Download Option B IB Chemistry Definitions HL

Chemistry: Definitions
Option B – Human Biochemistry - HL
Active site:
The part of the protein that is involved in the catalysis.
ADP:
Adenosine diphosphate. Made of base A, ribose, and two phosphate
groups. Addition of another phosphate group makes ATP.
ATP:
Adenosine triphosphate. Made up of base A, ribose, and three phosphate
groups bonded together by high-energy phosphate bonds. Breaking the
last of these bonds releases energy for use in cells, leaving ADP.
Chromosome:
A structure composed of DNA and associated proteins.
Codon:
Each of 64 permutations of the triplet code.
Coenzyme:
Organic cofactors. Example: B-vitamins. Two types:
1) permanent coenzymes (always bonded to enzymes);
2) non-permanent coenzymes (only bonded to enzymes during
catalysis).
Cofactor:
A substance that is a part of the active site, and that is involved in the
catalysis. Can be:
1) inorganic (metal ions);
2) organic (coenzymes).
Concentration, effect of:
1) Increasing concentration of the substrate: proportional
increase in rate, but eventually evens out as all active sites of enzyme
become saturated. 2) Increasing concentration of enzyme: proportional
increase in rate.
Cyanide:
A poison which works in the same way as CO: by forming irreversible
complexes with the iron in Hb. Taken up by the hemoglobin easier than
oxygen is.
Cytochrome:
Oxidizing enzymes in mitochondria. Contain Cu2+/Cu+.
Deoxyribose:
The pentose sugar found in DNA.
DNA profiling:
Using a small amount of cellular material, DNA is extracted and broken
down into minisatellites using restriction enzymes. Splits where there
are no coded messages in the base sequence are unique to the person
giving the sample, and so this can be used to identify them.
DNA replication:
DNA in cell begin to partly unzip as hydrogen bonds between the bases
break. New sugar base units are taken up from the aqueous solution.
Due to set pairs (AT and CG), the new strands will be identical to the
original one.
DNA:
Deoxyribonucleic acid. Double-stranded. Made up of nucleotides. Have –
charge due to phosphate group. Cannot penetrate nucleus.
Electron transport:
Occurs in inner membrane of mitochondria, which contains different
proteins and enzymes, incl. cytochromes. The H+ ions from the NADH2
(product from the citric acid cycle) move along cytochromes by
repeated redox reactions, due to presence of stronger oxidizing
agents. Enzyme cytochrome oxidase causes H+ ions, e- and O2 to react
to form water, releasing energy in the process.
Enzyme saturation:
When all the active sites of the enzymes are occupied by a substrate. At
this saturation, increasing substrate concentration has no effect.
Enzyme, factors affecting:
1)
Enzyme concentration;
2) substrate concentration;
3) temperature;
4) pH;
5) inhibitors (reversible/irreversible).
Enzyme:
Proteins that act as biological catalysts, for specific substrates.
Gene:
A specific sequence of DNA which codes for the synthesis of a protein.
Glycolysis:
First phase of breakdown of glucose in respiration. Occurs in cytoplasm.
Haemoglobin:
Found in RBC’s. Contains four large polypeptide groups and four Fe 2+ ions
surrounded by hem groups. At high oxygen concentrations, oxygen
bonds onto the iron in hem group as an extra ligand. At low
concentrations, the reverse occurs.
Hb
Heavy metal ions, effect of:
Can poison enzymes by reacting with –SH groups replacing the
hydrogen atom with a heavy metal atom or ion. Enzyme is denatured.
Induced fit theory:
The active site can alter its shape to allow for a better fit with the
substrate. An enzyme-substrate complex is created, and the catalyzed
reaction takes place, leaving an enzyme-product complex. The products
are released, and the enzyme reverts to its original shape.
Inhibition, competitive: Reversible inhibition. Resemble the substrate in shape, but cannot
react. Slow down reaction by occupying active site. Does not affect
Vmax but does affect Km.
