MCB 150 30-60 Lecture Notes: Starches, Glycogen, Lipids, Biomembranes, and Proteins

Starches

• Starches are discussed (slide 21).

Glycogen

• Found in muscle and liver cells of animals and serves as energy storage (slide 22).
• Helical, highly branched polymers of glucose.
  • Monomers within chains are covalently linked by α-1,4 glycosidic linkages.
  • Chains branch by connecting with other chains via α-1,6 glycosidic linkages.
• Glycogen is a polysaccharide used for energy storage in animal cells like liver and muscles (slide 23).
• It has a chemical structure showing α-glucose molecules linked by α-1,4-glycosidic linkages and α-1,6-glycosidic linkages at branch points.
• The three-dimensional structure is depicted as highly branched helices.

Lipids

• Defined by a physical property, not a chemical structure (slide 33).
• Vary widely in structure.
• Three primary functions and four primary types:
  • Energy Storage
  • Biomembrane Composition
  • Chemical Signaling
  • Triglycerides
  • Phospholipids & Glycolipids
  • Steroids

Monomers of Lipids

• Glycerol and Fatty Acids (slide 34).
• 3 Fatty Acids + Glycerol = Triglyceride.
• 2 Fatty Acids + Glycerol + Phosphate = Phospholipid (slide 35).

Phospholipids

• Variety in polar head groups (slide 36).
• Fatty acid tails in phospholipids can also vary in length and degree of saturation.
• Phospholipids are amphipathic (slide 37).
• In water, they spontaneously form micelles or bilayers (slide 37).
• Bilayers have exposed edges, and will fold into liposomes (slide 38).
• Lipid properties can be studied through artificial bilayers.
• Water is excluded at the bilayer interface due to the hydrophobic nature of the tails (slide 39).
• Some membrane lipids are glycolipids.

Steroids

• Can be used as circulating hormones like estrogen and testosterone, or as membrane components (slide 40).
• Animal cells have cholesterol in their biomembranes.
• Plants & fungi have different steroids; bacteria have none (slide 40).

Biomembranes

• Asymmetrical (slide 41).
• Have associated Proteins (Transmembrane, Membrane-associated, Lipid-linked, Peripheral) (slide 41).
• Proteins serve a variety of functions (slide 42):
  • Transport
  • Enzymatic activity
  • Signal transduction
  • Cell-cell recognition
  • Intercellular joining
  • Attachment to the cytoskeleton and extracellular matrix (ECM)
• Biomembranes are selectively permeable (slide 42).

Membrane Fluidity

• Biological membranes are fluid (slide 44).
• Lipids can move around within the membrane (slide 45).
• Membrane fluidity is temperature dependent (slide 45).
• The transition from fluid to gel phase is influenced by the lipid composition of the membrane.
• The cell can regulate membrane fluidity by changing (slide 46):
  • The number of unsaturated fatty acids
    • High level: increase fluidity
    • Low level: decrease fluidity
  • The tail length of fatty acids
    • Short chains: increase fluidity
    • Long chains: decrease fluidity
  • The number of cholesterol molecules (at low temperatures)
    • High level: increase fluidity
    • Low level: decrease fluidity

Nucleic Acids

• Two types: Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) (slide 46).
• Serve an information storage role in a cell.
• The monomers are Nucleotides: Base, Sugar, Phosphate.
• Numbering, labeling, and naming conventions (slide 47):
  • Base + Sugar = Nucleoside
  • Nucleoside + 1 Phosphate = nucleoside monophosphate
  • Nucleoside + 2 Phosphates = nucleoside diphosphate
  • Nucleoside + 3 Phosphates = nucleoside triphosphate
• The nucleotides of DNA and RNA differ in two important ways (slide 47):
  • Which nitrogenous bases are found in each nucleic acid?
    • RNA: Uracil, Cytosine, Adenine, Guanine
    • DNA: Cytosine, Thymine, Adenine, Guanine
  • Which 5-carbon sugar is found in each nucleic acid?
• Nucleotide nomenclature (slide 48):
  • Adenine (A), Guanine (G), Cytosine (C), Uracil (U), Thymine (T)
  • All nucleotides in DNA chain have the same 5-carbon sugar and a phosphate group.
  • All nucleotides in RNA chain have the same 5-carbon sugar and a phosphate group.
  • The designation of the nucleotide is the abbreviation of the base.

