Molecular biology

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What did the theory of vitalism state?
That living organisms were composed of organic chemicals that could only be produced in living organisms because a ‘vital force’ was needed. This theory was falsified by discoveries i.e. artificial synthesis of urea.
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According to the theory of vitalism it was predicted that urea could only be made in living organisms as it was an organic compound and required a ‘vital force’. How did Friedrich Wohler help to falsify the theory of vitalism?
In 1828, he used silver isocyanate and ammonium chloride to synthesize urea artificially. Didn’t disprove but falsified the theory of vitalism.
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What is metabolism?
Web of all enzyme catalysed reactions in a cell or organism (the sum of anabolic and catabolic reactions). Metabolic pathways = chains of reactions or cycles of reactions.
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What is Anabolism?
Synthesis of complex molecules from simpler molecules (i.e. monomers to macromolecules). Anabolic reactions = condensation reactions as water is produced.
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What is Catabolism?
Breakdown of complex molecules into simpler molecules (i.e. the hydrolysis of macromolecules into monomers). In Hydrolysis reactions water molecules are split.
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Polarity of molecules.
Where the nucleus of one of the atoms in a molecule (covalently bonded) is more attractive to the electrons than the other so the electrons aren’t shared equally –means part of mol has slight pos charge + part has slight neg charge.
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Describe the polarity of water molecules.
Hydrogen nuclei are less attractive to electrons than oxygen nuclei – H atoms =slight pos charge, O= slight neg charge. Water molecules have two poles-->show dipolarity.
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Why does water have a higher melting point than methane?
Methane (-182C) + water (0C). Hydrogen bonds restrict the movement of water particles + heat needed to overcome this.
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Why does water have a higher specific heat capacity than methane?
Methane (2.2J J/g/C) + water (4.2 J/g/C). Hydrogen bonds restrict movement --> more energy stored by moving molecules of water than methane.
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Why does water have a much higher heat of vaporization + boiling point than methane?
Methane (760 J/g)(-160C) + Water (2257 J/g)(100C). More heat energy needed to break hydrogen bonds + allow a water molecule to evaporate.
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Hydrophilic substances are ionic compounds/substances with polar molecules. Describe their solubility in water.
Dissolve in water as ions/molecules are more attracted to water than to each other + so form intermolecular bonds with water molecules.
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Why are hydrophobic substances insoluble?
Not because they are repelled by water but because water molecules are more strongly attracted to each other than to the non-polar molecules of hydrophobic substances.
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What are the 4 different properties of water?
Cohesive (molecules stick to each other-H bonds), adhesive (adhere to polar/hydrophilic surfaces), thermal (high m + b points, spec heat capacity + latent heat of v) and solvent (many substances dissolve in water).
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What are hydrogen bonds?
Intermolecular bond formed between the pos pole of one water molecule + the neg pole of another. Heat energy is used/transferred when broken –why sweat is used as a coolant (evap of water from sweat removes heat from body).
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How is water being a good solvent beneficial to living organisms?
Most chemical reactions take place with all of the substances involved in the reaction dissolved in water--> water is the medium for metabolic purposes.
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Anabolic reactions are condensation reactions. What are condensation reactions?
Two molecules are joined together to form a larger molecule plus a molecule of water i.e. polymerisation.
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What are glycerides?
Lipids formed when a fatty acid is linked to a glycerol in a condensation reaction. A maximum of 3 fatty acids can be linked to each glycerol to form a triglyceride.
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Catabolic reactions are hydrolysis reactions (incl those used to digest food). What are hydrolysis reactions?
When large molecules are broken down into smaller molecules and water molecules are split into –H and –OH groups. The –H and –OH are needed to make new bonds after a bond in the large molecule has been broken.
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What are monosaccharides?
Monosaccharides are basic sub-units of carbohydrates that contain only atoms of C, H + O in the ratio 1:2:1 i.e. glucose, ribose and galactose.
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What are polysaccharides?
i.e. cellulose, glycogen + starch that are all composed of glucose. The basic glycosidic bond is formed between the C4 of 1 glucose to the C4 (fourth carbon) of the next.
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Describe cellulose.
unbranched polymer of β-D glucose –orientation of the glucose molecules alternate so that the polymer is straight rather than curved -->allows groups of cellulose to be arranged in parallel with hydrogen bonds forming crosslinks.
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What are disaccharides?
Pairs of monosaccharides are linked together by condensation to form disaccharides. Glucose + glucose = maltose, glucose + galactose = lactose, glucose + fructose = sucrose. Molecules recognised by the double ring structure.
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How can cellulose be used in organisms?
The structures cellulose fibrils have enormous tensile strength and are the basis of plant cell walls.
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What is starch?
A polymer of α-D-glucose, with all of the glucose subunits in the same orientation, giving the polymer a helical shape. 2 forms =amylose (one has 1,4 linkages so is unbranched) + amylopectin has some 1,6 linkages so is a branched molecule.
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How is starch used by plants?
