Introduction; Dr. Morgan; 23/01
Practicals attending alternatingly. ETC-electron transport chain. All practicals are after the
lesson is learnt. Biochemistry and Molecular Biology-study of biology at molecular level with
emphasis on structure, function, and processes within the cell, with a focus on macromolecules
(proteins, nucleic acids, (and carbohydrates)).
Sugars and Carbohydrates
No drawing structures, just become familiar with. Sugars from fruits, vegetables, and dairy (lots
naturally). Sugars needed for energy, components of many structures and biological
macromolecules like DNA, membrane protein complexes (lots of proteins are
glycosylated-proteins attached), and key mono sugars from diet include glucose, fructose and
galactose from lactose milk.
Sugars are substances made from C, H, and O (1:2:1), usually in 5 or 6 membered rings
(sucrose has two-glucose and fructose). Basic unit is linear or ring form though. Attached to
chain of C is OH group and hydrogen; one C at the end may be in the form of a carbonyl group
(C=O). Can be simple or long chains or branched. Multiple forms of carbohydrates, sugar,
pasta, DNA. Bonding-takes place when OH of one molecule binds to H from another, forming
water (condensation). Glucose and fructose bind, and connection makes them lose a water
molecule (Is just O). Remaining O forms glycosidic bond linking two C from different sugars.
Breaking bonds-hydrolysis (add water). Number 1,4 or 1,2 or 1,6 refers to positions of carbon in
the glycosidic link. Alpha-alongside the ring centre and beta if below the ring centre. Glucose
and glucose makes maltose.
Glycogen-liver which stores glucose. Monosaccharide-one (glucose), disaccharide (sucrose),
oligosaccharides (3-20)-non digestible (prebiotics). Polysaccharides (>10), which can be homo
or hetero in front of the name. Unbranched starch-amylose or branched is it amylopectin.
Glycogen-frequent 8-10 branches, easier to break down than starch (20-30) by mammalian
enzymes. Dextran, found in bacteria, have complex branches. Alpha and beta forms differ (also
called D and L?)=glucose in its 6 membered ring form, it can be alpha (below the ring) or beta
(above), depending where the OH on C 1 is pointing. Alpha has H on top, OH on bottom. For
branches, can have 1,4 or 1,6 bonds, all about efficiency storing. Cellulose from plants has beta
glucose; human enzymes cannot digest 1,4 beta bonds. Strength of cellulose comes from H
Bonding between the chains. We store glucose as polysaccharide glucogen which has 1,4 and
1,6 linkages.
Sugars with 3 C triose, 5 C pentose, and 5 C hexose. Is either an aldose or ketose sugar (so
far...might be more). Cyclic forms of 5 membered and 6 membered sugar rings are termed
furanose (5) or pyranose (6), reflecting the heterocyclic compounds furan and pyran.
Ribose (pentose) is a key component of nucleic acid where ribose in RNA and deoxyribose is
one less oxygen. Hexose-vary according to position and number of hydroxyl groups;
fructose-C=O is on Carbon number 2 instead of the end.
Reactions: Reducing sugars-seen with mono sugars that can linearize. With alkaline conditions,
they can linearise and donate an electron (oxidation and reduction stuff). Electron acceptor is
usually copper (II) ions, reduced to copper (I) by the aldehyde groups in reducing sugars. The
sugar will gain another oxygen (glucose to gluconic acid). (C=O -H to C=O -OH on first Carbon).
Phosphorylation (adding a phosphate), key modification to saccharides, so CH2O at the end is
now CH2OPO3 2-, which can be used to make ATP (or ATP used to phosphorylate). Enzymes
,that do phosphorylation are kinases. Phosphatase loses a phosphate. Numbering is position of
phosphate. Sugar phosphates are intermediates of metabolic pathways; some act as control
points.
Practical: 3,5-dinitrosalicylic acid (DNSA) is used for the determination of the concentration of
reducing sugars in a sample. A reducing sugar is one where the pyran ring is NOT involved in
the α [1-4] link between the monomer molecules. This link opens up under alkaline conditions
and allows the oxidation of the aldehyde group. This reaction can be coupled to a reduction in
the DNSA reagent which results in a colour change, as measured at 540 nm. The reaction in
this case is 1 molecule of oxidised sugar results in 1 molecule of reduced DNSA. The glycosidic
link between sugars can be broken by acidic conditions and high temperature-why we cook.
Amino Acids and Proteins 30/01/20 Dr. Babis
Protein (macromolecule) made up of amino acids (monomer unit); nucleic acids (DNA/RNA)
made up of nucleotides, carbohydrates made of sugars, and lipids usually made of fatty acids.
Amino acids are also signalling molecules, they charge tRNAs, and cell senses it has energy. If
no, signals as energy crisis in the cell, so some things cease (growth, cell division). Signal for
signalling pathways-diabetes type 1 and 2 are affected. In a cell, made up of 60% proteins! Cell
invests lots of energy, lots of ribosomes in cells. Nucleic acids, only 5%, and study DNA, called
genomics-ways of assessing all of the DNA in the cell (not nucleus; in euk, about mitochondrial
DNA as well). Only RNA looking, called transcriptomics (product of transcription), proteins is
proteomics (most complex because 23k genes, but 100ks produced). Splicing-from one gene,
produces many proteins. Proteins do everything in the cell, cell
division/growth/communication/metabolism/defence/death (mitochondria are center of energy,
but they also control death-apoptosis) and also DNA binding (transcription factors), growth
factors, hormones/receptors, enzymes, antibodies, and proteases. PIC OF STRUCTURE.
