Basics of Molecular Biology

What is bioinformatics

• The science of collecting and analyzing complex biological data.

  • Central dogma of molecular biology: DNA (genomics) → RNA (transcriptomics) → protein (proteomics).

• Metabolomics: the study of all small molecules (metabolites) in a cell, tissue, or organism.

• Representation/storage/retrieval/analysis of biological data concerning:

  • Sequences (DNA, RNA, protein).

  • Structure (RNA, protein).

  • Function (protein).

  • Activity levels (mRNA, protein, metabolite).

  • Networks of interactions of molecules(metabolic pathways, regulatory pathways, signaling pathways).

  • Etc.

What are the important molecules that modern molecular biology studies?

• DNA, RNA, proteins, and metabolites.

• Most bioinformatics research studies DNA, RNA, and proteins.

  • They are “easier.”

  • Their primary structures are sequences.

  • The technologies for analyzing them have been developed.

  • More work emerges on metabolites.

DNA (tissue cells & regions of DNA on chromosomes)

• The structure and the four genetic letters code (A, G, T, C) are the same for all living organisms.

  • Four different nucleotides distinguished by four bases: adenine (A), cytosine (C), guanine (G) and thymine (T).

• Tissue cells have two set of chromosomes (one coming from each parent).

  • Maternal and paternal copy.

• Regions of DNA sequence along chromosomes encode instructions for the manufacture of proteins.

• DNA is a polymer:

  • Polymer = a large molecule consisting of nucleotides.

The double helix

• DNA typically consists of two strands arranged in a double helix structure

• In a double stranded DNA, each base has its own binding partner.

  • Adenine always bonds to Thymine.

  • Cytosine always bonds to Guanine.

Directions of the DNA strands

• Each DNA strand has two ends: 5’ and 3’.

• 5’ (five prime) and 3’:

  • 5' carbon has a phosphate group attached to it.

    • Picture = the one circled red.

  • 3' carbon a hydroxyl (-OH) group.

    • Picture = the one in the blue box.

• DNA polymerase (helps DNA replication) works in a 5' -> 3' direction.

  • DNA polymerase: enzyme, it recognizes the free -OH groups on the 3’ end and works from there to start the DNA synthesis. Synthesized DNA is always from 5’ to 3’.

Chromosomes (histones, nucleosomes, and chromatin)

• DNA is packaged into individual chromosomes.

• Histones: small proteins (H1, H2A, H2B, H3, H4); helps package and organize DNA into structural units.

• Nucleosomes (beads):

  • Histone + DNA.

• Chromatin (necklace of beads):

  • Made up of nucleosomes linked together.

Genome

• The complete DNA for a given species.

• Human genome consists of 23 pairs of chromosomes.

• Every cell (except sex cells and mature red blood cells) contains the complete genome of an organism.

Epigenome

• The complete set of chemical modifications to DNA and histone proteins that regulate gene activity.

  • Without changing the underlying DNA sequence.

• It is important because:

  • Explains why different cells (e.g., skin vs. muscle) behave differently with the same DNA.

  • Plays a role in development, aging, and diseases like cancer.

DNAs across individuals are not identical because of…

• Genetic variations are differences in the DNA sequence among individuals.

  • They make each person's genome unique.

  • They can affect everything from physical traits to susceptibility to disease.

• Genetic variations are generally permanent within an individual’s genome.

  • Unless altered by cancer cells or gene editing.

• Genetic variations range in size from a single DNA building block (single nucleotide) to a large segment of a chromosome.

Genetic mutation vs. genetic variation

• Genetic mutation is a change in the DNA sequence, while genetic variation refers to the differences in DNA among individuals.

• Genetic variations across individuals partly arise from accumulating genetic mutations over generations.

Gene mutations occur in two ways…

• Inherited from a parent (hereditary).

• Acquired during a person’s lifetime (somatic).

Hereditary mutations (germline mutations)

• Passed from parents to children.

• Present in the egg and sperm cells, which are also called germ cells.

• These variations are present in virtually every cell of a person's body from birth.

