Molecular Building Blocks Flashcards
Monosaccharides
One hydroxyl group
Generally exist as ring structure (cyclised)
Aldose has an aldehyde
Ketose has a ketone
Glycosidic bond
Hydroxyl group of a monosaccharide can react with an OH or NH to form a glycosidic bond
O-glycosidic bonds form…
Disaccharides, oligosaccharides and polysaccharides
N-glycosidic bonds found in…
Nucleotides in DNA
Disaccharides
Contain 2 monosaccharides joined by an o-glycosidic bond
Oligosaccharides
Contain 3-12 monosaccharides
Product of digestion of polysaccharides or part of a complex protein/lipid
Polysaccharides
Formed by thousands of monosaccharides joined by glycosidic bonds
Glycogen
Branched polysaccharides formed by glucose residues
Nucleotides
Made from nitrogenous base, sugar and phosphate
Bonds between bases hydrogen bonds
Bonds between nucleotides = phosphodiester bonds
Triglycerides
3 fatty acids bound to glycerol
Straight carbon chains with a methyl group and a carboxyl group at ends
Tends to be hydrophobic
Contain no oxygen in main chain
Unsaturated fatty acids
Double bonds are commonly cis, spaced at 3C intervals
Proteins
Amino acids linked by peptide bonds
Protein - if it is functional and synthesised by a cell
Peptide - bit of protein broken off
Folding of proteins
Linear chains fold in different shapes to form 3D structures
Determined by charged interactions, flexibility, amino acid sequence and physical dimensions
Primary structure
Linear sequence of amino acids
Secondary structure
Alpha helix or beta pleated sheets formation due to H+ bonds between amino acids-
Determine by local interactions between side chains and sequence of amino acids
Tertiary structure
Overall 3D conformation of a protein
Can change with temperature or pH
bonds between R -groups:
Disulfide bonds - strong covalent bonds that form between 2 cysteine R groups. Strongest within a protein so most resistant to temperature+pH changes but can be broken by oxidation
Ionic bonds - form between any carbonyl and amino R group weaker so broken by pH changes
Hydrogen bonds- form between strongly polar R groups
Hydrophobic interactions- form between hydrophobic non-polar R groups within interior of protein
It creates specific and flexible binding sites for ligands
Some conformational domains occur repeatedly and include barrels, bundles and saddle
Alpha helix
hydrogen bonds between each carbonyl oxygen atom and the amino hydrogen of an amino acid residue located 4 residues farther down the chain. Core of helix is tightly packed. Proline breaks the helix (ring and no H). Side chains look outwards
Beta pleated sheet
hydrogen binding between regions of separate neighbouring polypeptide strands aligned parallel to each other. Bonds are at an angle in the parallel beta-sheets (parallel if the polypeptide strands run in the same direction (as defined by their amino and carboxyl terminals)) are weaker than in the anti parallel beta-sheet (Antiparallel strands are often the same polypeptide chain folded back on itself, with simple hairpin turns or long runs of polypeptide chain connecting the strands)
Quaternary structure
proteins that contain more than one polypeptide chain joined by same bonds as in tertiary structure
Many proteins function in the cell as dimers, tetramers, or oligomers, proteins in which two, four, or more subunits, respectively, have combined to make one functional protein.
Proteoglycans
long unbranched polysaccharide radiating from a core protein, form (along with proteins such as collagen) the extracellular matrix cells exist on
Monosaccharide isomers
Asymmetric so have a chiral carbon- enantiomers. Monosaccharide stereoisomers are designated D or L based on position of hydroxyl group farthest from the carbonyl carbon that matches D or L glyceraldehyde
Sugar derivatives
Animosugars: contain an amino group instead of a hydroxyl group on one of the carbons (usually carbon 2)- often acetylated to form an N-acetylated sugar eg. Glucosamine
Alcohol sugars eg sorbitol
Sulfate groups eg Heparin, chondroitin sulphate
Phosphorylated at terminal carbons, which prevents transport out of cells eg Glucose-6-phosphate
Water
universal solvent (can dissolve ionic and polar substances)
• polarity leading to hydrogen bonding
• liquid range from O to 100 °C
• max density at 4°C
• Doesn’t interact with non-polar substances, lipids, aromatic groups - hydrophobic compounds
Hydrogen bonding = electronegative atoms such as O or N can attract hydrogen atoms from other molecules. Partial sharing of this proton leads to a mutual attraction between the 2 atoms. Weak on its own but strong in a collective
steroids
- contain a 4 ring structure called steroid nucleus. Can be synthesised from Acetyl Co-A. Hydrophobic and fat soluble. Cholesterol is the steroid precursor in human cells for steroid hormones and critical role in cell signalling - it is converted to amphipathic water-soluble bile salts such as cholic acid. Bile salts line surfaces of micelles in lumen of intestine where they keep the droplets emulsified in the aqueous environment.
