3.1 - BIOLOGICAL MOLECULES

Polymers

Large, complex molecules made of long chains of monomers

Monomers

Small, basic molecular units

Monomer examples

Monosaccharides, amino acids, nucleotides

Carbohydates contain ____

C, H, O

Monosaccharide examples

Glucose, fructose, galactose

Carbohydrates are (mono/polysaccharides)

Polysaccharides

Glucose

Hexose sugar - 6 C atoms per molecule

Has 2 isomers - alpha (α) and beta (β)

α-glucose structure

(alpha - H is on top)

β-glucose structure

(beta - H is on bottom)

Condensation reaction

Two molecules join with formation of new chemical bond

+ water molecule released

Monosaccharides are joined by ____

condensation reactions

Glycosidic bond

Bond between two monosaccharides

Sucrose

Disaccharide formed by glucose + fructose (via condensation reaction)

Lactose

Disaccharide formed by glucose + galactose (via condensation reaction)

Maltose

Disaccharide formed by glucose + glucose (via condensation reaction)

Hyrolysis reactions

Breaking of chemical bond between monomers using water molecule

What is starch made of?

Mixture of amylose + amylopectin - polysaccharides of α-glucose

Plants store excess glucose as ___

starch

Why is starch good for storage?

Insoluble in water → doesn’t affect water potential

• → doesn’t cause water to enter cells by osmosis

• → good for storage

Amylose

• Long, unbranched chain of α-glucose

• Angles of glycosidic bonds → coiled structure

  • → compact

  • → good for storage

Amylopectin

• Long, branched chain of α-glucose

• Side branches allow enzymes that break down molecule to reach glycosidic bonds easily

  • → glucose can be released quickly

Glycogen

• Polysaccharide of α-glucose

• Animals store excess glucose as glycogen

Glycogen structure

• Highly branched structure

  • → stored glucose can be released quickly

• Compact

  • → good for storage

Cellulose

• Made of long, unbranched chains of β-glucose

• When β-glucose molecules bond, they form straight cellulose chains

• Cellulose chains linked by H bonds to form microfibrils (strong fibres)

  • → strong fibres make cellulose a good structural support for cells

Which sugars are reducing sugars?

All monosaccharides + some disaccharides (e.g. maltose, lactose)

Test for reducing sugars

1. Add Benedict’s reagent (blue) to sample + heat in water bath at 100ᵒC

2. If positive test, coloured ppt forms

   • Higher conc. of reducing sugar = further colour change

Test for non-reducing sugars

If reducing sugar test negative, must do non-reducing sugar test

1. Get new sample of test solution, add dilute hydrochloric acid + heat in water bath at 100ᵒC

2. Add sodium hydrogencarbonate to neutralise

3. Carry out Benedict’s test (reducing sugar test)

4. If positive test, coloured ppt forms

5. If negative, solution stays blue → no sugar in solution

Test for starch

1. Add iodine dissolved in potassium iodide solution to sample

2. If positive test, sample changes from browny-orange → blue-black

Triglyceride structure

1 glycerol + 3 fatty acid

Fatty acid molecules

• Have ‘tails’ made of hydrocarbons

• Tails ‘hydrophobic’ (repel water)

  • → lipids insoluble in water

• All fatty acids have same basic structure, but hydrocarbon tail varies

Basic structure of fatty acid

What bond forms between glycerol + fatty acid?

Ester bond

Formation of triglycerides

• Ester bond forms between each fatty acid and the gycerol molecule

  • Each time, water molecule is released

• 3x condensation reactions

Saturated fatty acid

No double bonds between C atoms (in hydrocarbon tail/R group)

Unsaturated fatty acid

1+ double bond between C atoms

→ causes kinks in chain

Phospholipids

• Found in cell membrane

• 1 fatty acid replaced by phosphate group

• Phosphate group hydrophilic (attracts water)

Structure + function of triglycerides

Energy storage molecules

• Long hydrocarbon tails contains lots of chemical energy

  • → lots of energy released when they’re broken down

  • Lipids have 2x energy per gram than carbohydrates

• Insoluble

  • → don’t affect water potential and cause water to enter by osmosis

  • Triglycerides stay together as insoluble droplets in cells

    • → fatty acid tails hydrophobic so face inwards, shielded from water

Structure + function of phospholipids

Make up bilayer of cell membranes (which control what enters/leaves cell)

• Hydrophilic heads + hydrophobic tails

  • → form double layer with heads facing out towards water

• Centre of bilayer hydrophobic

  • → water-soluble substances can’t pass through easily

    • → membrane is barrier to those substances

Name of test for lipids

Emulsion test

Test for lipids

1. Shake test substance with ethanol for 1min so it dissolves, then pour solution into water

2. Any lipid shows up as milky emulsion

3. More lipid = more noticeable milky colour

What are the monomers of proteins?

