U1 - All Biological Molecules Sets

What does inorganic mean?

Compounds that don’t have carbon - most compounds in living organisms are organic

What does ion mean?

A particle with a charge

Where are H+ ions important in organisms?

The concentration of H+ ions is vita; as it determines pH (e.g. denaturing proteins)

Where are iron ions (Fe²+ / Fe³+) important in organisms?

The heme group of haemoglobin contains an iron ion used to reversibly bind to O2

Where are sodium ion (Na+) important in organisms?

All cells normally have a very low concentration of Na+ inside them. That concentration gradient can then be used to get an “action potential” in neurons and for co-transport

Where are phosphate ions (PO4³-) important in organisms?

Needed for phospholipids (cell membranes) but also for DNA / RNA / ATP and for calcium phosphate (bones and teeth)

Where are magnesium ions (Mg²+) important in organisms?

Viral part of chlorophyll (plants)

Where are potassium ions (K+) important in organisms?

Cells work hard to pump K+ ions into their cytoplasm. K+ ions move in an action potential

Where are calcium ion (Ca²+) important in organisms?

Used in teeth and bones. Also an important signalling molecule - Ca²+ concentration is normally very low inside cells.

What is the structure of an amino acid?

1. variable part (R)

2. amine part (H2N)

3. hydrogen

4. carbon

5. carboxylic acid group (COOH)

How do you make a dipeptide?

join 2 amino acids

What bond is made when joining amino acids?

Peptide bond

What do you make when you join many amino acids?

Polypeptide

What is the difference between a polypeptide and a protein?

A polypeptide is a simple chain of amino acids, whereas a protein has then folded into a specific 3D shape

What are the functions of a protein?

1. Structural roles

2. Enzyme

3. Carrier or channel proteins

4. Antibody

What is the primary structure of a protein?

The sequence of amino acids and the peptide bonds that join them (a simple linear chain with no folding) (each amino acid is joined by a peptide bond)

What is the secondary structure of a protein?

The amino acid chain starts to fold due to hydrogen bonds forming between the acid part of the amino acids and the amine part of other amino acids

What are the 2 secondary structures of proteins?

• Alpha helix

• Beta pleated sheet

Both are regular, repeating structures

What is the tertiary structure of a protein?

When the chain folds up ina very precise shape (that is unique to every protein) due to bonding between the variable side groups of different amino acids (often at very different points in the chain)

What are the types of bonds that can form in tertiary protein structures?

• Disulfide bridges (STRONG COVALENT BOND)

• Ionic bonds - positive variable side grpu[ attracts to another negative variable side group (QUITE STRONG)

• Hydrogen bonds (WEAK)

• Hydrophobic interactions (non-charged, non-polar hydrophobic amino acids cluster together in the middle of the molecule away from water 

What determines what bonds form and where within the protein to determine the tertiary structure?

The variable side groups - the sequence of aino acids - the primary structure

What is the quaternary structure of a protein?

Where more than one polypeptide chain makes the final protein, and/or there is a prosthetic group (part of a protein not made of amino acids)

What kinda of bonds are involved in quaternary structures?

• Disulfide bridges

• Ionic bonds

• Hydrogen bonds

• Hydrophobic interactions

What are the 2 types of lipids?

• triglycerides

• phospholipids

What 2 forms can triglycerides come in?

• Fats - solids at room temperature (used in animals)

• Oils - Liquids at room temperature (used in plants)

What are the elements in triglycerides?

• carbon

• hydrogen

• oxygen

What are triglycerides made of?

Glycerol + 3 fatty acids

What are the parts of a fatty acid?

1. variable part - the carbohydrate part that changes to give different fatty acids

2. carboxylic acid group - the part that in the same in all fatty acids

What is the bond when the glycerol and fatty acids join?

An ester bond

What are the 2 types of fatty acids?

● saturated

● unsaturated

What is a saturated fatty acids?

A fatty acids with no c=c double bonds

What is an unsaturated fatty acid?

A fatty acid with at least one c=c double bond

What is the difference between unsaturated and saturated fatty acids?

Triglycerides made with saturated fatty acids tend to be solid at room temperature (fats), while ones with unsaturated fatty acids tend to be liquid at room temperature (oils)

What is the structure of a phospholipid?

Glycerol head (hydrophilic) and fatty acid tails (hydrophobic)

Why is the head of a phospholipid hydrophilic?

