CELLBIO Macromolecules of the Cell

• Four Major Groups of Macromolecules

  1. Nucleic acid
  2. Carbohydrate
  3. Lipid
  4. Protein
• Level 1: Monomeric Units = nucleotides, amino acids, sugars

  Level 2: Macromolecules = DNA, protein, cellulose

  Level 3: Supramolecular Complexes = chromosome, plasma membrane, cell wall

  Level 4: The cell and its organelles
• Biomolecules

  • formed by joining many small units together to form a long chain (synthesis = water removed, hydrolysis = water added, breaks down)
  • several compounds required to continue to live
  • all are organic, contains carbon
  • forms strong covalent bonds
• Proteins

  • Class of extremely important and ubiquitous macromolecules in all organisms, occurring nearly everywhere in the cell.
  • Greek word proteios, meaning first place
• Classification of Proteins

  • Transport proteins = movement of other substances into, out of, and within the cell
  • Signaling proteins = communication between cells in an organism, hormonal
  • Receptor proteins = response to chemical stimuli
  • Defensive proteins = protection against disease
  • Storage proteins = reservoir of amino acids
• Classification of Proteins

  • Enzymes = catalysts that greatly increase the rates of the thousands of chemical reactions on which life depends
  • Structural proteins = physical support and shape to cells and organelles
  • Motility proteins = contraction and movement of cells and intracellular materials
  • Regulatory proteins = control and coordination of cellular functions
• Proteins are linear polymer of amino acids.

  • more than 60 different kinds of amino acids are typically present in a cell, but only 20 kinds are used in protein synthesis.
  • some proteins contain more than 20 different kinds of amino acids, but additional ones usually result from modifications that occur after the protein has been synthesized.
  • no two different proteins have the same amino acid sequence.
• The R group is different for each amino acid and gives each amino acid its distinctive properties. Except for glycine, all amino acids have four different groups attached to the alpha carbon
• All amino acids except glycine exist in two stereoisomeric forms that are mirror images of each other and cannot be superimposed. The two mirror images are called D- and L- amino acids.

  Only L- amino acids occur in proteins.
• Specific properties of various amino acids differ depending on the chemical nature of their R groups.
• From the 20 L- amino acids found in proteins:

  • Nine have nonpolar, hydrophobic R groups usually found in the interior or proteins when in aqueous environments.
  • The eleven remaining have hydrophilic R groups that are either distinctly polar or actually charged at the neutral pH values characteristic of cells which tend to occur on the surface of proteins in solution.
• The polymers are polypeptides and proteins.

  • process of stringing individual amino acids into a linear polymer involves the stepwise addition of each amino acid to the growing chain through a condensation/dehydration reaction.
  • the C-N bond linking two amino acids is known as the peptide bond.
  • N- (or amino) terminus = end of chain with amino acid
  • C- (or carboxyl) terminus = end of chain with carboxyl group
• • Protein synthesis = process of elongating a chain of amino acids
  • not entirely accurate because the immediate product of amino acid polymerization is not a protein but a polypeptide.
• • Protein = polypeptide chain with an attained unique, stable, three-dimensional shape and is biologically active.
  • final shape is due to the folding and coiling that occur spontaneously as the chain is being formed
  • monomeric protein = one polypepyide
  • multimeric protein = two or more polypeptides
  • In the case of multimeric proteins, protein synthesis involves not only the elongation and folding of the individual polypeptide subunits but also their subsequent interaction and assembly into the multimeric protein.
• A polypeptide is itself a polymer, the entire polypeptide is sometimes a monomeric unit of a multimeric protein.
• Several kinds of bonds and interactions are important in protein folding and stability.

  • The initial folding of a polypeptide into its proper shape, or conformation depends on several different kinds of bonds and interactions including covalent disulfide bond and several non covalent bonds and interactions.
  • Non covalent forces are diverse, numerous, and collectively exert a powerful influence on protein structure and stability.
  • hydrogen bonds, ionic bonds, van der Waals reactions, hydrophobic interactions.
• Non covalent bonds and interactions primarily involve R groups of the individual amino acid residues.
• The disruption of these interactions by heat, high salt, or chemical treatment can result in denaturation, or unfolding of the polypeptide.
• Usually, a protein is inactive in this denatured, unfolded state. Similarly, the folding polypeptides due to incorrect interactions can have serious biological effects. The presence of misfolded proteins in cells can cause human diseases such as Alzheimer's disease.
• Disulfide Bonds

  • A special type of covalent bond that helps stabilize protein conformation, forms between the sulfur atoms of two cysteine amino acid residues.
• Once formed, disulfide bonds confer considerable stability to the structure of the protein because of its covalent nature and can only be broken only by reducing it again.
• Disulfide bonds may be distant from each other along the polypeptide, but are brought close together by the folding process. Such intramolecular disulfide bonds stabilize the conformation of the polypeptide.

