Computational Biology
Midterm Study Guide

What Is Computational Biology?

Computational biology refers to the use of techniques in computer science, data analysis, mathematical modeling, and computational simulations to understand biological systems and their relationships (NIH BISTI, 2000). It sits at the intersection of computer science, biology, data science, applied mathematics, chemistry, and genetics.

Five Related Fields — Know the Difference

Applications of Computational Biology in Genetics

Biology vs Mathematics — Why Biology Is Different

Biology is dominated by observations; its rules are not yet fully universal, and mathematical representations are still evolving. Unlike math (where operations are precisely defined) or physics (where observations map cleanly to equations), biology requires pattern recognition across messy, context-dependent data. This is exactly why computational methods are so valuable.

Bio-Inspired Algorithms — CS from Biology

Levels of Biological Organization

Unifying Themes in Biology (Campbell Ch. 1)

• Evolution — the overarching framework; natural selection drives diversity.
• Information flow — DNA → RNA → Protein (Central Dogma).
• Energy transformation — all life transforms energy; photosynthesis captures it, cellular respiration releases it.
• Structure & function — form at every level correlates with function (e.g., enzyme active sites, membrane phospholipids).
• Emergent properties — life arises from interaction of non-living components; the whole is greater than the sum of its parts.
• Cell theory — the cell is the fundamental unit of life; all cells come from pre-existing cells.

All living organisms are built from chemicals based mostly on carbon. A compound containing carbon is an organic compound. Carbon's unique ability to form four covalent bonds allows it to build large, complex, varied molecules. The four classes of biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids.

Polymers and Monomers — The Core Concept

1. Carbohydrates (CH₂O)ₙ

Carbohydrates serve as fuel and building materials. Their molecular formula is generally multiples of CH₂O. They are classified by size into monosaccharides, disaccharides, and polysaccharides.

Key Terms

Important Polysaccharides

2. Lipids

Lipids are hydrophobic (water-fearing) molecules. Unlike the other three macromolecules, lipids are not true polymers — they don't form long repetitive chains of identical monomers. They are unified by being mostly nonpolar hydrocarbons that do not mix with water.

3. Proteins

Proteins are the most structurally and functionally diverse macromolecules. They are polymers of amino acids joined by peptide bonds. A protein's specific shape determines its specific function. Proteins carry out virtually every process in a cell.

Functions of Proteins

• Enzymes — biological catalysts that speed up reactions (e.g., amylase, DNA polymerase, ATP synthase).
• Structural — collagen (connective tissue), keratin (hair, nails), actin & myosin (muscle).
• Transport — hemoglobin (O₂), membrane transport proteins, channel proteins.
• Signaling — hormones (insulin), receptors, second-messenger proteins.
• Defense — antibodies (immunoglobulins) bind to foreign antigens.
• Gene regulation — transcription factors bind DNA to turn genes on/off.
• Motor proteins — kinesin, dynein move along cytoskeletal tracks.

Amino Acid Structure

All 20 amino acids share a central α-carbon bonded to: an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen (–H), and a variable R group (side chain). The R group determines the amino acid's chemical properties.

Four Levels of Protein Structure

4. Nucleic Acids — DNA & RNA

Nucleic acids store, transmit, and help express genetic information. They are polymers of nucleotides. Each nucleotide has three components: a 5-carbon sugar (deoxyribose in DNA, ribose in RNA), a nitrogenous base, and a phosphate group. Nucleotides are joined by phosphodiester bonds between the 3'-OH of one sugar and the 5'-phosphate of the next.

Nitrogenous Bases — Base-Pairing Rules

ATP — The Cell's Energy Currency

Adenosine triphosphate (ATP) is a nucleotide (adenine + ribose + 3 phosphates) that is the direct energy currency of all cells. The bond between the second and third phosphate is a high-energy phosphoanhydride bond. Hydrolysis of this bond releases ~7.3 kcal/mol of free energy under standard conditions.

Macromolecule Quick-Reference

Genetics at the molecular level explains how information is stored in DNA, copied faithfully during cell division, and converted into functional proteins. This section covers DNA replication, the Central Dogma (transcription + translation), gene regulation, and mutations — all relevant computational biology targets.

DNA Double Helix — Structure

• Watson-Crick model (1953): Two antiparallel polynucleotide strands coiled around a common axis. One strand runs 5'→3', the other 3'→5'.
• Sugar-phosphate backbones on the outside; nitrogenous bases stacked on the inside, perpendicular to the helix axis (~0.34 nm apart; one full turn = 10 base pairs = 3.4 nm).
• Base pairs stabilized by hydrogen bonds (A=T via 2; G≡C via 3) and by hydrophobic stacking interactions between adjacent base pairs.
• Major and minor grooves: Proteins that interact with DNA (transcription factors, restriction enzymes) typically bind the major groove where base-specific contacts are possible.

