P1 – Cell ChemistryBiomacromolecules

Key knowledgeThe nature and importance of biomacromolecules in the chemistry of the cell

Synthesis of biomacromolecules through the condensation reaction

Structure and function of lipids Structure and function of DNA and RNA, their

monomers and complementary base pairs The structure and functional diversity of proteins,

their levels of organisation and the nature of the proteome.

Organic vs. Inorganic

Organic: a compound which has the elements carbon and hydrogen. The atoms of carbon and hydrogen are bonded together within that molecule

eg: glucose.

Inorganic: a compound where carbon and hydrogen aren’t bonded together

eg: water, carbon dioxide etc.

Different kinds of bonding

Different kinds of bonding

Properties of Water:

Classes of MACROMOLECULES

Macromolecule Subunit

1. PROTEINS Amino Acid

2. NUCLEIC ACIDS Nucleotide 3. complex CARBOHYDRATES Simple

sugar (monosaccharide) 4. LIPIDS Triglyceride and

chains of fatty acids

Class of biomacromolecule

Sub units / monomers

Cellular functions

Lipids (hydrophobic)Lipids are not polymers

Fatty acids & glycerolEster Bonds between subunits

Energy store, component of cell membranes, signalling molecules

Complex carbohydratesInsoluble PolysaccharidesStarch, glycogen, cellulose, chitin

GlucoseGlycosidic bond between monomers

Energy store, structural components of cells

Nucleic AcidsPolynucleotidesDNA, RNA (various forms)

NucleotidePhosphodiester bond between monomers

Information molecules that constitute an organisms genetic material

ProteinsPolypeptides

Amino AcidPeptide bond between monomers

Proteins have many diverse roles. They control and regulate cellular processes, assist in transport of substances, act as receptors and as structural components

Synthesis of biomacromolecules Autotrophs – synthesise their own

organic requirements through chemical processes other than photosynthesis. Called chemosynthetic autotrophs.

Heterotrophs – have to synthesise their own biomacromolecules from existing organic compounds. E.g. we need to take in lots of organic compounds from food and then break them into smaller, simpler substances.

Biomacromolecules Mono (one) mer (unit) Poly (many) mer (units)

Monomers join up together to create a polymer.

The process by which this happens is known as condensation polymerisation.

Monomer ------------------- Monomer -------------------- Monomer

Building a polymer

As the polymer is built a H from one monomer joins with the OH of the next monomer

releasing a water molecule.

Biomacromolecules

Lipids are a macromolecule, however, they aren’t polymers.Not made up of similar subunits. They are made up of fatty acids and glycerol.

Monomer Polymer

Amino Acid Protein

Monosaccharide Polysaccharide/Carbohydrate

Nucleotide Nucleic Acid

Glycerol A water molecule is condensed out when the acid group reacts with the alcohol group. An ester bond is formed that links the two molecules together

Fatty acid Hydrocarbon chain

Fatty acid Hydrocarbon chain

Fatty acid Hydrocarbon chain

Glycerol has three OH groups. Hence each glycerol molecule can only accept a total of three fatty acids. There is no repetitive linkage: so lipids are NOT polymers

Carbohydrates/Polysaccharides

Formula: nCH2O e.g. Glucose C6H12O6

Subunit: monosaccharide

Monosaccharide + monosaccharide = disaccharide Monosaccharide + disaccharide = polysaccharide

Monosaccharide = fructose, glucose, hexose Disaccharide= sucrose, lactose, maltose Polysaccharide= glycogen, cellulose, chitin

Can join with other atoms or groups eg: glycoproteins (carbohydrate and protein)

GlucoseGlucose C6H12O6

Carbohydrate ratio: 1:2:1

In solution glucose forms a ring structure as shown

*Note the number of OH groups in each molecule. These OH groups make glucose highly soluble in water

Monosaccharide (simple sugar)

Eg: Maltose (grains), Sucrose (table sugar, sugar cane), Lactose (milk)

Disaccharide (sucrose)

Eg: Maltose (grains), Sucrose (table sugar, sugar cane), Lactose (milk)

Polysaccharide (cellulose)

Eg: Cellulose (structural component in plant cells most common organic chemical on Earth), Starch (plants – energy storage), Glycogen (animals – energy storage in muscles and liver), Chitin (exoskeleton of insects and crustaceans, cell walls of fungi).

