Download Macromolecules and Membranes

LS50 2015
INTRO TO CHEMISTRY WEEK: SEPTEMBER 14 – 18, 2015
Learning goals
By the end of this week, you should understand the following:
• The key findings and interpretations of some critical experiments that led to our current
understanding of atomic structure and electron configurations (Lecture 08)
• How electron configurations are related to chemical bonds and interactions (Lecture 09)
• How chemical bonds are related to assembly and structure of biological molecules (Lectures 0910)
• How molecular assembly and structure are related to molecular function (Lectures 11-12)
• How knowing molecular function facilitates prediction of the evolution of biological molecules
(Lecture 12)
Lecture 12 – Macromolecules and membranes
Learning goals
By the end of this lecture, you should be able to:
• Understand and describe the hydrophobic effect
• Explain primary, secondary, tertiary and quaternary protein structure, and describe the major
intermolecular forces involved
• Understand the role of entropy in protein folding
• Describe the makeup of nucleotides and oligonucleotides
• Define allosteric communication and its relationship to protein function
Hydrophobic effect
• Refers to the tendency of nonpolar substances to aggregate and exclude water molecules when
in aqueous solution
o e.g. oil and water
• The layer of water molecules on the outside of the protein is called the water cage (= solvation
shell)
o These water molecules have restricted mobility compared to the other water molecules in
the solvent
o By aggregating, the nonpolar molecules can reduce entropy in the system by minimizing
the loss of mobility of water molecules
• an important phenomenon because it drives membrane stability, protein folding and membrane
protein insertion
• also important to understand folding of proteins with hydrophobic amino acids (A, V, L, I, D, W, M,
P): hydrophilic proteins can have a hydrophobic core where side chains are never exposed to
ligand or solvent.
Higher order protein structure
• Primary structure
o This is the sequence of amino acids that makes up the protein
o Written from amino (N) terminus to carboxy (C) terminus
• Secondary structure
o Two most common types of secondary structural elements are α-helix and β-sheet
o Alpha helix
§ Provides backbone hydrogen bonds (side chains don’t generally participate in the
hydrogen bonding needed to construct the helix)
§ Amino acid side chains extend outwards from the helix
§ Has a dipole: δ+ towards N terminus
§ 3.6 amino acid residues per turn
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Beta sheet
§ Backbone atoms are essentially planar
§ Side chains alternately point above and below the plane of the sheet
§ Each strand has 5-10 amino acids
o All other regions are called “loops”
Tertiary structure
o Overall geometric shape of a single protein molecule ( = a single polypeptide chain):
spatial relationship of secondary structures to each other
o Relevant forces include the following:
§ formation of hydrophobic core (globular proteins)
§ hydrogen bonds
§ disulfide bonds
§ hydrophobic interactions
Quaternary structure
o shape or structure resulting from interaction with more than one protein molecule
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Protein folding, entropy
• Review Lecture 05 on equilibrium: realize that protein folding is a process where the enthalpy has
to overcome the entropy, as in other systems you’ve learned about
• To be able to calculate the Gibbs free energy of a protein folding, you’d need to know the relative
strengths of the various forces involved in folding
Next section:
• Continuing the theme of polymerization of molecules: until now we have talked a lot about
proteins, which are polymers of amino acids.
• In this lecture we will talk about two more biologically important polymers:
o Nucleic acids, polymers of of bases (nucleic acids)
o polymers of lipids that form membranes
Nucleic acids
• The monomeric “subunit” of nucleic acid polymers are nucleotides
• A nucleotide = 1 nitrogenous base + 1 5 carbon sugar + phosphate
o Sugar:
§ DNA contains deoxyribose
§ RNA contains ribose
o Nitrogenous base can be one of two types:
§ Purine (adenine and guanine in DNA)
§ Pyrimidine (cytosine and thymine in DNA; cytosine and uracil in RNA)
§ DNA uses four different such bases
• Nucleotides are linked together with a sugar-phosphate “backbone”
• DNA is two long polymers as described above, that are held together by many hydrogen bonds
between a purine on one of the polymers (strand) and a pyrimidine on the other
o A is held to T by two hydrogen bonds
o G is held to C by three hydrogen bonds
o When heated up the hydrogen bonds weaken and the two strands can separate (melt)
o When the temperature is cooled again, they match up perfectly.
o This is an example of self-assembly
• To distinguish between the strands and specify their directionality, we call the ends
o 5 prime
o 3 prime
• to represent graphically, show the top strand (by convention in a given) as 5 prime to 3 prime
• RNA tends to be single stranded, but base pair complementarity could still give rise to doublestranded conformations within an RNA molecule
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Membranes
• Membrane is not only a phospholipid bilayer: there are other lipids, proteins and other molecules
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embedded in it – these things can probably drift laterally within the bilayer pretty often (10
times/second) and very rarely flip-flop across the membrane
• Fluidity will depend on temperature and on the degree of saturation of the FA tails:
o Unsaturated FAs will be more fluid than saturated FAs
• Membrane associated proteins can be one of two types depending on their spatial relationship
with the membrane:
o Integral: penetrate the hydrophobic interior and can stick out the other side.
o Includes transmembrane proteins
o Peripheral: sticking to surface of membrane
• Membrane protein function: usually they do at least one of these main things:
o Transport across membrane
o Enzymatic activity
o Signal transduction
o Cell-cell recognition
o Intercellular joining
o Attachment to cytoskeleton and extracellular matrix
• Surface molecules are important for cell-cell recognition: membrane carbohydrates are among
these
• They could be covalently bonded to lipids à glycolipids, or to proteins à glycoproteins
• How can molecules get across the membrane? It is selectively permeable, and the method of
getting across is going to depend on the chemical properties of the membrane and the molecule
that is to cross it:
o Nonpolar molecules: can dissolve in lipid bilayer and pass through easily
o Polar molecules: will not be able to cross easily because of hydrophobicity of membrane
à they will need transport proteins to get across
Self-assembly
• Nucleic acids: pair bonding (creation of helix)
• Proteins: including microtubules, actin filaments, collagen fibers
Allosteric communication
• This is when binding properties of a macromolecule change as a consequence of a second ligand
binding the macromolecule
o The two ligands don’t have to be directly connected to each other
o If the two ligands are the same = homotropic allosteric effect
o If the two ligands are different = heterotropic allosteric effect
• Could generate cooperative behavior
• The macromolecule has two forms:
o Binds ligand with low affinity = T (tense) state
o Binds ligand with high affinity = R (relaxed) state
• T and R states are in equilibrium (remember Lecture 05): T ßà R
o If T>R because ligand binding increases the amount of R = positive cooperativity
o If T<R because ligand binding increases the amount of T = negative cooperativity
• Example: hemoglobin (works as a tetramer)
o O2 binding Fe2+ moves the Fe2+ atom into the plane of the porphyrin ring (a circular
organic compound: the one that binds to hemoglobin is called heme)
o The Fe2+ atom interacts with the (imixazole) side chain of the histidine residue, which
pull that residue towards the porphyrin as well
o The helix that contains this histidine residue gets pulled on as a result
o The strain from this pulling gets transmitted to the other three monomers of the tetramer,
which undergo similar conformational changes
o This makes O2 binding to the other monomers easier than before
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In summary, binding one O2 (first ligand) makes the molecule have an increased affinity for O2
(subsequent ligands)
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