mince sec 1

scientific method

meaning of each

flow

pasteur example of scientific method flow

Scientific method = scientific method is used to test a hypothesis based on observations, and a valid hypothesis must be testable. peer review and good science must be reproducible by other scientists

Term	Detailed meaning	Microbiology example
Observation	Something noticed in the world.	Broth becomes cloudy after sitting out, maggots on meat
Question	What you ask based on the observation.	Did microbes appear spontaneously, or did they enter from outside?
Hypothesis	A testable explanation. that you can support or reject w/ evidence	Microbes come from contamination in the air.
Prediction	What should happen if the hypothesis is true.	If dust/microbes are blocked but air enters, broth should stay clear.
Experiment	A controlled test of the hypothesis.	Pasteur’s swan-neck flask experiment.
Control	A comparison condition. shows what happens w/out tested change	Flask with intact neck vs flask with broken neck. a variable is any factor that can change or be changed, while a control (or controlled variable) is a factor kept intentionally constant to ensure a fair test. Variables drive the action and measurement of the test, while controls keep the test accurate and reliable
Variable	The factor being changed.	Whether microbes can physically reach the broth.
Data/evidence	The results observed.	Clear broth = no microbial growth; cloudy broth = growth.
Conclusion	What the evidence supports.	Microbes come from existing microbes, not spontaneous generation.

Flow chart:
observation → question → hypothesis → prediction → controlled experiment → data → conclusion → accepted/rejected explanation

Applied to Pasteur:
broth can grow microbes → ask where microbes come from → test air vs contamination → boil broth → allow air but block dust/microbes → broth stays clear → conclusion: air alone does not create life; microbes come from other microbes

Topic 1: Scientific Method, Early Microbiology, Golden Age, Epidemiology

what did the humans notice about food? what did they say about them?

which tool and how were they cleared of those misconceptions

which microbiologists (3 main) build germ theory

epidemiology

Humans noticed disease, death, food spoilage, and fermentation
→ they made early explanations like miasma, witchcraft, humors, and spontaneous generation
→ microscopes revealed an invisible microbial world
→ experiments showed that microbes come from preexisting life, not nonliving matter
→ Pasteur, Lister, and Koch helped build germ theory
→ epidemiology used disease patterns in populations to stop outbreaks.

what were the early beliefs about diseases like smallpox, malaria, influenza, and bubonic plague shaped human history, but people did not know what caused them?

8 reasons

flow chart

Term	Detailed meaning
Infectious disease	Disease caused by a pathogen that can enter the body, multiply, and cause harm.
Pathogen	A disease-causing microbe or infectious agent.
Miasma theory	Old idea that disease came from “bad air” or foul smells from rotting matter, sewage, or swamps. It was wrong, but it sometimes led to useful sanitation because removing filth also removed pathogens.
Malaria	The word comes from “bad air,” which reflects miasma theory. The disease is actually caused by a protozoan parasite transmitted by mosquitoes.
Humor theory	Old idea that disease came from imbalance in body fluids called humors. This was not correct but was historically important.
Witchcraft/supernatural causes	Some people believed disease was caused by curses, spirits, or punishment rather than natural causes.
Contagion	The idea that disease can spread from one person, object, or environment to another.
Sanitation	Practices that reduce exposure to waste/pathogens, such as clean water, sewage control, and handwashing.

people see disease spreading→ they do not know about microbes→ they explain disease using bad air, witchcraft, or humors→ cities improve sanitation partly because of miasma beliefs → later germ theory explains the real cause: pathogens

fermentation

flow chart

examples

why matters ? regarding germ theory and pasteur’s work

flow chart

Fermentation

Fermentation = a microbial process where organisms such as yeast, bacteria, or molds break down sugars and produce products like alcohol, acids, gases, and flavor compounds.

Flow chart:
sugar/carbohydrate in food → yeast/bacteria metabolize sugar → alcohol/acid/CO₂ forms → food changes taste, texture, preservation

Examples:
flour sugar → yeast → CO₂ → bread rises
milk sugar → bacteria → lactic acid → yogurt/cheese forms
grape sugar → yeast → ethanol → wine forms

Why it matters: because Pasteur studied fermentation and spoilage first. That helped him later propose that if microbes can cause changes in food, they might also cause disease.

fermentation/spoilage work → microbes cause chemical changes → microbes can contaminate materials → microbes may cause infection → germ theory

early microscopes

2 people

Robert Hooke, Antonie van Leeuwenhoek

Person	What he saw	Main importance
Robert Hooke	Cork compartments	Coined/used the term cells
Antonie van Leeuwenhoek	Living microbes/animalcules	First clear observations of microbes like bacteria/protists

Robert Hooke was an early microscopist who looked at thin slices of cork and used the word cells to describe the tiny compartments he saw. The lecture slide says he was the first to view and refer to “cells” as the tiniest components of life.

Important detail: Hooke was looking at dead cork cells, so he saw cell walls/empty chambers, not living internal cell activity.

Flow:
thin cork slice → microscope → box-like compartments → Hooke calls them “cells” → later cell theory develops

Antonie van Leeuwenhoek built powerful simple microscopes as a hobby and observed tiny living organisms. His lecture slide mentions that he looked at plaque, blood, capillaries, lymph vessels, and more.

OpenStax says Leeuwenhoek observed single-celled organisms in rainwater and called them animalcules or “wee little beasties”; based on his drawings, he was seeing bacteria and protists.

Flow:
better microscope → invisible organisms become visible → animalcules observed → microbial world becomes real → microbiology becomes possible

Contagion

importance

flow

Contagion = the idea that disease can spread from one person, object, or environment to another.

important because it pushed people toward quarantine, sanitation, and isolation even before germ theory was fully accepted.

Flow chart:
sick person/object/environment → invisible disease-causing factor spreads → new person becomes sick → people try containment

containment

flow chart

Containment = actions used to limit disease spread. Historically, this included quarantine, separating sick people, sanitation, and clean water systems.

Flow chart:
disease appears → people suspect spread → isolate sick people / improve sanitation / avoid contaminated sources → fewer new cases

Miasma theory

how did it help w/ reducing disease ?

flow chart

Miasma theory = the old idea that disease came from “bad air” or foul-smelling vapors from rotting matter, sewage, or swamps. I

wrong about the cause, but it sometimes led to useful sanitation practices because removing sewage and improving air/water quality really can reduce disease.

Flow chart:
rotting waste smells bad → people think bad air causes disease → they improve sanitation → disease may decrease, but the real reason is fewer pathogens/contaminated sources

Hippocrates

what he contributed to?

why it matters

Argued disease had natural causes, not supernatural causes.

Moves medicine toward observation and environment/body-based explanations.

Thucydides

what he contributed to?

why it matters

Noticed survivors of plague did not get reinfected while caring for sick people.

Early observation related to immunity.

Varro

what he contributed to ?

why it matters

Suggested invisible “minute creatures” from swamps could enter through mouth/nose and cause disease.

Early idea close to invisible microbes causing disease.

al Razi / Rhazes

what he contributed to? (3)

why it matters ?

Used experimental thinking in medicine; distinguished measles and smallpox; tested treatments.

Early evidence-based medicine.

Ibn Sina / Avicenna

whaty he contributed to ?

why it matters?

Described contagion and isolation of sick people.

Early foundation for quarantine/contagion thinking.

Birth of microbiology by who ?

what he found?

what are animalcules

flow

Antonie van Leeuwenhoek

Antonie van Leeuwenhoek used powerful simple microscopes and saw tiny living things in water, which he called animalcules. From his drawings, we now know he saw bacteria and protists. This matters because before microscopy, microbes were only suspected; after microscopy, invisible life became observable.

animalcules: Leeuwenhoek’s name for tiny organisms he observed

flow:

microscope improves → tiny organisms become visible → “animalcules” observed → invisible world becomes real → microbiology can become experimental science

when and what was golden age of microbio

2 most important figures

flow microscope —> vaccines

Golden Age of Microbiology = roughly 1857–1914, when scientists made major discoveries linking microbes to fermentation, spoilage, disease, vaccines, and laboratory methods. OpenStax specifically emphasizes Louis Pasteur and Robert Koch as central figures.