sphingolipids
formed from sphingosine (serine and palmitate) instead of glycerol. Sphingomyelin contains a phosphorylcholine group attached to ceramide and is a component of cell membranes and myelin sheath
Eicosanoids
synthesised from 20 C atoms. Acids with. 3,4,5 double bonds. biological functions
acylglycerols
comprise of glycerol with one or more fatty acids attached through ester linkages. Can be phosphorylated to form phosphoacylglycerols
Lipid aggregates
Micelle, Bilayer formed due to hydrophilic and hydrophobic interactions
Organisation
atoms → molecules → macromolecules (large molecules formed from simple molecules)
Water
universal solvent (can dissolve ionic and polar substances)
• polarity leading to hydrogen bonding
• liquid range from O to 100 °C
• max density at 4°C
• Doesn’t interact with non-polar substances, lipids, aromatic groups - hydrophobic compounds
Hydrogen bonding = electronegative atoms such as O or N can attract hydrogen atoms from other molecules. Partial sharing of this proton leads to a mutual attraction between the 2 atoms. Weak on its own but strong in a collective
Proteoglycans
long unbranched polysaccharide radiating from a core protein, form (along with proteins such as collagen) the extracellular matrix cells exist on
Amino sugars
contain an amino group instead of a hydroxyl group on one of the carbons (usually carbon 2)- often acetylated to form an N-acetylated sugar eg. Glucosamine
Alcohol sugars
Sorbitol
Sulfate groups on sugars
Heparin, chondroitin sulphate
Carbohydrate enantiomers
Asymmetric so have a chiral carbon- enantiomers. Monosaccharide stereoisomers are designated D or L based on position of hydroxyl group farthest from the carbonyl carbon that matches D or L glyceraldehyde
Lipids
straight chain C compounds (mostly 16-20) with a methyl group and a carbonyl group
• Melting point decreases with degree of unsaturation (fluidity) as kink prevents surface contact but increases with chain length
• Double bonds are commonly cis (hydrogen on same side of double bond) and spaced at 3 C intervals- trans fatty acids produced by hydrogenation of polyunsaturated fatty acids in vegetable oils
Nomenclature of lipids
18:1, (triangle)9
18 = number of carbon atoms
1 = number of double bonds
Triangle = the position of double bond (between 9th and 10th Carbon)
Also classified by distance of double band closest to w end eg
W-6 20:4 (triangle) 5,8,11,14
Amino acids
compounds that contain an amino group and a carboxylic acid group
• 20 naturally occurring
• Most naturally occur in L form
• Charge determined by R group, amino group and carboxylic acid group which changes with pH
• Polarity determined by R group
• At different pH, carboxylic and amino group (and some R groups) are ionised
• peptide bond formed by condensation reaction- cleaved by proteolysis enzymes (proteases or peptidases)
• very stable
• flexibility around C not involved in bond so multiple conformations
Zwitterion
React intramolecularly to form a zwitterion = both positively and negatively charged. Because of this, there are strong intermolecular forces of attraction between amino acids so they are soluble crystalline solids
Amino acids
Act as protein buffers as can accept or donate H+
Peptide bond
very stable
• Cleaved by proteolysis enzymes- proteases or peptidases
• Partial double bond
• Flexibility around C atom not involved in bond, allows multiple confirmations
• Usually one preferred native conformation, determined mainly by side chain and sequence of amino acids
Glycine
simplest amino acid R group= -H
Polypeptide starts at…
amine group and amino acids added to carboxylate group (N-terminus)
Globular proteins
compact, roughly spherical in shape+ soluble in water
Non-polar R groups orientate inwards with polar R groups on outside so are soluble and easily transported and involved in metabolic reactions.
Specific shapes and some are conjugated (prosthetic group) e.g. Enzymes + immunoglobulins
Fibrous proteins
long strands of polypeptide chains that have hydrogen bond cross-linkages
Insoluble due to large number of hydrophobic R groups
Repetitive sequence of amino acids eg. Collagen
How is protein structure determine
X-ray diffraction of protein crystals
How are protein structures represented
• backbone (line of peptide bonds- no side groups)
• cartoon (shows fundamental secondary structures)