Biological molecules (proteins) Flashcards
What is the general sturcture of an amino acid?
-COOH carboxyl/carboxylic acid group
-R variable side group consists of carbon chain and may include other functiona groups (benzene ring or -OH alcohol)
-NH2 amine/amino group
Describe how to test for proteins in a sample
Biuret test confirms presence of peptide bond
1. Add equal volume of sodium hydroxide to sample at room temperature.
2. Add drops of dilute copper (II) sulfate solution. Swirl to mix.
(steps 1 & 2 make Biuret reagent)
3. Positive result: colour changes from blue to purple
Negative result: solution remains blue
How many amino acids are there and how do they differ from one another?
20 (naturally occuring)
differ only by side R group
How do dipeptides and polypeptides form?
- Condensation reaction forms peptide bond (-CONH-) & eliminates molecule of water
- Dipeptide: 2 amino acids
- Polypeptide: 3 or more amino acids
How many levels of protein structure are there?
4
Define primary struture of a protein
.Sequence, number and type of amino acids in the polypeptide
.Determined by sequence of codons on mRNA
Define secondary struture of a protein
.Hydrogen bonds form between O- (slightly negative) attatched to -C=O and H+ (slightly positive) attatched to -NH
Describe the 2 types of secondary protein structure
a-helix:
* all N-H bonds on same side of protein chain
* spiral shape
* H-bonds parallel to helical axis
ẞ-pleated sheet:
* N-H & C=O groups alternate from one side to the other
Define tertiary structure of a protein. Name the bonds present
3D structure formed by further folding of polypeptide
.disulfide bridges
.ionic bonds
.hydrogen bonds
Describe each type of bond in the tertiary structure of proteins
.Disilfide bridges- strong covalent S-S bonds between molecules of the amino acid cysteine
.Ionic bonds- relatively strong bonds between charged R groups (pH changes causes these bonds to break)
.Hydrogen bonds- numerous and easily broken
Define quarternary structure of a protein
.Functional proeteins may consist of more than one polypeptide
.Precise 3D structure held together by the same types of bond as tertiary structure
.May involve addition of prosthetic groups (metal ions/phosphate groups)
Describe the structure and function of globular proteins
.Spherical and compact
.Hydrophilic R groups face outwards and hydrophobic R groups faced inwards= usually water-soluble
.Involved in metabolic processes (enzymes and haemoglobin)
Describe the structure and function of fibrous proteins
.Can form long cahins or fibres
.Insoluble in water
.Ueful for structure and support (collagen in skin)
Outline how chromatography could be used to identify the amino acids in a mixture
- Use capillary tube to spot mixture onto pencil origin line & place chromatography paper in solvent
- Allow solvent to run until it almost touches other end of paper. Amino acids move different distances based on relative attraction to paper & solubility in solvent.
- Use revealing agent or UV light to see spots.
- Calculate R, values & match to database
What are enzymes?
.Biological catalysts for intra and extracellular reactions
.Specific tertiary structure determines shape of active site, complementary to a specific substrate
.Formation of enzyme-substrate complexes lowers activation energy of metablic reactions
Explain the induced fit model of enzyme action
.Shape of active site is not directly complementary to substrate and is flexible
.Conformational change enables ES complexes to form
.This puts strain on substrate bonds,lowering activation energy
How have models of enzyme action changed?
.Initially lock and key model: rigid shape of active site complementary to only 1 substrate
.Currently induced fit model: also explains why binding at allosteric sities can change shape of active site
How could a student identify the activation energy of a metabolic reaction from an energy level diagram?
Difference between free energy of substrate and peak of curve
Name 5 factors that affect the rate of enzyme-controlled reactions
.enzyme concentration
.substrate concentration
.concentration of inhibitors
.pH
.temperature
How does substrate concentration affect rate of reaction?
Given that enzyme concentration is fixed, rate increases proportionally to substrate concentration
Rate levels off when maximum number of ES complexes form at any given time
How does temperature affect rate of reaction?
Rate increases as kinetic energy increases and peaks at optimum temperature
Above optimum, ionic and H-bonds in 3 degress struture break= active site no longer complementary to substrate (denaturation)
How does pH affect rate of reaction?
Enzymes have a narrow optimum pH range
Outside range H+/OH- ions interact with H-bonds and ionic bonds in 3 degrees structure= denaturation
Contrast competitive and non-competitive inhibitors
Competitive inhibitors
similar shape to substrate = bind to active site
do not stop reaction; ES complex forms when inhibitor is released
increasing substrate concentration in decreases their effect
Non-competitive inhibitors
bind at allosteric binding site
may permanently stop reaction; triggers active site to change shape
increasing substrate concentration has no impact on their effect
Outline how to calculate rate of reaction from a graph
.calculate gradient of line or gradient of tangent to a point
.initial rate: draw tangent at t=0
