Biological molecules

Structure of water

In water each hydrogen atom shares a pair of electrons with the oxygen atom forming a covalent bond.

There are two hydrogen atoms and one oxygen atom

Why is water described as being polar?

• Contains 2 slightly positive hydrogen atoms and 1 slightly negative oxygen atom (overall slightly positive charge)

• Results in an uneven distribution of charge = Polar

• Results in the formation of hydrogen bonds between adjacent water molecules

What is waters value as a solvent?

• Most of a cells reactions take place in aqueous solution

• Ability to act as a trasnport medium

• Effects on hydrophobic and hydrophilic molecules

What are buffers

Chemicals or substances that resist changes to pH and ensure that a particular environment maintains a certain pH

Give two examples of buffers

• Hydrogen carbonate ions

• Albumin (blood protein)

Calcium role

Calcium pectate in the middle lamella

Iron role

Haem group in haemoglobin -oxygen binds to this haem group

Magneisum role

Gives chlorophyll its light absorbing property

Potassium role

Maintains electrical gradients during nervous communication

Nitrate role

Are found in amino acids, nucleic acids (Nitrogenous base)

Phosphate role

Found in nucleic acids, phopholipds

Hydrogencarbonate role

Natural buffer

What are organic molecules

Complex carbon containing molecules

Examples of organic molecules

Carbohydrates, lipids and proteins

When monomers join to form polymers, this is known as

Polymerisation

Glucose is a hexose monosaccharide with the formula

C₆H₁₂O₆

in what glucose is hydorixde group below C1

alpha glucose

in what glucose is hydorixde group above C1

beta glucose (ABBA alpha below beta above)

Name another monosacchardie

Fructose

Why are these monosaccharides desribed as being isomers

Same chemical formula but different structural formula

How are disaccharadies? Name the reaction and the bond formed?

2 monosaccharides joined in a condesantion reaction with a 1-4 glycosidic bond.

What happnes during a codnesation reaction

joining of molecules (removing water)

what is the general formula for all disacchardies

C₁₂H₂₂O₁₁

Give two examples of disaccharides and how they are formed

1. Maltose- 2 alpha glucoses joined in a condesation reaction with a 1-4 glycosidic bond

2. Sucorse- 1 alpha glucose and 1 fructose joined in a condensation reaction with a 1-4 glycosidic bond

What is a polysaccharides

More than 2 monosaccharides joined in a condensation reaction with a 1-4 glycosidic bond

They aren’t sugars and are insoluble in water

what is starch

a polymer of a alpha glucose and storage molecule in plants

amylose vs amylopectin diagrams

	Amylose	Amylopectin
Elements,
Monomer
Bonds
Branched?
many terminal ends

	Amylose	Amylopectin
Elements,	C, H , O	C, H, O
Monomer	alpha glucose	alpha glucose
Bonds	1-4 glycosidic bonds	1-4 and 1-6 glycosidic bonds
Branched?	No	yes
many terminal ends	no, 2	many

One of the two chains of starch discussed has many terminal ends. Why is this an advanatge?

Allows for faster hydrolysis of glucose e.g to be used in respiration

Why is starch a good storage molecule

• Very compact (amylopectin)

• Insoluble - doesnt affect osmotic gradient

• Large- is retained within the cell as it is too large to pass through the membrane

• Amylopectin branching = many terminal ends for fasted hydrolysis of glucose

What is glycogen

storgae in animals, - liver, fungi cells (fungi)

Desribe the strucutre of glycogen

Formed of alpha glucose

contains 1-4 and 1-6 glycosidic bonds,

highly branched therefore many terminal ends for fast hydrolysis of glucose

Glycogen is similar to which starch?

Amylopectin

How are glycogen and amylopectin different?

Glycogen is more highly branched, many more terminal ends and therefore faster hydrolysis of glucose. This is is bcus animals are more metabollicaly active than plants.

