Protein Structure and Function Flashcards
Proteins
Composed of C, H, O, and usually S or P
polymers of amino acids
More varied roles than any other molecule in organisms
Monomer
Building blocks 20 amino acids
Amino acids has a central “C” with 4 attached groups
Amino acids form peptide bonds through condensation reaction
Properties of the R group
Determine inter- and intra- molecular interactions
Conjugated proteins
Involved in another type of molecule attached covalently or non- covalently
Small molecular weight materials ofter attached to proteins (metals- zinc)
Nucleoproteins- proteins + nucleic acid
Lipoproteins- lipids + protein
Glycoproteins- carbohydrates + proteins
Levels of protein structure
All levels of structure are ultimately determined by the primary level.
Primary, Secondary, Tertiary, Quaternary
Primary
All proteins must have primary structure
the order of the amino acids in the polypeptide chain
peptide bonds link amino acids together
Secondary
Results from interactions between proportions of polypeptide chain (particularly the R groups of adjacent amino acids)
Hydrogen bonds (H bonds)
Alpha helix: spiral shaped; H bond maximal; allows extensibility
Beta heet: flattened and extended sheet like shape
Tertiary
Results from interactions within a single chain between R groups so that the chain can be folded to from complex structures
H bonds; disulfide bonds: Van Der Waals interactions; ionic bonds; hydrophobic interactions
Domain- compact regions functioning semi- independently
Motif- substrate in the polypeptide chain with unique functions; usually motif is smaller than domain
Quaternary
At least 2 or more polypeptide chains
Result from R group interactions between multiple polypeptide chains (or substrate)
Assembly spontaneously and usually bound together by non covalent bonds
Homodimer- 2 identical subunits
Heterodimer- 2 non-identical subunits
Enzymes
Protein enzyme (names usually end in the suffix -ase)
Not altered during course of reaction (used over and over again)
Specific for its substrate
Catalyze reactions under mild temperature, near neutral pH and normally ionic concentration (between 6-8)
Catalyze reactions at extremely rapid rates
Enzyme kinetics
Study of reaction rates under experimental conditions
Leonor Michaelis and Maud Menten (1913): worked out mathematical relationship between substrate concentration and enzymic reaction velocity.
Rate of Reaction: V= Vmax [S/(S + Km)]
Curve is hyperbolic, at low substrate concentration (s), substrate concentration is rate-limiting
At high substate concentration, enzyme is saturated and works as fast as possible to reach maximum velocity
Michaelis Constant Km:
Km= the [s] when reaction velocity is 1/2 Vmax
serves as the measurement of enzyme affinity for substrate
Higher Km –> lower affinity
Lower Km –> higher affinity
Nucleic Acids (DNA and RNA)
Chemical nature of DNA
Gene- a segment of DNA involved in producing a polypeptide chain or RNA
Nucleotide= phosphate + base + sugar
Phosphate group- negatively charged
Sugars- 5 carbon (deoxyribose in DNA, ribose in RNA)
Base- pyrimidines (C and T in DNA ; U and C in RNA) –> 1 ring
- purines (G and A) –> 2 rings
- bases are nitrogen heavy
Polymerization occurs when 3’ -OH of sugars is linked by an ester bond to 5’ phosphate of next nucleotide in chain
- 3’-5’ phosphodiester linkage: Phosphates in backbone attached to 2 sugars by ester linkages.
Overall DNA is hydrophilic due to the negatively charged phosphate but, bases largely hydrophobic due to the rings.
Double Helix Structure of DNA
Watson- crick model
2 chains serial around the central axis of DNA molecule
The phosphate- sugar backbone is on outside molecule; bases of 2 chains project toward center
Chains held together by hydrogen bonds between adjacent bases of opposite strands
2 chains run in opposite directions (anti- parallel)
one 5’- 3’ and the other 3’-5’
H- bonds:
Larger number of H-bonds added together , strong, making the double helix:
-2 bonds between A:T pairs
-3 bonds between G:C pairs
