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3.1 Biological molecules Flashcards

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1
Q

What is a monomer?

A

Smaller / repeating molecules from which larger molecules / polymers are made.

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2
Q

What is a polymer?

A

Molecule made up of many identical / similar molecules / monomers.

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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

2 molecules join together
Forming a chemical bond
Releasing a water molecule

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5
Q

What is a hydrolysis reaction?

A

2 molecules separated
Breaking a chemical bond
Using 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

Two monosaccharides joined together with a glycosidic bond.
Formed by a condensation reaction, releasing a water molecule.

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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

Many monosaccharides joined together with glycosidic bonds.
Formed by many condensation reactions, releasing water molecules.

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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:
Energy store in plant cells.

Structure:
- Polysaccharide of α-glucose
- Amylose - 1,4 glycosidic bonds → unbranched
- Amylopectin - 1,4 and 1,6 glycosidic bonds → branched

How structures relate to function:
Amylose
- Helical → compact for storage in cell
- Large, insoluble polysaccharide molecule → can’t leave cell / cross cell membrane
- Insoluble in water → water potential of cell not affected (no osmotic effect)

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16
Q

What is the structure & function of the polysaccharide Glycogen?

A

Function:
Energy store in animal cells.

Structure:
- Polysaccharide made of α-glucose
- 1,4 and 1,6 glycosidic bonds → branched

How structures relate to function:
● Branched → compact / fit more molecules in small area
● Branched → more ends for faster hydrolysis → release glucose for respiration to make ATP for energy release
● Large, insoluble polysaccharide molecule → can’t leave cell / cross cell membrane
● Insoluble in water → water potential of cell not affected (no osmotic effect)

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17
Q

What is the structure & function of the polysaccharide Cellulose?

A

Function:
Provides strength and structural support to plant / algal cell walls.

Structure:
● Polysaccharide of β-glucose
● 1,4 glycosidic bond → straight, unbranched chains
● Chains linked in parallel by hydrogen bonds forming microfibrils

How structures relate to function:
● Every other β-glucose molecule is inverted in a long, straight, unbranched chain
● Many hydrogen bonds link parallel strands (crosslinks) to form microfibrils (strong fibres)
● Hydrogen bonds are strong in high numbers
● So provides strength to plant cell walls

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18
Q

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

A

For reducing sugars (monosaccharides + maltose, lactose):

  • 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 (sucrose):

  • 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

● 1 glycerol molecule and 3 fatty acids
● Condensation reaction
● Removing 3 water molecules
● Forming 3 ester bonds

How structures relate to function:
- High ratio of C-H bonds to carbon atoms in hydrocarbon chain
- So used in respiration to release more energy than same mass of carbohydrates
- Hydrophobic / non-polar fatty acids so insoluble in water (clump together as droplets)
- So no effect on water potential of cell (or can be used for waterproofing)

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22
Q

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

A

R-COOH
- Variable R-group - hydrocarbon chain (saturated or unsaturated)
- -COOH = carboxyl group

Saturated - no C=C double bonds in hydrocarbon chain; all carbons fully saturated with hydrogen.

Unsaturated - one or more C=C double bond in hydrocarbon chain (creating bend / kink)

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23
Q

What are the properties of triglycerides?

A

Function: energy storage molecules.

  • High ratio of C-H bonds to carbon atoms in hydrocarbon chain
  • So used in respiration to release more energy than same mass of carbohydrates
  • Hydrophobic / non-polar fatty acids so insoluble in water (clump together as droplets)
  • So no effect on water potential of cell (or can be used for waterproofing)
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24
Q

What are phospholipids formed from? What is their structure?

A

One of the fatty acids of a triglyceride is substituted by a phosphate-containing group.

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25
Q

What are the properties of phospholipids?

A

Function: form a bilayer in cell membrane, allowing diffusion of lipid-soluble (non-polar) or very small substances and restricting movement of water-soluble (polar) or larger substances.

