Biological Molecules

• Biological Molecules

  Carbon-based molecules (except for some small inorganic molecules) that are the basis of life
• Categories of biological molecules

  • Sugars
  • Amino acids
  • Nucleotides
  • Lipids/fats
• Macromolecules

  Large biological molecules
• Small molecules

  Often play at least two roles: as building blocks for macromolecules and as specific functions in their own right
• Macromolecules take up 26% of the total cell weight, with water taking up 70%, inorganic ions taking up 1% and small organic molecules taking up 3%
• Carbohydrates


  Organic compounds with the general formula CH2On, the most common organic compound on Earth, function as energy storage, fuel, metabolites and structural components
• Carbohydrates


  • Composed of monosaccharides, which are small molecules typically containing three to nine carbon atoms bound to hydroxyl groups
  • Monosaccharides can be used to form a large variety of oligosaccharide structures
  • Carbohydrates are information rich, and this information can enhance the diversity of proteins when attached

  
• Monosaccharides

  Simple carbohydrates that are the building blocks of carbohydrates, all having the empirical formula CH2On

  
• Monosaccharides

  • Can be ketone-based (ketose) or aldehyde-based (aldose)
  • The number of carbon atoms determines the name (triose, tetrose, pentose, hexose, heptose etc.)
  • Can exist in a variety of isomeric forms (constitutional isomers, stereoisomers, enantiomers, diastereoisomers)

  
• Glucose

  An aldose that is an essential energy source, has 6 carbon atoms (a hexose), and can exist in long chain or ring structures
• Glucose

  • Only naturally exists in D-configuration, can also exist in L-configuration but this is synthesized
  • Alpha and beta configurations are determined by the location of the OH group
• Oligosaccharides

  Built by the linkage of two or more monosaccharides by O-glycosidic bonds, have a directionality defined by reducing and non-reducing ends

  
• Oligosaccharides


  • Blood groups, ABO blood groups
• Disaccharides

  A type of oligosaccharide consisting of two sugars joined by an O-glycosidic bond, formed by a condensation reaction

  
• Polysaccharides

  Large polymeric oligosaccharides formed by the linkage of multiple monosaccharides, play vital roles in energy storage and structural integrity

  
• Polysaccharides


  • Glycogen, the storage form of glucose
• Amino acids

  The building blocks of proteins, consisting of a central carbon atom linked to an amino group, a carboxylic acid group, a hydrogen atom, and a distinctive R group (side chain)
• Amino acids

  • Are chiral, existing in L or D isomers
  • There are 20 kinds of side chains varying in size, shape, charge, hydrogen-bonding capacity, hydrophobic character and chemical reactivity
  • All proteins are constructed from the same set of 20 amino acids with only a few exceptions
• Amino acid reaction

  Amino acids react to form peptides, with a peptide bond formed between the carboxyl group of one amino acid and the amino group of another, releasing a water molecule
• Primary structure

  Amino acids linked by peptide/amide bonds to form linear polypeptide chains (proteins), with a directionality from the amino-terminal to the carboxyl-terminal
• Polypeptide chain

  • Consists of a regularly repeating backbone and variable side chains
  • The peptide bond is planar
• Secondary structure

  Polypeptide chains that can fold into regular structures such as alpha helices, beta sheets, and turns and loops, stabilized by hydrogen bonds between the peptide NH and CO groups

  
• Alpha helices


  • Coiled structures stabilized by intrachain hydrogen bonds, with a tightly coiled backbone and side chains extending outward in a helical array
• Secondary structures


  • Polypeptide chains that can fold into regular structures such as the alpha helix, the beta sheet and turns and loops
  • Although not periodic, these common loop or turn structures are well-defined and contribute with α helices and β sheets to form the final protein structure
  • α helices, β sheets and turns are formed by a regular pattern of hydrogen bonds between the peptide NH and CO groups of amino acids that are near one another in the linear sequence

  
• Polypeptide chains fold as a result of the R-groups of each of the amine acid chains

  
• Alpha Helices


  • Coiled structures stabilised by intrachain hydrogen bonds
  • Rod-like structures, with a tightly coiled backbone that form the inner part of the rod and the side chains extend outward in a helical array
  • Stabilised by hydrogen bonds between the NH and CO groups of the main chain
  • Except for AA near the ends of an α helix, all main-chain CO and NH groups are hydrogen bonded
• Beta Sheets

