Biological Molecules OCR A level Biology

What is a polar molecule? Give an example.

A combination of atoms in which the electrical charge is not distributed symmetrically. An example is H2O. Hydrogen and oxygen are bonded together by sharing electrons, but the oxygen atoms pulls the shard electrons closer to it, creating negative and positive sides of the water molecules.

What is a monomer?

Smaller units from which larger molecules are made

What is a polymer?

Made from lots of monomers bonded together

Name the molecules that are monomer and state the polymer they can form

- glucose —> starch, cellulose, glycogen

- amino acid —> protein

- nucleotide —> DNA and RNA

What are the two key chemical reactions

- condensation

- hydrolysis

What is condensation?

Joining two molecules creating a chemical bond and removing water

What is hydrolysis?

Breaks a chemical bond between two molecules and involves the use of a water molecule

Name the elements of carbohydrates

C, H, O

What is the shape of glucose

Hexose - need to know how to draw structure of it

What's a monosaccharide

A single sugar molecule

What's a feature of monosaccharides

Soluble in water due to hydroxyl groups being able to form hydrogen bonds with water - hydrophilic

What does hydrophilic mean

Water loving. All hydrophilic molecules dissolve in water

Name a pentose monosaccharide

Ribose - need to know how to draw structure of this

Name the elements of Lipids

C, H, O

Name the elecements of amino acids

C, H, O, N, (S in cystine)

Name the polysaccharides formed from C H and O elements

- starch

- cellulose

- glycogen

- amylose

- amylopectin

Describe a disaccharide

- made of two monosaccharides

- joined together by glycosidic bond

- formed by condensation reaction

Where is cellulose found in plants?

Cell wall

What form is glucose sorted in plants?

Starch

What form is glucose store in animals?

Glycogen

What is the monomer of starch

Alpha glucose

What's the function of starch

Store of glucose

What bond is formed between monomers of alpha glucose in starch?

1-4 glycosidic bonds in amylose

1-4 and 1-6 in amylopectin

What's the structure of starch

Made of 2 polymers:

- amylose - an unbranded helix

- amylopectin - a branched molecule - coiled

Explain how the structure of starch leads to its function

Helix can compact to fit a lot of glucose in a small space. Branched structure increases surface area for rapid hydrolysis back to glucose. Insoluble - won't affect water potential

What are the 2 isomers of glucose

Alpha and beta glucose

How is amylose formed

Long change of alpha glucose molecules, 1-4 glycolic bond between them which twist to form a helix which is held in place by hydrogen bonds - unbranded

What are the bonds between the beta glucose in cellulose

1-4 glycosidic bond

What's the monomer of glycogen?

Alpha glucose

What are macrofibrils

When cellulose chains group together

What's a fibril

Loads of macrofibrils grouped together

What's the structure of cellulose

Polymers form long chains. Chains are held in parallel by many hydrogen bonds to form fibrils

What's the location of glycogen

Animals - mainly in muscles and liver cells

What's the structure of glycogen

- Highly branched molecule

- formed from alpha glucose joined by 1,4 and 1,6 glycosidic bonds

Explain how the structure of glycogen leads to its function

Branched structure increases surface area for rapid hydrolysis back to glucose

Insoluble - won't affect water potential

What's phospholipids composed of

- phosphate group

- glycerol

- 2 fatty acids

What is the ester bond formed between

Hydroxyl (OH) group of glycerol and carboxyl group (-COOH) group of fatty acid

Describe the formation of triglyceride

Condensation between one molecule of glycerol and three molecules of fatty acid

What is phospholipids composed of?

Made of:

- 1 glycerol molecule

- 2 fatty acid chains

- 1 phosphate group (attached to the glycerol)

The two fatty acids also bond to the glycerol via two condensation reactions,resulting in two ester bonds

What are the properties of phospholipids

Hydrophilic 'head' due to negative charge on phosphate group

Attracts water and repels fats as it is charged

Fatty acid chain is not charged.

It is known as the hydrophobic 'tail' and it repels water, but will mix it with fats

Have two charged regions, so they are polar

In water they are positioned so that the heads are exposed to water and the tails aren't

This forms a phospholipid bilayer membrane around cellsde

How are polypeptides formed

By condensation of more than 2 amino acids

What is protein composed of

- amino group (NH2)

- r group -C-H

- Carboxylic group (-COOH)

What's the difference between a saturated and non saturated fatty acid

Unsaturated has at least 1 double carbon bond, whereas saturated fatty acids - the hydrocarbon chain has only single bonds between carbons

Describe the structure of the phospholipid bilayer

Composed of two layers:

- hydrophobic tails facing each together/inwards

- hydrophilic head facing outwards

This forms an intracellular and extracellular fluid layer in the cell membrane

What is the function of the phospholipid bilayer

All cell to be selectively permeable

What's a dipeptide

Formed when two amino acids join by a condensation reaction

Describe the secondary structure of protein

The sequence of amino acids causes parts of protein molecule to bend into alpha helix shapes or fold into beta pleated sheets.

