Biochemistry and Unity of Life Flashcards
What is Biochemistry
- study of life at a molecular level
- application of chemistry to explain biology
Living states can be considered from 4 perspectives:
- Chemical
- Energy
- Genetic
- Evolutionary
All living things are made of 4 common ingredients (98% of organisms)
- Carbon
- Oxygen
- Hydrogen
- Nitrogen
How does structure dictate function?
- molecules do what they do because of their structures
Conformation
flexible changes in structure that don’t break any bonds (spinning things around)
Configuration
fixed changes by breaking bonds
- conferred by double bonds and chiral centers
Geometric (cis-trans) isomers
have same chemical formula but differ in the configuration of groups with respect to a non-rotating double bond
- once carbons are double bonded they can no longer rotate
trans
“across” groups on opposite sides of the bond
- “z” shaped
cis
“on this side” groups on the same side of the double bond
- half circle shaped
chiral carbon
4 different groups that will attach to the central carbon that are all different
- chemical properties are identical but biological properties are distinct
- double bonds can’t be chiral carbons
Construction
often constructed from one stereoisomer
Ex. proteins are built from L-amino acids
Interactions
interactions between biomolecules, as well as between biomolecules and small molecules are stereospecific
Advantages of constructing biologicals and polymers:
- Simplicity
- Recycling
- Diversity
Simplicity
simple and conserved reactions for synthesis and degradation
- single unified system (all be broken down in the same way)
Recycling
biomolecules can be digested back to component building blocks
- once protein is used, it can be broken down to amino acids and build a new protein
Diversity
Complex molecules can be generated
4 major classes of biomolecules:
- Proteins
- Carbohydrates
- Nucleic acids
- Lipids
Proteins
- 20 different amino acids
- Peptide bonded linked groups that form linear chains that fold into complex patterns
- side chains differentiate the structures (activity)
Carbohydrates (polysaccharides)
- Monosaccharides link together to form linear or branched polymers
- Has lubricate joints and flexible
- serve many important biological roles including structural, energy storage, and cellular recognition
Nucleic acids
- Linear polymers of nucleotide building blocks for DNA and RNA
- Aspects of storage and genetic information
- Cytosine, uracil, thymine, adenine, guanine
Lipids
- aggregates of building blocks
- aren’t covalently linked to each other or locked into specific positions
- serve in energy storage , formation of membranes, and signalling
Prokaryotes
- small, simple, single-celled organisms (bacteria)
- Rapid growth allow adaptation to environment
Eukaryotes
- larger complex cells
- make up multicellular organisms
- membrane bound organelles to support specialized functions
- form particular biological functions
In vitro (in glass)
- studies behaviour of molecules outside the context of the cell and organism (inside test tube)
In vivo (in the living)
- studies occur within the complexity of the cell or organism (inside a living organism)
First Law of thermodynamics
Total amount of energy in the universe remains constant, although forms of energy may change
- energy cannot be made or destroyed
Second Law of thermodynamics
The tendency in nature is towards a greater disorder (continually increasing)
Ex. sand castle falling apart
Enthalpy
Energy contained within the bonds of a molecule
- depends on number of bonds and value of each
Entropy
Degree of randomness
- temperature dependent
Endergonic
Non-spontaneous process, needs input of energy to proceed
- Delta G > 0
Exergonic
Spontaneous process (occurs without input of energy), releases free energy which can be used to do work, proceeds until equilibrium is reached
- delta G < 0
Delta G = 0
system is at equilibrium, no change in free energy in the system
How can cells drive thermodynamically unfavourable reactions?
By taking a dis-favourable reaction and pairing it with a favourable reactions to make it favourable
Catabolic
- Breaking stuff down
- releases energy
Anabolic
- Builds stuff up
- Requires energy
ATP
- common energy currency
- serves as a link between catabolic and anabolic reactions
Perpetuation of life requires that genetic information be:
- stored in a stable form
- expressed accurately in the form of gene products
- reproduced with minimal errors
Linear sequence in DNA encodes three-dimensional protein structures:
- nucleotide sequence determines sequence of amino acids
- amino acid sequence dictates its structure
- structure of protein dictates its biological activity
- results in an active hexokinase
