biological molecules

Monomers and polymers

Monomers -smaller, repeating molecules /units from which larger molecules / polymers are made

●Polymers - molecules made from many (a large number) identical /similar monomer molecules

Condensation

reaction

●2 molecules join together

●Forming a chemical bond

●Releasing awater molecule

Hydrolysis

reaction

●2 molecules separated

●Breaking a chemical bond

●Using awater molecule

What are monosaccharides? Give 3 common examples

●Monomers from which larger carbohydrates are made

●Glucose,fructose,galactose

draw structure of glucose

Describe the difference between the structure of α-glucose and β-glucose

●Isomers -same molecular formula but differently arranged atoms

●OH group is below carbon 1 in α-glucose but above carbon 1 in β-glucose

What are disaccharides and how are they formed?

●Two monosaccharides joined together with a glycosidic bond

●Formed by a condensation reaction, releasing a water molecule

List 3 common disaccharides & monosaccharides from which they’re made

What are polysaccharides and how are they formed?

●Many monosaccharides joined together with glycosidic bonds

●Formed by many condensation reactions, releasing many water molecules

Starch Function

Energy storage molecule in plant cells

Starch Structure

• Polysaccharide made of α-glucose

• Amylose contains α-1,4 glycosidic bonds and forms a long, unbranched, helical/coiled chain

• Amylopectin contains α-1,4 and α-1,6 glycosidic bonds and is branched

Glycogen Function

Energy storage molecule in animal cells

Glycogen Structure

• Polysaccharide made of α-glucose

• Contains α-1,4 and α-1,6 glycosidic bonds

• Highly branched (more highly branched than amylopectin)

Starch (amylose and amylopectin) how the structures of starch relate to their functions

• Helical/coiled structure of amylose makes it compact, allowing lots to be stored in a small space

• Amylopectin is branched, making it compact and allowing more glucose molecules to fit into a small area

• Branches provide many ends for enzyme action, allowing faster hydrolysis and quicker release of glucose for respiration and ATP production

• Large polysaccharide molecules cannot diffuse out of the cell or cross the cell membrane

• Insoluble in water, so they do not affect the water potential of the cell (no osmotic effect)

What is the structure and function of amylose?

• Polysaccharide made of α-glucose

• Contains α-1,4 glycosidic bonds only

• Unbranched chain that coils into a helix

• Compact → suitable for energy storage in plants

• Fewer ends for enzyme action → slower hydrolysis and glucose release

What is the structure and function of amylopectin?

• Polysaccharide made of α-glucose

• Contains α-1,4 and α-1,6 glycosidic bonds

• Branched structure

• Compact → allows lots of glucose to be stored

• Many ends for enzyme action → faster hydrolysis and glucose release

Explain how the structures of glycogen relate to their functions

• Highly branched structure makes it compact, allowing large amounts of glucose to be stored

• More highly branched than amylopectin, so it has more ends for enzyme action and can be hydrolysed more rapidly to release glucose quickly for respiration and ATP production

• Large polysaccharide molecule, so it cannot diffuse out of the cell or cross the cell membrane

• Insoluble in water, so it does not affect the water potential of the cell (no osmotic effect)