Pasteur’s Germ theory

microscopes reveal microbes→ fermentation/spoilage linked to microbes→ microbes linked to disease→ antiseptics reduce infections→ specific pathogens linked to specific diseases→ vaccines and public health improve

Louis Pasteur

what he did (6)

flow

Pasteur was a French chemist. His importance is that he connected microbes to real processes: fermentation, spoilage, spontaneous generation, pasteurization, vaccines, and germ theory.

Contribution	Detailed meaning
Fermentation	Showed fermentation is caused by microorganisms, not just random chemical change.
Spoilage	Showed microbes can spoil wine/beer/food.
Swan-neck flask	Disproved spontaneous generation by showing sterilized broth stays sterile unless microbes enter.
Pasteurization	Developed briefly heating method to kill spoilage microbes without fully sterilizing the liquid = liquid lasts longer / disease transmission through contaminated liquid decreases
Vaccines	Worked on vaccines, including rabies.
Germ theory support	If microbes cause spoilage/fermentation, they may also cause infection/disease.

flow:

wine/beer spoils → Pasteur investigates → microbes are present → microbes cause fermentation/spoilage → heating can kill unwanted microbes → pasteurization protects products —> microbes can also explain infection → germ theory strengthened

Joseph Lister

what he did

what he introduced / brought to the table

define antiseptic , disinfectant , carbolic acid/ phenol, post surgical infection

flow

Joseph Lister applied Pasteur’s work to surgery.

If microbes in air/on hands/on instruments can contaminate wounds, then killing or reducing microbes should reduce surgical infection

pplied Pasteur’s work showing microbes are in the air and introduced chemical disinfectants, especially carbolic acid/phenol, to reduce surgical infections.

OpenStax adds that Lister insisted on handwashing and cleanliness and began using carbolic acid spray in 1867 to reduce postsurgical wound infections.

Term	Meaning
Antiseptic	Chemical used on living tissue to reduce microbes.
Disinfectant	Chemical used on nonliving surfaces to reduce microbes.
Carbolic acid / phenol	Chemical Lister used to reduce microbial contamination during surgery.
Postsurgical infection	Infection that occurs after surgery, often because microbes enter wounds.

surgery opens body tissues→ microbes from hands/tools/air can enter wound→ wound infection develops→ Lister uses cleanliness + phenol/carbolic acid→ fewer microbes enter wound→ postsurgical infections decrease

Robert Koch

what he did (5)

flow

bacteriology, causative agent, etiologic agent, pure culture, inoculation, susceptible host

Father of modern bacteriology

Koch was a German physician. His importance is that he showed specific microbes cause specific diseases

found causative pathogens/

etiologic agent (the specific microbe/ factors causing disease) of anthrax, TB, Cholera

Contribution	Detailed meaning
Pure culture logic	Needed to isolate one microbe type to connect it to one disease.
Anthrax	Identified Bacillus anthracis as the cause of anthrax.
Tuberculosis	Identified Mycobacterium tuberculosis.
Cholera	Identified Vibrio cholerae.
Koch’s postulates	Rules for proving that a specific pathogen causes a specific disease.

flow

disease observed → suspected microbe found → isolate/grow microbe → test disease causation → same microbe recovered → specific pathogen linked to disease

Term	Meaning
Bacteriology	Study of bacteria.
Causative agent	The organism or factor that causes a disease.
Etiologic agent	The specific microbe or factor causing the disease/pathogen responsible.
Pure culture	A lab culture containing only one type/species of organism.
Inoculation	Introducing a microbe into a host or growth medium.
Susceptible host	A host that can become infected/diseased by that pathogen.

Spontaneous generation vs biogenesis

what was it ?

examples ? why people believed it

flow

Biogenesis and flow

Spontaneous generation

Spontaneous generation = the old belief that living organisms can arise from nonliving matter.

Examples people believed:
maggots appear from rotting meat
mice appear from old grain/rags
microbes appear from broth

Why people believed it:
They saw organisms “appear” after time passed, but they did not see the eggs, microbes, spores, or contamination that caused them

Flow:
nonliving material sits out → living things appear → people assume life came from nonliving matter

Biogenesis

Biogenesis = life comes from preexisting life.

Flow:
flies lay eggs → maggots hatch
airborne microbes enter broth → microbes grow
cells come from cells

Term	Detailed meaning
Spontaneous generation	Old hypothesis that life can arise from nonliving material. Example: maggots arise from meat, microbes arise from broth.
Vital force	Supposed invisible life-producing force believed to make nonliving matter become alive.
Biogenesis	Life comes from preexisting life. Cells come from cells; microbes come from other microbes.
Falsified hypothesis	A hypothesis shown to be wrong by evidence. Spontaneous generation was falsified.

Aristotle and van Helmont

what theyt suggested

flow

Aristotle supported spontaneous generation, arguing life could arise from nonliving matter if some “vital force” was present. van Helmont later proposed that mice could arise from wheat and dirty rags.

flow

stored grain/rags → mice appear → wrong conclusion: mice formed from material → real explanation: mice were attracted to food/shelter

experiments that challenged spontaneous generation ? name them (4 microbiologist’s)

Redi, Needham, Spallanzani, Pasteur: experiment sequence

set up , result and what it meant

Redi flow

Needham flow and problem VS Spallanzani flow and conclusion

why was Pasteur stronger, flow

Redi’s meat experiment, Needham’s broth, Spallanzani’s sealed flasks, and Pasteur’s swan-neck flask as the key experimental sequence for this debate.

Redi disproved maggots-from-meat. Spallanzani challenged microbes-from-broth. Pasteur definitively disproved spontaneous generation with swan-neck flasks.

Scientist	Setup	Result	What it meant
Francesco Redi	Meat in open jars, sealed jars, and gauze-covered jars.	Maggots appeared only where flies could access meat or lay eggs.	Maggots come from flies, not meat.
John Needham	Briefly boiled broth, then sealed it. not boiled enough to kill all preexisting microbes	Broth became cloudy with microbes.	He argued microbes arose spontaneously.
Lazzaro Spallanzani	Boiled broth longer; kept some flasks sealed and some open.	Sealed boiled broth stayed clear unless opened.	Microbes came from air/contamination, not spontaneous generation.
Louis Pasteur	Boiled broth in swan-neck flasks that allowed air in but trapped dust/microbes.	Broth stayed sterile unless neck was broken/tilted so trapped microbes reached broth.	Definitively disproved spontaneous generation.

Redi flow

meat placed in jars → flies can enter open jar → flies lay eggs → maggots appear
sealed/gauze jars block flies → no maggots on meat → conclusion: maggots come from flies

Exam trap: Gauze allowed air but blocked flies. That matters because supporters of spontaneous generation could not just say “air was missing.”

Needham vs Spallanzani flow

Needham:

broth briefly boiled → sealed → later cloudy → Needham says spontaneous generation

Problem:
brief boiling may not kill all microbes/endospores → surviving microbes grow → cloudy broth

Spallanzani:

broth boiled longer → sealed flask stays clear → opened flask becomes cloudy → microbes entered from air
Needham’s criticism: extended boiling destroyed “life force,” and sealing prevented new life force from entering.

Pasteur flow

broth boiled → swan neck lets air enter → curved neck traps dust/microbes → broth stays clear → neck broken/tilted → microbes reach broth → broth becomes cloudy

Concluded: microbes came from contamination, not a life force.

Why Pasteur’s design was stronger: it allowed air in but blocked microbes, so it answered Needham’s “life force in air” objection.

Describe two contradictory hypotheses. Which was falsified, and what experiment/who did this work?

The two contradictory hypotheses were spontaneous generation and biogenesis. Spontaneous generation claimed that living organisms arise from nonliving matter through a vital force, while biogenesis claimed that living organisms arise from preexisting life. Spontaneous generation was falsified by Louis Pasteur’s swan-neck flask experiment, which showed that sterilized broth stayed sterile when air could enter but microbes were blocked.

cell theory as bridge to biogenesis

what did each if them did Robert Hooke, Schleiden, Schwann, remake, Virchow

why this matters?

cells are fundamental units of organisms, and all cells come from other cells,

Person	What she should know
Robert Hooke	First used the word “cells” after looking at cork.
Schleiden	Plants are made of cells.
Schwann	Animals are made of cells.
Remak	Published evidence that cells come from other cells.
Virchow	Popularized “all cells arise from cells.”