  
  

  In multimeric proteins, a disulfide bond may form between cysteine residues located in two different polypeptides. Such intermolecular disulfide bonds link the two polypeptides to one another covalently.
• Hydrogen bonds

  • formed between a covalently bonded hydrogen atom on one water molecule and an oxygen atom on another molecule.
• In hydrogen bonds:

  • the R groups of many amino acids have functional groups that are able to participate in hydrogen bonding.
  • this allows hydrogen bonds to form between amino acid residues that may be distant from one another along the amino acid sequence but are brought into close proximity by the folding of the polypeptide.
  • in polypeptides, hydrogen bonding is important in stabilizing helical and sheet structures.
• Hydrogen bond donors have a hydrogen atom that is covalently linked to a more electronegative atom.

  Hydrogen bond acceptors have an electronegative atom that attracts this hydrogen atom.
• The role of ionic bonds in protein structure:

  • Because of the opposite charges of the R groups of amino acids, polypeptide folding is dictated in part by the tendency of charged groups to repel groups with the same charge and to attract groups with the opposite charge.
  • Because ionic bonds depend on both groups remaining charged, they will be disrupted if the pH value becomes so high or so low that either loses their charge.
• Van der Waals Interactions

  • When two molecules that have dipoles are very close to each other and are oriented appropriately, they are attracted to each other.
  • Weak interaction but are important in the structure of proteins by binding two molecules together with complementary surfaces that fit closely together.
• Hydrophobic Interactions

  • Not a bond or interaction, but the tendency of hydrophobic molecules or parts of molecules to be excluded from interactions with water.
  • Polypeptide folding to form the final protein structure is, in part, a balance between the tendency of hydrophilic groups to seek an aqueous environment near the surface of the molecule and the tendency of hydrophobic groups to minimize contact with water by associating with each other in the interior of the molecule.
• Protein Structure

  1. Primary Structure = amino acid sequence ; covalent peptide bonds
  2. Secondary Structure = folding into alpha helix, beta sheet, or random coil ; hydrogen bonds between NH and CO groups of peptide bonds in the backbone
  3. Tertiary Structure = three-dimensional folding of a single polypeptide chain ; disulfide, hydrogen, ionic bonds, van der waals, and hydrophobic interactions
  4. Quaternary Structure = association of multiple polypeptides to form a multimeric protein ; disulfide, hydrogen, ionic bonds, van der waals, and hydrophobic interactions
• Primary Structure

  • formal designation for the amino acid sequence
  • specifying the order in which its amino acids appear from one end of the molecule to the other
  • first protein to have its complete amino acid sequence determined was the hormone insulin consists of two polypeptides called A subunit and B subunit
  • messenger RNA reflects DNA sequences in the gene that encodes the protein
  • primary structure of a protein is the result of the order of nucleotides in the DNA of the gene
• Secondary Structure

  • local regions of structure that result from hydrogen bonding between NH and CO groups along the polypeptide backbone
  • alpha helix and beta sheet conformations
• Alpha helix

  • spiral in shape backbone of amino acids linked by peptide bonds with specific R groups
  • 3.6 amino acids per turn
  • two or more alpha helices can coil together in a rope-like fashion to form a coiled coil
• Beta sheet

  • extended sheet-like conformation with successive atoms in polypeptide chain located at the "peaks" and "troughs" of the pleats
  • R groups of successive amino acids stick out on alternating sides of the sheet
  • hydrogen bonding can be intramolecular or intermolecular
  • parallel beta sheet = two regions run in the same N-terminus to C-terminus direction
  • antiparallel beta sheet = two regions run in the opposite N-terminus to C-terminus direction
• Proline

  • considered as a helix breaker because its R group is covalently bonded to its amino nitrogen
  • rarely found in a alpha helix but when present, introduces a bend in the helix
• • alpha-helical region is represented as either a spiral or a cylinder
  • beta-sheet region is drawn as a flat ribbon or arrow with the arrowhead pointing in the direction of the C-terminus
  • combinations of alpha-helices and beta-sheets are called motifs
• Tertiary Structure

  • comes about precisely because of the variety of amino acids present in proteins and very different chemical properties of their R groups
  • neither repetitive readily predictable, involves competing interactions between side groups with different properties
  • polypeptide chain will be folded, coiled, and twisted into its native conformation (most stable)
• Proteins can be divided into two categories:

  1. Fibrous proteins = extensive secondary structure, highly ordered and repetitive structure
  2. Globular proteins = polypeptide chains fold into compact structures rather than extended filaments, often folded locally into regions with alpha-helical or alpha-sheet structures giving its compact and globular shape ; folding is possible because regions of the beta-helix or beta-sheet are interspersed with random coils
• Higher levels of organization depend on the primary structure of the polypeptide exemplified especially by the condition sickle-cell anemia.
• Although we know that the primary sequence of a protein determines its final folded shape, the way a protein will fold cannot be predicted especially for large proteins.
• Quaternary Structure

  • concerned with subunit interactions and assembly
  • applies only to multimeric proteins
  • process of subunit assembly is often, but not always, spontaneous
  • often molecular chaperones are required to ensure proper assembly
  • a still higher level of assembly is possible in the sense that two or more proteins are organized into multiprotein complex (ex. pyruvate dehydrogenase complex), involved sequentially in a common multistep process