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biology > 3.1 Biological molecules > Flashcards

3.1 Biological molecules Flashcards

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1
Q

What is a monomer?

A

Small basic repeating unit from which larger molecules are made (polymers).

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2
Q

What is a polymer?

A

Large complex molecules made of long chains of repeating units (monomers) joined together.

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3
Q

What are the main examples of biological polymers and their monomers?

A

Carbohydrates/Polysaccharides - Monosaccharides
Proteins - Amino acids
Nucleic acids - Nucleotides

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4
Q

What is a condensation reaction?

A

Forms a chemical bond and joins two monomers, involving the elimination/release of a water molecule.

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5
Q

What is a hydrolysis reaction?

A

Breaks a chemical bond between two monomers, involving the use of a water molecule.

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6
Q

What are monosaccharides?
What are the common monosaccharides?

A

The monomers from which larger carbohydrates are made. Glucose, galactose and fructose are common monosaccharides.

These are respiratory substrates - release energy.

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7
Q

What does a condensation reaction between two monosaccharides form?

A

A glycosidic bond.

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8
Q

What does glucose (a common monosaccharide) look like?

A

Glucose has two isomers.
α-glucose & β-glucose

α-glucose β-glucose
H hexagon H H hexagon OH
HO OH HO H

(In β-glucose the OH and H are flipped on Carbon 1)
(Reference images if unsure)

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9
Q

How would you identify the other common monosaccharides?
(Since all three have the shared chemical formula of C6H12O6)

A

Galactose is, similar to glucose, a hexose sugar. But the OH & H in galactose are flipped on Carbon 4 compared to glucose.

Fructose’s displayed formula is a pentagon, not a hexagon.

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10
Q

What is a disaccharide?

A

Formed when 2 monosaccharides join together (via a condensation reaction).

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11
Q

What are the 3 main examples of disaccharides and what monosaccharides are they formed from?

A
  • Maltose formed by the condensation of 2 glucose molecules
  • Sucrose formed by the condensation of a glucose + a fructose molecule
  • Lactose formed by the condensation of a glucose + a galactose molecule
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12
Q

How do the monosaccharide displayed formulas join to form disaccharides?

A

From the OH (hydroxyl group) of the monosaccharides, OH & H are removed, forming a glycosidic bond at the remaining C-O-C. H2O is then added on (as it was removed).

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13
Q

What are polysaccharides?

A

Formed by the condensation of many glucose units.

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14
Q

What are the 3 main examples of polysaccharides and what monosaccharides are they formed from?

A
  • Glycogen & Starch formed by the condensation of α-glucose
  • Cellulose formed by the condensation of β-glucose
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15
Q

What is the structure & function of the polysaccharide Starch?

A

Function:
Cells get energy from glucose - plants store excess glucose as starch.

Structure:
Mixture of two polysaccharides of α-glucose.
- Amylose - long unbranched chain, coiled structure so compact (therefore good for storage). Contains hydrogen bonds & 1,4 glycosidic bonds.
- Amylopectin - long branched chain, it’s side branches allow the enzymes that break down the molecule to get at the 1,4 & 1,6 glycosidic bonds easily (therefore glucose can be released quickly).

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16
Q

What is the structure & function of the polysaccharide Glycogen?

A

Function:
Animals store access glucose as glycogen.

Structure:
Very similar to amylopectin but with more side branches (therefore glucose can be released quickly). Compact molecule (therefore good for storage).

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17
Q

What is the structure & function of the polysaccharide Cellulose?

A

Function:
Provides structural support for cells.

Structure:
Long unbranched chains of β-glucose (alternate glucoses flipped/rotated 180 degrees - inverted glycosidic bonds (1, 4)). When β-glucose molecules bond they form straight (not coiled) cellulose chains. These are linked together with hydrogen bonds forming strong fibres (microfibrils).

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18
Q

How do you complete the Benedict’s test for sugars?

