Chapter 3 - Biological Molecules

What does Ca2+ do?

Muscle contraction, nerve impule transmission

What does Na+ do?

Kidney function, nerve impulse transmission

What does K+ do?

Stomatal opening, nerve impulse transmission

What does H+ do?

Catalysis of reactions, pH determination

What does NH4+ do?

Production of nitrate ions by bacteria

What does NO3- do?

Nitrogen supply to plants (amino acid and protein formation)

What does HCO3- do?

Maintain blood pH

What does Cl- do?

Balance positive Na and K ions

What does PO43- do?

Cell membrane formation, bone formation, ATP and nucleic acid formation

What does OH- do?

pH determination, catalysis of reactions

What bonds are in a water molecule?

Covalent bonds and weak hydrogen bonds (many) that break/reform as molecules always moving

Why is water polar?

In the O-H bond, the hydrogen is slightly positive. Because polar molecules react weak hydrogen bonds form between molecules

Why does water have a high boiling point?

Many hydrogen bonds take a lot of energy to increase temperature and evaporate

Why is ice less dense than liquid water?

Hydrogen bonds fix molecule positions further apart than the average distance (when below 4oC)

Giant

Rigid open structure

Tetrahedral

So floats

Why is water a good solvent?

Due to polarity

Cohesive-moves as 1 mass (molecules all attracted to eachother-polarity). More cohesive to each other than air = surface tension

Adhesive-to each other and other polar molecules = capillary action (up against gravity)

Efficient transport medium and good for chemical reactions

Why is water a good coolant?

Can buffer temperature changes (cell reactions). Important for enzymes.

Why is water being stable important?

Doesn't change temperature/become a gas easily=constant environment e.g. ice pond insulation

What are carbo made of?

Carbon

Oxygen

Hydrogen

What type of sugar is glucose?

Hexose monosaccharide

What’s the difference between alpha and beta glucose?

Alpha-OH group below carbon 1

Beta-OH group above carbon 1

What reaction joins glucose and what is the bond formed?

Condensation (covalent)

1-4 glycosidic bond

Alternate beta glucoses flipped

Why is glucose soluble in water and why is this useful?

Polar so is soluble (between hydrogen and hydroxyl groups)

Glucose dissolved in cytosol=easy transport

Why type of sugars are fructose and galactose? Where are they found?

Hexose monosaccharides

Fructose-fruit

Galactose (+glucose) = lactose in milk

What type of sugar is ribose? Where is it found?

Pentose monosaccharide

RNA and DNA nucleotides (deoxyribose)

How many polysaccharides of starch does alpha glucose form?

2

Amylose

Amylopectin

Why is amylose a helix? What bonds does it have? Is it soluble?

Bond angles (1-4 glycosidic bond) create a helix (stabilised by hydrogen bonds)

Less soluble than glucose (compact).

Doesn't affect water potential.

What bonds does amylopectin have? What is its structure? Is it soluble?

1-4 and 1-6 glycosidic bonds

Branched structure

Insoluble (compact) doesn't affect water potential

Only in plants

What species is glycogen and energy store in? Why is it more compact than amylopectin. Why is storing and releasing glucose fast?

Animals and fungi

Many branches=compact (important as animals are mobile)

Many free ends so glucose easily added/removed. Speeds up storing/releasing glucose

What type of glucose makes cellulose? What is its structure? Why is it a good plant cell wall and for the digestive system?

Beta glucose

Can't coil/branch=straight chain molecule

Chains form hydrogen bonds : microfibrils, macrofibrils, cellulose fibres

Cell walls as is strong and insoluble (crystalline structure)

Humans can't break it down easily=healthy digestive system

What are reducing sugars and what is the test?

All monosaccharides and most disaccharides (can reduce, give elections)

Benedict: copper 2 sulphate solution (Cu2+) hot water bath, red Cu+ precipitate

More reducing sugar=more precipitate. Colour spends on reducing sugar concentration=quantitative

Can boil sucrose in HCl goes to glucose and fructose

How do you test for starch?

Iodine goes blue black (from brown) iodine dissolved in KI solution

Reagent strips-compare to chart to see glucose concentration

What are lipids made of?

Carbon

Hydrogen

Oxygen

Why don't lipids dissolve in water?

They are non-polar (outer shell electrons evenly distributed). No positive or negative regions.

What type of molecules are lipids?

Macromolecules (no monomers)

What are triglycerides made of?