Why this matters for spontaneous generation:
If cells come from cells, then living microbes do not just appear from nonliving broth. They come from preexisting cells or spores.

Miasma theory vs germ theory

flow

how was it helpful

germ theory

flow

Miasma theory

Miasma theory = disease comes from bad air or vapors from rotting organic matter, sewage, swamps, or filth.

Flow:
rotting matter/sewage → bad smell → people believe bad air causes disease

It was wrong, but not completely useless: cleaning sewage and improving sanitation can reduce disease because it removes pathogens, even if people had the wrong mechanism

Germ theory

Germ theory of disease = some diseases are caused by microorganisms infecting the body.

Flow:
pathogenic microbe enters host → microbe grows/damages tissue/produces toxins → signs and symptoms appear → disease spreads to others

OpenStax explains that miasma theory was widely accepted until the 19th century, when the work of people like Semmelweis, Snow, Pasteur, Lister, and Koch supported germ theory.

germ theory

flow

what each of these did ? flow

Girolamo Fracastoro

Ignaz Semmelweis

John Snow

Louis Pasteur

Joseph Lister

Robert Koch

Germ theory of disease = the idea that many diseases are caused by microorganisms entering the body, multiplying, damaging tissues, or producing toxins.

Semmelweis and Snow showed sanitation could prevent infection, while Pasteur, Lister, and Koch strengthened germ theory by connecting microbes to spoilage, infection, antisepsis, and specific diseases.

flow:

microbes exist→ microbes can contaminate food/wounds/water→ microbes can multiply→ microbes can cause disease→ sanitation, handwashing, antiseptics, pasteurization, and vaccines can prevent disease

Person	Detailed explanation	Flow chart
Girolamo Fracastoro	Early proposed that disease could spread by seed-like particles through contact, contaminated objects/clothing, or air. This was an early germ-theory-like idea, but it was not widely accepted then.	infectious “seeds” → contact/objects/air → new person sick
Ignaz Semmelweis	Noticed physicians/medical students went from autopsies to childbirth exams without washing hands. Maternal death from puerperal fever was much higher in physician wards than midwife wards. Handwashing with chlorinated lime greatly reduced mortality.	autopsy material on hands → exams on patients → puerperal fever → handwashing w/ chlorinated lime removes agent → deaths drop
John Snow	Tracked cholera cases in London and connected them to contaminated water, especially the Broad Street pump. Removing the pump handle helped stop the outbreak.	cholera cases mapped → cluster near pump → water source suspected → pump handle removed → outbreak controlled
Louis Pasteur	Showed microbes cause fermentation/spoilage and argued microbes could also cause infection. His swan-neck flask work destroyed spontaneous generation.	microbes cause spoilage → microbes can enter from environment → microbes can cause disease
Joseph Lister	Applied germ theory to surgery. Used handwashing, cleanliness, and carbolic acid/phenol antiseptic spray to reduce postsurgical infections.	surgery opens tissue → microbes contaminate wound → antiseptic kills/reduces microbes → fewer infections
Robert Koch	Developed postulates to prove a specific microbe causes a specific disease. Identified agents of anthrax, TB, and cholera.	specific disease → isolate microbe → culture → infect host → recover same microbe

John Snow

what did he do? what disease is he linked to?

flow

why can epidemiology save lives? regarding this case

John Snow tracked a cholera outbreak in London to the Broad Street pump, and cases diminished after he removed the pump handle.

Snow traced cholera outbreaks to sewage-contaminated water sources, demonstrating waterborne transmission and producing one of the first known epidemiological studies/public health responses

people die of cholera→ Snow maps deaths→ cases cluster near Broad Street pump→ pump water suspected→ pump handle removed→ people stop using contaminated water→ cases diminish

Snow did not originally know the full microbial cause, but his pattern analysis still helped stop transmission. That is why epidemiology can save lives even before the mechanism is fully proven

Semmelewis

what he did and what disses did he link it to?

hildbed fever / puerperal , incidence, antiseptic hand washing, transmission

flow

scientific method version

physicians and medical students moved from autopsies to childbirth exams without washing, Semmelweis suspected they transferred the causative agent, and chlorinated lime handwashing lowered physician-ward mortality to the midwife-ward rate.

Term	Meaning
Childbed fever / puerperal fever	Infection after childbirth; lecture connects it to Streptococcus pyogenes.
Incidence	New cases in a time period.
Antiseptic handwashing	Chemical handwashing to reduce microbes on hands.
Transmission	Movement of a pathogen from source to host.

flow:

physicians perform autopsies→ invisible infectious material remains on hands→ physicians examine childbirth patients→ patients develop childbed fever→ Semmelweis requires chlorinated handwashing→ infectious material reduced→ childbed fever deaths drop

scientic method version:

Observation: physician-attended patients died more often than midwife-attended patients
→ Hypothesis: physicians were transferring something from autopsies to patients
→ Experiment: require antiseptic/chlorinated handwashing
→ Data: infection/mortality rates dropped greatly
→ Conclusion: handwashing prevents disease transmission.

Koch’s postulates

4 steps

flow

what diseases did he link to?

association vs causation

limitations to it (7)

Koch’s postulates = a step-by-step test to prove that a specific microbe causes a specific disease.

Step	What it means
1	The suspected pathogen should be found in sick organisms and absent from healthy ones.
2	The pathogen should be isolated and grown in pure culture.
3	The cultured pathogen should cause the same disease when introduced into a healthy susceptible host.
4	The same pathogen should be recovered from the newly diseased host.

Flow chart:
sick host has suspected microbe → isolate it → grow pure culture → introduce into healthy host → same disease appears → reisolate same microbe

Koch moved microbiology from “microbes are associated with disease” to microbes can be proven to cause disease. OpenStax notes that Koch’s work linked diseases such as anthrax, tuberculosis, and cholera with specific causative agents

Association is not causation. Seeing a microbe near a disease is not enough. Koch’s postulates try to prove causation.

Exceptions/ Limitations :

• Some pathogens cannot be grown in pure culture.

• Some diseases are caused by viruses, which require host cells.

• Some pathogens only infect humans, so testing in healthy hosts can be unethical.

• Some people can carry pathogens without symptoms/ Asymptomatic carriers

• Some diseases are caused by multiple factors.

• One pathogen = many diseases may cause different disease syndromes depending on body site. Example from transcript: Streptococcus pyogenes can cause strep throat, scarlet fever, necrotizing fasciitis, childbed fever, etc.

• Different pathogens can cause similar diseases, like cold-like symptoms from different viruses.

Molecular Koch’s postulate

example

flow

molecular Koch’s postulates demonstrate that a gene responsible for virulence in a strain is the causative agent of disease.

example: some E. coli strains are harmless in the gut, but disease-causing strains may have extra virulence genes, such as toxin genes.

bacterial strain has virulence gene→ disease occurs→ remove/inactivate gene→ disease decreases→ restore gene→ disease returns→ gene supports virulence

epidemiology

flow

Population

Etiology

Etiologic agent / causative agent

Transmission

Morbidity

Mortality

Incidence

Prevalence

Incidence vs prevalence flow:

Epidemiology = the study of how disease occurs, spreads, and is maintained in populations, with the goal of recognizing and controlling outbreaks.

flow:

people get sick → cases are counted → patterns are mapped by person/place/time → source/transmission is suspected → studies test the cause → public health action controls spread

Term	Detailed meaning
Population	The group at risk for the disease. It can be a city, school, hospital, age group, behavior group, etc.
Etiology	The cause of disease. In infection, this often means the pathogen responsible.
Etiologic agent / causative agent	The specific microbe or factor causing the disease.
Transmission	How a disease spreads from source to host.
Morbidity	Illness burden: how much disease exists in a population.
Mortality	Death burden: how many people die from the disease.
Incidence	Number/rate of new cases in a time period.
Prevalence	Number/rate of total existing cases at a time or during a period.

