Option B: Biochemistry Flashcards
(92 cards)
1
Q
Metabolism
A
all the chemical processes that take place within a living organism to maintain life
2
Q
Anabolism
A
- the biosynthesis of complex molecules from simpler units
- requires energy, supplied by catabolic reactions or in photosynthesis is received in the form of light
- reduce their entropy
- cannot be spontaneous
3
Q
Catabolism
A
the breakdown of complex molecules in living organisms into simpler units that is usually accompanied by the release of energy.
4
Q
Metabolic pathway
A
A biochemical transformation of a molecule through a series of intermediates (metabolites) into the final product.
5
Q
Why is carbon the main element in organic molecules?
A
- it’s relatively small in size
- moderate electronegativity
- 2s2.2p2 in the ground state and 2s1.2p3 in excited state
- forms four single or multiple bonds with many elements including itself
- energies of these bonds are high enough to produce stable molecules and at the same time low enough to allow other substances to undergo various transformations
- allows for the formation of molecules of any size and complexity
6
Q
lipids
A
fatty acids → lipids
7
Q
proteins
A
amino acids → peptides → proteins
8
Q
nucleic acids
A
nucleic bases → nucleotides and sugars → nucleic acids
9
Q
polysaccharides
A
sugars → polysaccharides
10
Q
List four most common types of biochemical reactions
A
1) condensation
2) hydrolysis
3) oxidation
4) reduction
11
Q
Oxidation
A
loss of two hydrogen atoms or the gain of an oxygen atom
12
Q
Reduction
A
gain of two hydrogen atoms or loss of an oxygen atom
13
Q
2-amino acids
A
- simple proteins
- linear polymers
joined by amide linkages (or peptide bonds) - general formula: H2NCH(R)COOH
14
Q
Peptide
A
polycondensation polymers of 2-amino acids containing less than 20 structural units.
15
Q
Polypeptide
A
longer peptides with 20–50 structural units
16
Q
Proteins
A
polycondensation polymers of 2-amino acids with more than 50 structural units.
17
Q
Proteinogenic 2-amino acids
A
- 20
- all have an amino and carboxyl group attached to the same atom
- R, side-chain
18
Q
List 9 essential 2-amino acids
A
1) histidine
2) isoleucine
3) leucine
4) lysine
5) methione
6) phenylalanine
7) threonine
8) tryptophan
9) valine
19
Q
Zwitterion
A
2-amino acids with two ionized groups that has zero charge
- the -NH3^+ is the acidic centre that can lose a proton in strongly alkaline solutions and produce the anionic form of the amino acid
20
Q
Isoelectric point (pI) of amino acids
A
The pH at which the sum of the positive and negative charges of all forms of the amino acid is zero
21
Q
Gel electrophoresis
A
- Separates and identifies amino acids, peptides, proteins and other ionizable compounds
- gel is saturated with a buffer solution to maintain a constant pH during the experiment
- two lectrodes are connected to the opposite side of the gel and an electric current is applied. The negatively charged compounds move to positively charged electrode (anode) and positvely charged to the cathode.
- when separation is complete, th gel is developed with a locating agent, ninhydrin that form coloured compounds with amino acids.
22
Q
Paper chromatography
A
- identifies amino acids and other organic compounds
- a spot of liquid sample containing the amino acid is placed on the start line near the bottom of a chromatographic paper, which forms stationary phase.
- Paper is put into a beaker containing a suitable solvent - the mobile phase
- due to capillary action, the solvent rises up the paper and eventually reaches the spots of amino acids
- the amino acids partition between the stationary and mobile phases according to their affinities for the solvent - compounds with higher solubility spend more time in the mobile phase and move up faster
- witht eh solvent has reached the top of the paper, it is then dried and developed using a locating agent, ninhydrin to make spots visible.
- retention factor (Rt) is the ratio of the distances travelled by each spot to the distance travelled by the solvent.
23
Q
What are the most common solvents used for amino acid separation in paper chromatography?
A
moderately polar alcohols, esters or chlorinated hydrocarbons (the last one is avoided due to environmental concerns)
24
Q
Intermolecular forces in amino acids
A
- in the solid state amino acids exist as zwitterions held together by strong ionic forces between -NH3^+ and -COO^-
- in aqueous solutions the ionic forces are replaced by ion-dipole interactions and hydrogen bonds between zwitterions and polar water molecules
- molecules of non polar solvents can only form van der Waal’s interactions, which are too weak to overcome the lattice energy of ionic solids
25
At which end of an amino acid does the the synthesis of peptides occur?
