Unit 1 Chapter 3: Proteins (Structure and Function) Flashcards
What was the Miller-Urey experiment
Miller used 2 flasks (smaller one containing H2O and larger one containing CH4. NH3 and H2) and gas tubing to mimic Earth’s early atmosphere and oceans. He boiled the water in order for gases to circulate and also sent electrical discharges through (mimicking ancient lightning) to see if the early “prebiotic soup” would be recreated. After a day the solution was pink, and after a week it was red and cloudy. When he analyzed the solution he found large amount of hydrogen cyanide and formaldehyde (organic molecules)which were also present in the early prebiotic soup and are the building blocks of proteins and amino acids.
conclusion chem. evolution occurs readily if molecules with high free energy are exposed to kinetic energy
How many different amino acids are there
20
Structure of amino acids
amino group-c(bonded to h and side chain)-carboxyl
How do we count amino acids? Why?
from N to C, because N is the start of the chain when proteins are synthesized in cells
Non-Polar side chains
glycine, valine, alanine, leucine, isoleucine, tryptophan, methionine, phenylalanine, proline
Polar side chains
serine, threonine, asparagine, glutamine, cysteine, tryrosine
Electrically charged side chains (acidic/basic)
- acidic: aspartate, glutamate
- basic: lysine, arginine, histidine
An amino acid is polar if
it has a polar side chain
An amino acid is non-polar if
it has a non-polar side chain
What is a protein
polymers of amino acids
-folding is crucial and is influenced by the sequence of amino acids
What is polymerization
the process of linking monomers (ie. amino acids) to form polymers (ie. proteins)
What is a macromolecule
a large molecule made up of smaller molecules joined together
Are polymers more or less stable than monomers
less, positive free energy
What is a condensation (dehydration reaction)
- how monomers polymerize
- monomer in, water out
- HO on monomer attaches to free H on existing joined monomers and leaves
What is hydrolysis
-reverse of condensation
-breaks up polymers using H2O
-water in, polymer out
EXERGONIC
What type of bond links amino acids and where does it form
peptide bond, between the carboxyl of one amino acid and the amino group of another
Why are peptide bonds so stable
involved electrons are partially shared between peptide bond and neighbouring carbonyl functional group
What geometry does the peptide bond have
planar (double bond nature)
Links of amino acids are called
polypeptides
What are the 3 key points about the peptide-bonded backbone of the polypeptide
- orientation of R group (extend out making interaction with water easier)
- directionality- amino group (N-terminus) always on left and carboxyl (C-terminus) always on right
- flexibility, the whole peptide can’t rotate due to its double bond nature but the single bonds on the side can
What type of bonds form between polypeptide chains
H-bonds
What are the 6 main functions of proteins
catalysis (enzymes), defence(antibodies), movement(motor and contractile proteins ie. actin and myosin), signalling(ie. glucagon), structure,(ie.keratin), transport(ie.hemoglobin and membrane proteins)
Why can proteins have so many diverse functions
due to their diverse size and shape, and chemical properties of their amino acids
What is the primary structure of proteins
the sequence of its amino acids
What is the secondary structure of proteins
- created by H-bonds between primary structures (between carbonyl of one amino acid and H on amino group of another)
- alpha helix (coiled, R groups point outwards) or beta pleated sheet(segments bend 180 deg. and then fold in the same plane; R-groups point up and down)
- depends on primary struc.
H-bonding between sections of the polypeptide backbone is only possible when….
different parts of the SAME polypeptide bend in a way that puts the carbonyl and amino groups close together
Why does proline NOT fit in an alpha helix or beta sheet
it has a strange R group position (second covalent bond with amino group) which causes a kink and disrupts H-bonding
What is the tertiary structure of proteins
- depends on side chain interactions
- multiple secondary structures bonded together
What are the 5 types of side chain interactions
- H-bonding- between H atom and carbonyl group, and between H-atoms in side chains
- Hydrophobic-due to hydrophilic chains interacting with H2O and pushing hydrophobic ones together
- Van der Waals-hydrophobic side chains stabilized by electrical attractions “partial charges”
- Covalent-between S atoms to make disulphide “bridges” which occur with cysteine
- Ionic-between groups that have full and opposing charges ie. amino and carboxyl
What is the quaternary structure of proteins
the combination of polypeptide subunits; may be held together by bonds, r-group interactions or sections of their peptide backbone
- in simplest case= two identical subunits aka “dimer”
- based on tertiary struc.
A multi-enzyme complex is
a group of enzymes each of which catalyzes one reaction and that are physically joined to each other
-all involved in same task
Protein structure is
hierarchial
What is a coiled-coil
when 2 alpha helices have hydrophobic amino acids at every 4th position
Fibrous structural proteins consist mainly of
alpha helices arranged in coiled coils
Molecular chaperones are
specific proteins that facilitate folding, help keep proteins from inappropriately interacting with eachother
Heat-shock proteins are
proteins that speed the refolding of a protein after it was denatured
Protein turnover is
breakdown and resynthesis
Prions are
proteinaceous infectious particles; have odd shape due to improper folding and can cause normal proteins to change shape
Protein function depends on
shape/structure
Substrates are
reactant molecules
A transition state is
a combination of reactant/product bond
super unstable
Activation energy is
the amount of energy needed to reach the transition state
A catalyst is
a substance that lowers activation energy by lowering the free energy of the transition state, increases reaction rate and does not get used up in the reaction ie. enzymes
What do enzymes do
- bring reactant molecules together in specific orientations
- stabilize transition states
The active site is
where substrates bind and react/where catalysis occurs
Are enzymes rigid and static or flexible and dynamic
flex. and dynamic
What actually stabilizes the transition state and lowers the activation energy
interactions with R-groups at the active site
What are the 3 steps of enzyme catalysis
- initiation- enzyme brings reactants together as they bind in active site
- transition state facilitation-interactions between substrate and R-groups lower activ. energy/shape of enzyme may change
- termination-reaction products to not desire to be attached to active site as much as reactants do so they are released
Cofactors can be
- metal ions
2. small organic molecules
What do cofactors do
play a key role in stabilizing transition state
Competitive inhibition is
regulatory molecule binds to active site so substrate can’t bind
Allosteric regulation (more common) is
regulatory molecule binds to a different spot on the enzyme and changes the enzyme’s shape
- activation; active site becomes available
- deactivation: active site becomes unavailable
Rate of an enzyme catalyzed reaction depends on
- substrate concentration
- enzyme availability/affinity for substrate
- temperature(affects movement)
- pH(enzyme shape and reactivity)
Is allosteric activation or deactivation more efficient
deactivation (inhibition)
What is cooperative allostery
occurs between 2 or more subunits, as more subunits are bound the enzyme activity eventually decreases significantly( proportional to the # of subunits) as inhibitor concentration is increased
