Topic 1: Biological molecules

What is the primary structure of a protein

Amino acid sequence joined by peptide bonds in a polypeptide chain

Amino acid structure

• amino group

• Carboxyl group

• R group

  
  

How do 2 amino acids join

• condensation reaction, water molecule (H2O) is lost

• Forms a peptide bond

What breaks peptide bonds

Hyrdolysis

What is secondary protein structure

• Alpha Helix- peptide bonds form backbone, R group sticks out

• Beta pleased sheet- 2 or more parallel polypeptide chains forming pleats

What is tertiary protein structure

• Alpha or beta sheet folds into a complex 3D shape.

• Held together by 3 different types of bonds

3 types of tertiary bonds

• disulphide bond- covalent bond. Oxidation between sulfur groups

• Ionic bonds- electrostatic interaction between R groups

• Hydrogen bond- helps stabilise protein.

Quaternary structure of a protein

• multiple polypeptide chains to form one protein

Why is primary structure of a protein important

• amino acid sequence determines the final protein shape and fuction

Why is secondary structure of a protein important

Hydrogen bonding stabilises alpha helixes and beta pleated sheets

Why is tertiary structure of a protein important

Determines protein overall shape, properties and whether it is soluble

Why is quaternary structure of a protein important

Interactions between polypeptides produce a functional protein

What is a fibrous protein

• long elongated insoluble structure

What is a globular protein

Protein folded into a sphere, often soluble and adapted for transport roles

How does the structure of fibrous proteins relate to their properties

Long chains cause high tensile strength making them suitable for support

How does the structure of globular proteins relate to their properties

Fold compactly with hydrophilic R groups on the outside and hydrophobic R groups on the inside so they can interact with water

What type of protein is collagen and whats its basic structure

• fibrous protein

• 3 polypeptide chains form a triple helix joined by hydrogen bonds

How does collagens structure give it strength

Triple helix arranged into fibrils that join by cross links causing high tensile strength

What type of protein is haemoglobin and whats its is its quaternary structure

• globular protein

• 4 polypeptide subunits: 2 alpha chains 2 beta chains

What is a haem group in haemoglobin

Iron containing haem group that binds 1 oxygen molecule

How does haemoglobin’s quaternary structure help its function

• binding oxygen to one subunit causes a conformational change that increases affinity for binding

• Cooperative binding

• Easier for next oxygen to bind

Whats the difference between collagen and haemoglobin

• collagen- insoluble, fibrous with high tensile strength good for tendons and ligaments

• Haemoglobin- soluble, globular to transport oxygen in blood

What does it mean that water is a dipole?

Water has an uneven distribution of charge: the oxygen atom is slightly negative (δ−) and the hydrogen atoms are slightly positive (δ+).

Why is a water molecule a dipole?

Oxygen attracts the shared electrons more strongly than hydrogen, so the electrons spend more time near oxygen.

What is a hydrogen bond in water?

A weak attraction between the slightly positive hydrogen of one water molecule and the slightly negative oxygen of another water molecule.

How does water's dipole nature lead to hydrogen bonding?

The δ+ hydrogen of one water molecule is attracted to the δ− oxygen of a neighbouring water molecule.

What is meant by water's high specific heat capacity?

A relatively large amount of energy is needed to raise the temperature of water by 1°C.

Why does water have a high specific heat capacity?

Energy must be supplied to overcome hydrogen bonds between water molecules before their kinetic energy, and therefore temperature, increases significantly.

Why is water's high specific heat capacity important to organisms?

Water temperatures change slowly, helping aquatic habitats and organisms maintain relatively stable temperatures; this helps enzymes function within suitable temperature ranges.

Why is water a good solvent for ions and polar substances?

Water is polar, so its partial charges attract ions and polar molecules, surrounding them and allowing them to dissolve.

Give examples of biological substances transported dissolved in water.

Examples include glucose and amino acids in blood plasma, and mineral ions in plant transport fluids. Use examples relevant to the question.

Why is water useful as a medium for metabolic reactions?

Many substances can dissolve in water, allowing reactants to meet and reactions to occur in solution.

Why do non-polar substances such as lipids not dissolve readily in water?

They do not have charged or polar regions that interact sufficiently with polar water molecules.

What is cohesion between water molecules?

The attraction between water molecules caused by hydrogen bonding.

What causes water's surface tension?

Cohesion from hydrogen bonds makes water molecules at the surface resist being pulled apart, creating a surface that is difficult to break.

Why can some small insects move on the surface of water?

Water's surface tension provides a resistant surface that can support them if their weight is distributed sufficiently.

What does it mean that water is incompressible?

Its volume changes very little when pressure is applied.

Why is water's incompressibility useful to some organisms?