At the N-terminal
26
Properties of peptides
- similar to 2-amino acids
- N- and C-terminals together with the functional groups can be ionized to various extents
- depending on the pH of the solution - produce polyions with multiple positive and negative charges
- each peptide has a characteristic isoelectric point
- act as acid-base buffers
- maintain a constant pH of biological fluids
27
How can the primary structure of proteins be determined?
- protein sequencing, including mass spectrometry, NMR and sequential hydrolysis followed by gel electrophoresis or chromatography
28
What are secondary structures of proteins and how are they stabilised?
- α-helix and β-pleated sheet
- stabilised by intramolecular hydrogen bonds between carbonyl and amino fragments of peptide linkages
- in α-helix, C=O of each amino acid residue forms a hydrogen bond with the NH group of the amino acid residue situated four units ahead in the sequence
- in β-pleated sheet, contains two or more chains of amino acid residues (β-strands), which can run in the same or opposite directions - producing parallel and anti-parallel β-sheets. If only two strands are present then they are linked by hydrogen bonds in a ladder-like fashion. Hydrogen bonds between three or more strands form a regular 2D network.
29
Interactions in tertiary structure of proteins
- side-chains of amino acid residues can participate in intra- and intermolecular interactions
- two non-polar or slightly polar side-chains can interact via van der Waals' forces
- oppositely charged ionized groups can experience electrostatic attraction and form ionic bonds
- hydrogen bonds are formed between non-ionized hydroxyl and/or amino groups
- covalent bonds can be formed between certain functional groups of the side-chains, including additional peptide linkages between carboxyl and amino groups, ester bonds between carboxyl and hydroxyl groups and disulfide bridges between two -SH groups of cysteine residues.
- these interactions can cause additional folding of the molecule
30
ester bond
between carboxyl and hydroxyl groups
31
disulfide bridge
between two -SH groups of cysteine residues
32
Globular proteins
- compact globules with non-polar side-chains buried inside and polar groups facing outwards
- readily soluble in water
- easily transported by biological fluids
- often act as biological catalysts (enzymes), chemical messengers (hormones) or carriers of physiologically active molecules.
33
Fibrous proteins
- tend to adopt rigid, rod-like conformations
- insoluble in water
- usually perform structural or storage functions in living organisms
34
Prosthetic group
non-protein component of a in quaternary structure of a protein molecule , such as heme in haemoglobin or lipids in lipoprotein
35
Which forces hold the quaternary structure of proteins?
van der Waals' forces
36
Denatured protein
- do not posses their native 3D structure
| - unable to perform their physiological functions
37
What causes denaturation of proteins?
caused by organic solvents, heavy metal ions, high concentrations of inorganic salts or changes in pH or temperature
38
Substrate
Molecules that are modified by enzymes
39
Induced fit model
The active site and the substrate molecule do not fir exactly and during the initial enzyme-substrate interactions are relatively weak but sufficient to induce the conformational changes in the active site that strengthen the binding
40
Factors that influence the efficiency of an enzyme.
1) configuration and charge of its active site, which are sensitive to pH and temperature
- amino acid residues of both the enzyme backbone and active site contain ionizable side-chains that can undergo reversible protonation or deprotonation
- any change in pH affects the charges of these side-chains and their ability to form ionic and hydrogen bonds with one another
41
Which atoms are abundant in side-chans and polypeptide backbones of enzymes?
oxygen, nitrogen and sulfur - that can act as ligands and form chelate complexes with various metals
42
What happens during heavy metal toxicity?
Heavy metal ions, such as lead(II) or mercury(II), bind to the -SH groups in the side-chains of cysteine residues, disrupting the formation of disulfide bridges or replacing them with sulfur-metal-sulfur fragments.