A

For reducing sugars (which include all monosaccharides + some disaccharides):

  • Add Benedict’s reagent (blue) to a sample & heat in water bath that’s been brought to a boil
    Negative result - stays blue. Positive result - forms green, yellow, orange, brick-red precipitate.
    (To compare concentrations of reducing sugars accurately, filter solution, dry & weigh precipitate or remove precipitate & use colorimeter to measure absorbance of the remaining Benedict’s reagent)

(If reducing sugars test is negative)
For non-reducing sugars:

  • You first have to break them down into monosaccharides - Add dilute HCl & heat in water bath until boiling
  • Then neutralise it - Add sodium hydrogencarbonate
  • Carry out Benedict’s test as you would for reducing sugars
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19
Q

How do you complete the iodine test for starch?

A
  • Add iodine dissolved in potassium iodide solution
    Negative result - stays browny-orange. Positive result - turns blue-black.
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20
Q

What are lipids?

A

They all contain hydrocarbons (molecules that contain only hydrogen & carbon) but also contain other components relating to the lipids function (therefore not polymers).
2 types:
- Triglycerides - Phospholipids

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21
Q

What are triglycerides formed from? What is their structure?

A

The condensation of 1 molecule of glycerol & 3 fatty acids.
Removal of 3 water molecules.
Forms 3 ester bonds (C-O-C).
The fatty acids have long hydrocarbon ‘tails’ - hydrophobic so insoluble in water (repel water molecules).

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22
Q

What is the general structure of fatty acids?
What are saturated & unsaturated fatty acids?

A

All consist of the same basic structure but the hydrocarbon tail varies.
R - COOH

Saturated - don’t have any double bonds between their carbon atoms - the fatty acid is ‘saturated’ with hydrogen.

Unsaturated - do have double bonds between carbon atoms which cause the chain to kink.

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23
Q

What are the properties of triglycerides?

A

Mainly used as energy storage molecules.
- Long hydrocarbon tails contain lots of chemical energy = lots of energy released when they’re broken down.
- Insoluble in water = don’t affect the water potential of cell & cause water to enter by osmosis (which would make them swell).
- Bundle together as insoluble droplets in cells because the fatty acids tails are hydrophobic (water repelling) and face inwards, shielding themselves from water with their glycerol heads.

Non-polar (no charged phosphate group) so no parts are hydrophilic (attract water).

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24
Q

What are phospholipids formed from? What is their structure?

A

The condensation of 1 molecule of glycerol, 2 fatty acids & a phosphate group (hydrophilic & charged (polar)).
Forms 3 ester bonds (C-O-C).
The fatty acids have long hydrocarbon ‘tails’ - hydrophobic so insoluble in water (repel water molecules).

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25
Q

What are the properties of phospholipids?

A

Make up the bilayer of cell membranes.
- Phosphate group is charged (so is hydrophilic) = phospholipid is polar.
- Their heads are hydrophilic (attract water) & their tails are hydrophobic so they form a double layer with heads facing out towards the water on either side.
- The centre of the bilayer is hydrophobic - water-soluble substances can’t pass through it (the membrane acts as a barrier to these substances).

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26
Q

How do you complete the emulsion test for lipids?

A
  • Shake test substance with ethanol for about a minute & pour solution into water
    Positive result - milky emulsion.
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27
Q

What are amino acids?

A

The monomers from which proteins are made.

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28
Q

What is the general structure of amino acids?

A

The 20 amino acids common in all organisms only differ in their R group.
R (variable side
l chain)
H2N — C — COOH
(amine l (carboxyl
group) H group)

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29
Q

What are dipeptides formed from?

A

The condensation of 2 amino acids.
Forms a peptide bond (C-N) between NH2 & COOH.

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30
Q

What are polypeptides formed from?

A

The condensation of many amino acids.
Forms a peptide bond (C-N).
A functional protein may contain 1 or more polypeptide chains.

31
Q

What is the primary structure of a protein?

A

The sequence of amino acids in the polypeptide chain.

32
Q

What is the secondary structure of a protein?

