VCE Biology Unit 3

Biomolecules

Organic polymers (monomers joined in a long linear chain).

Four Major Molecules

Carbohydrates, Lipids, Proteins, and Nucleic Acid. 

Water

• Most abundant compound in organisms.

• H2O molecules are cohesive (attracted to each other) and adhesive (stick to surfaces).

• Acts as a solvent, dissolving hydrophilic or polar substances.

• Has a neutral pH of 7.

Carbohydrates

• Primary energy source.

• Monosaccharides (monomers): e.g., Glucose, Fructose, Galactose, Ribose, Deoxyribose.

• Disaccharides: Two monosaccharides joined, e.g., Maltose, Sucrose, Lactose.

• Polysaccharides: Multiple monosaccharides joined, e.g., Starch, Cellulose.

Lipids

• Not true polymers (e.g., hormones, phospholipids).

• Insoluble in water (hydrophobic, non-polar).

• Composed of fatty acids and glycerol.

Condensation Reactions

• Monomers join to form polymers, releasing water.

• Requires energy (ATP) and catalyzed by enzymes.

• Example: Protein synthesis from amino acids.

Nucleotide & Condensation Reactions

• Condensation reactions join nucleotides to form nucleic acids.

• These reactions create phosphodiester bonds between nucleotides.

Hydrolysis Reactions

• Polymers break down into monomers, catalyzed by enzymes.

• Example: Protein breakdown into amino acids.

Proteins

• Polymers made of amino acids (monomers).

• Synthesized at ribosomes, folded in the Rough ER, and modified in the Golgi body.

• Proteins differ in the sequence of amino acids, determining their function.

• Proteins are made of polypeptide chains folded into a specific 3D shape.

Peptides, Peptide Bonds, Polypeptides

Peptide bond: Link between two amino acids.

Peptides: Short chains of amino acids (not folded).

Polypeptides: Long chains of amino acids (not folded).

Protein Functions

• Enzymes – Speed up chemical reactions.

• Transport – Move substances across membranes (e.g., channel proteins).

• Structural – Provide support (e.g., keratin in skin, hair, nails).

• Hormones – Act as chemical messengers (e.g., insulin).

• Receptors – Detect environmental signals (e.g., hormone receptors).

• Defense – Destroy pathogens (e.g., antibodies).

• Motor – Enable movement (e.g., muscle contraction, cilia, flagella).

• Storage – Reserve metal ions and molecules.

• Signaling – Relay messages between cells.

Enzymes

Globular proteins that act as biological catalysts, speeding up chemical reactions without being consumed. They work by lowering activation energy, making reactions occur faster.

Substrate

•  The reactant molecule that the enzyme acts on.

Active Site

 A specific region on the enzyme where the substrate binds.

Enzyme Specificity

 Active sites are specific to certain substrates (some enzymes can act on multiple substrates).

Induced Fit Model

• The enzyme slightly changes shape when the substrate binds.

• This ensures a tighter fit, forming the enzyme-substrate complex.

• Weak bonds hold the substrate in place during the reaction.

Enzyme Activation Energy

• Enzymes speed up reactions that would otherwise be too slow at body temperature.

• They do this by reducing the activation energy needed for substrates to react.

• Example: Cellular respiration relies on enzymes to produce ATP efficiently.

Anabolic Reactions

• Build larger molecules from smaller ones.

• Example: Protein synthesis (amino acids → proteins).

Catabolic Reactions

• Break down larger molecules into smaller ones.

• Example: Digestion (starch → glucose).

• Enzymes often work in metabolic pathways, where the product of one reaction becomes the substrate for another enzyme.

Cofactors and Coenzymes

• Some enzymes require helper molecules to function:

  • Cofactors: Inorganic molecules (e.g., metal ions like Mg²⁺, Zn²⁺).

  • Coenzymes: Organic molecules (e.g., NADH, FADH₂, ATP).

Role of Coenzymes

• Bind to the active site and help with reactions.

• They donate or accept energy, protons (H⁺), electrons, or chemical groups.

• Recyclable: Once used, they must be reloaded with energy.

