Chapter 1- Chemical Basis Of Life Flashcards
What is biochemistry?
Scientific discipline that seeks to explain life at the molecular level
Most abundant elements in living systems
C, H, O, N
Second most abundant elements in living systems
An, K, Mg, Ca, P, S, Cl
Trace elements in living systems
V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, W, Cd, B, Al, Si, As, Se, Br, I
Structure of amino acid
Contain amino group, carboxyllic acid group, central carbon, and variable R group; under physiological conditions ionized to NH3+ and COO-
carbohydrates
aka monosaccharides, formula of (CH2O)n where n is greater than or equal to 3,
nucleotides
five-carbon sugar, nitrogen-containing ring, and one or more phosphate groups
lipids
cannot be described by singular structural formula, many different forms; all tend to be poorly soluble in water (hydro-carbon like)
formation of polymers
chemically linking individual units (monomers) into polymers, individual momomers become covalently linked in head-to-tail fashion; monomers called residues after incooporation into polymer
do lipids form polymers?
lipids do not form polymers, but they tend to aggregate together
what are the polymers of amino acids?
proteins
what links amino acid residues
peptide bonds, link between carbon of the carboxyllic acid and the nitrogen of the amine
what is the conformation of a protein?
the 3D shape, depends on the composition and sequence of amino acids
what is the polymer of nucleotides?
polynucleotides of nucleic acids, aka DNA and RNA; made from just four nucleotides; DNA has bases adenine, cytosine, guanine, and thymine; in RNA thymine is replaced with uracil
what is the linkage for nucleic acids?
phosphodiester bond, linkage between phosphate group on one nucleotide and sugar group of another
what is the polymer of monosaccharides?
polysaccharides, most are homogenous
how are glucose residues linked?
glycosidic bonds
what are the major functions of proteins?
carry out metablic reactions, support celllular structures
what are the minor functions of proteins?
store energy
what are the major functions of nucleic acids?
encode info
what are the minor functions of nucleic acids?
carry out metablic reactions, support cellular structures
what are the major functions of polysaccharides?
store energy, support cellular structures
what are the minor functions of polysaccharides?
encode information
what is the energy relevant to biochemical systems?
Gibbs free energy (G) (J/mol)
what is enthalpy?
(H) equivalent to the heat content of the system
what is entropy?
(S) (J/mol) measure of how the energy is dispersed within a system; measure of system’s disorder or randomness
Gibb’s free energy equation
ΔG= ΔH-TΔS
what is an exothermic reaction?
when heat is released to the surroundings (ΔH<0)
what is an endothermic reaction?
when heat is added to the system (ΔH>0)
what makes a reaction spontaneous?
when ΔG<0, a negative change of free energy; exergonic
what makes a reaction nonspontaneous?
when ΔG>0, a positive change of free energy; endergonic
Does spontaneity determine how fast a reaction will occur?
no, only whether it will occur as written, rate is dependent on other factors
what makes a reaction be in equilibrium?
when ΔG=0, rate of forward reaction is equal to the rate of the reverse reaction, no net change in system
when is a reaction spontaneous at all temps?
when there is a decrease in enthalpy and an increase in entropy
when is a reaction nonspontaneous at all temps?
when there is an increase in enthalpy and a decrease in entropy
how can nonspontaneous reactions occur in the body?
nonspontaneous reactions can be coupled with spontaneous reactions to achieve an overall spontaneous reaction, net change in free energy is negative (can add ΔG values)
what is the function of light in photosynthetic organisms?
excites certain molecules so that their subsequent chemical reactions occur with a net negative change in free energy; coupled with the unfavorable synthesis of monosaccharides from atmospheric CO2
what happens to carbon during the synthesis of monosaccharides?
it is reduced (gains electrons)
what happens to the carbon when the monosaccharide is broken down to be used as fuel?
it is oxidized (loses electrons), ultimately becomes CO2; process is thermodynamically favorable (can be coupled with unfavorable reactions)
what do catalysts (enzymes) do?
increases the rate of a reaction without itself undergoing any net change; almost all reactions occur with aid of catalysts
how do living organisms follow the laws of thermodynamics?
a living organism, with all of its organization, represents a state of low entropy, can maintain this thermodynamically unfavorable state as long as it continues to obtain energy from food
what does ΔG=0 indicate for an organism?
death, chemical reactions in cells reach equilibrium
scenario for emergence of life
inorganic molecules (H2, H2O, NH3, and CH4) could have given rise to simple bio molecules such as amino acids when sparked by lightning; lab experiments with same raw materials and electric discharges to simulate lightning do yield these molecules (other experiments suggest that HCN, HCOH (formedahyde) and phosphate could have been converted to nucleotides in the same fashion); over time molecular building blocks could have accumulated and formed larger structures (probs in shallow waters where evaporation would have led to concentration)
alternate scenario for emergence of life
first cells could have been developed in deep sea hydrothermal vents (w super high temp and gaseous H2S), in lab incubating a few small molecules in presence of iron sulfide and nick sulfide at 100C yields an organic molecule (acetic acid), stabalize in cooler water next to vent
how would the first biological building blocks polymerized?
organic molecules bearing amionic (negatively charged) groups aligned themselves on cationic (positively charged) mineral surface; in lab common clay promotes the polymerization of nucleotides into RNA
how could replication have occurred originally?
may have first made a copy of itself by first making a complement (mirror image) which could then make a complement of itself which would be identical to original molecule
what is natural selection?
phenomenon where the entities best suited to the prevailing conditions are the likeliest to survive and multiply
what would natural selection have favored early on?
replicator that was chemically stable with ready supply f building blocks and free energy, thus a membrane would be advantageous to prevent important molecules from diffusing away, favored replicating systems that developed the means for synthesizing their own building blocks and more efficiently harnessing sources of energy
how did the first cells harness energy?
most likely able to “fix”CO2 (convert it to reduced organic compounds, using free energy released in oxidation of readily available inorganic molecules)
how did later cells harness energy?
photosynthetic organisms used suns energy to fix CO2
how did the concentration of atmospheric O2 increase?
the concomitant oxidation of H2O to O2 when photosynthetic organisms fixed CO2; allowed aerobic organims to take advantage of this powerful oxidizing agent
what are prokaryotes?
small unicellular organisms that lack a discrete nucleus and usually contain no internal membrane; split into bacteria and archae which are similar in appearance but differ metabolically
what are eukaryotes?
usually larger cells that contain a nucleas and other membrane-bound cellular components, can be unicellular or multicellular, includes both microscopic and macroscopic organisms
how can we determine how long ago two groups of organisms diverged from a common ancestor?
number of sequence differences between two groups; species with similar sequences have a longer shared evolutionary history than species with dissimilar sequences
which organelles contain their own genetic material and protein-synthesizing machinery?
chloroplasts and mitochandria
how did the early eukaryotic cell develop?
from a mixed population of prokaryotic cells, over many generations of living in close proximity and sharing each other’s metabolic products, some of these cells became incorporated into a single larger cell; allowed division of labor