Hydrogen bonds hold the secondary structrue

What are the 4 levels of structure in a protein

- primary

- secondary

- tertiary

- quaternary

Describe the tertiary structure of protein

The further folding of the secondary structure. To form a. Unique 3D shape. Held in place by ionic, hydrogen and disulphide bonds

What is the strongest bond in tertiary structure of protein

- disulphide bonds

- ionic bonds

- hydrogen bonds

- hydrophilic/hydrophobic interactions

Describe the quaternary structure

A protein made up of more than 1 polypeptide chain. Alpha and beta subunits

What structure of proteins are enzyme

- tertiary

What's the function of enzymes

Lower activation energy of the reactions they catalyse speeding up the rate of the reaction

Describe how enzyme is adapted to its function

Active site/enzyme is specific and unique in shape due to the specific folded and bonding in the tertiary structure of the protein. The location of the bonds is determined by the primary structure.

Due to this specific active site, enzymes can only attach to substrates that are complementary in shape forming enzyme-substrate complex breaking substrate into products

Describe the models of enzyme action

Induced fit model - more appropriate nowadays

Lock and key model

Describe the induced fit model

When the enzyme active sit is induced, or slightly changes shape, to mould around the substrate

When the enzyme-substrate complex occurs, due to the enzyme moulding around the substrate it puts strain on the bonds and therefore lowers the activation energy. This breaks the substrate into products and leaves the active site

List the factors affecting enzymes

1. Temperature

2. PH

3. Substrate concentration

4. Enzyme concentration

5. Inhibitors

Describe how temperature affects rate of reaction

- If temperature is too low there is not enough kinetic energy for successful collisions between the enzyme and substrate

- if the temperature is too high enzymes denature, the active site changes shape and enzyme-substrate complexes cannot form

How does pH affect rate of reaction

Too high or low a pH will interfere with the charges in the amino acids in the active site. This can break the bonds holding the tertiary structure in place and therefore the active site changes shape

Therefore the enzyme denatures and fewer enzyme-substrate complexes form

Different enzymes have a different optimal pH

How do substrate and enzyme concentration affect rate of reaction

If there is insufficient substrate, then the reaction will be slower as there will be fewer collisions between the enzyme and substrate

Is there is insufficient enzymes, then the enzyme active sites will become saturated with substrate and unable to work any faster

Name the two types of enzyme inhibitors

- competitive inhibitors

- non-competitive inhibitors

What are competitive inhibitor?

- same shape as the substrate

- bind to the complementary active site

- prevents enzyme-substrate complexes

If you add more substrate it will flood/out-compete the inhibitor, knocking them out of the active site

What are non-competitive inhibitors?

- bind to the allosteric site

- causes the active site to change shape

- no enzyme-substrate complexes

The substrate can no longer bind, regardless of how much substrate is added

What is the test for starch

1. Add iodine

2. A +ve test observation = solution turns from orange to blue/black

What is the test for reducing sugars?

1. Add Benedict's reagent and heat

2. A +ve test observation = solution turns from blue to green,yellow,orange or brick red (more red = higher concentration of reducing sugar)

When is ATP made

During respiration from ADP + Pi by a condensation reaction and using the enzyme ATP synthase

ATP can be hydrolysed into ADP + Pi using enzyme ATP hydrolyse. This releases a small amount of energy

What is phosphorylation?

Inorganic phosphate released during the hydrolysis of ATP can be bonded onto different compounds to are them more reactive. ATP can also transfer energy to other compounds

What are the 5 key properties of water

- hydrogen bonds form between different water molecules between the oxygen and a hydrogen atom

The formation of these hydrogen bonds and the fact that water is depolarised results in 5 key properties of water:

1. It is a metabolite (e.g in condensation and hydrolysis reactions)

2. An important solvent in reactions

3. Has a high heat capacity, it buffered temperature

4. Has a large latent heat of vaporisation, providing a cooling effect with loss of water through evaporation

5. Has strong cohesion between water molecules ; this supports water columns and provides surface tension

Name the 4 types of inorganic ions and its role

- hydrogen ions: lowers the pH of solutions and impact enzyme function and haemoglobin function. Or role in chemiosmosis

- iron ions: a component of haemoglobin in the transport of oxygen

- sodium ions: involved in the co-transport of glucose and amino acids in absorption. Or role in generating action potentials

- phosphate ions: a component of DNA (forms phosphodiester bonds with deoxyribose) and ATP (makes ADP more reactive)

What is the test for non-reducing sugars

1. Following a -ve Bendcit's test, where the reagent remains blue

2. Add acid and boil - (this is hydrolysis)

3. Cool the solution then add an alkali to neutralise

4. Add Benedict's reagent and heat

5. A +ve test observation = solution turns from blue to orange or brick red (the more red the higher the concentration of non-reducing sugar

