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Dr Bhavsar's A level Biology > Biological molecules > Flashcards

Biological molecules Flashcards

1
Q

Describe the structure of a water molecule

A
  1. Two Hydrogen atoms joined to a single oxygen atom
  2. By covalent bonds
  3. Oxygen is more electronegative than Hydrogen so each bond is polar
  4. Resulting in oxygen being partially negative
  5. And both Hydrogens being partially positive
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2
Q

Explain how the properties of water are linked to its structure

A
  1. The polar O-H bonds result in the water molecule have a partially negative Oxygen and partially positive Hydrogens
  2. The Oxygen of one water molecule can be attracted to the Hydrogen of a different water molecule, forming a Hydrogen bond
  3. This results in intermolecular attractions between water molecules resulting in cohesiveness of water molecules
  4. Water has an unusually high boiling point, and is a liquid at room temperature (or most of the naturally occuring temperatures on Earth), due to the large amounts of energy that would be needed to break the Hydrogen bonds
  5. The polarity of water molecules also allows them to attract other surfaces, resulting in adhesiveness
  6. The polarity of water means it can interact with other polar or ionic substances and act as a solvent
  7. Due to the formation of Hydrogen bonds in a lattice structure, freezing causes water (ice) to be less dense than liquid water
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3
Q

Describe how the properties of water support life on Earth

A
  1. The cytoplasm of cells is primarily water, which means the substances involved in metabolic reactions (including biological molecules such as sugars, amino acids, proteins) can be stored, and transported because water is a solvent
  2. Water is also the main component of transport media in multicellular organisms. As water is a solvent it can transport many biological molecules. It can be moved around the body because its cohesive properties allow it to be a liquid
  3. The adhesiveness of water allows it to stick to the walls of xylem vessels, and the cohesion allows columns of water to move by capillary action
  4. The high-specific heat capacity of water means it has a stabilising effect on the temperatures of organisms (preventing rapid fluctuations), enabling enzyme-dependent reactions to proceed
  5. Water is also a habitat for organisms, which are protected from dramatic temperature changes
  6. Ice on the surface of large bodies of water has an insulating effect, preventing the whole body from freezing and thus maintaining ecosystems
  7. Some organisms live and feed on the surface of water due to its surface tension (as a result of cohesion of water molecules)
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4
Q

Be able to draw the structure of alpha glucose

A
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5
Q

Be able to draw the structure of beta glucose

A
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6
Q

Be able to draw the structure of ribose

A
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7
Q

Be able to draw the structure of deoxyribose

A
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8
Q

Be able to draw a condensation reaction between two alpha glucose molecules to form maltose

A
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9
Q

Be able to draw a condensation reaction between alpha glucose and fructose to form sucrose

A
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10
Q

Be able to draw a condensation reaction between galactose and beta glucose to form lactose

A
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11
Q

Describe the structure of starch

A
  1. Alpha glucose monomers joined by condensation reaction, and alpha 1-4 glycosidic bonds
  2. (the hydroxyl group on carbon one, undergoes condensation reaction with the hydroxyl group on carbon 4 of another glucose molecule)
  3. To form a polysaccharide
  4. Amylose is coiled and unbranched (only contains 1-4 glycosidic bonds)
  5. Amylopectin is branched, by having 1-4 and 1-6 glycosidic bonds
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12
Q

Relate the structure of starch to its function

A
  1. Function of starch is glucose storage in plants
  2. The glucose is used in respiration to release energy, generate ATP
  3. Starch polysaccharides are insoluble, so they don’t affect the water potential of the cell
  4. Both amylose and amylopectin store a large amount of glucose in a small space (compact)
  5. Amylopectin’s branched structure allows for a higher rate of hydrolysis and glucose mobilisation as well as storage
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13
Q

Describe the structure of glycogen

A
  1. Composed of alpha glucose monomers joined by condensation reaction
  2. Contain alpha 1-4 glycosidic bonds, and 1-6 glycosidic bonds
  3. To form a highly branched polysaccharide
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14
Q

Relate the structure of glycogen to its function

A
  1. The function of glycogen is the storage of glucose in animals
  2. The stored glucose can be mobilised for use in respiration to generate ATP
  3. Glycogen is an insoluble polysaccharide so it doesn’t affect the water potential of the cell
  4. High branch density means that it is a compact store of glucose
  5. High branch density means that glucose can be mobilised more quickly by hydrolysis, and stored more quickly
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15
Q