Incidence vs prevalence flow:
new diagnoses this month = incidence
everyone currently living with the disease = prevalence

Memory:
Incidence = incoming new cases.
Prevalence = present total cases.

Epidemiology vs Clinical Trial

main goal, groups, examples, main limitation, important time

flow

epidemiological studies look for associations in populations, while clinical trials set up defined groups and test an intervention.

Feature	Epidemiological study	Clinical trial
Main goal	Find patterns/associations in populations	Test whether an intervention works
Groups	Often naturally occurring groups	Usually assigned control vs experimental groups
Example from lecture	Smoking vs cancer; vaccination status vs disease rate	New headache medicine vs placebo/aspirin
Main limitation	Association does not always prove cause	Stronger for testing cause/effect if well designed
Important term	Association	Double-blind/placebo/control

Epidemiology:
observe population pattern → compare groups → find association → generate/test hypothesis

Clinical trial:
choose matched groups → give treatment/placebo → blind if possible → compare outcomes → decide if treatment works

what is one Epidemiology limitation

can it tell the cause of the disease

Cholera vs Zika virus examples

assosiation, causation , causative agent, correlation

Assosiation is not Causation

epidemiology can help stop disease spread, but it does not always tell the cause. It gives two examples: John Snow was right about cholera water but did not know why, and microcephaly appeared in areas where Zika virus was epidemic, but that alone did not prove Zika was the causative agent.

Term	Meaning
Association	Two things occur together more than expected.
Causation	One thing actually causes the other.
Causative agent	The pathogen/factor responsible for disease.
Correlation	Pattern where variables change together; does not automatically prove cause.

Zika outbreak + microcephaly increase→ association noticed→ lab studies needed→ if virus damages developing neurons, causation becomes stronger

4 disaese pattern

Sporadic

Endemic

Epidemic

Pandemic

flow

Term	Meaning	Example-style idea
Sporadic	Occurs occasionally, irregularly, scattered.	Rare scattered plague cases.
Endemic	Constantly present in a region/population.	Malaria in some regions.
Epidemic	More cases than expected in a region/time.	Unusually high flu cases.
Pandemic	Epidemic spread across countries/continents/worldwide.	HIV/AIDS, pandemic influenza, COVID-like coronavirus spread.

Flow:
(occur rarely without a geographic focus)scattered rare cases = sporadic → constant local presence = endemic → sudden above-normal regional rise = epidemic → worldwide spread = pandemic

public health cdc nndss, mmwr

what does each one of these do?

Public health

CDC

NNDSS

Notifiable/reportable disease

MMWR

Surveillance

flow

CDC oversees the National Notifiable Disease Surveillance System, where important diseases must be reported, and the CDC publishes updates in the Morbidity and Mortality Weekly Report.

Term	Meaning
Public health	Organized effort to protect the health of populations, not just one patient.
CDC	U.S. agency focused on disease control/prevention.
NNDSS	System for tracking nationally notifiable diseases.
Notifiable/reportable disease	Disease that legally must be reported to public health agencies.
MMWR	CDC report that updates disease trends and public health information.
Surveillance	Ongoing collection and analysis of disease data.

Flow:
doctor diagnoses reportable disease → case reported to public health → data enters surveillance system → CDC/state monitors trends → MMWR/public alerts guide action

epidemeology pioneers

John snow

flow

Florence Nightingale

John Snow

John Snow is called the father of epidemiology because he traced the 1854 London cholera outbreak to contaminated water from the Broad Street pump. OpenStax says he mapped cholera incidence, linked cases to water sources, and removal of the pump handle helped contain the epidemic.

Flow:
cholera outbreak → map cases → cases cluster around Broad Street pump → contaminated water suspected → pump handle removed → outbreak contained

Florence Nightingale

Nightingale collected and graphed death/cause data during the Crimean War. Her importance is careful recordkeeping + data visualization to identify preventable causes of death.

Flow:
soldiers dying → collect cause-of-death data → display patterns visually → sanitation/hospital conditions implicated → reforms reduce deaths

disease spread in epidemiology

Common source spread

Point source spread

Continuous common source

Intermittent common source

Propagated spread

Type	Meaning	Flow
Common source spread	Many people infected from one shared source.	contaminated source → many people exposed → many cases
Point source spread	Common source exposure occurs for a short time.	bad potato salad at picnic → people eat it → outbreak spike
Continuous common source	Source exposes people over a longer time.	contaminated water supply → repeated exposure → ongoing cases
Intermittent common source	Source appears/disappears.	well contaminated after rain → cases rise → source clears → later rain contaminates again
Propagated spread	Person-to-person spread; each case can infect others.	person 1 sick → person 2 sick → person 3 sick → outbreak continues

If removing one source stops the outbreak, think common source.
If sick people keep infecting new people, think propagated spread

epidemology study types (3)

flows

questions asked

analytical epidemology subtypes (5)

experimental (placebo, double blind study, bias, placebo effect)

Descriptive epidemiology

Analytical epidemiology

Experimental epidemiology / Clinical trials

Descriptive epidemiology = describing the pattern of the disease ,

first stage of outbreak investigation: describe who, where, and when.

Flow:
cases appear → interview patients → map locations → record timing → look for shared pattern → generate hypothesis

Questions asked:

• Who got sick?

• Where did they go?

• What did they eat/drink?

• When did symptoms start?

• Who did they contact

Analytical epidemiology = tests possible causes by comparing groups.

Flow:
hypothesis formed → compare exposed vs unexposed or sick vs not sick → look for association → support/reject suspected source

examples:

smokers vs nonsmokers → cancer rates
vaccinated vs unvaccinated → disease incidence
cell phone use vs brain cancer

subtypes

Study	Meaning
Retrospective	Looks backward at past exposures of people who are already sick.
Prospective	Follows people forward over time to see who becomes sick.
Cohort study	Follows a group with a shared characteristic/exposure.
Case-control study	Compares sick people to similar non-sick people.
Cross-sectional study	Looks at a population at one point in time; useful for prevalence.

Experimental epidemiology/ clinical trials = researcher manipulates something, like giving a treatment or intervention, and compares outcomes.

Flow:
group A gets treatment/intervention → group B gets placebo/no treatment →or blinded if possible → compare outcomes → determine whether intervention worked

Term	Meaning
Placebo	Fake treatment with no active ingredient.
Double-blind study	Neither subjects nor researchers know who got treatment vs placebo.
Bias	Systematic error that can distort results.
Placebo effect	Improvement because someone believes they received treatment, not because the treatment itself worked.

Coronavirus

flow

Respiratory transmission

Zoonotic spillover

Outbreak

Epidemic

Pandemic

Surveillance

Coronavirus = enveloped RNA virus group; some cause respiratory disease.

Flow:
respiratory virus emerges → people develop symptoms → cases reported → epidemiologists track person/place/time → outbreak classified → public health measures used

Term	Meaning
Respiratory transmission	Spread through droplets/aerosols/close contact.
Zoonotic spillover	Pathogen moves from animals into humans.
Outbreak	More cases than expected in a specific place/time.
Epidemic	Regional above-expected spread.
Pandemic	Global spread.
Surveillance	Monitoring cases to detect and control spread.

origins of microbial life

Prebiotic

Sterile

Primordial soup

Inorganic substrates

Biological molecules

Early Earth was prebiotic, meaning before life. The slides describe it as hot, volcanic, and “nasty.”

Term	Detailed meaning
Prebiotic	Before life existed. means early Earth had no living organisms yet, but had chemical conditions that could eventually lead to life.
Sterile	No living organisms present. Early Earth is described as sterile/prebiotic.
Primordial soup	The mixture of early Earth chemicals plus energy sources that may have allowed biological molecules to form. It is not literal soup; it is a model for early chemical conditions.
Inorganic substrates	Simple nonliving chemicals present before life, such as gases and minerals, that could become building blocks for biological molecules.
Biological molecules	Molecules associated with life, such as amino acids, nucleotides, sugars, and lipids.

earth is about how many years old? when was life existed? large macroscopic life ?

main timelines

earth forms

life present

large macroscopic life

humans

flow chart

Earth is about 4.5–4.9 billion years old, life has existed for at least 3.5 billion years, and large macroscopic plants/animals have existed for about 900 million years.

