Ch3 Proteins + Ch4 Nucleic Acids

Lecture #3 (Finish)

Proteins (Chapter 3)

Carbon-based Chemistry in Aqueous Solution

• Four Classes of Carbon Compounds Found in Cells:

  • Proteins

  • Nucleic Acids (DNA & RNA)

  • Carbohydrates

  • Lipids

Monomers and Polymers

• Condensation Reaction:

  • Definition: Monomer in, water out.

  • Example: Linking of monomers to form polymers.

• Many mid-sized molecules such as:

  • Amino acids,

  • Nucleotides,

  • Simple sugars

  • These individual units are called monomers.

• Polymerization: Monomers link together to form polymers, such as:

  • Proteins

  • Nucleic acids

  • Polysaccharides

• Macromolecules: Very large polymers made up of many linked monomers.

Proteins: Polymers of Amino Acids

• Proteins are made from 20 amino acid building blocks.

• Structure of Amino Acids:

  • Central carbon atom bonds to:

  • H (Hydrogen)

  • NH2 (Amino group)

  • COOH (Carboxyl group)

  • A variable side chain denoted as R-group.

• At pH 7 in water:

  • Amino group ionizes to NH3+.

  • Carboxyl group ionizes to COO–.

Example Amino Acids:

• Glycine (G): Gly

• Alanine (A): Ala

• Valine (V): Val

• Leucine (L): Leu

• Isoleucine (I): Ile

• Methionine (M): Met

• Cysteine (C): Cys

• Phenylalanine (F): Phe

• Tryptophan (W): Trp

• Proline (P): Pro

  • Structure Types of Amino Acids:

  • Nonpolar Side Chains: No charged or electronegative atoms to form hydrogen bonds.

  • Polar Side Chains: Partial charges can form hydrogen bonds.

  • Charged Side Chains: Acidic and basic groups that can form ionic and hydrogen bonds.

The Peptide Bond

• Peptide Bond:

  • Definition: Bonds the carboxyl group of one amino acid to the amino group of another amino acid.

• Polypeptide: A chain of amino acids linked by peptide bonds.

• Protein: A polypeptide that contains more than 50 amino acids.

• The sharing of electrons in the peptide bond makes it behave similarly to a double bond.

Characteristics of Polypeptides

• Backbone: Consists of alternating amino and carboxyl groups.

• R-group Sequence: The specific order of side chains in the polypeptide.

• Directionality (Polarity):

  • N-terminus: Free amino group on the left end.

  • C-terminus: Free carboxyl group on the right end.

Describing a Protein

• Proteins can be described by four basic levels of structure:

  • Primary Structure: Unique sequence of amino acids.

  • Secondary Structure: Hydrogen bonds stabilize interactions between parts of the backbone.

  • Tertiary Structure: Overall three-dimensional shape formed due to R-group interactions.

  • Quaternary Structure: Structure formed from the interaction of multiple polypeptide subunits.

Primary Structure

• Definition: Unique sequence of amino acids in a polypeptide.

• Possible structures:

  • Limitless due to 20 types of amino acids available.

  • Length ranges from 50 amino acids to tens of thousands.

Secondary Structure

• Definition: Stabilized by hydrogen bonds between carbonyl group of one amino acid and amino group of another.

• Two common secondary structures:

  • α-helices

  • β-pleated sheets

Tertiary Structure

• Resultant from:

  • Interactions between R-groups or between R-groups and peptide backbone.

• Types of R-group interactions include:

  • Hydrogen bonds

  • Hydrophobic interactions

  • Covalent disulfide bonds

  • Ionic bonds

Quaternary Structure

• Definition: Involves multiple distinct polypeptide subunits that form a single functional structure.

• Example Proteins:

  • Cro protein: Dimer.

  • Hemoglobin: Tetramer (composed of four polypeptide subunits).

Summary Table of Protein Structure

Questions and Discussion Points

• 1. Polarity of a polypeptide chain vs. polarity of a chemical bond: How they differ?

• 2. Distinction between secondary and tertiary structures of proteins:

  • Shape?

  • Stabilized by what bonds?

  • Location of these bonds?

What Do Proteins Look Like?

• Importance of size, shape, and structure diversity:

  • Shapes include:

  • Fibrous: Provides structural support (example: Collagen)

  • Saddle-shaped: Binds to DNA (example: TATA box-binding protein)

  • Globular: Handles binding substrates (example: Trypsin)

Functions of Proteins

• Catalysis: Enzymes speed up chemical reactions.

• Defense: Antibodies and complement proteins attack pathogens.

• Movement: Motor and contractile proteins facilitate movement in cells.