Describe the structure of cellulose

A
  1. Cellulose is a polysaccharide composed of beta-glucose monomers
  2. Joined by condensation reaction, joining carbon one of one beta glucose molecule to carbon four of the next beta glucose molecule with a beta glycosidic bond
  3. Every other beta glucose molecule is inverted (not rotated)
  4. This produces a linear, unbranched molecule (not coiled)
  5. 1Because they are linear, adjacent molecules can form hydrogen bonds to form bundles of molecules
  6. Forming microfibrils and then macrofibrils
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16
Q

Relate the structure of cellulose to its function

A
  1. It is insoluble, so continues to provide support while in contact with water
  2. Beta glycosidic bonds produce linear molecules, which can hydrogen bond to form bundles with a high tensile strength
  3. Cellulose has many polar (hydroxyl) groups, which allow cellulose fibres to be permeable to water, mineral ions, glucose, amino acids and plant hormones
  4. Cellulose molecules can be cross-linked, making them rigid, and withstanding hydrostatic pressure of turgid plant cells
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17
Q

Describe the structure of triglycerides

A
  1. Composed of three fatty acids chains and a molecule of glycerol
  2. The carboxyl group of each fatty acid undergoes condensation reaction with a hydroxyl group on the glycerol molecule
  3. Joining them via ester bonds (esterification)
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18
Q

Describe and discuss saturated and unsaturated triglycerides

A
  1. Fatty acids (gained from the diet) can be saturated or unsaturated
  2. Saturated fatty acids have no carbon-carbon double bonds, and have a straight chain
  3. Unsaturated fatty acids have one or more carbon-carbon double bonds, resulting in kinks in the chain
  4. Kinks in the chain cause lipids to pack less closely, reducing their density
  5. There is evidence to suggest diets high in saturated fats may cause cardiovascular disease.
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19
Q

Describe how the structure, properties and functions of triglycerides are related

A
  1. The fatty chains of lipids are composed of Carbon and Hydrogen, which makes them non-polar and hydrophobic
  2. The many C-H bonds can be broken down in aerobic respiration (Kreb’s cycle), to release energy for the production of ATP
  3. Triglycerides provides thermal insulation (due to low density)
  4. They also provide physical cushioning (protection) of organs (due to low density)
  5. They provide buoyancy to some aquatic animals such as whales (due to low density)
  6. Waterproof coating on animals and plants
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20
Q

Describe the structure of phospholipids

A
  1. Composed of two fatty acids chains, a phosphate group and a molecule of glycerol
  2. The carboxyl group of each fatty acid undergoes condensation reaction with a hydroxyl group on the glycerol molecule
  3. Joining them via ester bonds (esterification)
  4. The phosphate group is joined to the third hydroxyl group
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21
Q

Describe how the structure, properties and functions of phospholipids are related

A
  1. The fatty acid tails are extremely non-polar and hydrophobic
  2. The phosphate head is negatively charged and very hydrophilic
  3. As a result, phospholipids in water form bilayers
  4. Which forms the basis of biological membrane structures and compartmentalisation of organelles and selective permeability
  5. Electrical insulation (for example the Schwann cells which allow faster transmission of nerve impulses)
22
Q

Describe the structure and function of sterols such as cholesterol

A
  1. Structure contains four carbon rings
  2. And a hydroxyl group
  3. Arranged in a planar structure
  4. The hydroxyl group is polar and hydrophilic
  5. The carbon ring structure is hydrophobic
  6. Cholesterol regulates the fluidity of phospholipids in membranes
  7. Forms the basis of steroid hormones, vitamin D and bile
23
Q

Draw the generalised structure of an amino acid

A
24
Q

Describe the structure of an amino acid

A
  1. Four groups attached to a central carbon:
  2. Amine group, Hydrogen, carboxyl group and variable side-chain
  3. There are twenty different amino acid types characterised by a different side chain
25
Q

Draw a diagram to show how two amino acids are joined to form a dipeptide (and understanding the reverse of this process is called hydrolysis)

A
26
Q

Describe the primary structure of proteins

A
  1. Specific amino acids are joined together in condensation reactions, to form peptide bonds.
  2. The order of the amino acids in a polypeptide is the primary structure
  3. The polypeptide has an N terminus (amino group at one end of the chain)
  4. It also has a C terminus (carboxyl group at the other end)
  5. The side chains project outward along the length of the polypeptide
  6. The positions and types of these side chains is determined by the primary structure
27
Q