How structures relate to function:
- Phosphate heads are hydrophilic
- Attracted to water so point to water (aqueous environment) either side of membrane
- Fatty acid tails are hydrophobic
- Repelled by water so point away from water / to interior of membrane

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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
  • Dipeptide - 2 amino acids joined together
    ● Condensation reaction
    ● Removing a water molecule
    ● Between carboxyl / COOH group of one and amine / NH2 group of another
    ● Forming a peptide bond
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30
Q

What are polypeptides formed from?

A
  • Polypeptide - many amino acids joined together

A functional protein may contain one or more polypeptides.

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31
Q

What is the primary structure of a protein?

A

Sequence of amino acids in a polypeptide chain, joined by peptide bonds.

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32
Q

What is the secondary structure of a protein?

A
  • Hydrogen bonds form between the amino acids in the chain. Between NH (group of one amino acid) and C=O (group of another).
  • This makes it automatically coil into an alpha helix or fold into a beta pleated sheet.
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33
Q

What is the tertiary structure of a protein?

A

● 3D folding of polypeptide chain
● Due to interactions between amino acid R groups (dependent on sequence of amino acids)
● Forming hydrogen bonds, ionic bonds and disulfide bridges

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

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34
Q

What is the quaternary structure of a protein?

A

● More than one polypeptide chain
● Formed by interactions between polypeptides (hydrogen bonds, ionic bonds, disulfide bridges)

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

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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.
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36
Q

What are enzymes? What is their structure?

A

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

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37
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.
38
Q

What is the ‘lock and key’ model?

A

Active site a fixed shape, complementary to one substrate.

39
Q

What is the ‘induced fit’ model?

A
  • Substrate binds to (not completely complementary) active site of enzyme
  • Causing active site to change shape (slightly) so it is complementary to substrate
  • So enzyme-substrate complex forms
  • Causing bonds in substrate to bend / distort, lowering activation energy
40
Q

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

A
  • Specific tertiary structure determines shape of active site
  • Dependent on sequence of amino acids (primary structure)
  • Active site is complementary to a specific substrate
  • Only this substrate can bind to active site, inducing fit and forming an enzyme-substrate complex
41
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.
42
Q

How is enzyme activity measured?

A
  • How fast the product is made.
  • How fast the substrate is broken down.
43
Q

Describe the effect of temperature on enzyme activity.

A

As temp increases up to optimum, rate of reaction increases
- More kinetic energy
- So more E-S complexes form
As temp increases above optimum, rate of reaction decreases
- Enzymes denature - tertiary structure and active site change shape
- As hydrogen / ionic bonds break
- So active site no longer complementary
- So fewer E-S complexes form

44
Q

Describe the effect of pH on enzyme activity.

A

As pH increases / decreases above / below an optimum, rate of reaction decreases
- Enzymes denature - tertiary structure and active site change shape
- As hydrogen / ionic bonds break
- So active site no longer complementary
- So fewer E-S complexes form

45
Q

Describe the effect of substrate concentration on enzyme activity.

A

As substrate conc increases, rate of reaction increases
- Substrate conc = limiting factor (too few substrate molecules to occupy all active sites)
- More E-S complexes form
At a certain point, rate of reaction stops increasing / levels off
- Enzyme conc = limiting factor
- As all active sites saturated / occupied (at a given time)

46
Q

Describe the effect of enzyme concentration on enzyme activity.

A

As enzyme conc increases, rate of reaction increases
- Enzyme conc = limiting factor (excess substrate)
- More enzymes so more available active sites
- So more enzyme-substrate (E-S) complexes form
At a certain point, rate of reaction stops increasing / levels off
- Substrate conc = limiting factor (all substrates in use)

47
Q

What are competitive inhibitors?

A

As concentration of competitive inhibitor increases, rate of reaction decreases
- Similar shape to substrate
- Competes for / binds to / blocks active site
- So substrates can’t bind and fewer E-S complexes form
Increasing substrate conc reduces effect of inhibitors
(dependent on relative concentrations of substrate and inhibitor)

48
Q

What are non-competitive inhibitors?