- as a result the enzyme denatures
43
Lipids
A broad group of naturally occurring substances that are largely non-polar and thus insoluble in water
44
List five functions of lipids
1) energy storage
2) chemical messaging
3) transport
4) thermal insulation of the body
5) physical separation of the cell content from biological fluids
45
Fatty acids
- long-chain unbranched carboxylic acids
| - important component of tryglycerides and phospholipids
46
Physical properties of fatty acids
- melting point increase with their molecular masses
- saturated fatty acids with 10 or more carbon atoms are solid at room temperature due to close packing and multiple van der Waals' bonds between rod shaped carbon chains - the presence of double bond in unsaturaed fatty acids, prevents them from packing densely, which reduces the intermolecular forces and lowers the melting points
47
List two essential fatty acids
linoleic (omega 6) and linolenic (omega 3)
48
Triglycerides
fatty acids form esters with polyfunctional alcohols
- result of condensation reaction between three molecules of fatty acids and one molecule of glycerol (propane-1,2,3-triol)
49
Degree of unsaturation
Average number of double carbon–carbon bonds per unit mass of the fat or oil. This number can be determined by the reaction of a triglyceride mixture with elemental iodine or another reagent that quantitatively combines with C=C bonds via electrophilic addition reactions
50
Iodine number
The maximum mass of iodine in grams that can be consumed by 100 g of a triglyceride or other unsaturated substance
51
Saponification
The fat or oil is treated with a hot solution of sodium hydroxide until the hydrolysis is complete. The sodium salts of fatty acids are separated by precipitation and cooled in moulds to produce soap bars of the desired size and shape.
The reaction by-product, glycerol, is often added to the soap as a softening and moisturizing agent. The
52
Saponification number
the mass of potassium hydroxide in milligrams required for the complete hydrolysis of 1 g of a fat
53
Lipase
Enzyme that cleaves the ester bonds in triglycerides
| - produced in the pancreas and small intestine
54
Hydrolytic rancidity
caused by the hydrolysis of ester bonds in triglycerides and occurs when the food is exposed to moisture or has a naturally high water content.
-accelerated by lipases, organic acids and elevated temperatures
55
Oxidative rancidity
Process where carbon–carbon double bonds in unsaturated fatty acids and triglycerides can be cleaved by free-radical reactions with molecular oxygen
- accelerated by sunlight
- Free-radical oxidation of such oils produces volatile aldehydes and ketones with unpleasant odours.
56
Phospholipids
- aka glycerophospholipids
- structurally similar to triglycerides except that one residue of a fatty acid in a phospholipid is replaced with a phosphate group
- forms two ester bonds and one phosphate ester bond
57
Phospholipid bilayer
- In aqueous solutions amphiphilic molecules spontaneously aggregate into bilayers with hydrophilic “heads” facing out and hydrophobic “tails” facing inwards
- arrangement maximizes the van der Waals’ interactions between the hydrocarbon tails within the bilayer and at the same time allows the hydrophilic heads to form multiple hydrogen bonds and dipole–dipole interactions with water and one another
58
Steroids
class of lipids with a steroidal backbone
- Almost all steroids contain two methyl groups attached to the steroidal backbone at positions 10 and 13,
- other functional groups, usually at positions 3 and 17.
- many steroids have one or more double carbon–carbon bonds at positions 4, 5, and 6.
59
Steroidal backbone
characteristic arrangement of three six-membered and one five-membered hydrocarbon rings fused together
60
Cholesterol
an essential component of cell membranes and the main precursor of all steroidal hormones produced in the human body.
- embedded in cell membrane, cholesterol molecules increase the rigidity of cell membranes and regulate their permeability to metabolites.
- transported as lipoproteins
61
Lipoproteins
lipid–protein complexes used to transport lipids
62
Which tests to use to check for steroids and their metabolites in urine and blood samples?
combination of gas chromatography, high-performance liquid chromatography, and mass spectrometry
63
Anabolic steroids
usually refers to synthetic drugs that mimic the effects of testosterone and other hormones that accelerate protein synthesis and cellular growth, especially in the muscle and bone tissues.
64
Aldose
- aldehyde sugar
- carbony group is connected to the terminal carbon atom of the
monosaccharide
-reducing sugars due to carbonyl groups that get readily oxidised under mild conditions
65
Ketose
- ketone sugar
| - Monosaccharides with a carbonyl group at the second carbon atom
66
Why are monosaccharides in cyclic forms?
due to the presence of a carbonyl group and several hydroxyl groups in the saem molecule, straight-chain monosaccharides are unstable and undergo intramolecular nucleophilic addition (An) reactions to from cyclic forms of monosaccharides.
67
Alcoholic fermentation
glucose → ethanol + CO2
68
Maltose
glucose + glucose
69
Disaccharides
Condesation reaction in the presence of certain enzymes of two monosaccharides or their derivatives.