DNA Replication — Semiconservative Model

Each new DNA molecule consists of one original (template) strand and one newly synthesized strand — the semiconservative model (confirmed by Meselson-Stahl experiment, 1958).

For a visual overview of the replication process, see this excellent video!

[Video] DNA Replication Animation: https://www.youtube.com/watch?v=TNKWgcFPHqw

Key Enzymes & Proteins

Leading vs Lagging Strand

The Central Dogma of Molecular Biology

Transcription (DNA → mRNA)

Transcription produces an RNA molecule complementary to the DNA template strand (read 3'→5'), building mRNA 5'→3'. It occurs in the nucleus in eukaryotes. The resulting mRNA is the same sequence as the coding strand (except T→U).

1. Initiation: RNA polymerase binds the promoter (in bacteria: –10 and –35 sequences; in eukaryotes: TATA box ~25 bp upstream, recognized by transcription factors). The double helix unwinds locally.
2. Elongation: RNA polymerase moves along template strand 3'→5', synthesizing mRNA 5'→3' at ~40 nt/s. No proofreading mechanism. Ribonucleotides (ATP, UTP, GTP, CTP) are incorporated.
3. Termination: In bacteria: rho-independent (hairpin in mRNA) or rho-dependent termination. In eukaryotes: polyadenylation signal (AAUAAA) followed by cleavage and poly-A addition.

Eukaryotic Pre-mRNA Processing

• 5' Capping: Modified guanosine cap added to 5' end (protects from degradation; aids ribosome recognition).
• 3' Poly-A Tail: ~200 adenine nucleotides added to 3' end (stability; nuclear export signal).
• RNA Splicing: Introns (non-coding intervening sequences) are removed by the spliceosome. Exons (expressed sequences) are joined together. Alternative splicing of the same pre-mRNA can produce different protein isoforms.

Translation (mRNA → Protein)

Translation occurs at the ribosome (large + small subunit). It reads mRNA in the 5'→3' direction, in triplets called codons, to assemble a polypeptide from amino acids delivered by tRNA molecules. The genetic code is redundant (degenerative), universal (with minor exceptions), and unambiguous.

1. Initiation: Small ribosomal subunit binds mRNA at the 5' cap (eukaryotes) or Shine-Dalgarno sequence (bacteria). Initiator tRNA (Met-tRNA) pairs with AUG start codon in the P site. Large subunit joins. GTP hydrolysis used.
2. Elongation: Aminoacyl-tRNA enters the A site; peptide bond forms (peptidyl transferase activity of 23S/28S rRNA is a ribozyme!); ribosome translocates 3 nt in 5'→3' direction; empty tRNA exits via E site.
3. Termination: Stop codon (UAA, UAG, UGA) enters A site; release factor (not tRNA) binds; polypeptide released; ribosome dissociates. Polyribosomes (polysomes) = multiple ribosomes on one mRNA.

tRNA — The Adapter Molecule

tRNA has a cloverleaf secondary structure folded into an L-shape in 3D. The anticodon loop (3 nucleotides) base-pairs with the mRNA codon. The 3' CCA-OH end carries the specific amino acid, attached by aminoacyl-tRNA synthetase (one per amino acid).

Mutations — Types & Consequences

Gene Regulation

Not all genes are expressed at all times in all cells. Gene regulation occurs at multiple levels:

Computational Approaches to Genetics

Sequence Alignment — Key Concepts (Jones & Pevzner)

# Smith-Waterman local alignment (pseudocode)
def smith_waterman(seq1, seq2, match, mismatch, gap):
    H = [[0]*(len(seq2)+1) for _ in range(len(seq1)+1)]
    for i in range(1, len(seq1)+1):
        for j in range(1, len(seq2)+1):
            score = match if seq1[i-1]==seq2[j-1] else mismatch
            H[i][j] = max(
                0,
                H[i-1][j-1] + score,   # diagonal (match/mismatch)
                H[i-1][j]   + gap,      # gap in seq2
                H[i][j-1]   + gap       # gap in seq1
            )
    return H

# De Bruijn graph for genome assembly
# k-mer decomposition of a read
def kmer_decomp(seq, k):
    return [seq[i:i+k] for i in range(len(seq)-k+1)]

# Build De Bruijn graph: nodes=(k-1)-mers, edges=k-mers
def de_bruijn(kmers):
    graph = {}
    for kmer in kmers:
        prefix = kmer[:-1]
        suffix = kmer[1:]
        graph.setdefault(prefix, []).append(suffix)
    return graph

The plasma membrane is a selectively permeable barrier that regulates the passage of substances in and out of the cell. Its structure is described by the Fluid Mosaic Model (Singer & Nicolson, 1972): a fluid phospholipid bilayer with embedded proteins that can move laterally.

