!! Basics of Molecular Biology

!! What is bioinformatics

• The science of collecting and analyzing complex biology data.

  • Central dogma of molecular biology: DNA → RNA → protein.

• Transcriptomics:

• Proteomics:

• Metabolomics:

• 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.

Bioinformatics vs. computational biology

• Bioinformatics:

  • Development and application of software tools, algorithms, databases for managing and analyzing biological data

  • Key aspects:

    • Data storage, retrieval, and annotation (e.g., genome databases).

    • Sequence alignment, genome assembly, gene prediction.

    • Emphasis on informatics, data infrastructure, and tool building.

    • More about engineering.

  • Example tasks:

    • Creating a tool for RNA-seq analysis.

    • Developing a database to store DNA sequences.

    • Writing algorithms for DNA sequence alignment.

• Computational biology

  • Using mathematical modeling, theoretical approaches, and computational simulations to understand biological processes.

  • Key aspects:

    • Model biological processes (e.g., protein folding, population dynamics).

    • Systems biology, structural biology, evolutionary biology models,

    • More about discovery, biology-focused and theory-driven,

  • Example tasks:

    • Simulating how a protein folds.

    • Modeling gene regulatory networks.

    • Studying the evolution of genes using computational models.

Brief review of biology

• Modern molecular biology studies a few types of biologically important molecules: DNA, RNA, proteins, and metabolites.

• Most bioinformatics research studied 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: The code of life

• 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.

Bioinformatics and computational biology

• Highly interdisciplinary:

  • Computer science → tools, algorithms.

  • Statistics → numbers (quality control, normalization).

  • Biology → question.

  • Emphasis change over time.

• Applied:

  • From freshman to postdocs.

  • Useful training for biologists.

• Field evolving quickly:

  • Remove microarray.

  • Add scRNA-seq, scATAC-seq, Hi-C.

• Levels:

  • Level 0:

    • Modeling for modeling’s sake.

  • Level 1 (Entry):

    • Use published tools to analyze data and generate hypothesis for experimentalists.

  • Level 2 (Bioinfo):

    • Develop algorithms and databases for data analyses on new technologies, data integration and reuse.

  • Level 3 (CompBio):

    • Make biological discoveries from public data integration and modeling.

  • Level X:

    • Integrative studies from big consortia.

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

• 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.

  • Mosquitos have 3 pairs.

  • Camels have 35 pairs.

  • Adder's tongue ferns have 1440 pairs!

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

  • A sex cell, also called a gamete, is a reproductive cell that carries half the number of chromosomes of a normal (body) cell and is involved in sexual reproduction.

  • Mature red blood cells (RBCs) don’t have any DNA because they eject their nucleus during development.

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.

Genome vs. epigenome

• Genome: the full cookbook (your DNA).

• Epigenome = footnotes in the cookbook telling you which recipes to cook, skip, or adjust

DNAs across individuals are not identical

• 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.

Genetic mutations are not always inherited

• 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.

• The DNA is organized into many sections called genes.

• Each gene contains the instructions a cell needs to make a specific molecule, usually a protein.

  • Human genome usually comprises ~25,000 protein coding genes.

RNA

• 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 RNA.

• Transcription is like photocopying a gene from DNA so the cell can use it to make a protein.

• 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.

  • These complex structures physically move along an mRNA molecule, catalyze the assembly of amino acids into protein chains. They also bind tRNAs and various accessory molecules necessary for protein synthesis.

• Transfer RNA (tRNA):

  • Informational adaptor needed for translation.

  • 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

• After transcription, the sequence we get is called pre-mRNAs.

• It must undergo several processing steps before they are ready to be translated.

• 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,

  • Human can produce 10 of these; the other amino acids are supplied by food (essential 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.

• Types:

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

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

Available data

• Nucleotide sequences.

• Protein sequences.

• Protein structures.

• Genome databases.

• Gene expression.

• Protein expression patterns.

• Metabolic pathways.

• Interactions and regulatory networks.

• Sequence motifs.

• Haplotypes and disease associated mutations.

Human genome

• Human genome has ~ 3 billion (3x10⁹) base pairs (letters).

• A person takes >30 years to read and > 50 years to type these letters.