Lipids CHO (N and P, much less O than carbohydrates)

Subunit: fatty acid and glycerol (therefore lipids are not polymers)

make triglycerides

Synthesised by Smooth Endoplasmic Reticulum

Generally hydrophobic, but some lipids possess a polar end, making the

whole molecule partially polar (hydrophilic) and some lipids are both -

amphipathic.

Use:

Energy storage (stores 2 times more energy than carbohydrates)

Structural component

Transmission of signals

Saturated vs. Unsaturated

Animal Plant

At least one double bond between carbon atoms

Lipid

Types: fats, oils, terpenes, waxes Phospholipid – phosphate is

hydrophilic, fatty acid tail is hydrophobic.

Cholesterol – structural, prevents solidification of membrane at cold temps. Belongs to steroid group. Glycolipids – communication,project from membranes and arespecialised to detect and bindwith signalling molecules.

Lipids in membranesPhospholipids, another kind of fat, have two fatty acids attached to a glycerol molecule. They also have a phosphate group attached to the glycerol molecule 

The phosphate ‘head’ of a phospholipid molecule is attracted to water (hydrophilic). The fatty acid tails extend away from water (hydrophobic). Because of these properties, the molecules align so that they develop double-layered sheets, which are the cell membranes found in every living cell.

Lipid functionENERGY

Lipids have a high proportion of Hydrogen atoms relative to Oxygen atoms and yield more

energy than the same mass of carbohydrates. Excess triglycerides are stored as adipose

tissue.

THERMAL INSULATION

Triglycerides conduct heat very slowly. Marine animals often have a thick layer of subcutaneous

fat (located under the skin) called blubber which keeps metabolic heat inside the body.

ELECTRICAL INSULATION

The axon of a nerve cell is surrounded by a fatty material called myelin. It helps maintain nerve

conductivity by preventing signal loss. It also increases speed of nervous conduction by

increasing the diameter of the axon.

HOMEOSTASIS

Steroid hormones have a lipid component e.g. estrogen and testosterone.

BUOYANCY

Triglycerides are less dense than water. Marine organisms with a high lipid content are highly

buoyant.

Cell membrane

Nucleic Acid CHNOP Subunit: Nucleotide Made of 3 parts: phosphate, attached to a

sugar, which is attached to a nitrogenous base.

Codes for production of proteins – genetic material

Structural & Chemical Differences between DNA & RNA

RNA: Nitrogenous base Thymine (T) is replaced with Uracil (U)

DNA sugar (deoxyribose) = one less oxygen atom

DNA & RNADNA RNA

Double Stranded Single Stranded

Deoxyribose Sugar Ribose Sugar

Found in nucleus Found in nucleus, cytoplasm and ribosomes

Nitrogenous bases: Adenine, Guanine, Cytosine and THYMINE

Nitrogenous bases: Adenine, Guanine, Cytosine and URACIL

Linear (eukaryotes) or circular (prokaryotes)

3 types: mRNA, tRNA, rRNA

Involved in Transcription (protein synthesis)

Involved in Transcription and Translation (protein synthesis)

Base Pairing

Chromosomes are made up of genes that are made up of DNA.

DNA is double stranded.Bases undergo complementary base pairing.

Adenine-Thymine and Guanine-Cytosine

RNA doesn’t have T, it has U instead: A-U

DNA: G T C C T A T T A C G T A GDNA: C A G G A T A A T G C A T CRNA: G U C C U A U U A C G U A C

Phosphodiester bond

RNA Important in protein synthesis

Takes the information from the DNA strand and makes proteins – Gene expression

Information from genes on DNA are transferred to messenger RNA (mRNA)

Ribosomes read mRNA, one triple (codon) at a time and with the help of transfer RNA (tRNA) an amino acid chain is formed.

RNA is necessary to make a protein from the DNA instructions that can’t leave the nucleus.

Ribosomal RNA is found in the ribosomes (rRNA)

Proteins

Protein are large molecules made of amino acidsEach amino acid has one part of it’s molecule different from other amino acids.