1 glycerol and 3 fatty acids (alcohol and carboxylic acids)

What process joins fatty acids and glycerol?

Condensation reaction

Esterification

Ester bonds form O-C + 3 waters

What is a phospholipid made of?

Carbon

Hydrogen

Oxygen

Phosphorus

How many fatty acids does a phospholipid have?

2 and 1 phosphate group

Why are phospholipids soluble in water?

The phosphate gives extra electrons, so is soluble in water

Which part of a phospholipid is hydrophobic and hydrophilic?

Tail hydrophobic

Head hydrophilic-attracted to and interact with water

Why do lipids form a layer on top of water?

Heads stick in water, tails stick out of water

Surfactants

How do phospholipids form a bilayer?

Hydrophobic tails inwards, protected by hydrophilic heads. They form cell membranes as can separate an aqueous environment from cytosol in cells

What is a sterol?

Steroid alcohol

What is a sterols structure?

C ring structure with and OH group at one end

Why do sterols have dual hydrophobic/hydrophilic properties?

OH is polar = hydrophobic. Rest of molecule is hydrophilic

What is cholesterol and its structure?

Sterol

4 C rings and an OH group

Where is cholesterol made in the body?

Liver and intestines

What is cholesterol used for?

Formation of cell membranes-helps stability and regulates fluidity (membrane fluid is at a low temperature)

What are made using cholesterol?

Vitamin D, Bile, Steroid Hormones

If a molecule has a double bond what type is it?

Unsaturated

Why are unsaturated fatty acids not compact?

As they have a double bond so can't be compact (as can't bend). Oils at room temperature

What type of lipid do plants contain?

Unsaturated triglycerides

What can excess saturated fats lead to?

Coronary heart disease. (Any lead to obesity and heart strain)

Due to lipids being non polar, what can they do?

Form membranes and hydrophobic barriers

Produce hormones

Electrical insulation (for transmission)

Waterproofing

What do triglycerides do?

Thermal insulation to reduce heat loss (around organs and under skin)

Cushioning to protect vital organs

Buoyancy for aquatic animals

What test can identify a lipid?

Emulsion

How do you carry out an emulsion test?

Mix sample with ethanol

Add water and shake solution

White emulsion layer=lipid

How many amino acids are there?

20 found in cells

How many amino acids are essential?

9 from food

How many amino acids are conditionally essential?

6 only needed by growing children

How many amino acids are non essential?

5 as our bodies can make them from other amino acids

What is the bond between 2 amino acids?

Peptide bond

Which groups of amino acids react to form a dipeptide?

Amine (NH2) and Carboxyl (CO2H)

What type of reaction forms a peptide bond?

Condensation reaction

What is a condensation reaction in amino acids catalysed by?

Peptidyl transferase (made in ribosomes by protein synthesis)

What is primary protein structure?

Sequence of joined amino acids, by DNA. Only has peptide bonds. (Sequence determines how it folds so determines its final shape and function)

What is secondary protein structure?

Oxygen, hydrogen and nitrogen interact.

Hydrogen bonds may form= alpha helix.

Chains may lay parallel = beta pleated sheet. Secondary structure is a result of hydrogen bonds forming along protein molecules.

What is tertiary protein structure?

The coiling/folding of a protein into its final shape. This brings R groups together and may interact:

Hydrogen bonds-weak

Ionic bonds-between oppositely charged R groups

Disulfide bridges-strongest, covalent. Between sulfur containing R groups

Hydrophilic/Hydrophobic interactions-polar and non polar R groups

What is quaternary protein structure?

2 or more proteins associate. Subunits can be identical/different.

Enzymes are often 2 identical

Insulin is 2 different

Haemoglobin has 2 sets of 2 identical (4)

How does a hydrophobic/hydrophilic R group determine how a protein folds?

If hydrophilic is on the outside of the molecule

If hydrophobic is on the inside of the molecule

What are the features of a globular protein?

Compact

Water soluble (hydrophilic R groups on outside of molecule)

Spherical

What type of protein is insulin and how does it work?

Globular

Hormone transported in bloodstream

Need precise shape to fit to specific plasma membrane receptors

What are the features of a conjugated protein?

Is a globular protein with a prosthetic group (non-protein component)

There's different types of prosthetic groups (lipids/carbs, lipoproteins or glycoproteins)

Metal ions and molecules derived from vitamins can form prosthetic groups

What is a haem group?