Describe the secondary structure of proteins

A
  1. The secondary structure is the initial coiling or folding of the polypeptide chain due to
  2. The partially negative oxygen of one peptide group forms a Hydrogen bond with the partially positive Hydrogen of another peptide group further along the chain
  3. This forms ether alpha helical structures or beta-pleated sheets
28
Q

Describe the tertiary structure of proteins

A
  1. The three-dimensional folding of the polypeptide as a result of interactions between the side chains
  2. These interactions can be:
  3. Disulphide bonds: covalent bonds between sulphur atoms of different side chains
  4. Ionic bonds: attractions between oppositely charged side chains
  5. Hydrogen bonds: attractions between opposite partially charged atoms such as H, O, and N
  6. Hydrophilic and hydrophobic interactions, which is the effect that the aqueous environment has on the location of hydrophobic side chains (which move away from water) and hydrophilic side chains (which move to the surface of the protein to interact with water)
29
Q

Describe the quaternary structure of proteins

A
  1. This is the association of more than one polypeptide chains, in order to make a fully functioning protein
  2. The interactions that allow this to happen are the same as in the tertiary structure
30
Q

Describe the structure of globular proteins

A
  1. Globular proteins are roughly spherical, compact and water soluble
  2. They have a complex tertiary structure
  3. Hydrophobic side chains are in the core of the protein, away from water
  4. Hydrophilic side chains are on the surface, interacting with water
31
Q

State the functions associated with globular proteins

A
  1. Transport proteins, soluble so can be transported in blood plasma (e.g. haemoglobin)
  2. Enzymes, soluble so can easily interact with soluble substrates (e.g. catalase)
  3. Hormones, soluble so easily transported in various body fluids, plasma, tissue fluid, cytoplasm (e.g insulin)
32
Q

State what a conjugated (globular) protein is

A
  1. Globular proteins that contain a permanently associated non-protein component called a prosthetic group
  2. Prosthetic groups can be, lipids, carbohydrates, metal ions and vitamin derivatives
33
Q

Describe the structure of haemoglobin

A
  1. roughly spherical, compact and water soluble
  2. complex tertiary structure
  3. Hydrophobic side chains are in the core of the protein, away from water
  4. Hydrophilic side chains are on the surface, interacting with water
  5. Has four polypeptide chains in its quaternary structure
  6. Two alpha polypeptide and two beta polypeptides
  7. Each polypeptide has a haem prosthetic group contains an iron ion, which bind oxygen molecules
34
Q

Describe the structure of fibrous proteins

A
  1. Fibrous proteins tend to be long molecules, that are insoluble in watery environments
  2. There is a high proportion of amino acids with hydrophobic side chains (in the primary structure)
  3. There is a high proportion of amino acids with small side chains
  4. In a repeating sequence
  5. With relatively little tertiary folding
  6. To allow these polypeptides to associate more closely in their quaternary structure
  7. To form long fibres with properties such as high rigidity (Keratin), strength and flexibility (collagen), elasticity (elastin)
35
Q

Write the chemical symbol for and state the role of: calcium ions

A
  1. Ca2+
  2. Synaptic transmission: Diffuse into the synaptic knob and cause exocytosis of synaptic vesicles
  3. Muscle contraction: released from the sarcoplasmic reticulum, binds to troponin, and allows myosin heads to bind actin filaments
36
Q

Write the chemical symbol for and state the role of: sodium ions

A
  1. Na+
  2. Resting and action potentials/nerve impulses: diffuse into axons resulting in depolarisation
  3. Selective reabsorption and reabsorption of water: co-transported during the selective reabsorption of glucose and amino acids, used to lower the water potential of the medulla (loop of Henle)
37
Q

Write the chemical symbol for and state the role of: potassium ions

A
  1. K+
  2. Resting and action potentials/nerve impulses: leak out of axons to maintain resting potential, diffuse into axons during repolarisation of axons
  3. Involved in stomatal closing
38
Q

Write the chemical symbol for and state the role of: hydrogen ions

A
  1. H+
  2. Pumped using energy to establish proton gradients used in chemiosmosis in photosynthesis and respiration
  3. Affects intracellular and extracellular pH
39
Q

Write the chemical symbol for and state the role of: ammonium ions

A
  1. NH4+
  2. Nitrogen cycle: used by bacteria to produce nitrates
  3. Toxic waste product of amino acid deamination/converted to urea in ornithine cycle
40
Q

Write the chemical symbol for and state the role of: nitrate ions

A
  1. NO3-
  2. Nitrogen cycle: absorbed by plants and used to make amino acids (and so proteins)
41
Q