To store glucose in an insoluble form that doesn’t cause osmotic problems. By making the molecule branched it is possible to load/unload glucose more rapidly as there are more points on starch molecules to which glucose can be added/detached.
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What is glycogen?
A branched polymer of α-D-glucose. There are more 1,6 linkages than amylopectin so it’s more branched.
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How is glycogen used by mammals?
Stored in liver and muscle cells. As its insoluble, large amounts can be stored whereas if glucose was stored it’d cause water to enter the cells by osmosis and there would be a danger of them bursting.
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What are lipids?
Carbon compounds made by living organisms that are mostly/entirely hydrophobic .Three main types = triglycerides, phospholipids + steroids. Identified by 2 or 3 hc chains or the quadruple ring structure steroids.
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Describe triglycerides.
Made from 3 fatty acids and one glycerol by condensation so they have 3 hydrocarbon tails.
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Describe phospholipids.
Similar to triglycerides but only have two fatty acids linked to glycerol, with a phosphate group instead of the third fatty acid. Phospholipids are only partly hydrophobic and form the basis of membranes.
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Describe steroids (lipids)?
All steroids have a similar structure of four fused rings in their molecule. i.e. cholesterol, progesterone, oestrogen, testosterone.
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How would you draw a fatty acid?
2 parts: a carboxyl group that is acidic (-COOH) & an unbranched hydrocarbon chain (i.e.(-CH2).
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Describe the bonding in saturated and unsaturated fatty acids.
Saturated: all carbon atoms in chain connected by single cov bonds so no. of H atoms bonded to the carbons can’t be increased. Unsaturated=1 or more double bonds (more H atoms could be added if a double bond-->single).
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Describe monounsaturated and polyunsaturated bonds.
Monounsaturated (1 double bond). Polyunsaturated (2 or < dbs) In omega3 the db nearest to the CH3 is the 3rd bond from CH3 (in omega-6 fatty acids it’s the 6th from CH3).]
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Describe Cis unsaturated and Trans unsaturated bonds.
Cis unsaturated: Hydrogen atoms are bonded to carbon atoms on the same side of a double bond. Trans unsaturated: hydrogen atoms are bonded to carbon atoms on opposite side of a double bon
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Describe the four different groups in amino acids.
Hydrogen atom, amino group (NH2), carboxyl (-COOH) group and R group.
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Amino acids with hundreds of different R-groups could be produced in the lab, but how many do most living creatures have?
Twenty in the polypeptides synthesized by their ribosomes. The same 20 amino acids are used (showing that all living organisms have shared ancestry).
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What is a peptide bond?
A bond formed between the amine group of one amino acid and the carboxyl group of the next.
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What is the conformation of a protein?
Its three dimensional structure. The polypeptides of most proteins are folded up to produce a globular shape (determined by the sequence of amino acids). The structure is stabilized by intermolecular bonds between the amino acids.
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How can heat denature an enzyme?
Heat: causes vibrations with protein molecules that break intermolecular bonds and cause the conformation to change. pH change: breaks intermolecular bonds.
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Lipids vs Carbs for long term energy storage.
Amount of energy released per gram of lipids = double that of carbs. Same amount of energy stored as lipid rather than carb adds ½ as much body mass. Also, each gram of glycogen is associated with 2 grams of water:(
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What is a polypeptide?
An unbranched chain of amino acids. Over 2 mil discovered so far. Most have 50-20,000 amino acids. The amino acid sequence for a polypeptide is coded for by a gene
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What is a peptide?
Less than 40 amino acids linked together.
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What are proteomes and genomes?
Proteomes: all of the proteins produced by a cell, tissue or an organism. Genomes: all genes of an organism.
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What are the different functions of proteins?
Enzymes, hormones (insulin), antibodies (immunoglobins), Pigment (rhopsodin), structural protein (collagen).
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What are enzymes and substrate?
Globular proteins and biological catalysts that speed up + control the rate of reactions of metabolism. Substrate: reactant in an enzyme catalysed reaction.
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Provide a condition of catalysis.
Catalysis only occurs if the substrates are I a liquid so their molecules are in continual motion + there is a chance of collisions between the substrates + the active site (on surface of enzyme).
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What can collisions between substrates and the active site result in?
Binding as the shape + chemical properties of the active site complement those of the substrates (chemically attracted to each other) –enzymes are substrate-specific as molecules other than the substrate don’t fit.
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How can lactose free milk be produced?
Lactose can be hydrolysed into glucose + galactose by adding free lactase to the milk or using lactase that has been immobilized on a surface/beads of porous material.
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How is the binding of substrates to the active site useful?
As it reduces the energy needed for substrates to be converted into products
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Describe effect of substrate concentration on enzyme activity.
At low substrate concentrations, enzyme activity increases steeply as substrate conc. increases (more collisions) but high substrate concentrations most of the active sites are occupied so raising conc. has little effect.
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What are nucleotides?