Prosthetic group

Contain Fe2+ ions

Catalase and haemoglobin contain haem groups

What type of protein is haemoglobin and how does it work?

Conjugated

Quaternary protein, made of 2 alpha and 2 beta subunits (4 polypeptides).

Each unit has a prosthetic haem group. The Fe2+ ions can combine with oxygen reversibly.

Enables oxygen transport around the body.

What type of protein is catalase and how does it work?

Conjugated

Enzyme

Quaternary protein with 4 prosthetic haem groups. The presence of Fe2+ ion allows it to interact with hydrogen peroxide and speed up its breakdown. (Common byproduct of metabolism but can be damaging to cells if accumulates).

What are the features of a fibrous protein?

Long

Insoluble

High proportion of amino acids with hydrophobic R groups

Limited amino acid range

Usually small R groups

Amino acid sequence is repetitive = very organised structures

Strong

Not folded into a complex 3D structure

What type of protein is keratin and what does it do?

Fibrous

Large proportion of the amino acid cysteine (contains sulfur). Contains disulfide bridges = strong, inflexible, insoluble. Degree of bridges determines flexibility.

Hair, skin, nails

What type of protein is elastin and what does it do?

Fibrous

Found in elastic fibres e.g. Walls of blood vessels and alveoli. Have flexibility to expand and return to normal size.

Quaternary protein of tropoelastin

What type of protein is collagen and what does it do?

Fibrous

Skin, tendons, ligaments, nervous system (a connective tissue)

Many different forms, but is 3 polypeptides wound together=strong. Flexible and insoluble.

Covalent Bond

The sharing of electrons between two non-metals. The bonds are strong and they form new molecules.

Ionic bond

Ions with opposite charges attract one another. the electrostatic attraction is an ionic bond.

Hydrogen bond

These form when slightly negatively charged parts of a molecule comes close to a slightly positively charged hydrogen atom. There is a weak electrical attraction.

Polymer

A series of many linked identical repeating units known as monomers.

Important biological polymers

Proteins, carbohydrates, nucleic acid, lipids

Hydrolysis reaction

The addition of a water molecule can be used to 'split' chemical bonds linking molecules.

Condensation reaction

A reaction that occurs when two molecules are joined together with the removal of water.

Properties of water

Universal solvent, density changes depending on temp, high heat capacity, high surface tension, adhesive/cohesive, high latent heat of vaporization and fusion

Benedicts test for reducing sugars

When Benedicts regeant is added to a sample and then heated to 80'C it should go green, yellow, brown or brick for a positive result or blue for a negative result.

Benedicts test for non-reducing sugars

Hyrochloric acid is added to a sample then heated for a few minutes, then sodium hydrogen carbonate is added then Benedicts regeant. it is then heated to 80'C for five minutes. it should go green, yellow, brown or brick for a positive result and blue for a negative result.

Iodine test: test for starch

A few drops of iodine is added to a sample, if it goes blue/black starch is present. If it goes yellow/brown there is no starch present.

Emulsion test: test for lipids/fats

Ethanol is added to a sample and then shaken. water is then added and the sample is shaken again. If a cloudy white emulsion is formed there are lipids/fats present. if it goes clear no lipids/fats are present.

Biuret test: test for proteins

an equal volume of sodium hydroxide is added to a sample at room temp. Then a few drops of dilute copper sulfate solution is added and mixed. If proteins are present the solution will turn a lilac/purple colour. If they are not present the solution will be blue.

Chemical formula for monosaccharides

Cn(H2O)n

Glycosidic bond

A bond formed between two monosaccharides by a hydrolysis reaction (forms disaccharide)

Examples of diasaccharides

Sucrose (glucose + fructose), lactose (glucose + galactose), maltose (glucose +glucose)

precipitate

Is an insoluble solid that emerges from a liquid solution

emulsion

A mixture of two or more liquids where one liquid contains a dispersion of the other liquid, These two liquids do not normally mix.

polysaccharide

polymers of monosaccharides, consisiting of thousands of monosaccharides.

Cellulose properties

\-Each molecule forms hydrogen bonds with its neighbor. This produces bundles of molecules lying side by side. these are called microfibrils and they themselves form larger bundles called macrofibrils.

\-Only found in plant cells

\-Difficult to digest (very few animals have the enzymes to break the glycosidic bonds)

\-B(1-4) glycosidic bonds

\-Macrofibrils have great mechanical strength and are embedded in pectin to make cell walls.