Proteins, Nucleic Acids, Energy, ATP, Enzymes, Sugars, Lipids
Tertiary Structure
Overall 3D shape of polypeptide, final folding
Occurs due to side chain interactions
Interactions like: H-bonds between 2 chains, hydrophobic and van Der Waals interactions etc.
Disulfide Bridge
2 Cysteine side chains are close (in space, not chain) so the two S atoms bond
Bond via redox reaction
Rearranging of Hydrophobic Amino Acids
Rearrange themselves away from water
Hydrophobic amino acids face inside and hydrophilic will face outside
Coiled Coils
Arise when two alpha helices have hydrophobic amino acids at every 4th position
2 helices wrap around each other to avoid water
Very stable structure that shows up in hair and feathers (keratin protein)
If 2 helices from the same structure, will have a loop, tertiary structure
If 2 helices from different structures, no loop, quaternary structure
Quaternary Structure
Occurs when tertiary structures still do not have function
Final step of protein folding
Several polypeptides form a large protein complex
Ex. hemoglobin is made of 4
Amino Acid Sequence Importance
Proteins diluted in watery solution denature at high temperature (unfold)
Will renature (refold) when temperature is lowered
Thus, the primary structure is sufficient for folding and the function is encoded in the amino acid sequence
Ex. 1 amino acid mutation in hemoglobin causes sickle cell anemia
Protein Turnover
Breakdown and resynthesis, occurs constantly in cells
Every protein has a half life
Half life: the time after which half the proteins have broken down
Chaperones
Help proteins fold properly after synthesis or unfolding
Keep other proteins from interacting inappropriately with eachother
Nucleotides
Occur in RNA, DNA, and energy carries (ex. ATP)
Serve functions in signalling and energy storage as monomers
Made of a phosphate group, attached to the 5’ carbon on a 5-carbon sugar, and the 1’ carbon of the sugar is bonded to a nitrogenous base
Carbon Sugar in RNA vs. DNA
RNA: called ribose, with an OH attached to the 2’ carbon
DNA: called deoxyribose, with an H attached to the 2’ carbon
No oxygen makes it more stable
Phosphates in Nucleotides
Can be monophosphate, diphosphate, or triphosphate, for a single nucleotide in solution
Connects with the 5’ carbon on/in the sugar
Considered energy rich bonds because their hydrolysis (depolymerization) releases energy
ADP has 2, ATP has 3
Nitrogenous Bases
Pyrimidines: single aromatic ring
Cytosine, Uracil, Thymine
Purines: two aromatic rings (larger)
Guanine, Adenine
**In RNA Thymine is replaced by Uracil
Phosphodiester Linkage
When nucleotides polymerize (condensation reaction)
Polymerization occurs 5’ to 3’ direction
The 5’ phosphate on the incoming molecule forms a covalent bond with the 3’ hydroxyl
Thus, RNA/DNA molecules start with a 5’ phosphate and end with a 3’ hydroxyl
Sugar Phosphate Backbone
The backbone of RNA and DNA molecules, long chain of nucleotides
Made by phosphodiester linkage of nucleotides
The nitrogenous bases do not play a role in formation
Faces the outside while nitrogenous bases face inside
Protects them from reacting with other molecules, makes D/RNA stable
Nitrogenous Base Pairing Rules
Purine bases only pair with pyrimidine bases
Guanine → Cytosine form 3 H-bonds (most stable)
Adenine → Thymine form 2 H-Bonds (RNA)
Adenine → Uracil form 2 H-Bonds (RNA)
RNA vs. DNA Structure
RNA is made of one sugar phosphate backbone, has U not T, usually has a loop and folds over on itself
DNA is made of two antiparallel strands, forming a helix
RNA can occasionally execute info like proteins
Major and Minor Grooves
Occur in DNA double helices
Major Groove: the 2 sugar-phos backbones are more widely spaced, allowing DNA-binding proteins to recognize the nitrogenous bases in the interior
Important for transcription factors, enzymes etc.