What is the test for protein

1. Add biuret

2. A +ve test observation = solution turns from blue to purple

What is the test for lipids

1. Dissolve the sample in ethanol

2. Then, add distilled water

3. A +ve test observation = a white emulsion forms

What's the function for DNA

Codes for the sequence of amino acids in the primary structure of a protein, which in turn determines the final 3D structure and function of a protein

It is essential therefore that cells contain a copy of this genetic code and that it can be passed on to new cells without being damaged

The DNA polymer forms a double helix

What is nucleotide

The monomer that makes up DNA

What is nucleotide made of

Deoxyribose ( a pentose sugar)

Nitrogenous base - (guanine, cytosine,adenine and thymine)

Phosphate group

What is a polynucleotide

Polymer of nucleotide

How is polynucleotide created

Via condensation reactions between the deoxyribose sugar and the phosphate group of adjacent nucleotides, creating a phosphodiester bond

The DNA polymers occurs in pairs joined by hydrogen bonds between bases. This creates the double helix

Hydrogen bonds can only form between complementary base pairs

What are the complementary base pairs in polynucleotide

- cytosine and guanine

- adenine and thymine

What is RNA

Is a polymer of a nucleotide formed of ribose, a nitrogenous base and a phosphate group

Why is the ability of water to act as a solvent important for the survival of organisms?

- medium for (metabolic) reactions

- transport

- transport , medium / system , with a

named example of what is transported (e.g sodium chloride);

(organisms can) absorb / take in , (named) minerals /ions

Caused by polarity of water

What's the role of water in living organisms

- allow chemical reactions to occur ('solvent) - polarity of water

- transport medium ('solvent) - polarity of water

- allow water to be suitable habitat (high specific heat capacity) - many hydrogen bonds

- optimal temp maintained within cells and body (high specific heat capacity) - many hydrogen bonds

- coolant (high latent heat of vaporisation) - many hydrogen bonds

The nitrogenous bases in RNA

- adenine

- guanine

- cytosine

- uracil instead of thymine

What's the difference between RNA polymer and DNA polymer

- RNA is relatively shorter

- RNA is single stranded whereas DNA is double stranded

- RNA contain base uracil instead of thymine

What is the function of RNA

To transfer the genetic code from DNA in the nucleus to the ribosomes. Some RNA(rRNA) is also combined with proteins to create ribsomes

What's DNA replication

Before cells divide (by mitosis or meiosis) all the DNA must replicate to prove a copy of the new cell.

The process of DNA replication is semi-conservative replication

(In the daughter DNA one strand is form the parental DNA and one strand is newly synthesised)

Describe the steps in semi - conservative replication

Step 1:

DNA helicase breaks the hydrogen bonds between the complementary base pairs between the two stands within a double helix

This causes the DNA double helix to unwind

Step 2:

Each of the separated parental DNA strands acts as a template

Free floating DNA nucleotides within the nucleus are attracted to their complementary base pairs on the template strands of the parental DNA

Step 3:

The adjacent nucleotides are joined together (to form phosphodiester bond) by a condensation reaction

DNA polymerase catalyses the join in together of adjacent nucleotides

Step 4:

The 2 sets of daughter DNA (name given to the new DNA molecules'0 contains one strand of the parental (original) DNA and one newly synthesised strand

What is ATP

An immediate source of energy for biological processes. Metabolic reactions in cells must have a constant,steady supply of ATP

Which amino acid contains sulphur?

Cysteine

What is a polar atom group example?

OH

Explain why water can form hydrogen bonds

the attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge. Creating a relatively weak bond. Caused due to electronegativity differences and since water molecule is polar

What do Hydrogen bonds do in water?

makes water cohesive and give it its other unique characteristics. Hydrogen bonds constantly break and reform between water molecules.

What does adhesive mean in terms of water?

The water molecules are attracted to other materials.

What does cohesive mean in terms of water?

Water moves as one mass because the polar molecules are attracted to one another- allowing for capillary action, plants can draw it up through their roots.

Why does ice float?

It is less dense than water. This is caused through the hydrogen bonds fixing the positions of the polar molecules further apart than normal. This produces a giant, lattice structure.

Why does water have a high boiling point?

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

Why does the polarity of water allow it to sustain life?

Water acts as a solvent, the cytosol of prokaryotes and eukaryotes is mainly water. Water acts as a medium for chemical reactions.

How do cohesion and adhesion make water useful for sustaining life?

Water has Capillary action - it can rise against gravity.

Why does water's high specific heat capacity make it useful for sustaining life?

It provides a constant environment, when frozen ice provides an insulating layer to prevent the water below from freezing. Due to the presence of many hydrogen bonds

Difference between alpha and beta glucose?

on Carbon 1, alpha glucose has a OH group below the carbon ring and beta glucose has a OH group above the carbon ring.

- same molecule formula different structural formula

Are polar molecules soluable?

Yes, hydrogen bonds between OH groups allow it to dissolve.