Event	Approximate time
Earth forms	4.5–4.9 billion years ago
Life present	at least 3.5 billion years ago
Large macroscopic life	about 900 million years ago
Humans	very recent compared with microbial life

early Earth forms→ hot, volcanic, meteor impacts, storms→ no life yet = prebiotic→ simple chemicals present→ energy from heat/lightning/radiation→ biological molecules may form→ eventually first self-replicating systems/cells appear.

Miller Urey experiment

what they did

what did they not prove

flow

The Miller-Urey experiment tested whether early Earth-like conditions could produce biological molecules from simple nonliving chemicals

simulation of early Earth and found it is possible to produce biological molecules from likely inorganic substrates, but it was not necessarily exactly how life actually began.

Miller-Urey did not prove exactly how life began. It showed that biological molecules can form from simple inorganic molecules under early Earth-like conditions

simple early Earth chemicals→ exposed to heat + electrical sparks→ chemical reactions occur→ organic molecules form→ amino acids/biological building blocks detected→ supports the idea that life’s building blocks could form naturally.

RNA world hypothesis

what it is

why it matters? (2)

RNA

Nucleotide

Base pairing

Template

Replication

Mutation

Ribozyme

Genetic code

flow charts

why is RNA a good candidate

limitations

RNA World Hypothesis = early life may have started with RNA or RNA-like molecules that could store information and help catalyze reactions before DNA/proteins became dominant.

matters because modern RNA has two life-like roles:

RNA ability	Why it matters
Stores genetic information	RNA has a sequence of bases, so it can carry information.
Can catalyze reactions	Some RNA molecules, called ribozymes, can act like enzymes.

Term	Detailed meaning
RNA	Ribonucleic acid; a nucleic acid made of nucleotides. In modern cells, it helps connect DNA instructions to protein production.
Nucleotide	Building block of RNA/DNA. In RNA, the bases are A, U, C, and G.
Base pairing	Specific matching of bases: A pairs with U, and G pairs with C in RNA.
Template	A strand that guides formation of a complementary strand.
Replication	Copying genetic information.
Mutation	Random change in genetic sequence.
Ribozyme	RNA molecule that can catalyze a chemical reaction.
Genetic code	The information system that connects nucleic acid sequences to protein building.

early Earth chemistry produces random RNA-like chains→ some chains base-pair with free nucleotides→ complementary copies form→ occasional mutations occur→ some RNA shapes work better than others→ natural selection acts on replicating molecules→ RNA systems become more complex→ eventually DNA/protein/cell systems evolve

good candidate b/c:

RNA can carry information like DNA→ RNA can fold into shapes like proteins→ some folded RNAs become ribozymes→ ribozymes can help chemical reactions→ that gives a possible bridge from chemistry to early biology.

limitations:
The RNA World Hypothesis is a hypothesis, not fully proven. The lecture video emphasized that scientists still do not know every detail, especially how early RNA replication would happen without modern enzymes.

where did life originate: (3 reasons )

3 hypothesis main idea, why they consider it,

LUCA

LUCA flow chart

origin location flow chart

three possibilities: hydrothermal vents, warm little ponds, or life originating somewhere other than Earth.

Hypothesis	Main idea	Why scientists consider it	What she should remember
Hydrothermal vent hypothesis	Life began near deep-sea vents.	Vents provide heat, minerals, chemical gradients, and protected environments.	Current lecture says LUCA gene evidence points toward deep-sea hydrothermal vents, but it is not certain.
Warm little pond hypothesis	Life began in shallow surface ponds.	Wet-dry cycles could concentrate molecules and help RNA polymers form.	Darwin’s “warm little pond” idea; drying and re-wetting could help build polymers.
Panspermia	Life or life-building materials came from outside Earth.	Meteorites can contain organic molecules; life might be older than Earth.	It does not explain the ultimate origin of life; it only moves the origin elsewhere.

LUCA = Last Universal Common Ancestor.
It means the ancestral cell/population from which all modern cellular life descends.

The slide says 355 genes probably originated with LUCA and that those genes point toward deep-sea hydrothermal vents, but the conclusion is far from certain.

flow:

first living systems→ early cells/populations→ LUCA→ descendants split over time→ Bacteria, Archaea, and Eukarya.

origin location flow:

early biological molecules form→ possible setting: hydrothermal vents OR warm little ponds OR delivered from space→ self-replicating chemistry develops→ early cells form→ LUCA gives rise to major domains of life.

evidence of early life

early life existed b/c what evidence? (4)

Stromatolite flow chart

evidence flow chart

We know early microbial life existed because of fossils and the geological record. The slide lists bacterial fossils, stromatolites, sulfur bacteria, cyanobacteria, and chemical changes in early Earth as evidence

Evidence	What it means
Stromatolites	Layered rock structures formed by microbial biofilms, especially cyanobacteria, trapping minerals/sediment.
Sulfur bacteria fossils	Fossils showing bacteria existed before atmospheric oxygen became abundant.
Fossilized cyanobacteria	Fossil evidence of photosynthetic bacteria-like organisms.
Geological record	Rocks/minerals show Earth’s chemistry changed as life evolved.

sulfur fossil bacteria are 2.5 billion years old and predate oxygen, and stromatolites are 3.5 billion years old, formed when minerals were trapped between layers of cyanobacteria biofilms.

stromatolite flow chart:

cyanobacteria grow in layers/biofilms→ sticky microbial mats trap sediment/minerals→ layer builds on layer→ minerals harden over time→ stromatolite forms→ fossil stromatolites show ancient microbial life.

evidence flow chart:

microbes live on early Earth→ some form biofilms/stromatolites→ minerals preserve layered structures→ fossils remain in rock→ scientists date the rock → evidence shows life existed billions of years ago.

cyanobacteria and great oxygen catastrophe

what it was? what happened because of it

Cyanobacteria

Photosynthesis

Oxygenic photosynthesis

Anaerobe

Obligate anaerobe

Aerobe

Aerobic metabolism

Great Oxygen Catastrophe / Great Oxygenation Event

oxygen flow chart

why was oxygen both dangerous and useful

Early life was mostly anaerobic, meaning it did not use oxygen. Then cyanobacteria evolved oxygen-producing photosynthesis. This changed the entire planet.

Term	Detailed meaning
Cyanobacteria	Photosynthetic bacteria that produce oxygen. They were crucial in oxygenating Earth.
Photosynthesis	Process using light energy to convert CO₂ and water into sugars; oxygen is released in oxygenic photosynthesis.
Oxygenic photosynthesis	Photosynthesis that produces oxygen gas.
Anaerobe	Organism that does not use oxygen.
Obligate anaerobe	Organism harmed or killed by oxygen.
Aerobe	Organism that uses oxygen for metabolism.
Aerobic metabolism	Energy production using oxygen, often producing more ATP than anaerobic metabolism.
Great Oxygen Catastrophe / Great Oxygenation Event	Rise of atmospheric oxygen caused by cyanobacteria; toxic to many anaerobes but allowed aerobic life to evolve.

Oxygen flow chart:

cyanobacteria evolve photosynthesis→ use sunlight + CO₂ + water→ produce sugars + O₂→ O₂ first reacts with minerals like iron→ minerals become oxidized→ eventually mineral “sinks” fill up→ O₂ accumulates in atmosphere→ many obligate anaerobes die→ some organisms evolve oxygen tolerance/aerobic metabolism→ complex aerobic life becomes possible.

both dangerous and useful

dangerous: oxygen is reactive and toxic to organisms not adapted to it
useful: organisms that evolved oxygen-handling systems could use oxygen to extract more energy from food.

Evolution

whether the theory of evolution explains how life arose on Earth T or F

Descent w/ Modification

all living things have a

modifications Accumulate across

most modifications are and

rare advantageous modifications improve

over billions of years natural selection produces

Evolution

Common ancestor

Common descent

Descent with modification

Mutation

Fitness

Adaptation

Selection

flow chart

Evolution explains how life changes over time after life already exists. It does not explain how life first arose.