Metabolism
All chemical reactions in a cell, divided into two types:
Anabolic: make something, link simple molecules to make complex ones, energy storing reactions, require energy
Catabolic: break down complex molecules into simpler ones, release energy
Energy Conversion in Chemical Reactions
chemical bond energy in molecules (potential) → rapid molecular motions while joining (kinetic) → heat energy (heat)
What drives energy conversions?
Not energy content/potential energy
The drive of energy to become evenly distributed/dispersed pushes reactions forward
First Law of Thermodynamics
During any energy conversion, the total initial energy is the same as the total final energy, as energy cannot be created or destroyed.
Second Law of Thermodynamics
Energy spontaneously disperses from being localized to becoming spread out if it is not hindered from doing so, thus entropy increases.
Or, energy transformations always result in a state of higher probability (a more disordered state).
What is change in entropy/overall disorder in the universe?
The amount of energy released to drive a chemical reaction.
What are the two ways a cell can release free energy (drive a chemical reaction)?
Entropy (S) - directly increasing/creating disorder in the cell (or closed system)
Ex. digesting a polymer, cutting a protein
Enthalpy (H) - undergoing a chemical reaction that releases heat into the surroundings making the disorder occur outside the cell (or closed system)
Total Free Energy and delta G Explained
delta G: total free energy (cal or J)
delta H: enthalpy
delta S: entropy/disorder
T: absolute temperature
If delta G is:
Negative: energy is released (disorder created) and the reaction is favourable/spontaneous
Positive: energy is required, not spontaneous
Four Types of Reactions
Exergonic: heat is released (-H), disorder created (+TS), spontaneous (-G)
Most catabolic reactions
Heat is released (-H), disorder decreases (-TS), spontaneous (-G) ABOVE a certain temperature
Ex. in protein folding heat is released, but disorder decreases because you get a nicely folded protein, if temperature is too high it will never fold and makes (+G)
Heat is used up (+H), disorder created (+TS), spontaneous (-G) ABOVE a certain temperature
Ex. Dissolving NaCl in water since heat is needed to break the crystal lattice
Endergonic: heat is used up (+H), disorder decreases (-TS), never spontaneous (+G)
Most anabolic reactions
Reaction Coupling
Since anabolic (endergonic) reactions have a positive delta G, they must be coupled with catabolic (exergonic) reactions to make the overall delta G negative.
Equilibrium and Reversible Reactions
All reactions are theoretically reversible, by the law of mass action
If reactions are left alone, they reach an equilibrium point where forward and reverse reactions take place at the same rate (G=0)
Energy Transfer in Cells
All living cells use ATP for energy capture, transfer, and storage
Some of the free energy released by exergonic reactions is captured in ATP, which then can drive endergonic reactions
ATP Hydrolysis
ATP hydrolyzes to yield ADP and an inorganic phosphate ion
This reaction is very exergonic since the body has a very high ATP concentration and the ADP concentration is very low
ATP and ADP Reaction Cycle
ADP + Pi → ATP: Endergonic, energy required, so needs an exergonic reaction to provide energy
ATP → ADP + Pi: Exergonic, energy released, so needs an endergonic reaction to give the energy to
What can you predict about a reaction?
Direction of a reaction can be predicted if the delta G is known, but not the rate of the reaction
Activation Energy and Relevance to Exergonic Reactions
Activation Energy: the amount of energy needed to put molecules into a transition state (less stable state)
Exergonic reactions proceed only after the activation energy is added
Catalysts
Substance that seeds up a reaction but is not used up in it (ex. enzymes)
Only applicable to reactions with overall negative delta G
Delta G is not changed, only lowers the activation energy required
Explain Enzyme-Substrate Interactions
Reactants (substrates) bind to the active enzyme site
Enzyme undergoes conformational change that brings the substrates into a transition state, with lower activation energy, speeding up the reaction
Products leave the active site, and the enzyme reverts to its original shape, unchanged
How can you induce the transition state of a substrate?