Membrane Structure

Passive Transport — No Energy Required

Passive transport moves substances down their concentration (or electrochemical) gradient — from high to low concentration. No ATP needed; driven by thermodynamics (entropy increase).

Osmotic Terminology

Active Transport — Energy Required

Active transport moves substances against their concentration gradient — from low to high concentration. Requires ATP (primary active transport) or an ion gradient (secondary active transport).

Bulk Transport — Moving Large Molecules

Transport Comparison Table

Metabolism is the totality of an organism's chemical reactions. It is organized into metabolic pathways: ordered sequences of reactions, each catalyzed by a specific enzyme, transforming substrates into products. Metabolic pathways are either catabolic (degradation, releasing energy) or anabolic (biosynthesis, requiring energy).

Thermodynamic Foundations

Enzymes — Biological Catalysts

Enzymes are proteins (or ribozymes) that lower the activation energy (Eₐ) of reactions without being consumed. They do not change ΔG or the equilibrium; they only speed the rate at which equilibrium is reached.

Cellular Respiration — Overview

Cellular respiration is the controlled release of chemical energy from organic molecules to produce ATP. In the presence of oxygen (aerobic respiration), glucose is completely oxidized.

Stage 1: Glycolysis (Cytoplasm)

Glucose (6C) is split into two pyruvate (3C) molecules through 10 enzymatic steps. Occurs in cytosol. Requires no oxygen (anaerobic-capable).

Stage 2: Pyruvate Oxidation (Pyruvate Dehydrogenase Complex)

Stage 3: Citric Acid Cycle (Krebs Cycle) — per Acetyl-CoA

Stage 4: Oxidative Phosphorylation (Inner Mitochondrial Membrane)

NADH and FADH₂ donate electrons to the electron transport chain (ETC). Energy released is used to pump H⁺ across the inner mitochondrial membrane, creating a proton gradient (proton motive force). H⁺ flows back through ATP synthase (chemiosmosis), driving ATP synthesis.

ATP Yield Summary (per glucose)

Anaerobic Respiration & Fermentation

When O₂ is absent or insufficient, cells regenerate NAD⁺ from NADH via fermentation — allowing glycolysis to continue producing 2 ATP per glucose.

Photosynthesis — Capturing Light Energy

Photosynthesis converts light energy into chemical energy stored in glucose. Occurs in chloroplasts.

Metabolic Networks & Computational Biology

Metabolism can be modeled as a directed graph where nodes are metabolites and edges are reactions (enzyme-catalyzed). This is the basis of flux balance analysis (FBA) and systems biology tools used to predict metabolic phenotypes.

# Simplified metabolic pathway graph (glycolysis key nodes)
glycolysis = {
    'Glucose':     [('G6P', 'Hexokinase')],
    'G6P':         [('F6P', 'Phosphoglucose isomerase')],
    'F6P':         [('F1,6BP', 'PFK-1')],   # rate-limiting step
    'F1,6BP':      [('DHAP', 'Aldolase'), ('G3P', 'Aldolase')],
    'G3P':         [('1,3-BPG', 'GAPDH')],  # NADH produced here
    '1,3-BPG':     [('3PG', 'Phosphoglycerate kinase')],  # ATP
    '3PG':         [('2PG', 'Phosphoglycerate mutase')],
    '2PG':         [('PEP', 'Enolase')],
    'PEP':         [('Pyruvate', 'Pyruvate kinase')],  # ATP
}

def trace_pathway(graph, start, end, path=[]):
    path = path + [start]
    if start == end: return path
    for (neighbor, enzyme) in graph.get(start, []):
        result = trace_pathway(graph, neighbor, end, path)
        if result: return result
    return None

print(trace_pathway(glycolysis, 'Glucose', 'Pyruvate'))

Quick Recap — 5 Big Ideas

• CompBio is an intersection: CS + math + statistics applied to biological systems. Bioinformatics ≈ using computers to analyze DNA, RNA, proteins and big biological data.
• Four macromolecules: Carbohydrates (CH₂O; energy & structure), Lipids (hydrophobic; membrane & energy storage), Proteins (amino acid polymers; catalysis & structure), Nucleic acids (nucleotide polymers; information). All built by dehydration, broken by hydrolysis.
• Central Dogma: DNA (replication & template) → mRNA (transcription) → Protein (translation). Mutations change sequence; regulation controls when/where/how much.
• Membrane transport: Passive (down gradient: diffusion, osmosis, facilitated diffusion — no ATP) vs. Active (against gradient — requires ATP or ion gradient). Phospholipid bilayer is selectively permeable.
• Metabolism = energy transformation: Glycolysis (2 ATP, cytoplasm, anaerobic) → Pyruvate oxidation → CAC (2 ATP, NADH, FADH₂) → Oxidative phosphorylation (~26–28 ATP via chemiosmosis, inner mitochondrial membrane). Total: ~30–32 ATP/glucose.