Exam 1 Flashcards
Biochemistry
The study of the molecules that function in very specialized ways to sustain life
Where is Carbon found in a cell
Glucose, Protein, DNA, Fat,
Four most abundant elements in cells
Carbon (60%), Hydrogen (11%), Nitrogen (9%), Oxygen (6%)
Biomolecules
Organic molecules, including nucleic acids, carbohydrates, proteins and lipid
Order of organization in cells
the cell and its organelles, supramolecular complexes, macromolecules, monomeric units
Carbohydrates composed of
Polysaccharides contain disaccharides contain monosaccharides
Lipids composed of
Triglycerides composed of fatty acids and glycerol
Proteins composed of
Peptides composed of amino acids
Nucleic Acids include
RNA and DNA composed of nucleotides
High-Energy Compounds include
ATP composed of nucleotide and phosphate groups
Organic compounds
Molecules with covalently bonded carbon backbones (linear, branched or cyclic)
Carbon has
-4 unpaired electrons (up to 4 different atomic partners)
-can form single bonds with hydrogen
-can form single and double bonds with oxygen and nitrogen
What determines a biomolecules chemical properties?
Functional Group
Isomers
Molecules that share the same chemical formula
Stereoisomers
Two isomers with the same order of bonds but different spacial arrangements
How can stereoisomers differ
Configuration or conformation
Configuration
Different spatial arragements can only be achieved by breaking and making of bonds (disFIGURE requires breaking)
Conformation
Free rotation around a single bond- same molecule can assume many different spacial arrangements
Cis-Trans Stereoisomers (geometric stereoisomers)
Arise in presence of C=C (carbon-carbon double bonds)
-same structural formula and order of bonds
-different spatial arrangement of atoms/functional groups
-similar groups on same side of double bond axis - cis
-similar groups on opposite sides of double bond axis - trans
What is the basis of our vision
Rapid change in cis-trans configuration
Configurational Stereoisomers
Enantiomers & Diastereomers
When do configurational stereoisomers arise
In presence of tetrasubstituted, chiral carbons
Enantiomers
Chiral molecule, same structural formula, same order of bonds, different spatial arrangement, enantiomers are mirror images of each other
Diastereomers
more than 1 chiral center, not mirror images
Conformational Isomers
Related to one other by free rotation around a single bond
What does the combination of configuration and conformation dictate
Biochemical interactions
What do biochemical interactions give rise to
Structure of biomolecules
What does the structure of biomolecules give rise to
Biological activities
Why is conformation and configuration important
Sterochemical ‘fit’ of biomolecules with one another underlies most biochemical interactions and biochemical reactions
Group transfer reactions
Transfer of an eectrophilic group A from one nucleophile X to the other Y
Nucleophile
Atom or functional group with a pari of electrons that can be shared
Oxidation and Reduction Reactions
Involves the loss and gain of electrons
Oxidation is
Loss of electrons
Reduction is
Gain of electrons
Thermodynamics
the study of heat and energy exchanges between a ‘system’ and its surroundings
For a reaction to occur spontaneously ∆G must be
∆G >0
Entropy
the measure of disorder, more disorder, the increase in entropy
Gibbs Free Energy
∆G=∆H-T∆S
Kinetics
The study of reaction rates and depends on the activation energy barrier and is independent of ∆G
Properties of water
-bent molecule; tetrahedral geometry
-hydrogen partially positively charged
-oxygen partially negatively charged
Hydrogen Bond
Electrostatic interaction between the oxygen of one water molecule and the hydrogen of another water molecule
How many hydrogen bonds can form with 1 water molecule
4 because of the tetrahedral structure
What atoms can serve as H-bond donors and acceptors
Nitrogen, Oxygen, Sulfur, Chlorine, and Flourine
When are hydrogen bonds strongest?
When electrostatic interactions are maximized
Solubility
Ability of a solvent to interact more strongly with solute particles than the solute particles interact with each other
Ionic interaction
Forces between charged molecules
How does water dissolve compounds
By replacining ionic bonds with solute-water hydrogen bonds
Van der Waals
Attractive forces between small electric dipoles induced on uncharged atoms
Amphipathic Compounds
Contain both polar-uncharged/ionic (hydrophilic) and non-polar (hydrophobic) regions (e.g. in biology: lipids)
Micelles
All hydrophobic groups are sequestered from water; ordered shell of H2O molecules is minimized, and entropy is further increased
Acids
Proton donors e.g. HCl, H2SO4
Bases
Proton acceptors e.g. NaOH, KOH, NH3
Buffer
An aqueous solution that tends to resist changes in pH when small amounts of acid or base are added
Primary Protein Structure
sequence, proteins are built from a linear “string of amino acids”
Secondary Protein Structure
Alpha helix, beta sheet
Tertiary Protein Structure
Motifs, folds and domains
Quaternary
Assembly of multiple polypeptides
Peptides
Small amino acid chains including hormones and pheromones, neuropeptides, antibiotics, and toxins
Proteins
large chains of amino acids that are needed for catalysis, nutrient transport, structure and motility
Nonpolar, aliphatic group
Cannot make hydrogen bonds or have ionic interactions
Aromatic group
Can absorb UV light at 270-280nm
Positively charged group
higher pKa
What amino acids are ionizable
Aspartate, glutamate, lysine, arginine, histidine
