Biomolecules Flashcards
What is Biochemistry?
The scientific discipline that seeks to explain life at the molecular level. A means for determining how organisms “work” using the tools and terminology of chemistry. A practical science with wide-ranging applications in a range of life science subjects, in treatment of diseases, and in industry
What are the most common elements in Biochemistry
Hydrogen, Carbon, Nitrogen and Oxygen
What are the essential ions in Biochemistry
Sodium, Magnesium, Chlorine, Potassium and Calcium
What are The Major Classes of Biomolecules
- Amino acids (amino and an acid)
- Carbohydrates (carbon mixed with water usually)
- Nucleotides (carbohydrate aspect, aromatic base aspect, and phosphates)
- Lipids (hydrophobic, specialized structures, non-polar)
What is the alcohol organic compound
Oxygen attached to hydrogen which is then attached to the rest of the organic compound. R-O-H
What is the aldehyde organic compound
Carbon has a double bond with oxygen, the carbon also has a bond with hydrogen, this carbon is attached to the rest of the organic compound.
O=
R-C-H
What is the ketone organic compound
Carbon has a double bond with oxygen, the carbon is attached to the rest of the organic compound on either side
O=
R-C-R
What is the carboxylic acid organic compound
Carbon has a double bond with oxygen, this carbon also is attached to a hydroxyl functional group and finally attached to the rest of the organic compound
O=
R-C-OH
What is the thiol (sulfhydryl) organic compound
Sulphur has a single bond with hydrogen and then attached to the rest of the organic compound
R-SH
What is the hydroxyl functional group
It is a single bond between oxygen and hydrogen
-OH
What is the carbonyl functional group
It is a double bond between carbon and oxygen.
C=O
What is the carboxylate functional group
It is a double bond between carbon and oxygen and then a single bonded oxygen as well attached to the carbon
=O
C-O
What is the sulfhydryl functional group
It is a single bond between sulphur and hydrogen
-SH
What is the amino functional group
It is a bond between nitrogen and two hydrogens
-NH2
What is the phosphate functional group
It is a phosphate that has single bonds with four oxygens
O-
O-P-O
-O
What is the phosphoryl functional group
It is a phosphate that one double bond with oxygen and two single bonds with oxygen
=O
P-O
-O
What is the ester linkage in biochemical compounds
It is oxygen that is single-bonded between two carbons, with one of the carbons have a double bond with an oxygen
=O
C-O-C
What is the ether linkage in biochemical compounds
It is oxygen that is single-bonded between two carbons
C-O-C
What is the amide linkage in biochemical compounds
It is nitrogen bonded to carbon which has a double bond with oxygen
=O
N-C
What is the phosphate ester linkage in biochemical compounds
It is phosphate with three single bonds with oxygen, one double bond with oxygen, carbon is also attached to one of the oxygens
=O
C-O-P-O
-O
What is the phosphoanhydride linkage in biochemical compounds
It is two phosphates, each phosphate has a double bond with oxygen, two oxygens in a single bond and one oxygen between the two of them
=O =O
C-O-P-O-P-O
-O -O
What is “Directionality”?
All covalent bonds are in the same orientation
What do a group of amino acids become
A protein
How do amino acids form a protein
Peptide bonds (amide bonds: nitrogen attached to a carbonyl)
What do a group of nucleotides become
Nucleic acids
How do nucleotides become nucleic acids
Phosphodiester bond (carbon and phosphorous or a phosphate group)
What is the shape that an H2O molecule takes
Tetrahedral
What are donor atoms
Atoms that donate their electrons easier
What are the accepter atoms
Atoms that are electronegative with a lone pair in a hybridized orbital
What do the hydrogen bonds in ice look like
Regular lattice of hydrogen bonds
What do the hydrogen bonds in water look like
Fluctuating hydrogen bond structure
How do hydrogen bonds in water work
~3 hydrogen bonds per water molecule. Potential for 4 hydrogen bonds
2 hydrogen bonds works as an acceptor (the bonds from lone pairs of oxygen)
2 hydrogen bonds work as a donor (the hydrogens)
What are the electrostatic forces
Ionic interactions, hydrogen bonds, Van de Waals and hydrophobic effects
What is Van der Waals Interactions
Dipole-dipole interactions and London dispersion forces
What are dipole-dipole interactions
Between polar non-charged groups. Weaker than Hydrogen bonds
What are London dispersion forces
Between nonpolar molecules. Weaker than dipole-dipole interactions
What is the bond strength in biological molecules in an aqueous environment from strongest to weakest
- Covalent bond
- Ionic interaction
- Hydrogen bond
- Van der Waals interaction
Explain electronegativity in atoms
Different atoms have different electronegative affinities. Atoms bonded (covalently) with significantly different electronegativities create a permanent dipole
What do amphiphilic/amphipathic molecules experience
Hydrophilic interactions and the hydrophobic effect
What is the hydrophobic effect
Non-polar compounds tend to associate with each other in aqueous environments. This reduces the amount of surface area exposed to water, increasing the entropy of the water. Energy goes down as the molecules come together. The hydrophobic effect does not occur in a nonaqueous solution.
What happens in a beaker that is less favourable and lower entropy
Each one of the molecules orders water molecules on its surface. This is more dispersed
What happens in a beaker that is more favourable and higher entropy
It has order water molecules on exposed surface. It is more ordered.