Loaded VS Unloaded Coenzymes

• Loaded coenzyme: Can release stored energy (e.g., ATP → ADP + Pi).

• Unloaded coenzyme: Lacks energy but can be reloaded to be reused.

Temperature Affecting Enzyme Activity

• Optimal temperature: Enzymes work best at a specific temperature (36-38°C in humans, optimal = 37°C).

• High temperature (>optimum):
  Enzymes denature (lose shape), making the active site non-functional.

• Low temperature (<optimum):

  • Enzymes and substrates move slower → fewer collisions.

  • Reaction rate decreases but no denaturation occurs. Enzymes regain function when reheated.

pH Affecting Enzyme Activity

• Enzymes have an optimal pH range (varies depending on the enzyme).

• Extreme pH levels → denaturation (active site shape is permanently changed).

• Example: Pepsin (stomach enzyme) works best at pH ~2, whereas amylase (saliva) works best at pH ~7.

Substrate Concentration Affecting Enzyme Activity

• Higher substrate concentration → faster reaction, as more substrates can bind to enzymes.

• However, the reaction rate plateaus once all enzyme active sites are occupied.

Enzyme Concentration Affecting Enzyme Activity

• Higher enzyme concentration → faster reaction, as more active sites are available.

• Lower enzyme concentration → slower reaction due to fewer available active sites.

Competitive Inhibition

• Inhibitor competes with the substrate for the active site.

• Blocks the substrate from binding, reducing reaction rate.

• Can be reversible or irreversible.

Non-Competitive (Allosteric) Inhibition

• Inhibitor binds to a different site (allosteric site), changing enzyme shape.

Active site no longer fits the substrate, permanently or temporarily stopping the reaction.

Reversible Inhibitors

• Bind weakly to the enzyme, effects can be reversed.

• If substrate concentration increases, it can outcompete the inhibitor.

Irreversible Inhibitors

• Bind permanently, preventing the enzyme from functioning.

  • Increasing substrate concentration will not restore function.

Enzyme Regulation of Biochemical Pathways

• Enzyme inhibitors help regulate how much of a product is made.

• Cells can increase or decrease enzyme activity as needed.

• Example: Feedback inhibition → The final product of a pathway inhibits an earlier enzyme to prevent excess production.

Amino Acid Structure

Monomers or subunits of proteins.

• Made of a central carbon atom (C), attached to:

  • A hydrogen atom (H),

  • A carboxyl group (COOH),

  • An amine group (NH2),

  • An R group (side chain).

R Groups

The R group varies between amino acids, creating unique properties.

• Hydrophobic R groups (non-polar) will tend to bond with other hydrophobic amino acids.

• Charged amino acids: Negatively charged R groups are likely to bond with positively charged R groups, forming ionic bonds.

Hierarchical Level of Proteins

Primary Structure

• A long chain of amino acids formed at the ribosomes.

• Peptide bonds form between adjacent amino acids.

• At this stage, the protein is not functional.

Secondary Structure

• Coiling and folding of the amino acid chain due to hydrogen bonds.

• Usually occurs in the Rough ER.

  • Alpha Helices (⍺-helix): Tight coils (e.g., keratin in wool, giving elasticity).

  • Beta Pleated Sheets (β-pleated sheets): Folding forms (e.g., silk, non-flexible).

  • Random Coiling: Sharp turns in coils, often seen at the active site of enzymes (e.g., myoglobin).

Tertiary Structure

• The polypeptide continues to fold into a functional, complex 3D shape.

• Composed of many secondary structures.

• A change in just one amino acid in the primary structure can alter folding, affecting protein function.

Quaternary Structure

• Two or more polypeptide chains bond to form a functional protein.

• Held together by hydrogen bonds, ionic bonds, or covalent bonds.

• Occurs in the Rough ER.

• Conjugated Proteins: Some proteins are bound with other molecules (e.g., nucleoproteins, which combine proteins with nucleic acids).

  • Example: Hemoglobin, which has four tertiary structures bound with a heme group (containing iron).

• This final modification step occurs in the Golgi body.