Amino acids

Dipeptide

2 amino acids joined together

Polypeptide

3+ amino acids joined together

Proteins are made of…

One or more polypeptides

Structure of amino acid

Same general structure:

• Carboxyl group (-COOH)

• Amino group (-NH₂)

• R group (variable group)

How many amino acids are there?

20 - all living things share a bank of 20 amino acids

Differences in amino acids

Only difference is R group

Formation of polypeptides

What is the name of the bond between amino acids?

Peptide bond

What is released during condensation reaction?

Water molecule

Primary structure of proteins

Sequence of amino acids in polypeptide chain

Secondary structure of proteins

• Polypeptide chain isn’t flat + straight

• H bonds form between amino acids in chain

  • → chain coils/folds automatically

Types of secondary structure in proteins

Can coil into alpha (α) helix

or fold into beta (β) pleated sheet

Tertiary structure of proteins

• Coiled/folded amino acid chan is coiled/folded further

• More bonds form between different parts of polypeptide chain, incl. H bonds + ionic bonds (attractions between -ve and +ve charges on different parts of molecule)

• For proteins made from single polypeptide chain, tertiary structure forms their final 3D structure

Example of tertiary structure in proteins

Disulfide bridges form whenever 2 molecules of amino acid cysteine come close together - S atom of one cysteine bonds to S atom of other

Quaternary structure of proteins

• Some proteins made of several different polypeptide chains held together by bonds

• Quaternary structure is the way polypeptide chains are assembled together

• For proteins made from 1+ polypeptide chain (e.g. haemoglobin, insulin), quaternary structure = proteins final 3D structure

Function of proteins as enzymes

• Usually a roughly spherical shape due to tight folding of polypeptide chains

• Soluble - often have roles in metabolism, e.g. some enzymes break down larger food molecules

• Some enzymes help to synthesise large molecules

Function of proteins as antibodies

• Involved in immune response

• Made of 2 light (short) polypeptide chains + 2 heavy (long) polypeptide chains bonded together

• Have variable regions - amino acid sequences in these regions vary greatly

Function of proteins as transport proteins

e.g. channel proteins in cell membranes

• Channel proteins contain hydrophobic + hydrophilic amino acids

  • → protein folds up to form channel

• Transport molecules + ions across membranes

Function of proteins as structural proteins

• Physically strong

• Have long polypeptide chains lying parallel to each other with cross-links between them

• Include keratin (in hair + nails) and collagen (in connective tissue)

Test for proteins

1. Add drops of sodium hydroxide solution (solution must be alkaline)

2. Add copper(II) sulfate solution

• Protein present = purple solution

• No protein = solution stays blue

Enzymes are known as…

biological catalysts

Enzymes are what type of biological molecule?

Proteins

Enzymes

• Catalyse metabolic reactions

  • at cellular level (e.g. resp.) and for organism as a whole (e.g. digestion)

• Can affect structures (e.g. involved in production of collagen) and functions (e.g. resp.)

• Intracellular (within cells) / extracellular (outside cells)

Why are enzymes specific?

• Have active site with specific shape

  • Active site = part of enzyme where substrate molecules bind to

• Highly specific due to tertiary structure

Activation energy

Energy that must be supplied for reaction to start - often provided as heat

How do enzymes catalyse reactions?

• Lowering activation energy

  • → reactions occur at lower temp.

    • → increases RoR

Why does formation of enzyme-substrate complex lower activation energy?

• If two substrate molecules need to be joined:

  • → being attached to enzyme holds them close together

    • → reduces repulsion between molecules

      • → can bond more easily

• If enzyme is catalysing breakdown reaction:

  • → fitting into active site puts strain on bonds in substrate

    • → substrate molecule breaks up more easily

Induced fit model

Substrate doesn’t only have to be right shape to fit active site, also has to make active site change shape in the right way

Enzyme’s tertiary structure

• Enzymes very specific - usually only catalyse one reaction

  • because only one complementary substrate fits into active site

• Active site shape is determined by enzyme’s tertiary structure (which is determined by primary structure)

• Each enzyme has different tertiary structure → different shaped active site

• If tertiary structure is altered in any way, shape of active site changes

  • → substrate won’t fit in active site → no enzyme-substrate complex → reaction not catalysed