False because evolution explains change in living populations, not the original chemical origin of life

Descent with modification = offspring descend from ancestors but are not exact copies; over many generations, small genetic changes accumulate.

all living things have a common ancestor, modifications accumulate across generations, most modifications are detrimental and selected against, rare advantageous modifications improve survival/reproduction, and over billions of years natural selection produces species adapted to different environments.

Term	Detailed meaning
Evolution	Change in the genetic makeup of populations over generations.
Common ancestor	An ancestral organism/population shared by descendant groups.
Common descent	Idea that all living organisms are related through shared ancestry.
Descent with modification	Offspring inherit traits from parents but with changes; changes accumulate over generations.
Mutation	Random change in DNA/genetic code.
Fitness	Ability to survive and reproduce in a particular environment.
Adaptation	Trait that improves survival/reproduction in a specific environment.
Selection	Process where some traits become more common because organisms with those traits reproduce more.

ancestor reproduces→ offspring have small genetic differences→ most changes are neutral or harmful→ rare changes are helpful in that environment→ helpful trait increases survival/reproduction→ more offspring inherit it→ population changes over generations→ evolution occurs.

Mutuation

3 outcomes

Natural selection

mutuation vs natural selection distinction

can individuals evolve

does evolution have an end goal

is a trait always good

mutations are random changes in DNA and can have three outcomes: beneficial, neutral, or detrimental. Beneficial mutations are rare; neutral and detrimental mutations are common.

Mutation outcome	Meaning
Beneficial	Helps survival/reproduction in that environment; rare.
Neutral	Has no major effect; common.
Detrimental	Harms survival/reproduction; common.

Natural selection

Natural selection = nonrandom selection of random genetic variation based on environmental conditions.

Mutuation is random but selection is not random because the environment determines which traits help survival.

individuals do not evolve, populations do; evolution has no end goal; traits can be advantageous or disadvantageous; and the environment specifies what is advantageous.

natural selection flow chart:

random mutation occurs→ trait changes→ environment “tests” trait→ harmful trait decreases because organism reproduces less→ neutral trait may stay or drift→ helpful trait increases because organism reproduces more→ population changes over time.

A trait is not “good” in every situation.

trait helps in hot desert→ selected for in desert but same trait hurts in freezing environment → selected against in cold.

random genetic changes occur first → environment selects which changes persist.

why new microbial diseases keep appearing?

reasons (4)

environmental changes / how they spread across in the world ?

flow

New diseases continue to appear because microbes evolve quickly.

They have short generation times, large populations, random mutations, and genetic exchange. Environmental changes, human travel, animal-human contact, climate change, and antibiotic/antiviral selection pressures can favor new variants or bring existing microbes into new hosts.

flow

microbes reproduce quickly→ many mutations occur→ some mutations improve survival/transmission→ environment or human behavior changes→ selected microbes spread→ new strains/diseases appear.

Taxonomy and classification

Taxonomy

Classification

Phylogeny

Phylogenetic tree / tree of life

Nomenclature

Species

Genus

flow

Taxonomy = classification, description, identification, and naming of organisms.

OpenStax defines taxonomy this way and explains that classification organizes organisms into groups based on shared characteristic

the goal of taxonomy is to create a phylogenetic system, group organisms based on evolutionary relatedness, allow identification, and provide a system of nomenclature.

Term	Detailed meaning
Taxonomy	Science of classifying, identifying, describing, and naming organisms.
Classification	Grouping organisms based on shared traits or relatedness.
Phylogeny	Evolutionary history/relatedness of organisms.
Phylogenetic tree / tree of life	Diagram showing how organisms are thought to be evolutionarily related.
Nomenclature	Naming system for organisms.
Species	Most specific/basic taxonomic unit in classic taxonomy.
Genus	Taxonomic group above species; first word in a scientific name.

organisms are diverse→ scientists need organization→ compare traits/genetic sequences→ group organisms by relatedness→ give standardized names→ identify organisms more accurately.

5 kingdom model vs 3 domain system

5 kingdom model , what it included

why it changed?? flow

the older five-kingdom model included:

Plantae, Fungi, Animalia, Protista, and Prokaryota/Monera.

The slide says the five-kingdom model is no more.

OpenStax explains that Whittaker’s five-kingdom tree included Animalia, Plantae, Protista, Fungi, and Monera, and that it was considered standard for many years.

The old model grouped organisms partly by appearance and cell type. Once scientists could compare genetic sequences, they realized that “prokaryotes” were not one simple group. Archaea and bacteria are both prokaryotic, but they are genetically and evolutionarily very different.

old classification based on visible/phenotypic traits→ prokaryotes grouped together as Monera → DNA/rRNA sequencing becomes available→ archaea found to be deeply different from bacteria→ five-kingdom model replaced by three-domain system.

Carl Woese and the three-domain system

what did Carl Woese did?

when was 3 domain proposed

which is more closely related to Eukarya?

Molecular clock

rRNA

16S rRNA

18S rRNA

Domain

Bacteria

Archaea

Eukarya

3 domain flow chart

Carl Woese used ribosomal RNA sequences as a molecular clock to reorganize all life into three domains: Bacteria, Archaea, and Eukarya.

three-domain system was proposed in 1990, based on molecular clocks/ribosomal RNA sequences, using 18S rRNA for Eukarya and 16S rRNA for prokaryotes.

Woese and Fox created a genetics-based tree of life using small subunit rRNA gene sequences and found that archaea, bacteria, and eukaryotes form three domains. It also notes that Archaea and Eukarya are more closely related to each other than either is to Bacteria.

Term	Detailed meaning
Molecular clock	Method using sequence differences in conserved molecules to estimate evolutionary relatedness.
rRNA	Ribosomal RNA; part of ribosomes, essential for protein synthesis, evolves slowly, useful for comparing organisms.
16S rRNA	Small subunit rRNA used to compare bacteria/archaea.
18S rRNA	Small subunit rRNA used to compare eukaryotes.
Domain	Highest major taxonomic grouping above kingdom.
Bacteria	Domain of prokaryotes with bacterial cell features.
Archaea	Domain of prokaryotes distinct from bacteria; often associated with extreme environments.
Eukarya	Domain containing organisms with eukaryotic cells: animals, plants, fungi, protists.

all cellular life shares ancient ancestry→ compare rRNA sequences→ three major groups appear→ Bacteria→ Archaea→ Eukarya

What are the three domains of life? What molecule did Carl Woese use? Which domain is most closely related to Eukaryotic organisms?”

The three domains are Bacteria, Archaea, and Eukarya. Carl Woese used ribosomal RNA sequences, especially small-subunit rRNA, as a molecular clock. Archaea are more closely related to Eukarya than Bacteria are.

rRNA sequences and much of their information-processing machinery reveal a much closer evolutionary connection to eukaryotes

Archaea

what are they and their factors

cell type? diseases?

Archaea

Extremophile

Methanogen

Halophile

Thermophile/hyperthermophile

Pseudopeptidoglycan

flow

Archaea are prokaryotes, but they are not bacteria.
They form their own domain and are often associated with extreme environments. archaea as extremophiles. OpenStax adds that archaea are unicellular prokaryotes with cell walls/membranes/metabolism different from bacteria, can live in extreme environments, and none have been shown to be human pathogens.

Term	Meaning
Archaea	One of the three domains of life; unicellular prokaryotes distinct from bacteria.
Extremophile	Organism that thrives in extreme conditions, such as high heat, high salt, or extreme acidity.
Methanogen	Archaeon that produces methane; some live in guts.
Halophile	Salt-loving archaeon.
Thermophile/hyperthermophile	Heat-loving archaeon.
Pseudopeptidoglycan	Archaeal wall material similar to but different from bacterial peptidoglycan.

prokaryotic cell→ no nucleus→ not bacteria→ unique membrane/wall chemistry→ often survives extreme environments→ some produce methane→ no known human pathogens.

