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BioAtlas

BIO 113 · Fall 2026 · Dr. Chinmay Tikhe

Microbiology,
drawn.

An atlas for BIO 113. The bacterial cell in cutaway, the Gram stain step by step, and every calculation on the syllabus worked out line by line rather than answered.

Start with the cellSit the mock exam
Capsule / slime layerCell wallCytoplasmic membraneCytoplasmNucleoidPlasmidFimbriaeRibosomes (70S)EndosporeInclusionsConjugation pilusFlagellum
Fig. 1A bacterial cell in cutaway, with everything Chapter 3 asks you to name. Not to scale: the cell is about 1 µm long, and the ribosomes are drawn far larger than they are. The full drawing is interactive on the cell page.

This week

Week 3 — Sep 7 – 11

Ch. 3 — Cell Structure and Function

Lab 5 — Gram Stain

Next exam

Exam 1 — 7 days

Wednesday 16 September, 2:30 pm

50 points · Chapters 1–4

The format

35–40 points multiple choice on Canvas under LockDown Browser, 10–15 points of essay written on paper in class.

Hand in the paper part or the Canvas part is not graded either.

What Exam 1 covers

Four chapters. Chapter 2 is chemistry, and it lives on the sister site — everything else is here.

Chapter 1

A Brief History of Microbiology

How we learned that microbes exist and that they cause disease — from Leeuwenhoek’s lenses to Koch’s postulates.

Chapter 2

The Chemistry of Microbiology

Atoms, bonds, water and the four macromolecules, as they matter to a cell.

Covered at chem.rcvbot.xyz.

Chapter 3

Cell Structure and Function

What a bacterial cell is made of, from the glycocalyx down to the nucleoid, and how that differs from a eukaryote.

Chapter 4

Microscopy, Staining, and Classification

Seeing microbes, colouring them so they can be told apart, and naming them.

Everything is drawn, and everything shows its working

No page here tells you an answer without showing how it got there. Reagents in order, colour at each step, and the mechanism underneath.

Open the Gram stain →
Step 1 · Primary stainCrystal violet≈ 1 minuteGram-positiveGram-negative
Everything takes up the primary stain.
Step 2 · MordantGram's iodine≈ 1 minuteGram-positiveGram-negative
Iodine binds the crystal violet into a large complex that cannot slip out through thick peptidoglycan.
Step 3 · DecolouriserAlcohol or acetone10–20 seconds — the critical stepGram-positiveGram-negativeWhere they part
Alcohol dissolves the Gram-negative outer membrane and washes the complex out through its thin peptidoglycan.
Step 4 · CounterstainSafranin≈ 1 minuteGram-positiveGram-negative
Safranin stains anything that lost the crystal violet.
Fig. 2The Gram stain, step by step. Both cell types are identical until the alcohol goes on, which is why step three is the one that goes wrong.

Every page

Fifteen of them, grouped by what they are for.

Cell biology

Bacterial cellEvery structure, labelled, with what it doesProkaryote vs eukaryoteWhat each one has, and what it does not

Microscopy & staining

Gram stainThe four steps, the mechanism, and what goes wrongStaining methodsSimple, negative, differential and structural stainsMicroscopyMagnification, resolution, and the parts of the scopeShape and arrangementCocci, bacilli, spirilla and how they group

Culture & counting

Dilution and plate countsSerial dilutions and CFU per millilitreGrowth and generation timeBinary fission, doubling, and the growth curveCulture mediaGeneral, selective, differential and enriched

Reference

History and KochWho proved what, and the postulatesNaming and classificationDomains, taxa, and how to write a species nameReference sheetsPrintable: structures, stains, media, terms

Practice

DrillRapid recall on the terms and structuresPractice questionsExam-style questions with the reasoning shownMock Exam 1A 50-point paper in the real format, MCQ plus essay

The run-up

Weeks 1 to 4, as the syllabus sets them out. Lecture on the left, lab on the right.

WeekDatesMondayWednesdayLabsDue
1Aug 24 – 28Course introduction; Ch. 1Ch. 1 — A Brief History of MicrobiologyLab 1 — Universal Precautions; Specimen Transport · Lab 2 — Microscopy: Care and Use of the Microscope—
2Aug 31 – Sep 4Ch. 2 — The Chemistry of MicrobiologyActive Learning 1Lab 3 — Cultivation of Microbes; Environment and Skin · Lab 4 — Isolation of Bacteria by Dilution TechniquesHW 1 — Sep 6
3Sep 7 – 11No class — Labor DayCh. 3 — Cell Structure and FunctionNo lab Monday or Tuesday — Labor Day · Lab 5 — Gram StainHW 2 — Sep 13
4Sep 14 – 18Ch. 4 — Microscopy, Staining, and Classification / ReviewEXAM 1Lab 6 — Acid-Fast and Structural Staining · Lab 7 — Morphological Unknown—

Textbook: Bauman, Microbiology with Diseases by Body System, 5th edition. Chapter titles and dates are quoted from the syllabus; the Exam 1 format is quoted from the Week 3 slides.