Factors Affecting Protein Folding/Function

• Temperature OR Ph above optimum 

• Primary structure determines how it will fold to 3D structure 

• Post-translational modification - Proteins can undergo a variety of chemical modifications after translation, which can affect their shape and function. Eg: Phosphorylation (addition of a phosphate group)

• Mutations in DNA causing substitutions, deletions, or insertions of amino acids in the primary structure can lead to alterations.

Proteome

• The complete/entire set of proteins expressed by an organism’s genome.

• It varies between cell types because different genes are turned on or off.

• Cell structure and function is determined by its proteins. Cells regulate which genes are switched on and expressed into proteins.

How the Proteome Contributes to Diversity

1. Gene Expression Regulation: switch on/off specific genes by transcription factors (proteins) that are unique to cell. (slide show 2E)

2. Epigenetic Modifications: Changes to DNA packaging (not bases), eg DNA methylation and histone modifications, influence gene expression without altering genetic code. (Unit 2)

3. Post-translational Modifications: After a protein is made, it can be modified which further influences its function. Eg The addition of a phosphate group (PO₄²⁻)

Nucleic Acids

• Composed of C, H, O, N, and P.

• Nucleic acids (polymer) are made up of nucleotides (monomer).

• Two main types of nucleotides:

  • DNA nucleotides (Deoxyribonucleic acid)

  • RNA nucleotides (Ribonucleic acid)

• Nucleic acids store genetic information and help in the production of proteins necessary for survival.

Nucleotide Structure

1. Nitrogenous base (a compound containing nitrogen)

2. Phosphate group

3. Pentose (5-carbon) sugar

Purines

Adenine (A), Guanine (G)

Pyrimidines

 Cytosine (C), Uracil (U) (RNA), Thymine (T)

Base Pairing

• Complementary base pairing ensures a consistent three-ring width in the double helix.

  • Cytosine pairs with Guanine by three hydrogen bonds.

  • Adenine pairs with Thymine (DNA) or Uracil (RNA) by two hydrogen bonds.

    

DNA Coding and Template Strands

During transcription, mRNA bases pair with the template strand, so the mRNA sequence is the same as the coding strand (except thymine (T) in DNA is replaced with uracil (U) in RNA).

DNA strands have:

• 5' end – ends with a phosphate group.

• 3' end – ends with a sugar.

• The two DNA strands run antiparallel, meaning one strand runs from 3' to 5', and the other runs from 5' to 3'.

DNA Function

1. Replication – to reproduce itself.

2. Protein synthesis – to manufacture proteins in living organisms.

Where is DNA Found in Cells

• DNA is visible in cells as chromosomes.

• In eukaryotic cells, DNA is found in the nucleus, while in prokaryotic cells, it is found in the cytoplasm.

DNA Packaging

• DNA wraps around histone proteins to form a nucleosome.

• Nucleosomes coil to form chromatin, and further supercoiling creates condensed chromosomes visible under a microscope.

Histone and Nucleosome Structure

• Histones are basic proteins with a positive charge, allowing them to bind to the negatively charged DNA.

• Each nucleosome consists of DNA wrapped around an octamer of histones (8 histone proteins, including H2A, H2B, H3, and H4).

RNA

A single-stranded polymer of RNA nucleotides. Nitrogenous bases are (A, U, C, G).

mRNA

A complementary copy of the template DNA strand. Carries genetic information from the nucleus to the ribosome, where it gets decoded to make proteins.

• mRNA consists of codons (groups of 3 bases), where each codon codes for one amino acid.

• Created during transcription. 

• CODONS ARE RNA

rRNA

A key component of the ribosome, which synthesizes proteins.

Ribosomes have two subunits, each containing rRNA and ribosomal proteins.

Functions of rRNA

Structural support: Maintains ribosomal integrity and function.

Catalysis: Catalyzes the formation of peptide bonds between amino acids during translation.

tRNA

Delivers amino acids from the cytoplasm to the ribosome for protein synthesis. Each tRNA is specific to a particular amino acid.

Anti-codon

A sequence of 3 bases on tRNA that pairs with the complementary codon in mRNA.

Genes

• Found in the nucleus, mitochondria, and chloroplasts (eukaryotes); cytosol (prokaryotes).

