BioChemistry Flashcards
Why is carbon extremely versatile?
- it has a large structural diversity and therefore also a large functional diversity (bind to different receptors)
Orbitals
the shapes/volume in which electrons are distributed
S, P, D, F
Explain a covalent bond in terms of orbitals
1 orbital for each atom (carrying an unpaired electron) fuses into a molecular orbital which now contains 2 electrons
Triple bonds are…
instable
Chiral center
region in a molecule where C is bound to 4 distinct chemical groups
(achiral, also 4, but 2 are the same)
Enantiomers
2 different configurations of a molecule, with a chiral center (mirror images of each other)
Conformations
different forms/projections of molecules (e.g. single or double bonds)
Double bonds don’t allow…
for a rotation to take place
Single bonds allow…
free rotation
Staggered conformation has … potential energy
lower
Eclipsed conformation has … potential energy
maximum
Conformation
the (potentially flexible) spatial arrangement of atoms around fixed bonds in molecules
- can readily be interconverted
Configuration
the FIXED arrangement of atoms dictated by the bonds of molecules
- cannot easily be interconverted
Catabolism
the conversion of potential energy in food -> energy used by cells to work
- generates energy and waste
Anabolism
the synthesis of biomolecules from building blocks
- uses up energy
Lithnotrophs
require inorganic molecules for fuel
Energy
the capacity to do work
1st law of thromodynamics
- constant amount of energy in the universe
- energy cannot be created or destroyed, but can change its form
2nd law of thermodynamics
- energy is transferred in a way that increases the randomness (entropy) of the universe
Gibbs free energy formula
G = H - TS
G - free energy (the energy that is available to do work)
H - enthalpy
T - temp. (kelvin)
S - entropy
Enthalpy
total energy of the system (including bonds)
a system with a lot of free energy is
unstable
Spontaneous process
decrease in free energy (between substrate and product) as the system moves to a more stable state
delta G is negative
Exothermic
negative change in enthalpy, heat is released
Endothermic
positive change in enthalpy
Non-spontaneous (endergonic) reaction
products are less stable than substrates because they have a higher potential energy
Characteristics of a reaction:
- spontaneity
- equilibrium constant
- directionality
- velocity
Equilibrium constant (Keq)
when there is no net change in the concentrations of P or S
Directionality
most directions are reversible (move in both directions)
- determined by Le Chatelier’s principle: when a dynamic equilibrium is disturbed, it changes to counteract the disturbance
Le Chatelier’s principle
when a dynamic equilibrium is disturbed, it changes to counteract the disturbance.
Protein
a linear polypeptide of amino acids linked by peptide bonds
What are the 4 groups coming off the central carbon in amino acids?
- hydrogen group
- amino acid group
- carboxylic acid group
- r group/ side chain
Zwitterion
has both a positive and a negative charge
3 main types of non-covalent interactions
Non-directional:
- Van de Waals (weakest)
- Salt bridges (strongest)(between pairs of charged ions)
Directional:
- Hydrogen (only between polar. groups with permanent dipoles)(H donor and acceptor)
A proteins functions are determined by its…
range movement / conformational flexibility
Elements in amino acids
N, H, O, C, and sometimes sulfur
Polar
can readily form H-bonds
Aliphatic compound (proteins)
- long chains (C in the middle, H attached)
- usually only single bonds
Aromatic compounds (proteins)
- rings
3 Secondary protein structures
- Beta sheet (multiple H-bonds)
- Alpha helix
- Loops
3 peptide bonds
- Cis (2 H side chains are parallel and tend to clash) (unfavorable)
- Trans (2 H side chains are adjacent)
- Omega
In proteins ….. always comes before C
N
In proteins ….. always comes before psi
phi
Dihedral angles
between 2 intersecting planes or planes
- Phi (between N and alpha carbon)
Psi (between the alpha and the carbonyl carbons)
Imino acid
contains both imine and carboxyl functional groups
Molecular models:
Red is:
Blue is:
oxygen
nitrogen
Tertiary structure of a protein
arrangement of helices, sheets, and loops within the polypeptide
Motif vs domain? (proteins)
Motif: assembly of several secondary structures
- a commonly repeating arrangement of a few secondary structure elements
Domain: 1+ motifs assembled to form a globular structure
- independent folding unit of a protein
Loop regions usually hold the … of enzymes
active sites
Protein fold
arrangement of secondary structure elements of a domain or protein
Proteins only fold in…
aqueous environments (as it is entropically favorable to mask hydrophobic residues from water)
What is the main force against protein folding
the loss of entropy (lot of conformational entropy when unfolded)
Hydrophobic effect (proteins)
increase in the conformational entropy of water as less of it is interacting with the buried side chains
…. stabilizes secondary structures
H-bonding
3 favorable energetic components:
- hydrophobic effect
- non-covalent interactions
- reduction in entropy (going from many conformational options to a single one)
2 main forces that promote protein folding:
- hydrophobic effect
2. enthalpy
Main force that disfavors protein folding
chain conformational entropy
Why does urea denature proteins
- it is very polar
- alters H-bonds in the water, reduces hydrophobic effect
Thermodynamic hypothesis
the most stable thermodynamic conformation of a protein is its native fold
Folding is a … process
spontaneous
During which part of protein folding is there the least free energy?
when a protein is in its native structure
Protein structure is determined by…
its primary sequence
Levinthal’s paradox (proteins)
the protein has no time to explore all the possible conformations as it would take longer than the existence of the universe
How are the best protein conformations found?
through cooperativity, when one residue folds it makes it more favorable for another to fold as well
2 models for how protein folding beings:
- Diffusion collision model
- secondary structure forms and then the rest of the
protein arranges itself
- secondary structure forms and then the rest of the
- Nucleation condensation model
- first the hydrophobic core collapses, and the the
secondary structures follow
- first the hydrophobic core collapses, and the the
Cytosol
the aqueous component of the cytoplasm
- is actually quite crowded with a lot of proteins and RNA, leading to the risk of aggregation
Aggregation
when misfolded proteins clump together
Chaperons
proteins that prevent aggregation, and help protein folding
- prevent teenagers from getting too tangled up before they become adults
…. interactions often lead to aggregation
hydrophobic interactions
Are H-bonds directional?
yes
Rapid protein folding may occur because of:
- hydrophobic interactions in the core
2. H-bonding networks in secondary structures
Catalyst (enzyme) determine….
the speed of the reaction
Substrate to enzyme equation
E + S <=> ES <=> EP <=> E + P
ES - enzyme-substrate complex
EP - enzyme-produce complex
3 reasons why enzymes are good catalysts:
- formation of transient covalent bonds between substrate and enzyme (lowers activation energy)(decreases entropy)
- formation of weak covalent bonds (binding releases energy, decreases activation energy)
- exquisite specificity (induced fit)
What are the functions of the rest of the enzyme?
- 3D fold allows for the correct positioning of residues (conformational change during binding)
- region for induced fit of substrate
- regulating and coordinating the enzyme
- regions involved in protein-protein interactions
- enzyme complexes
How are enzymes regulated?
- signals in the cell
Stochastic
randomly determined
Zymogens / proenzymes
- synthesized as inactive precursors
- cleaving activates them
- reduce potential cell toxicity but allow for the quick release of active proteins
Proteolysis
partial breaking down of proteins
- activates some proteins
Insulin
released by the pancreas when there are high levels of glucose in the blood, stimulates glucose uptake by liver, adipose tissue, and muscles
How do enzymes work?
decrease activation energy and then catalyze the reaction
DO NOT impact the equilibrium of reactions
Reaction velocity
the amount of products formed over time PR the amount of substrate consumed