A

Hydrogen bonds form between the amino acids in the chain.
This makes it automatically coil into an alpha helix or fold into a beta pleated sheet.

33
Q

What is the tertiary structure of a protein?

A

More bonds formed between different parts of the polypeptide chain (hydrogen bonds & ionic bonds). disulphide bridges also form whenever two molecules of amino acid cysteine come close together.

For proteins made from a single polypeptide chain, the tertiary structure forms their final 3D structure.

34
Q

What is the quaternary structure of a protein?

A

For proteins made from more than one polypeptide chain, the quaternary structure forms their final 3D structure.

35
Q

How do you complete the biuret test for proteins?

A
  • Test solution needs to be alkaline - so first add a few drops sodium hydroxide solution
  • Add some copper (II) sulphate solution
    Positive result - turns purple. Negative result - stays blue.
36
Q

How would you use chromatography to separate a mixture from amino acids?

A
37
Q

What are enzymes? What is their structure?

A

Each enzyme lowers the activation energy of the reaction it catalyses.
Enzymes are proteins - they have an active site which has a specific shape.
They are highly specific due to their tertiary structure.

38
Q

How do enzymes speed up reactions?

A

Activation energy - the amount of energy needed to be supplied to the chemicals before the reaction starts (often provided as heat).
Enzymes lower the amount of activation energy needed (often reactions happen at a lower temperature than they would without an enzyme) = speed up rate of reaction.

39
Q

When a substrate binds to an enzymes active site, it forms an enzyme-substrate complex?
Why does this lower the activation energy?

A
  • If 2 substrate molecules need to be joined (Anabolic), being attached to the enzyme holds them close together, reducing any repulsion between the molecules so they can bond more easily.
  • If enzyme is catalysing a breakdown reaction (Catabolic), fitting into the active site puts a strain on bonds in the substrate, so it breaks down more easily.
40
Q

What is the ‘lock and key’ model?

A

Substrate fits into enzyme the same way a key fits into a lock - the active site & substrate have a complimentary shape.

41
Q

What is the ‘induced fit’ model?

A

Explains why enzymes are so specific - the substrate doesn’t only have to be the right shape to fit the active site, it has to make the active site change shape in the right way as well.
As the substrate binds, the active site changes shape so that it is complementary to the substrate, locking the substrate even more tightly to the enzyme.

42
Q

What are the properties of enzymes? (Relating to their tertiary structure)

A

Very specific - will usually only catalyse 1 reaction (only 1 complimentary substrate will fit into its active site - shape of a.s determined by enzymes tertiary structure, which is determined by its primary structure).
If the tertiary structure of a protein is altered in any way - the shape of active site will change = enzyme will no longer function.

43
Q

What are the factors that could alter the tertiary structure of an enzyme?

A
  • pH
  • Temperature
  • Mutation of a gene that determines proteins primary structure.
44
Q

How is enzyme activity measured?

A
  • How fast the product is made.
  • How fast the substrate is broken down.
45
Q

Describe the effect of temperature on enzyme activity.

A

Increased temperature, increased rate of enzyme activity.
More heat = more kinetic energy = molecules move faster = substrate molecules more likely to collide with enzymes active sites + collide with more energy = each collision more likely to result in enzyme-substrate complex formation.

If temperature too high, enzymes denature.
More heat = enzymes molecules vibrate more = vibration breaks some of the bonds that hold enzyme in shape = active site changes shape = enzyme + substrate no longer fit.

46
Q

Describe the effect of pH on enzyme activity.

A

All enzymes have an optimum pH.
Above & below optimum - H^+ & OH^- ions found in acids + alkalis can disrupt the ionic & hydrogen bonds that hold the enzymes tertiary structure in place (enzymes denature).

47
Q

Describe the effect of substrate concentration on enzyme activity.

A

Increased substrate concentration, increased rate of enzyme activity.
More substrate molecules = substrate molecules more likely to collide with enzymes active sites = more enzyme-substrate complexes being formed = more active sites occupied.