A

As concentration of non-competitive inhibitor increases, rate of reaction decreases
- Binds to site other than the active site (allosteric site)
- Changes enzyme tertiary structure / active site shape
- So active site no longer complementary to substrate
- So substrates can’t bind so fewer E-S complexes form
Increasing substrate conc has no effect on rate of reaction as change to active site is permanent

49
Q

What is DNA?
What is RNA?

A

Deoxyribonucleic acid - holds the genetic material in all living cells.
Ribonucleic acid - transfers genetic info from DNA to the ribosomes.

50
Q

How are ribosomes formed?

A

Formed from RNA & proteins.

51
Q

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

A

Nucleotides.

52
Q

What is the basic structure of a nucleotide?

A

Each nucleotide is formed from a pentose, a nitrogen-containing organic base & a phosphate group.

53
Q

What are polynucleotides? What is their structure?

A
  • Many nucleotides joined together via condensation reactions, removing water molecules
  • Forms a phosphodiester bond (2 ester bonds) between the phosphate group of one nucleotide and the sugar of another
54
Q

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

A

DNA nucleotide:
- Deoxyribose sugar
- A phosphate group
- 1 of: Adenine, Cytosine, Guanine, or Thymine (A C G T)

RNA nucleotide:
- Ribose sugar
- A phosphate group
- 1 of: Adenine, Cytosine, Guanine, or Uracil (A C G U)

55
Q

What is the general structure of DNA?

A

A double helix with 2 antiparallel polynucleotide chains held together by hydrogen bonds between specific complementary base pairs (A-T & G-C).
(This means there are always equal amounts of A & T and G & C)
2 hydrogen bonds form between A & T and 3 form between G & C.

56
Q

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

A

Cause chain to coil/twist into double helix.
- Compact so can fit into nucleus
- Stabilises the molecule

57
Q

What is the general structure of RNA?

A

A relatively short polynucleotide chain.

58
Q

What are the 4 main differences between DNA & RNA?

A

DNA - 2 polynucleotide chains stabilised by hydrogen bonds.
RNA - Single polynucleotide chain.

DNA - Deoxyribose sugar.
RNA - Ribose sugar.

DNA - A, T, C, G bases.
RNA - A, U, C, G bases.

DNA - Long molecule.
RNA - Relatively short molecule.

59
Q

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

A

Due to its relatively simple chemical composition. Some argued the genetic code must be carried by proteins (much more chemically varied).

60
Q

Why does DNA replicate?

A

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

61
Q

What is semi-conservative replication?

A

Each new DNA molecule consists of one original / template strand and one new strand
This means there is genetic continuity between generations of cells.

62
Q

What are the steps in DNA replication?

A
  1. DNA helicase breaks hydrogen bonds between complementary bases, unwinding the double helix
  2. Both strands act as templates
  3. Free DNA nucleotides attracted to exposed bases and join by specific complementary base pairing
  4. Hydrogen bonds form between adenine-thymine and guanine-cytosine
  5. DNA polymerase joins adjacent nucleotides on new strand by condensation reactions
  6. Forming phosphodiester bonds
63
Q

How does the enzyme DNA polymerase work?

A
  • DNA has antiparallel strands
  • So shapes / arrangements of nucleotides on two ends are different
  • DNA polymerase is an enzyme with a specific shaped active site
  • So can only bind to substrate with complementary shape (5’ end of developing (primer) strand)
  • So new strand is made in a 5’ to 3’ direction & DNA polymerase moves down the template strand in a 3’ to 5’ direction

Because the strands in DNA are antiparallel, the DNA polymerase working on 1 template strand moves in the opposite direction to the other one.