Monomers of DNA/RNA consisting of 3 parts (phosphate group, pentose sugar + base). Pentose sugar = ribose in RNA, deoxyribose in DNA. There are 4 possible bases Adenine, cytosine, guanine + 4th base (uracil in RNA + thymine in DNA).
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Describe one more difference between DNA and RNA.
RNA usually has one strand + DNA usually has 2 strands. The nucleotides in DNA/RNA are linked together by covalent bonds between the pentose sugar of one nucleotide + the phosphate group of the next.
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What is complementary base pairing?
The 2 strands in DNA are antiparallel (run alongside each other but in opp directions) + are linked by hydrogen bonding between their bases –each base will only form hydrogen bonds with 1 other base so that only 2 base pairs are possible.
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Provide the 3 stages of DNA replication.
Helicase unwinds the double helix + separates the 2 strands by breaking hydrogen bonds. DNA polymerase links nucleotides together to form new strands, using the pre-existing strands as templates. Daughter DNA molecules rewind into a double helix.
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What is transcription?
The copying of the base sequence of a gene by making an RNA molecule. (DNA-->mRNA) –process begins when RNA polymerase binds to a site on the DNA at the start of a gene.
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Describe the first 3 stages of transcription.
RNA polymerase moves along the gene separating the DNA into 2 single strands. RNA nucleotides assemble along 1 of the 2 strands + are linked together by covalent bonds between the pentose sugar of 1 nucleotide to the phosphate of the next.
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Describe the final 2 stages of transcription.
RNA strand separates from the DNA strand as it is produced + released completely when the end of the gene is reached. DNA strands pair up again + twist into a double helix.
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What is translation?
The synthesis of polypeptides on ribosomes using mRNA (determines amino acid of polypeptides according to the genetic code) and tRNA.
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Describe the first 3 stages of translation.
mRNA binds to a site on the sub-unit of the ribosome. tRNA carries the amino acid corresponding to its special triplet of bases (called anti-codon). tRNA anti-codons bind to complementary codons on the mRNA –bases on codon & anti-codon link by hydrog
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Describe the final stage of translation.
Amino acids carried by the tRNA molecules are bonded together by peptide linkage--> dipeptide formed. Ribosome moves along the mRNA to the next codon + another tRNA carrying amino acids binds-->chain of 3 amino acids form +repeat until polypeptide fo
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Describe the polymerase chain reaction.
Used for copying DNA artificially (in small tubes called eppendorfs). DNA polymerase used to copy the original molecule –Taq DNA polymerase (heat stable) has to be used. Millions of copies produced by PCR in a few hours due to high temps used.
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Why is it useful to be able to copy DNA artificially?
For gene transfer procedure where many copies of the desired gene are needed or in forensic analysis when only a small sample is available.
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Define cell respiration.
The controlled release of energy from organic compounds (glucose/fat) to produce ATP (Adenosine triphosphate). Pro: ATP is immediately available as an energy source in the cell as it can diffuse to any part of the cell and release its energy in a sec
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Why is anaerobic respiration used in muscles carrying out very vigorous exercise (i.e. weight lifting)?
Though it produces fewer molecules of ATP it can supply ATP at a more rapid overall rate for a short time as it isn’t limited by how fast oxygen is supplied. Lactic acid + hydrogen ions produced. Only used for 2 mins.
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What is a respirometer?
Any device used to measure respiration rates.
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Provide 2 instruments normally used in a respirometer.
A sealed glass or plastic container in which the organism/tissue is placed. A capillary tube containing fluid, connected to the container which allows the volume of air inside the respirometer to be monitored.
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What is also often used in a respirometer?
An alkali (i.e KOH) which absorbs CO2 produced by cell respiration. The volume inside the respirometer should therefore reduce as a result of O2 being used in cell respiration by the organisms in the respirometer.
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What is photosynthesis?
The production of carbon compounds in cells using light energy. CO2 + water + light energy --> glucose + oxygen.
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What is needed to convert CO2 into carbohydrates + other carbon compounds?
Light energy. Electrons also needed to convert CO2 into carbs + are obtained by photolysis (the splitting of water molecules -->produces waste produce of O2).
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What is a spectrum?
A range of wavelengths of electromagnetic radiation (violet light with shortest wavelength to red light with the longest). An absorption spectrum: a graph showing the range of wavelengths absorbed by a pigment.
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Why do structures containing chlorophyll appear green to us?
As chlorophyll absorbs red + blue light most effectively & small amounts of green light are absorbed but most is reflected.
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Card 2

Front

According to the theory of vitalism it was predicted that urea could only be made in living organisms as it was an organic compound and required a ‘vital force’. How did Friedrich Wohler help to falsify the theory of vitalism?

Back

In 1828, he used silver isocyanate and ammonium chloride to synthesize urea artificially. Didn’t disprove but falsified the theory of vitalism.

Card 3

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What is metabolism?

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Card 4

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What is Anabolism?

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Card 5

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What is Catabolism?

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