Water can provide support and transmit pressure; for example, fluid in a hydrostatic skeleton helps an animal maintain shape and move.

At what temperature is liquid water at its maximum density?

4°C.

Why is water most dense at 4°C, and what happens as it cools below 4°C?

As water cools below 4°C, hydrogen bonding holds molecules in a more open arrangement, so water expands and becomes less dense.

Why does ice float, and why is this biologically important?

Ice is less dense than liquid water because its hydrogen bonds form an open structure. Ice floats and insulates the water below, helping aquatic organisms survive cold conditions.

what is a monosaccharide

a single sugar monomer

what is a disaccharide

two monosaccharides

what is a polysaccharide

two or more monosaccharides

how do monosaccharides join together to make disaccharides and polysaccharides

by a condensation reaction which forms a glycosidic bond

3 monosaccharides

• glucose

• galactose

• fructose

what is glucose

• monosaccharide

• hexose

• formula C₆H₁₂O₆

what are the two isomers of glucose

• alpha glucose

• beta glucose

Difference between alpha and beta glucose structures

• Alpha- H above, -OH below (the ring)

• Beta- -OH above, H below (the ring)

what reaction forms glycosidic bonds

condensation reaction (removes water molecule)

what reaction breaks glycosidic bonds

hydrolysis reaction (adds water molecule)

3 types of disaccharides

• maltose= glucose + glucose

• sucrose= glucose + fructose

• lactose= glucose + galactose

pentose ribose structure

alpha hexose glucose structure

beta hexose glucose structure

Polysaccharides to know

• glycogen and starch= condensation of alpha glucose

• cellulose= condensation of beta glucose

composition of starch

amylose + amylopectin

where is glycogen used

energy store in animals

where is starch used

• energy store in plants

where is cellulose used

• plant cell walls

amylose structure

• alpha glucose

• 1 → 4 bonds

• unbranched

amylopectin structure

• alpha glucose

• 1 → 4 and 1→6 bonds branched

glycogen structure

• alpha glucose

• 1→4 and 1→6 bonds highly branched

cellulose structure

• beta glucose

• 1→4 bonds

how does starch/glycogen structure relate to its function

• compactness maximise energy stored

• branches allow hydrolysis for respiration

how does branching in amylopectin and glycogen relate to its function

• allows rapid glucose release

how does cellulose structure relate to its function

• hydrogen bonding creates microfibrils

• strong fibres for cell wall allow expansion without lysis

what forms a nucleotide

• a phosphate group

• deoxyribose sugar

• nitrogenous base

what are the 4 bases of dna

• adenine

• guamine

• cytosine

• thymine

what are the purine bases

• Adenine and guanine

what are the pyrimidine bases

• cytosine and thymine

what bases pair together in DNA

• adenine + thymine- 2 hydrogen bonds

• cytosine + guanine - 3 hydrogen bonds

structure of DNA

• two polynucleotide strands coiled into a double helix

what makes a poynucleotide strand

a sugar-phosphate backbone with nucleotides, joined by phosphodiester bonds

How do DNA strands run

• antiparallel

• run in opposite directions (3’ →5’ and 5’→3’)

what is semi-conservative DNA replication

• DNA replication produces 2 DNA molecules, each has one original strand and one new strand

when does DNA replication take place

during the S stage of interphase

What is the role of DNA helicase

• it breaks the hydrogen bonds between complementary bases and separates the strands

What is the role of the original strand in a new DNA molecule

• The original strand acted as a template for the new complimentary strand

What is the role of DNA polymerase

joins nucleotides together to form a new strand

what is the role of DNA ligase

joins sections of the sugar- phosphate backbone which seals breaks between DNA fragments

what is a gene

• a sequence of bases on DNA which codes for a sequence of amino acids on a polypeptide chain

• the sequence of bases determines the sequence of amino acids

how many bases code for one amino acid

• 3 bases code for 1 specific amino acid

what is a codon

a triplet of bases on mRNA strand

whats the purpose of start and stop codons

signal the beginning and end of translation

what are non coding regions

• region of DNA that doesn’t code for a protein

Structure of RNA nuceotides

• phosphate group

• ribose sugar

• nitrogenous base

what are the bases of RNA

• Adenine

• uracil

• cytosine

• guanine

what is mRNA

• a single stranded molecule with a sugar-phosphate backbone

• contains codons (of 3 bases)

function of mRNA

• carries a copy of genetic information from the nucleus to a ribosome

function of tRNA

carries a specific amino acid to the ribosome

what bonds hold tRNA together

• tRNA folds into a specific shape held partly by hydrogen bonds

what is an anticodon

• tRNA has this, 3 bases complimentary to an mRNA codon

role of an anticodon

• allows the correct tRNA to pair with the codon of mRNA