Bacteria

classic classification relies on which factors (3)

modern classification depends on

Phenotype

Morphology

Gram stain

Physiological needs

Metabolic traits

Genotyping

Sequence analysis

Lateral/horizontal gene transfer

microbes are difficult to classify so how they do it?

flow chart

why genetics matters more now

Bacteria are hard to classify by appearance because they are small and structurally simple.

classic prokaryotic classification relies on phenotypic traits such as morphology, Gram stain, gaseous/physiological needs, but

modern microbial classification depends on genotyping, including DNA, rRNA, and protein sequence analysis.

Term	Meaning
Phenotype	Observable traits, such as shape, staining, metabolism, and growth requirements.
Morphology	Shape/structure of cells, such as cocci or bacilli.
Gram stain	Stain method that helps classify bacteria by cell wall structure.
Physiological needs	Conditions needed for growth, such as oxygen, temperature, pH, nutrients.
Metabolic traits	How bacteria use nutrients and what waste products they produce.
Genotyping	Classification/identification based on genetic information.
Sequence analysis	Comparing DNA, rRNA, or protein sequences.
Lateral/horizontal gene transfer	Movement of genes between organisms, especially common in prokaryotes.

microbes are difficult to classify visually, so biochemical tests, serological tests, DNA sequencing, and rRNA sequencing are used for identification and classification

unknown bacterium→ look at morphology→ Gram stain→ test growth needs→ test metabolism/waste products→ compare DNA/rRNA/protein sequences→ identify/classify more accurately.

matters more now>:

two bacteria may look almost identical→ but have major genetic differences→ or may exchange genes horizontally→ phenotype alone can mislead→ genetic analysis gives better evolutionary classification.

microbes what counts and doesn’t count

all microbes causes disease?

Microorganism / microbe

Bug

Germ

Pathogen

Microbiota

Microbiome

types of microbe

microorganisms = microbes = bugs, but “germs” is misleading because most microbes are not pathogenic; only a small minority cause disease, and most are useful or essential for life.

Term	Meaning
Microorganism / microbe	Organism or infectious agent usually too small to see without magnification.
Bug	Informal lab word for a microbe; not actually an insect.
Germ	Informal word often meaning disease-causing microbe, but misleading because most microbes are not harmful.
Pathogen	Disease-causing organism or agent.
Microbiota	Microbes living in/on a body site or environment.
Microbiome	The total microbial community and/or its genetic content in a body site/environment.

basic chem terminology

Atom

Proton

Neutron

Electron

Covalent bond

Ionic bond

Anion

Cation

Hydrogen bond

Electronegativity

pH

Term	Exam-ready meaning
Atom	Basic unit of matter. Made of protons, neutrons, and electrons.
Proton	Positively charged particle in the nucleus.
Neutron	Neutral particle in the nucleus.
Electron	Negatively charged particle around the nucleus; involved in bonding.
Covalent bond	Atoms share electrons. Strong bond. Example: O-H bonds inside one water molecule.
Ionic bond	Attraction between oppositely charged ions after electrons are transferred. Example: Na⁺ and Cl⁻.
Anion	Negatively charged ion. Example: Cl⁻.
Cation	Positively charged ion. Example: Na⁺.
Hydrogen bond	Weak attraction between a slightly positive H and a slightly negative atom nearby, often O or N. Important in water and proteins.
Electronegativity	How strongly an atom pulls electrons toward itself.
pH	Measure of acidity/basicity; important because proteins and cells only function in certain pH ranges.

what type of bonds between different water molecules vs inside one water molecules

Inside one water molecule:
H—O bonds = covalent bonds.

Between different water molecules:
water molecule → hydrogen bond → nearby water molecule.

The slides ask both: oxygen and hydrogen inside one water molecule are connected by covalent bonds, while two water molecules interact through hydrogen bonds

what are the 2 major categories of chemical rxns

what did each of them do

ana vs catabolism , hydrolysis vs dehydration synthesis

The two major categories are catabolism and anabolism.

decomposition/catabolism

synthesis/anabolism builds large molecules from smaller molecules and usually requires energy.

Process	Meaning	Energy connection	Example
Catabolism	Breaking larger molecules into smaller molecules.	Usually releases or generates usable energy.	Breaking glucose down during metabolism.
Anabolism	Building larger molecules from smaller molecules.	Usually requires energy input.	Building starch from glucose or proteins from amino acids.
Hydrolysis	Uses water to break a bond.	Common in digestion/breakdown.	Starch + water → smaller sugars.
Dehydration synthesis	Removes water while forming a bond.	Common in building polymers.	glucose + glucose → maltose + water.

he slide connects hydrolysis with catabolism and dehydration reactions with anabolism. It also says hydrolysis substrates are usually oxidized and dehydration substrates are usually reduced

hydrolysis = break down; dehydration synthesis = build up.

Catabolism:
large nutrient molecule → hydrolysis/breakdown → smaller molecules → energy can be released

Anabolism:
small building blocks + energy → dehydration synthesis → larger molecule/polymer → cell structure or storage

give an example of how anabolism and catabolism works in bacteria? or their connection to this class ?

bacteria find nutrient polymer outside cell→ secrete enzymes→ polymer is broken into smaller molecules→ small molecules enter cell→ catabolism releases energy→ anabolism uses energy/building blocks to build new cell parts.

why do cell depends on water

Water is not one of the carbon macromolecules, but it is essential because life’s chemistry happens in water. The slide says water is the solvent, is inorganic, and is polar.

Term	Meaning
Solvent	Liquid that dissolves other substances. Water is the main solvent of cells.
Solute	Substance dissolved in a solvent. Example: Na⁺, Cl⁻, glucose.
Solution	Solvent + solute mixed together.
Polar	Uneven charge distribution. In water, oxygen is slightly negative and hydrogens are slightly positive.
Hydrophilic	Water-loving; polar/charged substances interact well with water.
Hydrophobic	Water-fearing; nonpolar substances do not mix well with water.

why water is polar

oxygen is more electronegative than hydrogen→ oxygen pulls shared electrons closer→ oxygen becomes slightly negative→ hydrogens become slightly positive→ water molecules attract each other through hydrogen bonding.

water dissolving salts flow chart

NaCl crystal enters water→ water’s oxygen side faces Na⁺→ water’s hydrogen side faces Cl⁻→ ions separate→ ions become surrounded by water→ salt dissolves

Water as a temperature buffer flow charts

The lecture slide says hydrogen bonds allow water to absorb a lot of energy before changing state, giving water a high specific heat capacity and helping oceans stabilize Earth’s temperature.

Flow:
many hydrogen bonds between water molecules→ heat energy first disrupts bonds/movement→ temperature changes more slowly→ cells and environments stay more stable.

organic molecules

what is carbon skeleton

flow chart

Organic molecules are carbon-based molecules.
OpenStax says organic chemistry is carbon-based chemistry, and biochemistry studies the chemistry of life. It also says organic molecules contain carbon, are usually organized around carbon chains, and are generally larger/more complex than inorganic molecules.

organic molecules have a carbon skeleton and functional groups, and functional groups are responsible for most of the chemical properties of organic molecules

Carbon skeleton = the carbon backbone of an organic molecule.
Carbon is special because it can form four covalent bonds, letting it build straight chains, branched chains, and rings. OpenStax explains that carbon’s bonding properties allow many different molecular sizes and shapes

carbon atom can make 4 bonds→ carbon atoms bond to each other→ chains/rings/branches form→ functional groups attach→ many different biomolecules are possible.

functional groups

Hydroxyl / alcohol

Aldehyde

Ketone

Methyl

Amino

Carboxyl

Phosphate

Sulfhydryl

Ester

Ether

Functional group = a specific group of atoms attached to a carbon skeleton that gives the molecule predictable chemical behavior.
OpenStax defines functional groups as groups of atoms categorized by their chemical composition and reactions, regardless of the molecule they are part of.

Functional group	Structure clue	Why she should care
Hydroxyl / alcohol	–OH	Makes molecules more polar; common in carbohydrates.
Aldehyde	terminal C=O	Found in some sugars; helps make reducing sugars.
Ketone	internal C=O	Found in sugars/metabolic intermediates.
Methyl	–CH₃	Affects DNA regulation and metabolism.
Amino	–NH₂ / –NH₃⁺	Found in amino acids/proteins.
Carboxyl	–COOH / –COO⁻	Found in amino acids, fatty acids, organic acids.
Phosphate	–PO₄	Found in ATP, DNA/RNA, phospholipids.
Sulfhydryl	–SH	Can form disulfide bonds in protein structure.
Ester	C–O–C=O pattern	Important in triglycerides and membranes.
Ether	C–O–C	Important in archaeal membranes.