Inhibition, irreversible: The inhibitor reacts with a part of the enzyme, and a covalent bond is
formed between the inhibitor and enzyme. Enzyme activity is
permanently destroyed. Example: nerve gases work by alkylation of an
OH-group in the active site of an enzyme.
Inhibition, non-competitive:
Reversible inhibition. Prevents enzyme reactions by binding to
another part of the enzyme than the active site. This causes the
enzyme to alter its shape and be unable to receive its substrate. Does
not affect Km but does affect Vmax.
Inhibition, reversible: The inhibitor makes weak (intermolecular) bonds with the enzyme. The
enzyme can become biologically active again. Two types:
1)competitive;
2) non-competitive.
Metal ions:
Examples of important ions: Na+ and K+ (nerve impulses and water
balance); Ca2+ (bones and teeth); Cu2+ (enzymes); Co2+ (vitamin B12);
Fe2+ (Hb). All depend on one of the following:
1) difference in charge density between two ions;
2) variable oxidation states;
3) forming complexes with ligands.
Michaelis-Menten constant:
The substrate concentration when the rate of the reaction is at
½ Vmax. The constant will always be the same for a particular enzyme
and particular substrate.
Km
mRNA:
Messenger of genetic information (transcription).
Nucleotide:
Repeating base-sugar-phosphate units that make up the nucleic acids.
The base can be one of four nitrogen-containing bases, adenine (A),
guanine (G), cytosine (C) or thymine (T). In RNA, uracil (U) replaces T.
The phosphate bonds to the C4, while the base bonds to the C1.
pH, effect of:
The pH value affects the tertiary structure. Enzymes have an optimum
pH; outside of this, they can be denatured.
Phosphodiester bond: Bonding between nucleotides in a polynucleotide. Each nucleotide is
joined between the C3 of the sugar and the neighboring phosphate
group.
Phosphorylation:
Protein synthesis:
Addition of phosphate group. Phosphorylation in the sodium-potassium
pump causes shape of pump to change.
Happens in ribosomes.
1) Transcription in nucleus; followed by
2) processing by mRNA;
3) translation by ribosome.
Ribose:
The pentose sugar found in RNA. Same as deoxyribose, except with an
extra O bonded to the C2.
Ribosome:
Particle that causes protein synthesis. Sequence of aa’s determined by
nucleotide sequence in mRNA.
RNA:
Ribonucleic acid. Single stranded. Contains base U instead of DNA’s base
T. Two functions:
1) transcription (messenger of genetic information);
2)
translation
(translating
gene
information
into
protein
synthesis).
Sodium-potassium pump:
Protein structure in cell membrane act as valves pumping Na+
ions out of cell and K+ ions into the cell. Works due to difference in
charge density between Na+ and K+. The Na+ binds to three sites on the
protein molecule. Energy is extracted from ATP by hydrolyzing to ADP,
and the phosphorylation causes the pump to change its shape. Na + ions
are expelled, and K+ ions bind to two sites on the protein molecule. The
loss of the phosphate causes the pump to change its shape again,
expelling the K+ ions into the cell.
Substrate:
The substance on which an enzyme acts.
Temperature, effect of:
Increasing temperature will initially increase rate of enzyme-
catalyzed reactions (greater proportion of reactants will have the
minimum activation energy). Optimum temperature for most enzymes is
ca. 40C. Above this temperature enzymes rapidly denature.
Transcription:
Copying of DNA onto a strand of RNA by unwinding temporarily due to
the action of RNA polymerase. Takes place in nucleus.
Translation:
The reading of the base sequence of the mRNA by ribosomes to make a
sequence of aa’s to form a polypeptide.
Triplet code:
A sequence of three bases that represents one aa.
tRNA:
RNA that brings the right aa’s to the ribosomes.
Vmax:
The maximum rate at which enzyme activity can occur, given a constant
enzyme concentration. This is when the active sites of the enzyme are
saturated.