Write the chemical symbol for and state the role of: hydrogencarbonate ions

A
  1. HCO3-
  2. Affects blood pH: detected by chemoreceptors in wall of carotid arteries and aorta (control of heart rate during exercise)
  3. form in which carbon dioxide is transported from body tissues to the heart/lungs
42
Q

Write the chemical symbol for and state the role of: chloride ions

A
  1. Cl-
  2. Cofactor for the enzyme amylase
  3. Chloride shift: chloride ions diffuse into red blood cells as hydrogen carbonate ions diffuse out (to maintain electrical balance)
  4. Balances the positive charge of sodium and potassium ions
43
Q

Write the chemical symbol for and state the role of: phosphate ions

A
  1. PO43-
  2. Required for synthesis of phospholipids, nucleotides, ATP
  3. Used to phosphorylate proteins (and change their activity) in the cell as part of hormone-induced cell signalling
44
Q

Write the chemical symbol for and state the role of: hydroxide ions

A
  1. OH-
  2. Affects cellular and extracellular pH
45
Q

Describe a positive test for the presence of proteins

A
  1. Biuret test
  2. Add Biuret reagent to the test solution
  3. If protein is present the reagent should turn from blue to purple
  4. Suitable controls would be solutions known to contain no protein, or known to contain protein
46
Q

Describe a positive test for the presence of reducing sugars

A
  1. Benedict’s test
  2. Add Benedict’s reagent to the test solution
  3. Heat the mixture to about 70C
  4. If reducing sugar is present, the blue reagent (Cu2+) should change colour due to the presence of brick red Cu+ ions.
  5. According the concentration of reducing sugar, the colour change should be in the order: blue (none), green, yellow, orange, red (high concentration)
  6. Suitable controls would be solutions known to contain no reducing sugar, or known to contain reducing sugar
47
Q

Describe a positive test for the presence of non-reducing sugars

A
  1. Benedict’s test for non-reducing sugar
  2. If Benedict’s test result is negative
  3. Boil in the presence of dilute hydrochloric acid (to hydrolyse the glycosidic bond)
  4. Add sodium hydroxide to neutralise the acid
  5. Repeat Benedict’s test by adding Benedict’s reagent and warming
  6. A positive result at this stage confirms the presence of a non-reducing sugar originally
48
Q

Describe a positive test for the presence of Starch

A
  1. Iodine test
  2. Add some drops of iodine (potassium iodide solution)
  3. If Iodine changes from brown to blue/black, starch is present
49
Q

Describe a positive test for the presence of lipids

A
  1. Emulsion test
  2. The sample is mixed with ethanol (to dissolve any lipids present)
  3. Water is added and then shaken
  4. The ethanol dissolves in the water, and the lipids form an emulsion
  5. Visible as a white (not clear) layer at the top of the tube
50
Q

Describe how colorimeter can be used to carry out quantitative tests for biological molecules

A
  1. Ensure the correct filter is inserted (which has the ‘opposite’ colour the one being detected)
  2. Use water to calibrate the colorimeter (to zero absorbance)
  3. Measure the absorbance of solutions of known concentrations (on which the test has been carried out), to produce a calibration curve
  4. Carry out the test for the biological molecule for the unknown solution
  5. Measure the absorbance and compare to the calibration curve to determine the concentration
51
Q

Explain how Biosensors can be used to make quantitative measurements of biological molecules

A
  1. The sample contains a particular biological molecule
  2. A protein (enzyme or antibody) is immobilised to the transducer (or to test strip)
  3. When a specific interaction takes place between the sample molecule and the protein, the change in shape is produces a signal from the transducer (or colour change in test strip)
  4. The intensity of the signal is proportional to the concentration of the biological molecule
  5. (or in a test strip, the extent of colour change)
52
Q

Describe how thin layer chromatography can be used to separate a mixture of amino acids

A
  1. Draw a horizontal line near the bottom of the chromatography paper or plate
  2. Draw spots to indicate the initial positions of the mixtures
  3. Use a capillary tube to spot the mixture onto the paper/plate
  4. The bottom of the paper/plate is placed in the solvent
  5. The solvent is allowed to move up the paper/plate
  6. Another horizontal line is drawn at this level
  7. The plate/paper is sprayed with ninhydrin to visualise the position of the amino acids
  8. Rf values are calculated by dividing the distance travelled by the amino acid by the distance travelled by the solvent
  9. Due to unique solubility in the solvent different amino acids travel specific distances and therefore have unique Rf values

Dr Bhavsar's A level Biology (9 decks)

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