Somatic mutations

• Occur in the DNA of individual cells at some time during a person’s life.

• Caused by mistakes as DNA copies, sometimes by environmental factors.

• In non-reproductive somatic cells (cells other than sperm and egg cells).

• Somatic mutations can accumulate over an individual's lifetime within specific cell line, but generally do not pass to the next generation.

Genes

• A gene is a segment of DNA sequence that carries the information required for constructing a particular protein.

  • A gene encodes a protein.

RNA (bases and strand)

• Four bases: adenine (A), cytosine(C), Guanine(G), and uracil(U).

  • Base pairs A-U, C-G.

• Single-stranded (notated as s.s. or ss).

• Single stranded structure is not stable.

  • Intramolecular base pairing is common.

    • RNA folding.

    • Secondary structure.

    • RNAfold: prediction of secondary structure.

Transcription

• The biological process through which the information in a gene's DNA sequence is copied into mRNA.

• Transcription occurs in the 5′ to 3′ direction.

  • The direction in which the new mRNA strand is synthesized.

• The sense strand is the strand of DNA that has the same sequence as the mRNA.

RNA types

• Messenger RNA (mRNA):

  • Information transfer from genes to proteins.

• Ribosomal RNA (rRNA):

  • Ribosome structure.

• Transfer RNA (tRNA):

  • RNA consisting of folded molecules which transport amino acids from the cytoplasm of a cell to a ribosome.

• Regulatory RNAs:

  • Non-coding RNA which does not lead to any proteins. In the form of RNA, they can regulate the expression of other genes.

  • MicroRNAs (miRNAs): a small regulatory RNA that helps silence genes through RNA interference.

RNA splicing & alternative splicing

• Introns and exons:

  • Spliceosomes can recognize sequences at the 5′ and 3′ end of the intron and cut the introns out precisely.

  • Introns are removed and exons (coding regions) are connected.

• Alternative splicing:

  • When one gene’s RNA can be cut and rearranged in different ways, so the same gene makes different proteins.

  • The cell can choose to:

    • Skip certain exons.

    • Include extra exons.

    • Use different splice sites within an exon or intron.

Proteins

• A chain of amino acids (also known as polypeptide).

• There are 20 amino acids.

• Amino acids are classified by their physical and chemical properties.

  • These properties play an important role in the function of proteins.

Translation: RNA to protein

• mRNA carries the genetic code from DNA in sets of three bases called codons.

• Each codon corresponds to one amino acid, matched by tRNA during translation.

• Ribosomes read the mRNA and link amino acids together to form a protein.

• Translation begins with the start codon (AUG).

• Translation ends with the stop codon (UAA|UAG|UGA).

• Open reading frame (ORF):

  • Groupings of codons.

  • Picture: there are 3 possible reading frames on an mRNA.

    • Option 3 is correct.

Protein structure

• Primary structure: sequences (CAAUG, etc.).

• Secondary structure: regular substructures (alpha-helix/beta sheets).

• Tertiary structure: 3-D structure of a single protein molecule.

• Quaternary structure: larger assembly of several protein molecules or polypeptide chains, usually called subunits in this context.

• Functional: transcription factors, receptors, ligands, signaling proteins, kinases, etc.

Post-translational modifications

• Chemical changes that occur to proteins after translation.

• PTMs occur at distinct amino acid side chains or peptide linkages, and they are most often mediated by enzymatic activity.

Protein functions

• Structural support.

• Storage of amino acids.

• Transport of other substances.

• Coordination of an organism’s activities.

• Movement.

• Response to cell to chemical stimuli.

• Protection against diseases.

• Etc.

Metabolites

• A chemical substance produced when the body breaks down food, drugs, chemicals, or its own tissue.

  • Glucose, lactate, fatty acids.

• This process is called metabolism, and it produces energy and materials for growth, reproduction, and maintaining health.

• Categories of molecules that the body uses or produces in metabolic processes:

  • Amino acids, lipids, peptides, nucleic acids, carbohydrates, vitamins, and minerals.

• Proteins function as enzymes in metabolism, catalyzing and regulating the chemical reactions.