64
Q

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

A
  1. Bacteria grown in medium containing heavy nitrogen (15N) and nitrogen is incorporated into DNA bases
    ● DNA extracted & centrifuged → settles near bottom, as all DNA molecules contain 2 ‘heavy’ strands
  2. Bacteria transferred to medium containing light nitrogen (14N) and allowed to divide once
    ● DNA extracted & centrifuged → settles in middle, as all DNA molecules contain 1 original ‘heavy’ and 1 new ‘light’ strand
  3. Bacteria in light nitrogen (14N) allowed to divide again
    ● DNA extracted & centrifuged → half settles in middle, as contains 1 original ‘heavy’ and 1 new ‘light’ strand; half settles near top, as contains 2 ‘light’ strands
65
Q

What is ATP?

A

Adenosine triphosphate.

66
Q

What is the structure of ATP?

A

● Ribose bound to a molecule of adenine (base) and 3 phosphate groups
● Nucleotide derivative (modified nucleotide)

67
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.

68
Q

How is ATP broken down?

A

● ATP (+ water)→ ADP (adenosine diphosphate) + Pi (inorganic phosphate)
● Hydrolysis reaction, using a water molecule
● Catalysed by ATP hydrolase (enzyme)

69
Q

Give two ways in which the hydrolysis of ATP is used in cells.

A

● Coupled to energy requiring reactions within cells (releases / provides energy) e.g. active transport, protein synthesis
● Inorganic phosphate released can be used to phosphorylate (add phosphate to) other compounds, making them more reactive

70
Q

How is ATP resynthesised?

A

● ADP + Pi → ATP (+ water)
● Condensation reaction, removing a water molecule
● Catalysed by ATP synthase (enzyme)
● During respiration and photosynthesis

71
Q

Why is ATP a suitable energy source for cells?

A

● Releases energy in (relatively) small amounts / little energy lost as heat
● Single reaction / one bond hydrolysed to release energy (so immediate release)
● Cannot pass out of cell

72
Q

What are the properties of water?

A
  • Metabolite
  • Solvent
  • High specific heat capacity
  • High latent heat of vaporisation
  • Strong cohesion between water molecules
73
Q

What is the structure of water?

A

Hydrogen bonds between water molecules
● Water is polar molecule
● Partially negatively charged oxygen atoms attract partially positively charged hydrogen atoms of other water molecules

74
Q

Describe the benefits of water being a metabolite.

A

Used in condensation / hydrolysis / photosynthesis / respiration
- hydrolysis requires water molecule to break a bond
- condensation releases water molecule as new bond forms

75
Q

Describe the benefits of water being a solvent.

A
  • A lot of important substances in biological reactions are ionic. Because water is polar, the δ+ end will be attracted to the positive ion & the δ- end will be attracted to the negative ion. This means the ions will get completely surrounded by water molecules (dissolve).
  1. Allows metabolic reactions to occur (faster in solution)
  2. Allows transport of substances eg. nitrates in xylem, urea in blood
76
Q

Describe the benefits of water having a relatively high heat capacity = buffers changes in temp.

A

When water heated, lots of energy used to break H bonds so less heat energy available to actually increase the temp of water = high specific heat capacity (can gain / lose a lot of heat / energy without changing temperature)
- Good habitat - temp under water likely to be more stable than on land.
- Water inside organisms also remains stable temp - helps maintain constant internal body temp (optimum enzyme activity).

77
Q

Describe the benefits of water having a relatively large latent heat of vaporisation.

A

Water evaporates when H bonds break. Allows water on surface to escape into air as a gas.
Takes a lot of energy to break these H bonds = high latent heat of vaporisation.
- Means living organisms can use water loss through evaporation to cool down without losing too much water
- So helps organisms maintain a constant internal body temperature

78
Q

Describe the benefits of water having strong cohesion.

A

Because they are polar, water molecules have strong cohesion.
- Water can flow - supports columns of water eg. transpiration stream through xylem in plants
- Produces high surface tension when in contact with air, supporting small organisms (to walk on water)

79
Q

Where are inorganic ions found in the body?

A

In solution in cytoplasm and body fluid, some in high concentrations and others in very low concentrations.

80
Q

What are some examples of the roles of inorganic ions?

