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P1 – Cell Chemistry. Biomacromolecules. Key knowledge. The nature and importance of biomacromolecules in the chemistry of the cell Synthesis of biomacromolecules through the condensation reaction Structure and function of lipids

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p1 cell chemistry

P1 – Cell Chemistry

Biomacromolecules

key knowledge
Key knowledge

The 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 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.
classes of macromolecules
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
synthesis of biomacromolecules
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
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
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.

biomacromolecules1
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.

glycerol
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
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)
glucose
Glucose

Glucose 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
Monosaccharide (simple sugar)

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

disaccharide sucrose
Disaccharide (sucrose)

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

polysaccharide cellulose
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
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
Saturated vs. Unsaturated

Animal

Plant

At least one double bond between carbon atoms

lipid
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 are

specialised to detect and bind

with signalling molecules.

lipids in membranes
Lipids in membranes

Phospholipids, 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 function
Lipid function

ENERGY

  • 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.
nucleic acid
Nucleic Acid
  • CHNOP
  • Subunit: Nucleotide
  • Made of 3 parts: phosphate, attached to asugar, which is attached to a nitrogenous base.
  • Codes for production of proteins – genetic material
structural chemical differences between dna rna
Structural & Chemical Differences between DNA & RNA
  • RNA: Nitrogenous base Thymine (T) is replaced with Uracil (U)
  • DNA sugar (deoxyribose)= one less oxygen atom
base pairing
Base Pairing

Phosphodiester bond

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 G

DNA: C A G G A T A A T G C A T C

RNA: G U C C U A U U A C G U A C

slide29
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
Proteins

Protein are large molecules made of amino acids

Each 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

proteins1
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.
amino acids subunit of a protein
Amino Acids – subunit of a protein

All have same basic structure

  • A central carbon atom attached to a hydrogen atom
  • A carboxyl acid group (COOH)
  • An amine group (NH2)
  • R group
  • The R group differentiates one amino acid from another
  • R 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 protein1
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 proteins
Amino Acids  Proteins

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

amino acids aa proteins
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 proteins1
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 proteins2
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 proteins3
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 globular

Fibrous 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.

Fibrous or Globular
changing the nature of proteins
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 denatureor 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
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:

Transcription: Occurs in the nucleus and involves DNA and mRNA

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

Protein Synthesis
questions
Questions

Complete the following Questions in your workbook

Heinemann Biology 2 Textbook:

Questions 14 – 17a, 18, 19. Page 19