Only true up until a ‘saturation point’.
Too many substrate molecules = all enzyme active sites are full = adding more has no further affect.

48
Q

Describe the effect of enzyme concentration on enzyme activity.

A

Increased enzyme concentration, increased rate of enzyme activity.
More enzyme molecules = substrate molecules more likely to collide with enzymes active sites = more enzyme-substrate complexes being formed = more active sites occupied.

Only true until amount of substrate is limited.
Will reach point where there are more than enough enzyme molecules to deal with available substrates = adding more has no further effect.

49
Q

What are competitive inhibitors?

A

Have a similar shape to that of the substrate.
Compete with the substrate molecules to bind to the active site.
They occupy and therefore block the active site so no substrate molecules can bind = stops enzyme substrate complexes forming.

High concentration of inhibitor = less chance of substrates getting to enzymes = decrease in enzyme activity.

High concentration of substrate = more chance of substrates getting to enzymes before inhibitors = increase in enzyme activity.

50
Q

What are non-competitive inhibitors?

A

Bind to enzyme away from its active site.
Cause active site to change shape so substrate molecules can no longer bind to enzyme as the active site is no longer complementary = stops enzyme substrate complexes forming.
Don’t compete with substrate molecules to bind to active site as they are a different shape.

Higher concentration of substrate = has no effect - enzyme activity still inhibited.

51
Q

What is DNA?
What is RNA?

A
52
Q

How are ribosomes formed?

A
53
Q

What are the monomers of DNA and RNA (nucleic acids)?

A
54
Q

What is the basic structure of a nucleotide?

A
55
Q

What are polynucleotides? What is their structure?

A

Many nucleotides joined together via condensation reactions.
Forms a phosphodiester bond between the phosphate group of one nucleotide and the sugar of another.

56
Q

What is the structure of a DNA nucleotide?
What is the structure of a RNA nucleotide?

A
57
Q

What is the general structure of DNA?

A
58
Q

What are the benefits of the 2 polynucleotide chains in DNA being antiparallel?

A
59
Q

What is the general structure of RNA?

A
60
Q

What are the 4 main differences between DNA & RNA?

A
61
Q

Why did many scientists have doubts around DNA carrying the genetic code when it was first observed?

A
62
Q

Why does DNA replicate?

A

It copies itself before cell division so that each new cell has the full amount of DNA.

63
Q

What is semi-conservative replication?

A
64
Q

What are the steps in DNA replication?

A
65
Q

How does the enzyme DNA polymerase work?

A
66
Q

What was Meselson and Stahl’s experiment to show DNA replicated using the semi-conservative method?

A
67
Q

What is ATP?
Why do we need it?

A

Adenosine triphosphate.

Plants + animals cells need energy for biological processes to occur - this is released from respiration. A cell can’t get its energy directly from glucose so the en the energy released from glucose in respiration is used to make atp.

68
Q

What is the structure of ATP?

A

Made from the nucleotide base adenine, a ribose sugar & 3 phosphate groups.
Nucleotide derivative (modified nucleotide).

69
Q

Where is the energy in ATP stored?

A

This energy in atp is stored in high energy bonds between the phosphate groups.
It is released via hydrolysis reactions.

70
Q

What happens when energy is needed in a cell?

A

Once atp is made, it diffuses to the part of the cell that needs energy.
ATP is broken down into ADP (adenosine diphosphate) and Pi (inorganic phosphate) via a hydrolysis reaction.
A phosphate bond is broken & energy is released.

This reaction is catalysed by the enzyme ATP hydrolase.

71
Q

ATP hydrolysis can be ‘coupled’ with other energy requiring reactions. Why?

A

This means the energy released can be used directly to make the coupled reaction happen rather than it being lost as heat.

72
Q

How can Pi be used (the inorganic phosphate)?

A

Can be added to another compound (via phosphorylation) which makes the compound more reactive.

73
Q

How is ATP resynthesised?

A

In a condensation reaction between ADP & Pi.
This happens during both respiration & photosynthesis and is catalysed by the enzyme ATP synthase.

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