• Provide instructions for protein synthesis.

• The sequence of nitrogenous bases in DNA specifies the amino acid sequence of proteins.

• Not all genes are expressed in every cell.

Endosymbiotic Theory

• Eukaryotic cells may have evolved through mutualism.

• Mitochondria and chloroplasts were once free-living prokaryotes.

• They enter host cells via phagocytosis or as parasites.

• The host provided a safe, nutrient-rich environment.

• The organelles produce energy for the host cell.

Degeneration

Some amino acids are coded for by multiple triplet codes (codon).

• Each codon specifies only one amino acid or stop signal.

• This helps protect vital genes from mutations and improves protein synthesis efficiency.

• Multiple tRNAs with different anticodons can recognize the same codon.

Gene Structure in Eukaryotic Organisms

Upstream regions:

• Enhancers/silencers regulate gene expression.

• Promoter region: Binds transcription factors & RNA polymerase.

• TATA box: Defines transcription direction.

• 5' UTR: Regulates gene expression (transcribed but not translated).

Flanking region: After the coding region.

• 3' UTR: Signals the end of coding & stabilizes mRNA.

• Terminator sequence: Ends transcription.

Coding region components:

• Start codon (DNA: TAC, mRNA: AUG) → Begins translation, codes for methionine.

• Stop codon (DNA: ACT, mRNA: UGA)

Exons & Introns:

• Introns: Non-coding sequences removed during RNA processing.

Exons: Coding sequences that determine protein structure.

Eukaryotic Coding Strand

Gene Structure in Prokaryotic Organisms

• Operon: Structural genes with a common function are grouped and controlled by the same promoter and operator, allowing simultaneous transcription or repression.

Upstream Region - Prokaryotic

• Regulatory gene: Produces proteins to activate or repress structural genes.

• Promoter region: Binds transcription factors and RNA polymerase.

• TATAAT box: Defines transcription direction.

• 5' UTR (Leader): Transcribed but not translated; regulates gene expression.

Coding and Downstream Region - Prokaryotic

• Coding region: Contains exons only (no introns).

  • Starts with TAC or CAC.

• Downstream region: Located after the gene.

  • 3' UTR (Trailer): Regulates mRNA stability.

Terminator sequence: Signals transcription end.

Prokaryotic Template Strand

Regulatory Genes

Control whether another gene is expressed or not.

• Produce proteins (e.g., transcription factors) that regulate structural genes.

Usually located upstream of the gene they control.

Structural Genes

Code for proteins with structural or functional roles in the cell or organisms.

Examples: Enzymes, antibodies.

Gene Expression

The processes by which the instructions in DNA are converted into a functional protein product.

Transcription Factors

Transcription factors are proteins that help turn specific genes "on" or "off" by binding to nearby DNA called a promoter region.

• Activators turn on a gene and activate transcription. 

Repressors decrease/prevent transcription and thus turn off a gene.

Transcription

Occurs in the nucleus of eukaryotic cells and the cytosol of prokaryotic cells.

1. RNA polymerase attaches to the promoter region

2. DNA unwinds, exposing the bases of the template strand of DNA

3. RNA nucleotides pair with the DNA template strand and join to form pre-mRNA.

RNA Processing

Occurs only in eukaryotic cells and is modified before leaving the nucleus.

1. Add a methyl cap to the 5’ end of mRNA

2. Add a poly-A tail to the 3’end of mRNA

3. Splice/cut out introns by spliceosome

4. The final product is mRNA.

The cap and tail stabilize the mRNA, preventing it from degrading and allowing it to bind to the ribosome during translation.

Translation (3 Steps)

Initiation, Elongation, Termination

Initiation

• The ribosome binds to the mRNA (5' end of the mRNA and moves along mRNA in the  5'→3' direction until it reaches the start codon) 

• The ribosome reads the mRNA molecule

• The tRNA with the anticodon to the start codon (AUG) will bind to the mRNA and the amino acid methionine will be delivered to the ribosome.

Elongation

• The mRNA moves through the ribosome to the next codon.

• The next amino acid is delivered by the specific tRNA. The amino acid binds to methionine by a peptide bond.