A

Hydrogen ions (H+)
● Maintain pH levels in the body → high conc = acidic / low pH
● Affects enzyme rate of reaction as can cause enzymes to denature

Iron ions (Fe^2+)
● Component of haem group of haemoglobin
● Allowing oxygen to bind / associate for transport as oxyhemoglobin

Sodium ions (Na+)
● Involved in co-transport of glucose / amino acids into cells
● Involved in action potentials in neurons
● Affects water potential of cells / osmosis

Phosphate ions (PO4^3-)
● Component of nucleotides, allowing phosphodiester bonds to form in DNA / RNA
● Component of ATP, allowing energy release
● Phosphorylates other compounds making them more reactive
● Hydrophilic part of phospholipids, allowing a bilayer to form

81
Q

3.3 temporarily here

A
82
Q

Explain what happens in digestion.

A

● Large (insoluble) biological molecules hydrolysed to smaller (soluble) molecules
● That are small enough be absorbed across cell membranes into blood

83
Q

Describe how starch is digested.

A

● Amylase (produced by salivary glands / pancreas) hydrolyses starch to maltose
● Membrane-bound maltase (attached to cells lining ileum) hydrolyses maltose to glucose
● Hydrolysis of glycosidic bond

84
Q

Describe how disaccharides are digested.

A

● Membrane-bound disaccharidases hydrolyse disaccharides to 2 monosaccharides:
- (Maltase) maltose → glucose + glucose
- (Sucrase) sucrose → fructose + glucose
- (Lactase) lactose → galactose + glucose
● Hydrolysis of glycosidic bond

85
Q

Describe how lipids are digested, including the action of bile salts.

A

● Bile salts (produced by liver) emulsify lipids causing them to form smaller lipid droplets
● This increases surface area of lipids for increased / faster lipase activity
● Lipase (made in pancreas) hydrolyses lipids (eg. triglycerides)→ monoglycerides + fatty acids
● Hydrolysis of ester bond

86
Q

Describe how proteins are digested.

A

● Endopeptidases - hydrolyse internal (peptide) bonds within a polypeptide → smaller peptides
- So more ends / surface area for exopeptidases
● Exopeptidases - hydrolyse terminal (peptide) bonds at ends of polypeptide → single amino acids
● Membrane-bound dipeptidases - hydrolyse (peptide) bond between a dipeptide → 2 amino acids
● Hydrolysis of peptide bond

87
Q

Why are membrane-bound enzymes important in digestion?

A

● Membrane-bound enzymes are located on cell membranes of epithelial cells lining ileum
● (By hydrolysing molecules at the site of absorption they) maintain concentration gradients for absorption

88
Q

Describe the pathway for absorption of products of digestion.

A

Lumen (inside) of ileum → cells lining ileum (part of small intestine) → blood

89
Q

Describe how amino acids and monosaccharides are absorbed.

A

Co-transport:
1. ● Na+ actively transported from epithelial cells lining ileum to blood (by Na+/K+ pump)
● Establishing a conc gradient of Na+ (higher in lumen than epithelial cell)
2. ● Na+ enters epithelial cell down its concentration gradient with glucose against its concentration gradient
● Via a co-transporter protein
3. ● Glucose moves down a conc gradient into blood via facilitated diffusion

90
Q

Describe how lipids are absorbed, including the role of micelles.

A

● Micelles contain bile salts, monoglycerides and fatty acids
- Make monoglycerides and fatty acids (more) soluble in water
- Carry / release fatty acids and monoglycerides to cell / lining of ileum
- Maintain high concentration of fatty acids to cell / lining
● Monoglycerides / fatty acids absorbed (into epithelial cell) by diffusion (lipid soluble)
● Triglycerides reformed in (epithelial) cells and aggregate into globules
● Globules coated with proteins forming chylomicrons which are then packaged into vesicles
● Vesicles move to cell membrane and leave via exocytosis
- Enter lymphatic vessels and eventually return to blood circulation

biology (9 decks)

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