. 5 Carbon Sugar

   • Ribose

   • Deoxyribose

3. Phosphate Group

   • 1-3 (polymers have 1)

Pyrimidines

• Single Ring

• Cytosine, Thymine (DNA)

• Uracil (RNA)

Purines

• Double Ring

• Adenine, Guanine (DNA/RNA)

Nitrogen Base Bonding

Purines can form hydrogen bonds to Pyrimidines

C-G → 3 H-bonds

A-T,U → 2 H-bonds

Cytosine - Guanine bond

3 H-bonds

Adenine - Thymine/Uracil bond

2 H-bonds

Nucleoside

• Nitrogen Base + Sugar (ribose or deoxyribose)

Nucleoside ; sugar

Nucleotide

• Nitrogen base + Sugar + Phosphate Group (1-3)

Numbering the Sugar Carbons

Count clockwise from the oxygen

Polymer Structure (DNA)

Outside: Phosphate Backbone

Inside: Complementary Nitrogen Bases

• double helix

• Each strand has 5’ and 3’ end

  • run in opposite directions

  • new nucleotides are added to 3’ end

  • created in 5’→3’ direction

DNA is created in which direction?

5’→3’

new nuceotides added to 3’ end

DNA vs. RNA (Eukaryotes)

Function

• DNA carries genetic info

• RNA is involved in protein synthesis

DNA vs. RNA (Eukaryotes)

Location

• DNA: stays in nucleus

• RNA: leaves nucleus

DNA vs. RNA (Eukaryotes)

Structure

• DNA: double helix

• RNA: usually single-stranded

DNA vs. RNA (Eukaryotes)

Stability

• DNA more stable than RNA

DNA vs. RNA (Eukaryotes)

Sugar

• Deoxyribose vs. Ribose

DNA vs. RNA (Eukaryotes)

Pyrimidines

• DNA: C, T

• RNA: C, Uracil

DNA vs. RNA (Eukaryotes)

Purines

• both A, G

Central Dogma of Genetics

• DNA → mRNA → Protein

Transcription: DNA → mRNA

Translation: mRNA → protein

Transcription

DNA → mRNA

Translation

mRNA → Protein

ATP

Adenosine Triphosphate

• universal energy storage molecule