Macromolecules I Quiz: Proteins & Nucleic Acids

Macromolecules I

• Proteins and nucleic acids are macromolecules.
• The structure of proteins and nucleic acids are discussed.
• The monomeric components of proteins and nucleic acids are examined.
• The synthesis of polymers (proteins and nucleic acids) is described.
• The properties and functions of polymers (proteins and nucleic acids) are explored.

Assumptions Regarding Chemistry

• Basic information regarding atomic structure is assumed.
• Chemical bonds, common bond types, and polarity are considered.
• The chemical nature of common functional groups is understood.

The Macromolecules of the Cell

• Amino acids (20 types) are monomers of proteins, found in cells at a concentration of 20.
• Aromatic bases (5 types) form components of nucleic acids, present in cells at a concentration of 5, including adenine, cytosine, guanine, and thymine.
• Sugars (variable quantities) are components of RNA (ribose) and DNA (deoxyribose), and energy sources such as glucose. Cellular quantities of sugars vary.
• Lipids (variable quantities) include fatty acids, cholesterol, and components of phospholipids. Cellular lipid amounts vary.
• Most biological macromolecules are created from about 30 common small biological molecules.

Diversity of Protein Function

• Enzymes speed up chemical reactions.
• Structural proteins provide support.
• Motility proteins enable movement.
• Regulatory proteins control cell function.
• Transport proteins move substances.
• Signaling proteins allow communication between cells.
• Receptor proteins enable response to stimuli.
• Defensive proteins protect against disease.
• Storage proteins hold amino acids.

All Proteins Are Polymers with Common Structural Characteristics

• Only 20 amino acids are used in protein synthesis.
• No two different proteins have the same amino acid sequence.
• Every amino acid has the same basic structure.

L-Amino Acid vs. D-Amino Acid

• Amino acids have distinct L and D forms.
• Glycine is the only non-polar amino acid with no separate L and D isomers.

Amino Acids

• (Detailed structural representations and group categorization [group A, B, C] for different amino acids are included.)

The Polymers Are Polypeptides and Proteins

• Amino acids link to form linear polymers via dehydration/condensation reactions, creating peptide bonds.

Which of these represents an important distinction between a polypeptide and a protein?

• "Protein" implies function, "polypeptide" is a structural term.

Monomeric and Multimeric Proteins

• Monomeric proteins have a single polypeptide chain.
• Multimeric proteins are composed of two or more polypeptides.
• Dimers and trimers represent proteins with 2 and 3 polypeptide chains respectively.
• Hemoglobin is a tetramer (2α and 2β subunits).

Several Kinds of Bonds and Interactions Are Important in Protein Folding and Stability

• Covalent and noncovalent interactions are essential for protein shape (conformation).
• These same bonds are involved in multimeric protein formation.
• Interactions involve amino acid groups (e.g., carboxyl, amino, R groups).

Levels of Organization of Protein Structure

• Primary structure: Amino acid sequence.
• Secondary structure: Local folding (α-helix, β-sheet, random coil).
• Tertiary structure: Three-dimensional folding of a polypeptide.
• Quaternary structure: Association of multiple polypeptides.

The Importance of Primary Structure

• The primary structure is genetically determined by the order of nucleotides in messenger RNA.
• The primary structure is read from the N-terminus to the C-terminus.
• The order and identity of amino acids influence higher-order structure.

Secondary Structure

• Secondary structure results from hydrogen bonding between the polypeptide backbone's NH and CO groups.
• Common patterns are the α-helix and the β-sheet.

The α Helix

• The α-helix is a spiral shape.
• Hydrogen bonds stabilize the helical structure.
• R groups protrude from the helix.

The β Sheet

• The β-sheet is a flat, extended structure.
• Hydrogen bonds stabilize the β-sheet.
• β-sheets can be parallel or antiparallel.

Common Secondary Motifs

• β-α-β motif, hairpin loop motif, helix-turn-helix motif

Proline

• Proline is a "helix breaker".
• It lacks a hydrogen atom, disrupting hydrogen bonding in α-helices.

Tertiary Structure

• The tertiary structure is determined by interactions of R groups.
• Hydrophobic and hydrophilic interactions, ionic bonds, disulfide bonds, and van der Waals forces influence tertiary shape.

Several Kinds of Bonds and Interactions Are Important in Tertiary Protein Structure

• Bonds and interactions for tertiary structure include disulfide bonds, hydrogen bonds, ionic bonds and van der Waals forces and hydrophobic nature of some amino acid.

Fibrous Proteins

• Fibrous proteins have extensive secondary structures, resulting in a highly ordered, repetitive structure.
• Fibroin (protein in silk) is predominantly made of β-sheets.
• Keratin (protein in hair) is composed of many α-helices.

Globular Proteins

• Most proteins are globular.
• Compact structures with unique tertiary structures.
• Most enzymes are globular proteins.

Quaternary Structure

• The quaternary structure is the interaction and assembly of subunits.
• Multimeric proteins have more than one polypeptide chain.
• Types of subunits and bonds involved are similar to those influencing tertiary structure.

Nucleic Acids

• Nucleic acids are crucial for storing, transmitting, and expressing genetic information.
• They are polymers of nucleotides.
• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are two key types.

Nucleic Acid Components

• Nucleotides include a phosphate group, a 5-carbon sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base (purine or pyrimidine).
• Purines (adenine and guanine) and Pyrimidines (cytosine, thymine, uracil).

Nomenclature

• Nucleotides with one or more phosphate groups are nucleoside monophosphates (e.g., AMP).
• Examples of nucleotides with more phosphates are ADP and ATP.

Table 3-4 The Bases, Nucleosides, and Nucleotides of RNA and DNA

• A table listing bases, nucleosides, and nucleotides for RNA and DNA.

The Polymers Are DNA and RNA

• Nucleic acids are linear polymers linked by phosphodiester bridges (3', 5').
• The polynucleotide has directionality (5' phosphate to 3' hydroxyl).
• Nucleotide sequences are written in the 5' to 3' direction.

Nucleic Acid Synthesis

• A template molecule is crucial for precisely adding nucleotides.
• Complementary base pairing dictates the order of incoming nucleotides. (A-T/U, G-C)

Complementary Relationships Between Purines and Pyrimidines

• Complementary base pairs (A-T/U, G-C) form hydrogen bonds.
• These interactions stabilize the structure of nucleic acids.

Complementary Base Pairing

• A-T (or U) and G-C are the complementary base pairs in molecular biology.
• DNA has a double-helix structure.
• RNA can form secondary structures.

The DNA Molecule Is a Double-Stranded Helix

• The DNA molecule is a double-stranded helix.
• Hydrogen bonding between bases stabilizes the double helix.
• Components and structure of the double helix are displayed.

Base Pairing and RNA

• RNA is typically single-stranded.
• Base pairing influences RNA structure, although less extensive than in DNA. It occurs between regions of the same molecule.