Describe the basic function and structure of cellulose

Function

• Provides strength and structural support to plant and algal cell walls

Structure

• Polysaccharide made of β-glucose

• β-1,4 glycosidic bonds form long, straight, unbranched chains

• Every other β-glucose molecule is inverted

• Parallel chains are linked by many hydrogen bonds, forming microfibrils

Explain how the structure of cellulose relates to its function

• Straight, unbranched chains run parallel to each other

• Many hydrogen bonds form between parallel chains, creating strong microfibrils

• Large numbers of hydrogen bonds give cellulose high tensile strength

• Strong microfibrils provide rigidity and support to the cell wall

• Prevents the plant cell from bursting when water enters by osmosis

Describe the test for reducing sugars

1. Add Benedict’s solution (blue) to sample

2. Heat in a boiling water bath

3. Positive result = green / yellow / orange / red precipitate

Reducing sugars

monosaccharides, maltose, lactose

Describe the test for non-reducing sugars

1. Do Benedict’s test (as above) and stays blue / negative

2. Heat in a boiling water bath with acid (to hydrolyse into reducing sugars)

3. Neutralise with alkali (eg. sodium bicarbonate)

4. Heat in a boiling water bath with Benedict’s solution

5. Positive result = green / yellow / orange / red precipitate

Non-reducing sugars

sucrose

Suggest a method to measure the quantity of sugar in a solution

●Carry out Benedict’s test as above, then filter and dry precipitate

●Find mass /weigh

Suggest another method to measure the quantity of sugar in a solution

1. Make sugar solutions of known concentrations

(eg. dilution series)

2. Heat a set volume of each sample with a set

volume of Benedict’s solution for the same time

3. Use colorimeter to measure absorbance (of

light) of each known concentration

4. Plot calibration curve -concentration on xaxis,

absorbance on yaxis and draw line of best fit

5. Repeat Benedict’s test with unknown sample and

measure absorbance

6. Read off calibration curve to find concentration

associated with unknown sample’s absorbance

Describe the biochemical test for starch

1. Add iodine dissolved in potassium iodide (orange / brown) and shake / stir

2. Positive result = blue-black

Name two groups of lipid

Triglycerides and phospholipids

Describe the structure of a fatty acid (RCOOH)

●Variable R-group -hydrocarbon chain (this may be saturated or unsaturated)

●-COOH =carboxyl group

Describe the difference between saturated and unsaturated fatty acid

●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 a bend / kink)

Describe how triglycerides form

●1 glycerol molecule and 3 fatty acids

●3 condensation reactions

●Removing 3 water molecules

●Forming 3 ester bonds

Explain how the properties of triglycerides are related to their structure

function: energy storage

●High ratio of C-H bonds to carbon atoms in hydrocarbon chain

○So used in respiration to release more energy than the same mass of carbohydrates

●Hydrophobic / non-polar fatty acids so insoluble in water (clump together as droplets, tails inwards)

○So no effect on water potential of cell (or can be used for waterproofing)

Describe the difference between the structure

of triglycerides and phospholipids

One of the fatty acids of a triglyceride is

substituted by a phosphate-containing group

function of phospholipid

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

Describe how the properties of

phospholipids relate to their structure

●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

Describe the test for lipids

1. Add ethanol,shake (to dissolve lipids), then add water

2. Positive result = milky white emulsion

Describe / draw the general

structure of an amino acid

How many amino acids are common in all organisms? How do they vary?

The 20 amino acids that are common in all organisms differ only in their side group (R)

Describe how amino acids join together

●Condensation reaction

●Removing a water molecule

●Between carboxyl group of one

and amine group of another

●Forming a peptide bond

What are dipeptides and polypeptides?

●Dipeptide -2amino acids joined together

●Polypeptide -many amino acids joined together

A functional protein may contain one or more polypeptides

Describe the primary structure of a protein

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

Describe the secondary structure of a protein

●Folding (repeating patterns) of polypeptide chain eg.

alpha helix / beta pleated sheets

●Due to hydrogen bonding between amino acids

●Between NH (group of one amino acid) and C=O (group)

Describe the tertiary structure of a protein

●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

Describe the quaternary structure of a protein

●More than one polypeptide chain

●Formed by interactions between polypeptides

(hydrogen bonds, ionic bonds, disulfide bridges)

Describe the test for protein

1. Add biuret reagent (sodium hydroxide + copper (II) sulphate)

2. Positive result = purple / lilac colour (indicating presence of peptide bonds)

How do enzymes act as

biological catalysts?