Cellulose role

structural role, in plant cell walls

Structure of cellulose

Long chains of beta glucose monomers held withing 1-4 glycosidic bonds. Adjacent chains are held together with hydorgen bonds to form microfibrils. Every second beta glucose in inverted (flipped 180°) to allow for 1-4 glycosidic bond to be formed.

How does the structure of cellulose relate to its function

Microfibrils provide tensile strenth in cell walls

	Amylose	Amylopectin	Glycogen	Cellulose
Monomer
Bonds
Branching
Terminal ends
Location
Function

	Amylose	Amylopectin	Glycogen	Cellulose
Monomer	α glucose	α glucose	α glucose	β glucose
Bonds	1-4 glyco	1-4 + 1-6	1+4 + 1-6	1-4
Branching	no	yes	yes- more highly	no
Terminal ends	2	many	many more	nope
Location	chloroplasts of cells	chloroplasts of cells	animals - liver muscle fungi	plant cell walls
Function	storage of glucose	storage of glucose	storage of glucose	proivde tensile strength

what are the properties of lipids

• They contain carbon hydrogen oxygen

• They are not polymers

• They are not soluble in water (hydrophobic) , but they are soluble in organic solvents such as ether or ethanol

• The main types of lipids are triglycerides, phospholipids, waxes and steroids

What are triglycerides made up of

1 glycerol and 3 fatty acids tails

What are triglycerides function

Energy store, insulation , protection

How is the triglyceride formed

Condensation reaction between each fatty acid tails and the glycerol

What bond is formed in a triglyceride

Ester bond formed between fatty acid tails and an OH group on the glycerol

What reaction takes place to create a triglyceride

Condensation

Describe the structure of a phospholipid

1 glycerol, 2 fatty acid chains and a phosphate group

How does a phospholipid differ to a triglyceride

Instead of a 3rd fatty acid chain it has a phosphate group

What part of the phospholipid is hydrophobic

Fatty acid tails

What part of the phospholipid is hydrophilic

the phosphate head

What is the orientation of phospholipids and what is created (what is a the function)

Phosphate headed oriented towards water and fatty acid tails away from water.

Phospholipid bilayer that forms the cell surface membrane is created as a result with fatty acid tails away from water (cytoplasm and fluid) and phosphate head towards.

What’s the different between a saturated and an unsaturated fatty acid

Unsaturated has a C=C

A fatty acid with one C=C bond is a

Monounsaturated fatty acid

A fatty acid with more than one C=C is a

polyunsaturated fatty acid

Unsaturated fatty acids are _____ at room temperature and why

Liquid because the C=C makes the unsaturated fatty acid more fluid

Saturated fatty acids are ________ at room temperature

Solid

What elements do proteins contain

Carbon, hydrogen, oxygen, nitrogen and sometimes Sulfur

What are proteins

proteins are large polymers of amino acids joined in a condensation reaction and held with a peptide bond

Amino acid diagram

What is the role of the R group

Allow bonding in the tertiary structure

If the R group is Sulfur, what bond can be formed between similar R groups

Disulfide bond

What is a dipeptide bond

2 amino acids joined together in a condensation reaction and held with a peptide bond. The peptide bond forms between the carboxyl group on one amino acid and the amino group on the other.

What is a polypeptide

Many amino acids joined together in a condensation reaction and held with peptide bonds

Describe the structure of a primary structure protein

A sequence of amino acids in the polypeptide chain

Desribe the structure of a secondary structure protein

Alpha helix vers

Hydrogen bonds are formed between amino acids at regular intervals. These bonds twist the polypeptide chain into a helical shape. Making an alpha helix

How are betapleated sheets formed

• Folding of the polypeptide chain caused by the sections of the polypeptide chain lying in opposite directions

• More rigid and less flexible

• Hydrogen bond between C=C and NH group

How is the tertiary structure formed

Further folding of secondary structure

What bonds are involved in the tertiary structure

• Hydrogen (weakest)

• Ionic ( break when pH moves from optimum)

• Disulphide (if sulphur group is present)