• Signaling: Convey information within and between cells.

• Structure: Define cell shape and form body structures.

• Transport: Carry materials across membranes and control molecular movement into/out of cells.

Folding and Function: Denaturation

• Significance of shape on function: Proper folding necessary.

• Denaturation: Unfolded proteins lose normal function due to:

  • Incorrect temperature,

  • Wrong pH,

  • Other disruptive conditions.

• Example: Ribonuclease before/after denaturation.

Regulatory Mechanism in Folding and Function

• Shape determines function: Correct folding essential.

• Influences on folding: The presence of certain ions or conditions can regulate function.

Implications of Mutation on Protein Function

• Mutation in amino acid sequence can affect shape and function:

  • Example: Normal vs. sickled red blood cells due to mutations in hemoglobin.

Conceptual Questions for Further Consideration

• 1. How does a high fever interfere with protein function?

• 2. What role do hair straighteners play in protein denaturation?

  • Possible explanation: Disruption of specific bond types in α-keratin.

• 3. Drug impacting protein structure: Level of structure affected by covalent bond cleavage between cysteine residues.

Lecture #4

Nucleic Acids (Chapter 4)

Nucleotides and Nucleic Acids

• Nucleic Acids: Polymers formed from nucleotide monomers.

• Nucleotide Composition:

  • A phosphate group,

  • A five-carbon sugar (ribose for RNA and deoxyribose for DNA),

  • A nitrogen-containing base.

Types of Nucleotides

• Ribonucleotides:

  • Contain ribose, form RNA.

• Deoxyribonucleotides:

  • Contain deoxyribose, form DNA.

Nitrogenous Bases in Nucleotides

• There are two groups of nitrogenous bases:

  • Purines (Adenine, Guanine)

  • Pyrimidines (Cytosine, Thymine in DNA, Uracil in RNA)

  • Purines are larger than pyrimidines.

ATP as an Activated Nucleotide

• Example of biological energy currency:

  • Contains phosphates that increase potential energy of the monomer due to added phosphate groups.

Polymerization of Nucleotides

• Polymerization occurs through condensation reactions, catalyzed by enzymes.

• Phosphodiester Linkage: Bond formation between 5′ phosphate of one nucleotide and 3′ hydroxyl of another.

Sugar-Phosphate Backbone

• Directionality:

  • One end has an unlinked 5′ phosphate.

  • Another end has an unlinked 3′ hydroxyl.

• Nucleotide sequence written in 5′ to 3′ direction.

Watson and Crick Model of DNA

• Characteristics of DNA:

  • Two antiparallel strands,

  • Form a double helix.

  • Sugar-phosphate backbone faces outwards; nitrogenous bases face inwards.

• Complementary Base Pairing:

  • Purines always pair with pyrimidines (A-T, G-C).

Structure of DNA

• Base Pairing:

  • A-T pairs with 2 hydrogen bonds,

  • G-C pairs with 3 hydrogen bonds.

• Structural Measurements:

  • Base spacing: 0.34 nm

  • Helix width: 2.0 nm

  • Length of one turn: 3.4 nm (10 base pairs per turn).

DNA Replication Process

• Key Insight: Complementary base pairing allows for replication.

• Steps in DNA Replication:

  • Separation of the double helix.

  • Base pairing of deoxyribonucleotides to template strands.

  • Phosphodiester bond formation for new strands.

DNA and Biological Information

• DNA is key for storing biological information related to organism growth and reproduction.

• Central Dogma: Information flow from DNA to RNA to proteins, dictating phenotype based on genotype.

RNA Structure and Function

• RNA's primary structure consists of a sugar-phosphate backbone formed by phosphodiester linkages.

• Contains nitrogenous bases: A, C, G, and U.

• Differences from DNA:

  • Uracil replaces thymine.

  • Ribose sugar instead of deoxyribose.

• 2′-OH group on ribose makes RNA more reactive and less stable.

Secondary Structures of RNAs

• RNA can exhibit secondary structures such as hairpins, formed by folding back on itself:

  • Stem: Double-stranded region

  • Loop: Single-stranded region.

Tertiary Structures of RNAs

• RNAs can also display distinctive three-dimensional tertiary structures, enhancing their functional capabilities.

Summary Table of DNA and RNA Structures

Conceptual Questions

• 1. Polymers: Protein is a polymer of ___?

• 2. What is a nucleotide?: Sequence of deoxyribonucleotides can lead to variance in biological information?

• 3. Define Polarity: How is it indicated in both proteins and nucleic acids?

• 4. Inquiry into base pairing and nucleotide sequence relationships for DNA and RNA.