Forming a glycosidic link, e.g. in maltose between C-1 atom of the first glucose residue and C-4 atom of the second glucose unit → 1, 4-glycosidic link.
70
Sucrose
α-glucose + β-fructose
71
α-Lactose
α-glucose + β-galactose
72
How does galactose differ from glucose?
By the orientation of the hydroxyl group at the C-4 atom
73
Ring-chain tautomerism
When the cyclic forms of monosaccharides lactose and maltose become open-chained as they are oxidised by copper(II) ions.
74
Iodine test for starch
In aqueous solutions of potassium iodide, elemental iodine forms orange coloured tri- and polyiodide ions. When the orange solution is added to starch, the tri- and polyiodide ions react with amylose and produce blue-black complexes
75
Glycogen
- short-term energy store in human body
- structurally similar to amylopectin but is more densely branched
- contains up to a million glucose residues
- concentrated in the liver and muscle tissue, where it is hydrolysed into glucose when needed
- total mass in a healthy adult is 300-400g
76
Cellulose
- major structural polysaccharide in plants
| - important healthy diet component
77
Vitamins
- organic micronutrients that cannot be synthesized by the organism in sufficient amounts, ie must be obtained from suitable foods
78
How are vitamins classified?
- according to their biological functions rather than their chemical structures.
79
What are some of the functions of vitamins?
- many vitamins bind to enzymes as prosthetic groups or cofactors
- some act as hormones or antioxidants
- some facilitate the transfer of functional groups and electrons
80
Vitamin A
- several compounds: retinoids and carotenes
- electron conjugation makes retinoids and carotenes efficient antioxidants that readily react with molecular oxygen and free radicals
- absorb visible light
- contain long hydrocarbon chains with very few or no polar functional groups, ie. hydrophobic and insoluble in water
81
Retinol
a long-chained alcohol with an extensive system of alternating single and double bonds, ie. sp2 hybridization, the π-electron clouds of adjacent double bonds partly overlap with one another and form a large cloud of delocalized electrons
82
Vitamin C
- ascorbic acid
- oxygen-rich organic molecule containing multiple polar functional groups
- important for biosynthesis of collagen, which is the main component of connective tissue in the body and is primarily affected by vitamin C deficiency
- powerful antioxidant and reducing agent
83
Vitamin D
- cholecalciferol and three other structurally similar organic compounds with a partially broken steroidal backbone
- biosynthesis of cholecalciferol takes place in the skin and requires UV light to open the second six-membered ring of 7-dehydrocholesterol
84
Xenobiotics
Chemical compounds that had no natural sources and therefore are foreign to living organisms, such as pesticides and medicinal drugs
85
What affects the rate of decomposition of xenobiotics in the environment?
- the nature of the functional groups and overall polarity of a xenobiotic molecule
- e.g. polar synthetic molecules are quickly metabolised by living organisms due to solubility in water or undergo photochemical oxidation
- non-polar, hydrophobic xenobiotics easily pass through biological phospholipid membranes and tend to accumulate within the cells or in fatty tissues
86
Give three examples of heavy metals
mercury
cadmium
lead
87
Biomagnification
When certain non-polar compounds that accumulate in cells or fatty tissues, like certain xenobiotics, are passed along the food chain, their concentration may increase exponentially and reach very high levels in top predators.
88
Heavy metal toxicity
- some heavy metals cause denaturation of proteins, inhibit enzymes and affect the redox balance in cells
- undergo biomagnification
89
Biological detergents
- contain a variety of enzymes extracted from thermophilic microorganisms, which facilitate the breakdown of fats, proteins, starch and other organic molecules, even in cold water.
- more resistant to thermal denaturation
- easily biodegradable
90
host-guest complexes
- mimic structures of enzyme-substrate complexes, where the synthetic analogue of the enzyme (host) and the environmental pollutant (guest) are held together by multiple non-covalent interactions, including van der Waals' forces, ionic bonds and hydrogen bonds
- this is done because some enzymes are unstable in the environment
91
List 5 common practices of green chemistry
1) aqueous or solvent-free reactions
2) renewable starting materials
3) mild reaction conditions
4) regio- and steroselective catalysis
5) utilization of any by-products formed during the synthesis
92
Give two examples of atom-efficient reactions.
1) hydrogenation of alkenes
| 2) hydrogenation of unsaturated fats