●Each enzyme lowers activation

energy of reaction it catalyses

●To speed up rate of reaction

Enzymes catalyse…?

a wide range of

intracellular and extracellular reactions

that determine structures and functions

from cellular to whole-organism level

how to identify activation energy with/without enzyme and energy released during a reaction on a graph

Describe the induced-fit model of enzyme action

1. Substrate binds to (not completely complementary) active site of enzyme

2. Causing active site to change shape (slightly) so it is complementary to its substrate

3. So enzyme-substrate complex forms

4. Causing bonds in substrate to bend / distort, lowering activation energy

Describe how models of enzyme action have changed over time

●Initially lock and key model (now outdated)

○Active site a fixed shape,complementary to one substrate

●Now induced-fit model

Explain the specificity of enzymes

●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

Describe and explain the effect of enzyme concentration on

the rate of enzyme-controlled reactions

●As enzyme concentration increases,rate of reaction increases

○Enzyme concentration =limiting factor (excess substrate)

○More enzymes so more available active sites

○So more enzyme-substrate complexes form

●At a certain point, rate of reaction stops increasing / levels off

○Substrate concentration =limiting factor (all substrates in use

Describe and explain the effect of substrate concentration on

the rate of enzyme-controlled reactions

●As substrate concentration increases,rate of reaction increases

○Substrate concentration =limiting factor (too few substrate

molecules to occupy all active sites)

○More enzyme-substrate complexes form

●At a certain point, rate of reaction stops increasing / levels off

○Enzyme concentration =limiting factor

○As all active sites saturated / occupied (at a given time

Describe and explain the effect of temperature on

the rate of enzyme-controlled reactions

●As temperature increases to optimum, rate of reaction increases

○More kinetic energy

○So more enzyme-substrate complexes form

●As temperature exceeds 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 enzyme-substrate complexes form

Describe and explain the effect of pH on

the rate of enzyme-controlled reactions

●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 enzyme-substrate complexes form

Describe and explain the effect of concentration of competitive inhibitors on

the rate of enzyme-controlled reactions

●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

○So fewer enzyme-substrate complexes form

●Increasing substrate concentration reduces effect of inhibitors

(dependent on relative concentrations of substrate and inhibitor)

Describe and explain the effect of concentration of

non-competitive inhibitors on the rate of enzyme-controlled reactions

●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 enzyme-substrate complexes form

●Increasing substrate concentration has no effect on rate of

reaction as change to active site is permanent

Describe the basic functions of DNA and RNA in all living cells

DNA

Holds genetic information which codes for polypeptides (proteins)

RNA

Transfers genetic information from DNA to ribosome

Name the two types of molecule from which a ribosome is made

RNA and proteins

Draw and label a DNA nucleotide and an RNA nucleotide

Describe the differences between a DNA nucleotide and an RNA nucleotide

Describe how nucleotides join together to form polynucleotides

●Condensation reactions, removing water molecules

●Between phosphate group of one nucleotide and deoxyribose / ribose of another

●Forming phosphodiester bonds

Why did many scientists initially doubt that DNA carried the genetic code?

The relative simplicity of DNA - chemically simple molecule with few components

Describe the structure of DNA

●Polymer of nucleotides (polynucleotide)

●Each nucleotide formed from

deoxyribose, a phosphate group and a

nitrogen-containing organic base

●Phosphodiester bonds join adjacent

nucleotides

●2polynucleotide chains held together by

hydrogen bonds

●Between specific complementary base

pairs -adenine / thymine and

cytosine / guanine

●Double helix

Describe the structure of (messenger) RNA

●Polymer of nucleotides (polynucleotide)

●Each nucleotide formed from ribose, a phosphate

group and a nitrogen-containing organic base

●Bases - uracil, adenine, cytosine, guanine

●Phosphodiester bonds join adjacent nucleotides

●Single helix

Compare and contrast the structure of DNA and (messenger) RNA

Suggest how the structure of DNA relates to its functions

●Two strands →both can act as templates for semi-conservative replication

●Hydrogen bonds between bases are weak →strands can be separated for replication

●Complementary base pairing →accurate replication

●Many hydrogen bonds between bases →stable / strong molecule

●Double helix with sugar phosphate backbone →protects bases / hydrogen bonds

●Long molecule →store lots of genetic information (that codes for polypeptides)

●Double helix (coiled) →compact

Suggest how you can use incomplete information about the frequency of

bases on DNA strands to find the frequency of other bases

1. % of adenine in strand 1 = % of thymine in strand 2 (and vice versa)

2. % of guanine in strand 1 = % of cytosine in strand 2 (and vice versa)

Because of specific complementary base pairing between 2 strands

Why is semi-conservative replication important?