• This continues for each codon in the mRNA, resulting in a long chain of amino acids (which form the primary structure of the protein)

Termination

• Once the ribosome reaches the stop codon on the mRNA, translation ends and the polypeptide (chain of amino acids) is released.

Translation Using tRNA molecules

• tRNA molecules are made of RNA and have a specific amino acid binding site at one end and a 3-nucleotide anticodon sequence at the other.

• tRNA loaded with a specific amino acid will move to the ribosome where its anti-codon will pair momentarily with the complementary mRNA codon.

• This ensures the coded for amino acid is put in the correct position in the growing amino acid chain at the ribosome.

• The tRNA anti-codon is complementary to the mRNA codon.

Protein Processing

• The amino acid sequence emerges from the ribosome as a primary structure protein, and the folding process begins.

• Proteins called molecular chaperones help a newly synthesized protein fold into its final functional 3D shape.

• The folding is done in the endoplasmic reticulum rough and modifications/additions to Golgi body.

Tryptophan

• Humans cannot synthesise it

• Prokaryotes can take in trp or make trp using the trp operon

• It can be free-floating or attached to a specific tRNA.

Trp Operon

Contains 5 structural genes that code for 5 proteins that eventually combine to make 3 enzymes that catalyse the production.

• Makes enzymes that turn chorismate into the amino acid trp.

• Has a promoter, operator, trp Leader, 5 structural genes, terminator

  

Difference Between Promoter and Operator in Trp Operon

Promoter: Nucleotide sequence that enables a gene to be transcribed. It is where RNA polymerase binds.

Operator: A segment of DNA where a repressor protein can bind to control the expression of structural genes.

Trp Operon Repression

• A specific trp regulatory gene is located upstream of the trp Operon.

• This trp regulatory gene codes for a trp repressor protein that can control the transcription of the operon.

• Under certain conditions, the repressor protein can bind to something called the operator, which can stop transcription.

• Repression prevents transcription from starting/occurring

• Dependent on the levels of free floating trp in the cell

Repression in High Free TRP in Cytosol

• If the trp repressor protein binds to free trp in the cytoplasm, the trp repressor protein will undergo a shape (conformational) change.

• The new shape can bind to the operator

• This prevents RNA polymerase from moving along the DNA and stops transcription from beginning/initiating.

Repression in Low Free TRP in Cytosol

• Trp repressor protein does NOT bind to free trp, the trp repressor protein will keep its shape.

• The trp repressor protein will NOT bind to the operator and RNA polymerase can successfully move along the DNA and transcription occurs.

Trp Operon Leader

Leader: Region of DNA of the trp Operon located between the operator and the first structural gene (trpE).

• The leader is made up of 4 regions

• Leader region 1 codes a short peptide with two trp amino acids 

• The leader peptide does not serve a long-term functional role but acts as part of a regulatory feedback mechanism determining if the operon will be fully transcribed.

Trp Operon Leader Region 1

• If repression does not occur and transcription begins, region 1 of the Leader DNA is transcribed into mRNA 

• DNA/mRNA of region 1 contains two triplet codes (codons) for trp]

Trp Operon Leader Region 2,3,&4

• Can be transcribed under certain conditions but NOT by ribosomes.

• If the DNA of regions 2, 3 and 4 get transcribed into mRNA, region 2 & 3 contain RNA bases that can complementary pair to each other and form an ‘anti-terminator’ hairpin

AND

• mRNA regions 3 & 4 contain RNA bases that can complementary pair to each other and form a ‘terminator’ hairpin

Trp Operon Attenuation (Synthesis)

• Attenuation provides additional fine control during transcription. It regulates how much of the operon is transcribed and prevents transcription from completing based on trp levels.

• Helps in high tryptophan conditions.

• Occurs when free trp is low, but Trp-tRNA levels are high.

Attenuation in High Trp-tRNA

• Transcription begins (as repression does not occur)

• The leader is the first area to undergo transcription to mRNA straight away.

• A ribosome attaches to the Leader mRNA in region 1.

• If there is plenty of trp attached to tRNA (trp-tRNA), translation of region 1 is quick.