R is a variable compound, it can be hydrophobic or hydrophilic resulting in some proteins being soluble while others are not.

Peptide bond –releases a water molecule

Proteins

CHNOPS eg: C708H1130N180O224S4

Subunit: amino acid (20 used to make proteins and are obtained through diet)

Examples and use: Enzymes – speed up cellular reactions Haemoglobin – transport oxygen Insulin – lower glucose levels Antibodies – immune response Keratin and Collagen – structure – provides

strength and support Actin and myosin - muscle movement.

Function of Proteins

Amino Acids – subunit of a proteinAll have same basic structureA central carbon atom attached to a hydrogen atomA carboxyl acid group (COOH)An amine group (NH2)R group

The R group differentiates one amino acid from anotherR group can be polar or charged (hydrophilic on the outside of protein molecule) or non polar (hydrophobic – inside of protein molecule)

Amino Acids – subunit of a protein

Type

*Non Polar =hydrophobic regions*Usually inside protein molecule away from aqueous external environment

R Group

Type

*Polar = hydrophilic regions*Usually on surface of protein molecule because they like aqueous

external environment

R Group

Amino Acids ProteinsAdditional bonding: covalent, ionic, hydrogen and disulphide bridges are used to create 3D shape.

Amino Acids (AA) Proteins 4 Levels from Amino Acid to Protein

Primary Structure (the order of AA in the polypeptides) DNA determines sequence of AA in the

polypeptide (protein). AA bond together by condensation

polymerisation and form peptide bonds between each AA

Amino Acids (AA) Proteins Secondary Structure

Hydrogen bonding causes coiling & folding Tight coils = α-helices Folding forms = β-sheets Coils & Sheets connected by random loops. Random Loops remain unchanged. β-sheets & random loops = basis of active site in enzymes

Amino Acids (AA) Proteins Tertiary Structure - (Determines the function of the protein – biological functionality.)

“Like attracts like” Hydrophilic R groups attract hydrophilic R groups Hydrophobic R groups attract other hydrophobic R

groups. This causes further folding and coiling into the proteins

functional shape.

R group interactions ionic bonds, hydrogen bonds & disulfide bridges between adjacent cysteine amino acids.

Protein molecules with the same AA sequence will fold into the same shape. One AA change will change the shape of the protein & possibly its function.

Amino Acids (AA) Proteins Quaternary Structure

Some large protein structures can consist of 2 or more polypeptide chains.

Chains are held together by hydrogen, ionic and covalent bond.

Makes their shape and function more complex.

haemoglobin

Protein channel

Fibrous or GlobularFibrous Proteins Basic tertiary structure. Long parallel

polypeptide chains. Cross linkages at

intervals forming long fibres or sheets.

Usually insoluble. Many have structural

roles. E.g. keratin in hair and

the outer layer of skin, collagen (a connective tissue).

Globular Proteins Have complex tertiary

and sometimes quaternary structures.

Folded into spherical (globular) shapes.

Usually soluble as hydrophobic side chains in centre of structure.

Roles in metabolic reactions.

E.g. enzymes, haemoglobin in blood.

Changing the nature of proteins Proteins are functional due to their 3D

conformation. This CAN be compromised.

High Temperatures Strong Salty Solutions Acidic or Alkaline Conditions

Such things denature or change the shape of the protein

Minor changes may be reversed, major changes cannot.

Important: Low temperatures can slow protein activity, but does not alter shape or denature the protein.

Proteome This is the structure and properties of all the

proteins produced by an organisms genetic material (genome).

Proteomics is the study of the structure and function of proteins, including the way they work and interact with each other inside cells.

It is important to study proteins together as they interact with one another.

Protein Synthesis DNA codes for proteins.

RNA is needed to copy the DNA sequence in order to get proteins made.

Two types of RNA needed for protein synthesis: mRNA and tRNA

Protein Synthesis occurs in two stages:

1. Transcription: Occurs in the nucleus and involves DNA and mRNA

2. Translation: Occurs in the cytoplasm and involves mRNA, ribosomes, tRNA and amino acids

Questions

Complete the following Questions in your workbook

Heinemann Biology 2 Textbook:Questions 14 – 17a, 18, 19. Page 19