Due to the charged phosphate group

Why does the tails of a phospholipid being hydrophobic mean?

They will spontaneously form particular shapes in water (emulsions or bilayers)

What are the similarities between triglycerides and phospholipids?

1. Both have fatty acids

2. Both have glycerol

3. Both have ester bonds

4. Both have carbon, hydrogen and oxygen

What are the differences between triglycerides and phospholipids?

1. Phospholipids have a phosphate group but triglycerides have an extra fatty acid (3 rather than 2)

2. Triglycerides are used for long term energy storage, or insulation, or for protecting organs but Phospholipids are used for cell membranes

3. Triglycerides are totally hydrophobic, but Phospholipids have a hydrophilic phosphate head and hydrophobic fatty acid tails

How do you test for lipids?

1. Add ethanol and shake

2. Add water and shake

3. if lipids is present a cloudy emulsion will be present

What are the key words when talking about enzymes?

• Complementary shape

• Active site

• Denature

• Tertiary structure

• Enzyme-substrate complex

• Shape

What is an enzyme?

A protein which acts as a biological catalyst for a specific reaction

What are the 2 types of reaction enzymes catalyse?

• Catabolic - where we split things apart (hydrolysis)

• Anabolic - where we put things together (condensation)

What is activation energy?

Energy needed to break bonds to start a reaction

What do enzymes do to a reaction?

Catalyse them by providing an alternate pathway with a lower activation energy

Why are enzymes important?

• There are thousands of different enzymes in ever cell

• The rate of metabolism at room temperature would be far too low to sustain life without enzymes

What is the “lock and key” theory?

Only the correct substrate is complementary to the shape of the active site. (formed due to the enzymes tertiary structure and so can form an enzyme-substrate complex)

What is the “iinduced fit” model?

In some enzymes, the substrate can force the enzymes active site to change shape slightly. The enzyme can form an enzyme-substrate complex with more than one substrate

What is the induced fit model necessary?

Some enzymes don’t just work on one reaction, but instead could catalyse a narrow range of similar reactions

What 5 factors effect the rate of enzyme controlled reactions?

• Substrate concentration

• Enzyme concentration

• Temperature

• pH

• Concentration of inhibitors

Describe the graph for the effect of substrate concentration on the rate of reaction of and enzyme controlled reaction?

• If substrate concentration is 0, rate of reaction is 0

• Increasing the substrate increases rate of reaction in direct proportion

• But, at very high substrate concentrations, the rate of reaction plateaus

Explain (more detail) the graph for the effect of substrate concentration on the rate of reaction of and enzyme controlled reaction?

• With no substrate, there is nothing to react

• As we increase substrate ocncentration, the chance of collision between enzyme and substrate (to form an ES complex) gets higher and higher, so the rate increases

• But, if the substrate concentration is already very high, the active site of the enzymes become saturated - always in an ES complex and so the rate plateaus

Describe the graph for the effect of enzyme concentration on the rate of reaction of and enzyme controlled reaction?

• If enzyme concentration is 0, rate of reaction is 0

• Increasing the enzyme increases rate of reaction in direct proportion

• But, at very high enzyme concentrations, the rate of reaction plateaus

Explain the graph for the effect of enzyme concentration on the rate of reaction of and enzyme controlled reaction?

• Only with an enzyme is there enough energy at room twmperature for the reaction to proceed

• More enzymes means more chnace of collisions to form enzyme-substrate complexes

• At very high enzyme concentrations all substrate is immediately used up, so adding more enzyme has no effect

Describe the graph for the effect of temperature on the rate of reaction of and enzyme controlled reaction?

• At 0°C, rate of reaction is 0

• As temperature increases, rate of reaction increases is direct proportion but then plateaus

• If the temperature is too high , rate rapidly decreases back to 0°C

Explain the graph for the effect of temperature on the rate of reaction of and enzyme controlled reaction?

• At 0°C, water freezes, so particles can no longer collide

• As temperature increases, particles move faster, so they have more kinetic energy, so collide more often and collisions are more likely to have enough energy to break bonds and react

• At fairly high temperatures, enzymes become denatured. This high temperature breaks bonds in the tertiary structure (hydrogen and ionic especially), changing the chape of the active site so the substrate is no longer complementary and enzyme-substrate complexes can no longer form

Describe the graph for the effect of pH on the rate of reaction of and enzyme controlled reaction?

