Nucleic Acids + Proteins

Year 12 Biology U3 AOS 1

Nucleic Acids

information molecules that encode instructions for the synthesis of proteins and are large linear polymers of nucleotides

Types of nucleic acids

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

Nucleotides

monomers of nucleic acids (DNA and RNA), which differ depending on which nucleic acid it is — phosphate group, pentose sugar, and nitrogenous base

Genetic Code

a universal triplet code that is degenerate

Monomers

small, simple molecules that bind chemically to other molecules

Polymers

large, complex molecules made up of repeating smaller units (monomers)

Proteins

a type of bio-macromolecule made of amino acid chains folded into a 3D shape

Amino acids

building blocks of proteins

• 20 different types of amino acids make all the proteins in the body

• Are joined together to form chains (polypeptides) which form proteins

Condensation Polymerisation

the reaction that joins amino acids to form a polypeptide

• The carboxyl group of one amino acid is joined to another, forming a peptide bond

• Releases water (condensation) + requires an input of energy (anabolic)

4 Structures of Protein

Primary, secondary, tertiary, and quaternary

Primary structure of protein

sequence of a chain of amino acids

Secondary structure of protein

local folding of the polypeptide chain into a-helices (helix) or b-pleated sheets, sections in between are called random loops

Tertiary structure of protein

3D folding pattern of a protein due to side chain interactions

• Most proteins become functional

• Due to the electric charge of R group → attraction/repulsion between sections of polypeptide chain, making it fold into 3D shape

• Change of protein can indicate biological INACTIVITY

Quaternary structure of protein

proteins made of two or more polypeptides joined together

• Not all proteins will have a quaternary structure — many are functional at the tertiary level

What can happen to Protein Structure?

if there is a change to the specific shape of a protein due to incorrect addition of an amino acid OR environmental change, the enzyme will not function properly

Proteome

the whole set of proteins produced by an organism or cell

• Proteome of a cell is different to its genome — not all cells make the same proteins, yet they all contain the same genes

Structure of DNA

made up on smaller ones called nucleotides — made up of 3 parts:

• a phosphate group, pentose sugar (deoxy/ribose), a nitrogenous base (Adenine, Guanine, Cytosine, Thymine/Uracil)

3 main forms of RNA

messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA)

messenger RNA (mRNA)

messenger strand made in nucleus that carries the genetic information for protein synthesis from nucleus to ribosomes

• specifies the order of amino acids in the polypeptide chain

ribosomal RNA (rRNA)

strand of RNA which is synthesised in the nucleus + binds to proteins within the cell to form ribosomes

transfer RNA (tRNA)

attached to specific amino acids + transports amino acids to the ribosome during protein synthesis

transcription

process (in the NUCLEUS) by which genetic information in a specific segment of DNA (a gene) is copied into a complementary mRNA strand by RNA polymerase

FIRST step of Transcription

Initiation

• RNA polymerase binds to the promoter (near the start of the gene)

• The DNA double helix unwinds, exposing the template strand

SECOND step of Transcription

Elongation

• RNA polymerase moves along the DNA template strand. synthesising a complementary RNA strand by adding RNA nucleotides (A U C G) in the 5’ to 3’ direction

• RNA strand is complementary to the DNA template strand + identical to DNA coding strand except RNA uses uracil instead of thymine

THIRD step of Transcription

Termination

• Transcription ends when RNA polymerase reaches a termination sequence in the DNA

• The newly synthesised RNA (pre-mRNA in eukaryotes) is released and RNA polymerase detaches from the DNA

Importance of Transcription

• First step of the central dogma of molecular biology (DNA → RNA → Protein)

• Allows cells to selectively express genes + produce the proteins needed for specific functions

Alternative Splicing

a process (in the nucleus) where a single pre-mRNA can be cut and joined in different ways to produce multiple mRNA variants — allowing one gene to make different proteins

FIRST step of Alternative Splicing

1. As the pre-mRNA is transcribed, a 5’ cap is added to the beginning of the RNA molecule

• The cap is a modified guanine nucleotide (methylated) attached to the 5’ side

• Function: Protects mRNA from degradation + helps ribosome bind during translation

SECOND step of Alternative Splicing

2. Near the end of transcription, a poly-A tail is added to the 3’ end of the pre-mRNA

• The tail is a long chain of adenine nucleotides (AAAAA…)

• Function: Stabilises the mRNA, protects it from degradation + helps it exit the nucleus

THIRD step of Alternative Splicing

3. The spliceosome (a molecular machine) removes introns (non-coding regions) and joins exons (coding region) together to form mature mRNA

• Spliceosome can include or skip certain exons, creating different mRNA variants from the same pre-mRNA

Importance of Alternative Splicing

• Increases diversity of proteins without needing more genes

• Allows cells to produce different proteins for different tissues or stages of development

Translation

a process (in RIBOSOMES) by which the genetic information carried by mRNA is decoded to produce a specific protein

FIRST step of Translation

Initiation

• The small ribosomal subunit binds to the mRNA at the start codon (AUG, which codes for MET)

• The initiator tRNA, carrying MET, binds to the start codon

• The larger ribosomal subunit joins, forming a complete ribosome

SECOND step of Translation

Elongation

• The ribosome moves along the mRNA, reading each codon one by one

• tRNA molecules, each carrying a specific amino acid, bind to the corresponding codons on the mRNA

• The ribosome catalyses the formation of peptide bonds between amino acids, building a polypeptide chain