Stereoisomers-only L isomers are found in proteins (PIC). The L and D isomers are mirrored
images (ammonia on the left side).
Amino acids can be acid, base, or neutral (protonated or deprotonated). The H is lost on the
ammonia and carboxyl group if gone to basic; carboxyl is lost in partial (neutral). Different R
group defines the amino acid, 20 common ones found in proteins, but we have many amino
acids in a human cell. Protegenic amino acids-20. Urea cycle, more amino acids than
participate in protein genetics. Classes of amino acids: nonpolar, polar, acidic, and basic.
Nonpolar and polar are aromatic (have a ring), polar can be phosphorylated (important!
Targeting proteins in the components of the cell). Hydrophobic nonpolar amino acids, isoleucine
and methionine are examples (methionine-all proteins start with them). First codon (Aug) is
usually codon for methionine. No hydroxyl groups or anything in the side chain. Polar does have
hydroxyl groups. Serine and threonine for example of polar. Basic are lysine, arginine, and
histidine (pos charged, have bases in R group; stored in different compartments in cell
(especially first two-in yeast/plant species, in vacuoles. Animal cells do have small ones, but
equivalent is lysosome; they are signalling molecules, and arginine is an indicator for enough
amino acids and can do translation. Cells read amount of energy through arginine.
Acidic-aspartate and glutamate (glutamate-one of the most abundant in the cell, signalling for
enough energy, but stored in cytoplasm, carboxyl group is acidic part). Aromatic amino
acids-tryptophan (nonpolar) or tyrosine (polar). Ones with hydroxyl group, like serine and
tyrosine, can be phosphorylated (phosphoserines-way to intervene. We can make amino acids
, permanently phosphorylated (genetic engineering can activate/deactivate the pathway)). We
know a pathway goes to a disease,so changing a molecule can cure a disease.
We cannot store proteins by the body (60g required a day as an adult, quite low). Surplus,
excess amino acids undergo either deamination to urea or transamination to other amino acid.
Kidneys filter urea out. Deamination is a process to break down amino acid, take away amino
group and make ammonia. Keto diets-keto acid is product of deamination (not preferable food).
Preferable carbon source is carbohydrates. Cannot rewire metabolism after all this evolution.
Ammonia is highly toxic, must be removed. Keto acids may enter the Krebs cycle and electron
chain, but is not preferable. Ornithine cycle is what happens to ammonia, ammonia is combined
with CO2 and converted to urea through the ornithine cycle. Urea cycle, orithine cycle,
describes the conversion reactions of ammonia to urea. Ornithine is an amino acid, but does not
participate in genetic code, but is important in metabolism. Ornithine gets one ammonia and one
CO2, makes citrulline (with an ornithine carbamoyl transferase enzyme). With aspartate, make
an argininosuccinate. Then the lyase breaks it down to fumarate, then makes into arginase and
produce urea-PIC. Do not need to know this cycle though, nor enzymes; remember the
ammonia plus CO2 goes to urea and water.
Transamination; proteins are degraded and synthesised within all tissues on a regular basis.
Some amino acids can be recycled and synthesised by the liver in the process of
transamination. You need the corresponding ketoacid of the amino acid. Take the amino group
and make the corresponding ketoacid, then transfer the amine group. We cannot do this for all
of them, but esentially make one amino acid from another. General transamination-amino acid A
plus keto acid B makes keto acid A and amino acid B. Literally just switch R group I think.
Alanine plus alpha oxoglutaric acid makes pyruvic acid and glutamic acid is an example.
Glutamic acid used in Krebs cycle if no carbohydrates or lipids.
PIC OF PROTEIN PEPTIDE BOND. Amino acids can be linked via peptide bonds; DO NOT
FORGET THE WATER WHEN PEPTIDE BOND IS FORMED. Hydrolysis to get to separate
amino acids, condensation to make the peptide bond. Hydrolysis happens through enzymes
with 37 degrees or acidic areas, or with proteases. Peptide, short protein. N terminus is the
ammonia, and C terminus is carboxyl group. First amino acid is methionine! Cystine can form
disulphide bonds (bridges), with oxidation the S-H from cysteine can be separated to make S-S
plus 2H and 2e’. Insulin, small hormone, formed by two amino acid chains; kept together with
disulphide bridges. Our antibodies are made up of chains that are kept together with disulphide
bridges.
Peptide bonds are with C-N, and is like a single bond. However, the N has 2 electrons, which
are not coupled; those electrons can be donated, so the single bond between C and N or with
the two electrons can form a double bond with C=N and have a single bond then with the O.
Resonance! O=C-N to O-C=N. Those atoms can be in one plane (surface), and cannot rotate;
confines the protein since they cannot move. No planar rotation in that bond, but on the C and N
chains, they can start turning so there is rotation there. Static-there is space, and cannot be
together in the same space. R groups on opposite sides is trans (transform since they are
away). Cis if both R groups are next to eachother, same side. Trans arrangement favoured in
nature, but with this static inhibitions, there must be a rule; do we have spaces/arrangements
we see mostly in the amino acids in space? Yes. The R groups of two adjacent amino acids can
sterically hinder the rotation of the alpha carbon and thus favour the trans arrangement.