Ensures genetic continuity between generations of cell?

Describe the process of semi-conservative DNA replication

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

Semi-conservative

- each new DNA molecule consists of one original / template strand and one new strand

Use your knowledge of enzyme action to suggest why DNA polymerase

moves in opposite directions along DNA strands

●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 (phosphate end of developing strand

Name the two scientists who proposed models of the chemical structure of

DNA and of DNA replication

Watson and Crick

Describe the work of Meselson and Stahl in validating the Watson-Crick

model of semi-conservative DNA replication

. Bacteria grown in medium containing heavy nitrogen (15N) so

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

What is ATP?

Adenosine triphosphate

Describe the structure of ATP

●Ribose bound to a molecule of adenine

(base) and 3 phosphate groups

●Nucleotide derivative (modified nucleotide)

Describe how ATP is broken down

●ATP (+ water) →ADP (adenosine diphosphate) + Pi (inorganic phosphate)

●Hydrolysis reaction, using a water molecule

●Catalysed by ATP hydrolase (enzyme)

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

●Coupled to energy requiring reactions within cells (releases energy)

○eg. active transport, protein synthesis

●Inorganic phosphate released can be used to phosphorylate

(add phosphate to) other compounds, making them more reactive

Describe how ATP is resynthesised in cells

●ADP + Pi →ATP (+ water)

●Condensation reaction, removing a water molecule

●Catalysed by ATP synthase (enzyme)

●During respiration and photosynthesis

Suggest how the properties of ATP make it a suitable immediate source of

energy for cells

●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

Explain how hydrogen bonds occur between water molecule

●Water is polar molecule

●Slightly negatively charged oxygen atoms attract slightly positively

charged hydrogen atoms of other water molecules

a property of water that are important in biology- Metabolite

Used in condensation /hydrolysis /photosynthesis /respiration

a property of water that are important in biology- solvent (Can dissolve solutes)

1. Allows metabolic reactions to occur (faster in solution)

2. Allows transport of substances eg. nitrates in xylem, urea in blood

a property of water that are important in biology - (Relatively) high

specific heat capacity

●Buffers changes in temperature

●As can gain / lose a lot of heat / energy without changing temperature

1. Good habitat for aquatic organisms as temperature more stable than land

2. Helps organisms maintain a constant internal body temperature

a property of water that are important in biology - (Relatively) large

latent heat of

vaporisation

●Allows effective cooling via evaporation of a small volume (eg. sweat)

●So helps organisms maintain a constant internal body temperature

a property of water that are important in biology - Strong cohesion between water molecule

1. Supports columns of water in tube-like transport cells of plants

eg. transpiration stream through xylem in plants

2. Produces surface tension where water meets air, supporting small

organisms (to walk on water

Where are inorganic ions found in the body?

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

describe the role of hydrogen ions

●Maintain pH levels in the body →high concentration = acidic / low pH

●Affects enzyme rate of reaction as can cause enzymes to denature (topic 1.4.2

describe the role of iron ions

●Component of haem group of haemoglobin

●Allowing oxygen to bind / associate for transport as oxyhaemoglobin (topic 3.4.1

describe the role of phosphate ions

1. Component of nucleotides, allowing phosphodiester bonds to form in DNA / RNA

2. Component of ATP, allowing energy release

3. Phosphorylates other compounds making them more reactive (topic 1.6)

4. Hydrophilic part of phospholipids, allowing a bilayer to form (topic 1.3 / 2.3