• Tertiary structure may be altered by changes in pH + temp

Primary structure of a protein is determined by ____

a gene

Mutation in gene could change tertiary structure of enzyme

Effect of temperature on enzyme activity

• Higher temp → enzyme molecules vibrate more

• Temp above certain level → vibrations break bonds that hold enzyme in shape

  • → active site changes shape

  • → enzyme denatured

Effect of pH on enzyme activity

• Enzymes have optimum pH

• Above and below optimum, H⁺ and OH⁻ ions in acids and alkalis damage ionic bonds + H bonds holding enzyme’s tertiary structure in place

  • → active site changes shape

  • → enzyme denatured

Effect of enzyme concentration on enzyme activity

• More enzyme molecules → more likely for substrate molecule to collide and form enzyme-substrate complex

  • → increase enzyme conc. = increase RoR

• If amount of substrate limited, there is a point where enzyme molecules > substrate → more enzyme = no effect

Effect of substrate concentration on enzyme activity

• Higher substrate conc. = faster reaction

  • → more likely to have collisions

  • only true up to ‘saturation’ point

    • all active sites are full → more substrate = no effect

• Substrate conc. decreases with time

  • → if no other variables change, RoR decreases over time

    • → initial RoR is highest

Competitive enzyme inhibitors

• Similar shape to substrate molecules

• Compete with substrate to bind to active site, but no reaction occurs

• Block active site so no substrate molecules can fit

Effect of competitive inhibitor concentration on enzyme activity

• High conc of inhibitor → take up nearly all active sites → substrate can’t get to enzyme

• Higher substrate conc. → substrate’s chances of getting to active site before inhibitor increase

  • → increasing substrate conc → increase RoR (up to a point)

Non-competitive enzyme inhibitors

• Bind to enzyme away from active site

  • → active site changes shape

  • → substrate can’t bind

Effect of non-competitive inhibitor concentration on enzyme activity

• Increasing substrate conc. has no effect on RoR - enzyme activity still inhibited

DNA

(deoxyribonucleic acid)

Stores genetic info - instructions needed for organism to grow + develop

RNA

(ribonucleic acid)

One main function is to transfer genetic info from DNA → ribosomes

Ribosomes function

Carry out protein synthesis

Read DNA to make polypeptides (proteins) during translation

What are ribosomes made from?

RNA + proteins

What are the monomers of DNA and RNA?

Nucleotides

Nucleotide structure

• A pentose sugar (sugar with 5 C atoms)

• A nitrogen-containing organic base

• A phosphate group

DNA nucleotides

• Pentose sugar in DNA nucleotide = deoxyribose

• Each DNA nucleotide has same sugar + phosphate group

  • Base varies

Possible bases in DNA nucleotides

• Adenine (A)

• Thymine (T)

• Cytosine (C)

• Guanine (G)

RNA nucleotides

• Pentose sugar in RNA nucleotide = ribose

• Like DNA, RNA nucleotide has phosphate group + one of four bases

Possible bases in RNA nucleotides

• Adenine (A)

• Uracil (U)

• Cytosine (C)

• Guanine (G)

Polynucleotide strand

How do nucleotides bond together?

Condensation reaction between phosphate group of one nucleotide + sugar of another

What is the name of the bond between nucleotides?

Phosphodiester bond (consists of phosphate group + 2 ester bonds)

Sugar-phosphate backbone

Chain of sugars + phosphates in polynucleotide

DNA structure

• Two DNA polynucleotide strands join by H bonding between bases

• Bases join with complementary base pairing

  • → always equal amounts A + T and equal amounts C + G in DNA

• Two antiparallel (opposite directions) polynucleotide strands twist to form DNA double-helix

Complementary base pairs in DNA

Adenine with thymine (A-T)

Cytosine with guanine (C-G)

How many bonds form between each base pair?

A-T = 2 H bonds

C-G = 3 H bonds

RNA structure

Single polynucleotide chain

Shorter than most DNA polynucleotides

What was scientist’s previous understanding of DNA?

• DNA first observed in 1800s

  • Scientists at the time doubted it could carry genetic code due to its relatively simple chemical composition

    • → thought genetic info was carried by proteins (more chemically varied)

• By 1953, experiments showed DNA was carrier of genetic info

• Double-helix structure was also discovered that year, by Watson and Crick

Semi-conservative replication

• DNA copies itself before cell division → each new cell has full DNA

• Half of strands of new DNA molecule are from original DNA molecule

  • → genetic continuity between generations of cells

Genetic continuity

Cells produced by cell division inherit their genes from their parent cells