Binding them in the correct orientation
Exposing reactants to a differently charged environment, promoting catalysis
Inducing a strain on the substrate to break a covalent bond
Enzyme Cofactors
Some enzymes require cofactors to function
Can be metal ions (zinc), small organic molecules (not amino acids), temporarily or permanently bonded
What does it mean when an enzyme is saturated?
All active sites are occupied
A higher substrate concentration does not increase the rate of product formation
The maximum reaction rate is achieved
Three Categories of Carbohydrates
Monosaccharides
Disaccharides: two monosaccharides
Polysaccharides: 3 or more monosaccharides (up to 100,000s)
Functions of Sugar
Energy storage, building block for nucleic acids, structural component (ex. in wood)
General Sugar Formula & Structure
Multiples of CH2O
An aldose, carbonyl group at the end of the carbon chain
A ketose, carbonyl group in the middle of the carbon chain
Aldose and ketose are isomers
Isomers
Compounds that have the same molecular formula but are structurally different
Usually a functional group attached to a different carbon
Optical Isomers
Occur when a carbon has four different groups attached (chiral centre)
Non-super imposable mirror images of each other
Glucose and Galactose
Optical Isomers of each other
The hydroxyl on the fourth carbon is flipped
What happens to glucose in solution?
The straight chain forms another covalent bond, becoming a ring
This makes the first carbon asymmetric, giving two isomers
Alpha and beta glucose
When the molecule is a monomer it can change between both isomers freely, it links and unlinks
Glycosidic Linkage
When 2 glucose monomers link through the oxygen on the fourth carbon on the incoming molecule
The oxygen attaches to the first carbon of the other molecule, replacing the OH
The OH and the H on the incoming molecule form one molecule of water
Once monomers link in a beta or alpha orientation they can no longer change
Glucose Alpha 1-4 Linkage, Properties in Plants vs. Animals
2 glucose molecules with alpha 1-4 linkage makes maltose
More of these links make starch, links have same orientation
Unbranched, in plants = amylose
Moderately branched, in plants = amylopectin
Lightly branched, in animals = glycogen
Bulky CH2OH groups are all on the same side, resulting in the shape of a spiral
Glucose Beta 1-4 Linkage, Properties in Plants vs. Animals
2 glucose molecules with beta 1-4 linkage makes cellobiose
More of these links makes cellulose, each link flips orientation
Thus, linear, symmetrical, and always unbranched
Better H-bonding and can form parallel strands
Oligosaccharide
10-20 sugar molecules linked together
Lipids
Fats (solid) or oils (liquid)
Hydrophobic, since few H atoms
Most energy dense cell in the body
Takes longer to mobilize than starch
Fats and Oils Structure
Made of three fatty acids and one glycerol connected by ester linkages, formed through dehydration reactions.
Fats have NO double bonds, packed together closer, van Der Waals is stronger
Fats have AT LEAST one double bond, packed together less closely, van Der Waals is weaker
Fatty Acids
1 carboxyl group and a long hydrocarbon chain
Amphiphilic: hydrophobic hydrocarbon chain, hydrophilic carboxyl group
Found in soap
Phospholipids
Very amphiphilic: hydrophilic head group, attached to glycerol, attached to 2 fatty acid tails
Have the ability to self-assemble into lipid bilayers
Lipid Bilayers
Phospholipid heads interact with water (hydrophilic)
Tails face inwards (hydrophobic)
Movement in lateral direction, rarely flip to other side
Bilayer sheets form a sealed compartment/sphere that is energetically favourable
Unsaturated Fatty Acid
Contain a double bond, creating a kink in the tail
Cannot be packed as close together
Increasing fluidity and permeability of the membrane
Unsaturated Fatty Acids in Fish and Plants
Fish and plants adjust the number of double bonds in phospholipids to keep membrane fluidity stable over a variety of temperatures.