• The ribosome reaches the stop codon at the end of region 1, then overlaps the mRNA of Leader regions 1 and 2.

• Region 2 is prevented from complementary bonding with region 3. 

• Regions 3 and 4 complementary pair and a termination hairpin is produced, causing the ribosome and RNA polymerase to be released and transcription of the trp operon STOPS.

• The trp structural genes are not transcribed or translated, and NO trp is produced.

The main organelles involved in the protein secretory pathway:

• Ribosomes

• Rough endoplasmic reticulum

• Golgi body/apparatus

• Transport and secretory vesicles

The protein secretory process:

1. Proteins are synthesised at the ribosome by translation.

2. Proteins that will be secreted are usually synthesised at ribosomes attached to the rough endoplasmic reticulum. This RER then folds the protein (into secondary, tertiary and quaternary)

3. Once folded, the protein leaves the RER in a transport vesicle. This vesicle fuses with the Golgi apparatus and releases the protein.

4. Once at the Golgi apparatus, the protein can be modified (sometimes molecules are added or removed) and then packaged into intracellular membranes that bud off as secretory vesicles. 

5. Secretory vesicles bud off the Golgi apparatus and travel through the cytoplasm to the plasma membrane. 

6. The secretory vesicle fuses with the plasma membrane.

7. The protein then leaves the cell via exocytosis.

The Protein Secretory Pathway Summarised

Nucleus -> ribosome -> rough endoplasmic reticulum -> transport vesicle -> golgi apparatus -> secretory vesicles -> cell membrane

Exocytosis

• Exocytosis moves large substances, such as proteins, to the outside of the cell (secretion).  

• This is an active process and thus requires energy.

• A vesicle will fuse with the plasma membrane, and its contents will be released into the extracellular fluid.

Plasmids

A small circular loop of DNA separate from a chromosome, typically found in bacteria.

Endonucleases

• Restriction enzymes that cut DNA

• Target specific recognition sequences with each enzyme recognising a different sequence

• They cleave (cut) the phosphodiester bonds of the backbone

• Sourced from bacteria

Recognition Sequences

The recognition site of a restriction endonuclease is usually four to six nucleotides in length, specific to each enzyme.

Generally, recognition site sequences are palindromes, meaning the 5’ to 3’ sequence of the template strand is the same as the 5’ to 3’ sequence of the non-template strand.

Blunt Ends

Result in a straight edge cut and no overhanging nucleotides. The unpaired nucleotides will be attracted to a complementary set of unpaired nucleotides.

Sticky Ends

Result in a staggered cut with overhanging, unpaired nucleotides. The unpaired nucleotides will be attracted to a complementary set of unpaired nucleotides.

Restriction Sites

• Scientists who want to cut out a fragment of human DNA from a human genome must find restriction sites that are upstream and downstream of the target gene they want to cut out. 

• Sticky ends are more useful because the DNA fragments can be inserted into the plasmid in the right direction. 

• If a blunt cut is used, the fragment might be inserted head-to-tail or tail-to-head into the plasmid.

Ligases

• Enzymes that join two fragments of DNA/RNA together.

• Catalyse the formation of phosphodiester bonds between sugars and phosphate groups.

• Not specific and can join any two fragments of DNA, regardless of whether they have blunt/sticky ends.

• DNA ligase joins DNA, RNA ligase joins RNA.

Polymerase

• Synthesises nucleic acids from nucleotides

• RNA polymerase is used in synthesis and transcription

• DNA polymerase is used in synthesis and replication 

Polymerase requires a primer to attach to the start of the template strand of DNA. Primers are short, single chains of nucleotides that are complementary to the template. Once attached to the primer, the polymerase enzyme can read and synthesise the complementary strand in a 5’ to 3’ direction.

Polymerase Chain Reactions (PCR)

A DNA manipulation technique that amplifies DNA by making multiple identical copies, used when there is an insufficient amount of a DNA sample for testing.  After undergoing the polymerase chain reaction, scientists can run further analyses on the DNA such as:

• Paternity testing

• Forensic testing samples of bodily fluids

• Analysing gene fragments for genetic diseases.