  • Stabilised by hydrogen bonding between polypeptide strands
  • Composed of two or more polypeptide chains called β strands, which is almost fully extended rather than being tightly coiled as in the alpha helix
  • A β sheet is formed by linking two or more β strands lying next to one another through hydrogen bonds
  • Strands next to each other in a β sheet can run in opposite directions (anti-parallel β sheet) or in the same direction (parallel β sheet)
  • In the anti-parallel arrangement, the NH group and the CO group of each AA are respectively hydrogen bonded to the CO group and the NH group of a partner on the adjacent chain
  • For the parallel structure, the hydrogen bonding scheme is a bit more complicated: for each AA, the NH group is hydrogen bonded to the CO group of one AA acid on the adjacent strand, whereas the CO group is hydrogen bonded the NH group on the AA two residues farther along the chain
  • β sheets can be almost flat but most adopt a somewhat twisted shape and is an important structural element in many proteins
• Turns and Loops

  • Polypeptide chains can change direction by making reverse turns and loops
  • Most proteins have compact, globular shapes due to reversals in the direction of their polypeptide chains
  • Many of these reversals are accomplished by a common structural element called reverse turn (aka the β turn or hairpin turn)
  • In many reverse turns, the CO group of residue i of a polypeptide is hydrogen bonded to the NH group of residue i+3
  • More elaborate structures are responsible for chain reversals, called loops (sometime omega (Ω) loops) to suggest their overall shape
  • Turns and loops invariably lie on the surfaces of proteins and thus often participate in interactions between proteins and other molecules
• Tertiary structure

  • Water soluble proteins that fold into compact structures with nonpolar cores and are 3D structures, stabilised by hydrogen bonds, hydrophobic, hydrophilic and Van der Waalʼs forces
  • Hydrophilic amino acids are typically going to be found on the outside of a protein, as opposed to something that is hydrophobic, e.g. hydrophobic AA, which would be found on the inside of the protein to form the structure

  
• Quaternary structure


  • Spatial arrangement of subunits, which is a polypeptide chain, and the nature of their interactions
  • Organisation of macromolecules into assemblies, often stabilised by ionic bonds
  • A dimer is the simplest type of quaternary structure, which consists of two identical subunits
• Nucleotides

  • DNA and RNA are long linear polymers, called nucleic acids, that carry information in a form that can be passed from one generation to the next
  • Macromolecules consist of a large number of linked nucleotides, each of which are formed by a combination of a sugar, base and a phosphate group
  • Sugars linked by phosphates form a common backbone that plays a structural role, whereas the sequence of bases along a nucleic acid strand carries genetic information
  • Each monomer unit within the polymer is a nucleotide and a single nucleotide unit is made from a sugar, a phosphate and one of four bases: adenine, guanine, cytosine and thymine
  • The sequence of bases in the polymer unique characterised a nucleic acid and constitutes a form of linear information
  • Ribonucleotide combines to form RNA while deoxyribonucleotide combines to form DNA; the absence of a single oxygen distinguishes between a RNA and DNA nucleotide
  • When nucleotides come together to form DNA/RNA, water is lost
• Body Fats

  • Act predominantly as food reserves (i.e. for energy)
  • Where sugars are the individual units for producing ATP in the body, body fats are more capable of producing more ATP than just the sugars themselves
  • Combo of a glycerol ester and fatty acids
  • Fatty acids are long hydrocarbon chains of various lengths and degrees of unsaturation that terminate with carboxylic acid groups
  • Saturated fatty acids have no double bonds while unsaturated (trans) — has a double bond and H atoms are on opposite sides and unsaturated (cis) — has double bond and H atom on same side (bent configuration)
  • Being in cis or trans configuration can change the overall structure of the fatty acid
  • Triglycerides are the fats themselves and storage molecules
• Phospholipids


  • An important and special type of lipid that come together to form the membranes of cells
  • Combo of a glycerol backbone with two fatty acid chains and a phosphate group, which is linked to a head group
  • Inside of a membrane is hydrophobic (hating water) whereas the phosphate head is hydrophilic (loving water)
  • Cell membrane is a phospholipid bilayer

  
• Cholesterol


  • Limits the movement of bilayer sheets
  • A steroid
  • Can intercalate into the membrane
  • OH group interact with the polar lipid heads
  • Its steroid scaffold interact with the fatty acids
  • Decreases fluidity and increases flexibility of the membrane
  • Reduces permeability for soluble molecules
• Proteins that denature (loss of structure) or are mutated (chance structure)

  Affect function
• Cancer mutations can lead to hyperactivity function of the enzyme
• If we get too hot, it could cause the denature of the interactions of those proteins
• Starch and glycogen


  Major energy sources for humans
• We cannot digest cellulose (different glucose polymer), due to the different orientation individual monosaccharides are coming together to bind
• Single oxygen difference makes DNA much more stable than RNA