THIRD step of Translation

Termination

• Ends when the ribosome reaches a stop codon (UAA, UAG, or UGA) on the mRNA

• The polypeptide chain is released and the ribosome disassembles

Importance of Translation

• Converts the genetic code into functional proteins, which perform most of the work in cells

• Essential for gene expression and proper functioning of cells and organisms

Gene Regulation

the process of turning genes “on” and “off”

• Allows cells to save energy by not producing unnecessary proteins + to specialise

Two mechanisms of gene regulation

Repression and attenuation

• Both occur within E.coli bacteria in a section of DNA — “trp operon”

Two types of genes

• Regulatory genes — DNA sequences that code for proteins that control the expression of other genes

• Structural genes — DNA sequences that code for proteins that are not regulatory proteins

Components of the Operon — gene expression in prokaryotes

• Operon — a set of adjacent genes and nearby regulatory sequences that can affect transcription of the genes

• Promoter — section of DNA where RNA polymerase binds + transcription beings

• Operator — section of DNA where proteins that control transcription bind (repressor proteins)

Trp operon

a group of genes that code for enzymes that make the amino acid “trp” and regulatory sequences that control their expression

Repression of Trp Operon — HIGH Trp levels

• Trp acts as a corepressor and binds to the Trp repressor protein

• Active repressor-corepressor complex binds to the operator region

• Blocks RNA polymerase from binding to promoter, preventing transcription of structural genes

• RESULT → Trp synthesis enzymes ARE NOT producted

Repression of Trp Operon — LOW Trp levels

• Trp repressor protein cannot bind to operator without tryptophan

• RNA polymerase can bind to promoter + transcribe structural genes

• RESULT → Trp synthesis enzymes ARE produced

Attenuation of Trp Operon — HIGH Trp levels

• Ribosomes quickly translate the leader peptide sequence, which includes two tryptophan codons

• Forms a terminator hairpin in the mRNA, halting transcription prematurely

• RESULT → Transcription of structural genes is STOPPED EARLY

Attenuation of Trp Operon — LOW Trp levels

• Ribosomes stall at the tryptophan codons in the leader sequence

• Forms an anti-terminator hairpin in the mRNA, enabling RNA polymerase to continue transcription

• RESULT → Structural genes are fully transcribed and tryptophan synthesis enzymes ARE produced

Importance of Gene Regulation

• Ensures that tryptophan is synthesised only when needed, saving energy + resources

• Demonstrates how bacteria can efficiently regulate gene expression in response to environmental conditions

Exocytosis

a cellular process that involves the transport of materials OUT of the cell

• a form of bulk transport

• essential for the secretion of hormones, enzymes and waste products + incorporation of proteins and lipids into the cell membrane

Exocytosis — Process

• Vesicles containing the material to be exported move toward the cell membrane

• The vesicle membrane fuses with the cell membrane

• The contents of the vesicle are released outside the cell

Exocytosis — Energy Requirement

an active process, requiring energy in the form of ATP (Adenosine Triphosphate)

Exocytosis — Role in the Cell

• Allows cells to secrete large molecules (proteins/hormones) that cannot pass the cell membrane via diffusion or other passive transport

• Helps maintain the cell membrane by adding new lipids + proteins

Endocytosis

a cellular process that allows cells to take in large molecules by engulfing them

• a form of bulk transport

• imports materials into the cell

• essential for nutrient uptake, cell signalling, and immune responses

Endocytosis — Process

• The cell membrane folds inwards, forming a pocket around the material to be imported

• The pocket pinches off, creating a vesicle inside the cell that contains the engulfed material

• The vesicle then transports the material to the appropriate location within the cell

Endocytosis — Energy Requirement

an active process, requiring energy in the form of ATP (Adenosine Triphosphate)

Types of Endocytosis

• Phagocytosis — engulfs large solid particles (bacteria/dead cells)

• Pinocytosis — takes in extracellular fluid containing dissolved substances (absorption of nutrients)

• Receptor-Mediated — specific molecules bind to receptors on cell membrane, triggering formation of vesicle

Endocytosis — Role in Cell

• Allows cells to take in essential nutrients (lipids and proteins)

• Plays a role in immune defence by enabling cells to engulf pathogens

• Helps regulate cell signalling by internalising receptor proteins

Secretory Pathway

a cellular process involving the synthesis, modification and transport of proteins and lipids for secretion from the cell or incorporation into the cell membrane

• Includes endoplasmic reticulum + Golgi apparatus + vesicles

Secretory Pathway — Process

1. Synthesis — Proteins are made by ribosomes on the rough ER and pushed inside its lumen

2. Modification — Proteins are folded and modified (e.g glycosylation) in the rough ER

3. Transport — Proteins are packaged into vesicles + sent to Golgi apparatus

4. Sorting + Packaging — In the Golgi, proteins are further modified, sorted + packed into secretory vesicles

5. Release — Vesicles fuse with cell membrane, releasing proteins outside the cell (exocytosis) OR inserting them into the membrane

Properties of the Genetic Code

• Triplet Code

• Universality

• Redundancy/degeneracy

• Non-ambiguous

Triplet Code

each sequence of three nucleotide bases in DNA (or RNA, called a codon) specifies a particular amino acid or a signal to start or stop protein synthesis

Universality

the same sequence of three-base codons specifies the same amino acid in almost all living organisms

Redundancy/Degeneracy

each amino acids is encoded by more than one mRNA codon

Non-Ambiguous

each specific will always code for only one particular amino acid or a start/stop signal