Nucleic Acid Properties

• DNA (slide 49):
  • Deoxyribose sugar (H at 2' carbon)
  • Pyrimidine bases: Cytosine (C) and Thymine (T)
  • Purine bases: Adenine (A) and Guanine (G)
  • Monomers are called deoxyribonucleotides (or deoxyribonucleoside triphosphates, or dNTPs)
  • Usually double-stranded
• RNA (slide 49):
  • Ribose sugar (OH at 2' carbon)
  • Pyrimidine bases: Cytosine (C) and Uracil (U)
  • Purine bases: Adenine (A) and Guanine (G)
  • Monomers are called ribonucleotides (or ribonucleoside triphosphates, or NTPs)
  • Usually single-stranded
• Polymerization of Nucleic Acid (slide 50).

Proteins

• The product of our proteins and protein activity (slide 51).
• The study of proteins and protein activity is called Proteomics.
• Proteins account for most of the dry weight in the cell (slide 51).
• Proteins are involved in nearly all categories of cellular function (slide 52):
  • Movement (Actin/Myosin)
  • Defense (Antibodies)
  • Structure (Keratin)
  • Transport (Hemoglobin)
  • Signaling (Glucagon)
  • Catalysis/Regulation/Metabolism
• Most of our (useful) genetic information instructs the cell how to build proteins or regulates that process.

Amino Acids

• Monomers of Proteins (slide 52).
• Basic structure of an amino acid (ionized form):
  • Carboxyl (or C) Terminus
  • Amino (or N) Terminus
  • Side Chain, or R-Group
  • The R group—the only part that differs—is what makes one amino acid different from another.
• Peptide bond formation (slide 53):
  • Condensation/Dehydration
• During protein synthesis, ribosomes link amino acids by constructing covalent PEPTIDE BONDS that join the NH2 (or NH3+) group of the incoming amino acid to the COOH (or COO-) group of what was already there, in the N→C direction (slide 53).
• Terminology (slide 54):
  • Two amino acids = DIPEPTIDE
  • A few amino acids = OLIGOPEPTIDE
  • A long chain of amino acids = POLYPEPTIDE
  • A polypeptide with a purpose = PROTEIN
• 20 different amino acids commonly found in proteins (slide 54):
  • Differ only in R groups, which confer distinct properties to that amino acid
  • Large number of amino acids makes possible a huge number of different amino acid sequences
    • 20^2 (=400) possibilities for dipeptides
    • 20^3 (=8,000) possibilities for tripeptides
    • 20^5 (=3,200,000) possibilities for pentapeptides
    • most proteins are >100 amino acids!!
• Amino acid R-groups (4 classes based on charge) (slide 55):
  • Uncharged, but polar
  • Uncharged and non-polar (hydrophobic)
  • Positively-charged (basic)
  • Negatively-charged (acidic)
• Polar amino acids (slide 55).
• Nonpolar (hydrophobic) amino acids (slide 56).
• Basic (positively-charged) amino acids (slide 56).
• Acidic (negatively-charged) amino acids (slide 57).
• Charged amino acids (slide 57).

Protein Structure

• Proteins exist in a virtually infinite number of 3-dimensional conformations (slide 58).
• That conformation is critical to the functioning of each protein.
• The consequence of folding improperly is usually very significant (slide 58).
  • Alzheimer’s, CF, Parkinson’s, Mad Cow –– all caused by errors in protein folding → accumulation of toxic insoluble “gunk” (e.g. “plaques” in Alzheimer’s)
• To describe how linear protein chains fold into their 3-D conformations, protein structure is organized into 4 different categories (slide 58):
  • 1° (pronounced ‘primary’)
  • 2° (pronounced ‘secondary’)
  • 3° (pronounced ‘tertiary’)
  • 4° (pronounced ‘quaternary’)
• Primary structure (1°, or primary sequence) (slide 59):
  • Linear sequence of amino acids from N → C (“beads on a string”)
  • All proteins have a UNIQUE primary structure
• Secondary Structure (2°) (slide 59):
  • First level of folding
  • Stabilized by (relatively weak) hydrogen bonds between peptide linkages
    • Peptide backbone is polar (N-H is partially +, C=O is partially –)
  • Independent of R groups, so found in most proteins
  • α-helix and β-pleated sheet are 2 major types
• Secondary Structure (2°) (slide 60).