• Each enzyme only works well over a narrow range of pH values - different enzymes work well at different pH’s

Explain the graph for the effect of pH on the rate of reaction of and enzyme controlled reaction?

• If the pH is “wrong” - the tertiary structure of the enzyme will be affected (especially hydrogen and ionic bonds)m which changes the shape of the active site so the substrate is no longer complementary, so enzyme-substrate complexes can no longer form - the enzyme is denatured

What is inhibition?

• Stopping something from working

• In enzymes it means making them less effective at catalysing a reaction

What is a specific and a non-specific inhibitor?

• Specific - Only inhibit a particular enzyme

• Non-specific - Will inhibit most / all enzymes (e.g. heavy metals)

(we almost always are talking about specific inhibitors)

What is competitive inhibition?

The inhibitor has a similar shape to the substrate, and so can also bind to the active site, blocking the actual substrate from binding.

What is Vm?

Fastest possible rate of reaction

What is Km?

Concentration of substance which gives ½ Vm

What is non-competitive inhibition?

• The inhibitor binds away from the active site

• This results in changes in the shape of the active site due to change in tertiary structure of the enzyme

• The substrate and enzyme are no longer complementary

• Enzyme-substrate complexes can’t form

What is a monomer?

Smaller units from which larger molecules are made

What is a polymer?

Molecules made from large numbers of monomers joined together in a chain during a process called polymerisation

What are two important reactions that occur to form covalent bonds in molecules?

• Condensation reactions

• Hydrolysis reactions

What is a condensation reaction?

A reaction that occurs when monomers combine by covalent bonds to form polymers or macromolecules, and water is removed

What does hydrolysis mean?

“lyse” = to break

“hydro” = with water

What happens in a hydrolysis reaction?

In the hydrolysis of polymers, covalent bonds are broken when water is added.

What is a monosacharride?

A single reducing sugar monomer

What elements do all carbohydrates contain?

• Carbon

• Hydrogen

• Oxygen

What are some examples of monosacharrides?

• Glucose

• Fructose

• Deoxyribose

What do monosacharrides join together to form?

• Disacharrides 

• Polysacharrides

How can sugars be classified and why?

• Reducing

• Non-reducing

Classification into these groups is dependent on the sugars ability to donate electrons

Can reducing sugars donate electrons?

yes

Can non-reducing sugars donate electrons?

No

How do you test for reducing sugars?

Add benedict’s solution and heat

blue > green > yellow > orange > brick red

What are some examples of reducing sugars?

• Glucose

• Fructose

• Galactose

Fructose and galactose have the same molecular formula as glucose however, they have a different structural formula

How do you test for non-reducing sugars?

1) Test using benedict’s solution - if negative…

2) Boil with concentrated acid to hydrolyse the glycosidic bond

3) Neutralise the acid with a base

4) Test again with benedict’s solution and heat - if positive, non-reducing sugars are present… if negative again, there is no sugar at all.

What is an xample of a non-reducing sugar?

Sucrose

What are the two forms of glucose?

• Alpha

• Beta

Where is the hydroxyl (OH) groups on carbon 1 located in alpha glucose?

Below the ring

Where is the hydroxyl (OH) groups on carbon 1 located in beta glucose?

Above the ring

What is a disacharride?

Two monosaccharides joined together with a glycosidic bond with a biproduct of water

What is a polysaccharide?

Many monosaccharides joined together with a glycosidic bond with a biproduct of water

What are 3 examples of polysaccharides?

• Starch

• Glycogen

• Cellulose

What type of glucose is starch made from?

Alpha glucose

What type of glucose is glycogen made from?

Alpha glucose

What type of glucose is cellulose made from?

Beta glucose

How are disaccharides and polysaccharides formed?

When two hydroxyl (-OH) groups (on different saccharides) interact to create a strong covalent bond called the glycosidic bond

What is maltose made up of?

2 alpha glucose molecules

What is sucrose made up of?

An alpha glucose molecule and a fructose molecule

What is lactose made up of?

An alpha glucose molecule and a galactose molecule

How is a glycosidic bond broken?

When water is added in a hydrolysis reaction

What are some examples of disaccharides?

• Maltose

• Sucrose

• Lactose

What is starch?

The storage polysaccharide of plants

How is starch stored?

As granules in plastids (e.g. chloroplasts)

Why does starch take longer than glucose to be digested?

Because there are many monomers in it

What 2 polysaccharides is starch constructed from?

• Amylose

• Amylopectin