• Peptide (in all structures)

• Hydrophobic interactions are involved

Describe the quaternary structure

2 or more polypeptide chains bonded together

Some protein structures contain prosthetic groups, what does this mean

Non protein

What are these proteins known as

Conjugated protein

Give an example of a conjugated protein and describe its structure

Haemoglobin consists of 4 polypeptide chains (2 alpha helixes, 2 beta pleated sheets) with a haem group (prosthetic group) attached to each

Oxygen bonds to the haem group for transport

What is another example of a conjugated protein

Glycoprotein

Give details and examples of fibrous

Collagen - 3 polypeptide chains held with H bonds (alpha helices) wound around each other and is therefore a quaternary structure protein. The structure of collagen gives it tensile strength for its function in tendons that link muscle to bone.

give details and example of globular

Globular have a specific function and are 3D e.g enzymes, hormones, antibodies, haemoglobin

What are prions

A particular type of protein found in mammals and some other animal groups. They are found in the nervous system and are thought to be involved in synapic transmisson.

What is the normal form of prion protein?

PrP^C

What is the formula for the disease causing Prion

PrP^sc

How can the disease casuing form PrP^sc be identified

Has a higher proportion of beta pleated sheets than the normal

How can diseases associated with the diseas causing form PrP^sc form arise.

• Eating contaminated meat

• Mutation

• Arise spontaneously 

Prions diseases includes

• Scrapie in sheep

• BSE - (bovine spongiform encephalopathy) in cattle

• vCJD - human form of BSE

What are the two key features of disease causing proteins 

• infectious

• can replicate 

What is the subunit of nucleic acids?

nucleotide

name the three components a nucleotide consits of

1. phosphate group

2. nitrogenous base

3. pentose sugar

nucleotide diagram

What does DNA stand for

Deoxyribonucleic Acid

What does RNA stand for

Ribonucleic acid

Describe the structure of RNA

• Ribose pentose sugar

• phosphate group

• nitrogenous base

single stranded contains vracil instead of Thymine

its shorter than DNA

There are 3 types of RNA, name them at give their role

1. mRNA - carries code from the DNA in nucleus to a ribosome in the cytoplasm where protein synthesis takes place

2. tRNA - transfers amino acids to the mRNA (clover shaped)

3. rRNA - made in nucleoulus and forms overhalf the mass of each ribosome.

Desribe the structure of DNA

Double helix, 2 antiparralel strands of DNA are held to hydrogen bonds following base pairing rules.

What are base pairing rules

Adenine bonds to thymine

Cytosine bonds to guanine

Mammals have very similar/ the same percentages of base pairs in their DNA. So, what makes them different to each other?

Order of bases/ base sequence

Describe the steps in DNA replication

1. The enzyme DNA helicase ‘unzips’ the two strands of DNA by breaking hydrogen bonds between the complementary base pairs.

2. Each original strand becomes a template.

3. Free DNA nucleotides are linked to the template strands following base pairing rules and hydrogen bonds form.

4. The nucleotides of the new strand are joined together by the enzyme DNA polymerase which forms phosphodiester bonds between them.

What is semi- conservative replication?

New DNA contains one original strand and one newly synthesised strand of DNA.

What were the two alternate methods of replication?

1. Conservative model

2. Semi Conservative model

Density - gradient centrifugation was used. Describe how

To separate the bacterial DNA following sampling based on density.

Samples are spun at a high speed.

Lighter 14 N accumulates at the top of the centrifuge tube Heavier 15 N accumulates near the

One geneartion 

– The DNA positions in the middle as all of the DNA contains one strand of 14N bases and one strand of 15N bases.

Two generations

Half of the DNA consists of mixed DNA (14N and 15N) and the other half only contains 14N.

How can these results by explained by the semi - conservative model?

After one generation the DNA contained one original template strand and one new strand (one 14N strand and one 15N strand)

Describe the composition of a third generation.

The light 14N band would get thicker and the mixed 14N and 15N band would remain the same.