Isomers

Structural isomers

Stereoisomers

Enantiomers

Chirality

Isomers are molecules with the same molecular formula but different arrangements of atoms.
OpenStax says structure is directly related to function, so slight changes in atom arrangement can cause very different properties.

Isomer type	Meaning	Example
Structural isomers	Same formula, different bonding sequence.	glucose, galactose, fructose all C₆H₁₂O₆.
Stereoisomers	Same bonds, different 3D arrangement.	D-glucose vs L-glucose.
Enantiomers	Mirror-image stereoisomers that cannot be superimposed.	D- and L- forms.
Chirality	“Handedness”; mirror-image molecules are not identical in 3D.	Like right hand vs left hand.

why dextrose is used for the biologically relevant isomer of glucose.

Dextrose refers to D-glucose, the biologically common form of glucose. “Dextro” relates to the right-handed/d-form naming idea, connected to optical isomers.

OpenStax explains that enantiomers can rotate polarized light, and the d and l labels come from Latin words meaning right and left.

same formula→ atoms arranged differently=→ different shape→ enzymes/receptors may recognize only one form→ biological effect changes.

Biological macromolecules:

monomers and polymers

Small organic molecules can combine into large macromolecules. The lecture slide says macromolecules are polymers made of many repeating smaller molecules called monomers

OpenStax says many macromolecules are formed by linking many identical or similar monomers into polymers, often by dehydration synthesis, which forms water as a byproduct.

Word	Meaning
Monomer	Small building block molecule.
Polymer	Large molecule made of many monomers.
Macromolecule	Large biological molecule.
Dehydration synthesis	Builds polymers by removing water.
Hydrolysis	Breaks polymers by adding water.

macromolecule

Carbohydrates

Lipids

Proteins

Nucleic acids

flow

OpenStax lists carbohydrate, lipid, nucleic acid, and protein functions: carbohydrates for energy/storage/structure/receptors, lipids for energy storage/membranes/hormones, nucleic acids for genetic information, and proteins for enzymes/structure/receptors/transport

Macromolecule	Building block	Main roles
Carbohydrates	monosaccharides	energy, storage, cell structures, receptors
Lipids	fatty acids + glycerol or lipid units	membranes, energy storage, hormones
Proteins	amino acids	enzymes, transport, movement, structure, toxins
Nucleic acids	nucleotides	DNA/RNA genetic information; not main focus in this lecture

Flow:
monomers → dehydration synthesis → polymer/macromolecule
polymer → hydrolysis → monomers

Carbohydrate

carbohydrate terms

Carbohydrate

Saccharide

Monosaccharide

Disaccharide

Oligosaccharide

Polysaccharide

Glycosidic bond

Hexose

Glycan

Carbohydrates are sugars and sugar polymers used for energy, energy storage, and structure.
The lecture lists sugars, starch, glycogen, and cellulose, says they function in cell structures and energy sources, and says many have the formula (CH₂O)n. OpenStax says carbohydrates are the most abundant biomolecules on Earth and are important in food, structural polymers, DNA/RNA components, and energy storage as starch/glycogen.

Term	Detailed meaning
Carbohydrate	Biomolecule made mainly of carbon, hydrogen, and oxygen; often used for energy or structure.
Saccharide	Another word for sugar/carbohydrate unit.
Monosaccharide	One sugar unit; carbohydrate monomer.
Disaccharide	Two monosaccharides linked together.
Oligosaccharide	Short sugar chain; lecture says 2–20 monosaccharides.
Polysaccharide	Large sugar polymer made of many monosaccharides.
Glycosidic bond	Covalent bond linking sugar monomers.
Hexose	Six-carbon sugar, such as glucose, galactose, fructose.
Glycan	Another term often used for polysaccharide/sugar chain.

Monosacchrides

Glucose

Fructose

Galactose

Mannose, fucose, GlcNAc

NAG / GlcNAc

flow

Monosaccharides = simple sugars, usually 3–7 carbons in this lecture.
OpenStax says monosaccharides are classified by the number of carbons and uses the suffix -ose, such as triose, pentose, and hexose. D-glucose is the most abundant monosaccharide in nature.

Monosaccharide	Importance
Glucose	Major energy sugar; monomer of starch, glycogen, cellulose.
Fructose	Fruit sugar; combines with glucose to make sucrose.
Galactose	Combines with glucose to make lactose.
Mannose, fucose, GlcNAc	Important in glycans/cell-surface carbohydrates.
NAG / GlcNAc	Important in chitin and bacterial cell wall peptidoglycan.

Flow:
simple sugar enters cell→ glycolysis/metabolism→ ATP + carbon intermediates → energy or building blocks for growth.

Disaccharide

Sucrose

Lactose

Maltose

The lecture lists these exact disaccharides: sucrose = glucose + fructose, lactose = glucose + galactose, maltose = glucose + glucose. OpenStax says glycosidic bonds form between hydroxyl groups of two saccharides by dehydration synthesis.

Disaccharide	Monomers	Common meaning
Sucrose	glucose + fructose	table sugar
Lactose	glucose + galactose	milk sugar
Maltose	glucose + glucose	grain sugar / starch breakdown product

monosaccharide + monosaccharide→ dehydration synthesis→ glycosidic bond forms→ disaccharide + water.

Polysaccharide

Starch

Glycogen

Cellulose

Chitin

Peptidoglycan

made of main role and details

amylose vs amylopectin

which has faster digestion why

alpha 1, 4 linkages vs alpha 1,6 linkages vs beta 1,4 linkages which ones are digestable and why?

The lecture says polysaccharides are tens or hundreds of monosaccharides; starch, glycogen, and cellulose are glucose polymers; chitin is a polymer of N-acetylglucosamine. OpenStax adds that polysaccharides are generally not sweet, usually not water-soluble, and are linked by glycosidic bonds.

Polysaccharide	Made of	Main role	Important detail
Starch	glucose	plant energy storage	alpha linkages; digestible.
Glycogen	glucose	animal/bacterial energy storage	highly branched; alpha linkages.
Cellulose	glucose	structural support in plant walls	beta linkages; humans cannot digest.
Chitin	N-acetylglucosamine	fungal cell walls, insect exoskeletons	structural polymer.
Peptidoglycan	NAG + NAM + peptides	bacterial cell wall	important for bacteria; antibiotic target later.

Amylose is a straight, unbranched chain of glucose. Amylopectin is a highly branched chain of glucose.

Uses α-1,4 linkages for straight lines and α-1,6 linkages to create branching points.

3. Digestion Speed

• Amylose: Digests slowly because the straight chains pack tightly together, making it harder for enzymes to reach.

• Amylopectin: Digests quickly because the open, branched structure gives enzymes many points to attack at the same time.

• α-1,4 Linkages: These bonds form the main straight chains of glucose molecules in both starch (amylose and amylopectin) and glycogen. Our saliva and pancreatic juices secrete Amylase to cleave these specific bonds. [1, 2, 3, 4]

• α-1,6 Linkages: These bonds create the branch points in amylopectin (found in starch) and glycogen. Specialized debranching enzymes in our gut break these bonds to finish digestion. [1, 2, 3]

• Why Beta linkages fail: Unlike alpha bonds, plant structural polysaccharides like cellulose use beta-1,4 linkages. Humans lack the enzyme (cellulase) needed to fit and break beta configurations, which is why we cannot digest fiber

Starch vs cellulose

flow

The slide says starch has alpha linkages and is digestible, while cellulose has beta linkages and is not digestible.

same glucose monomers→ different glycosidic linkage orientation→ different 3D shape→ different enzymes can/cannot break it→ starch digestible, cellulose not digestible by humans.

Glycogen

flow

The slide says glycogen is the storage form of glucose in animals, used for short-term energy storage in liver and muscles, has alpha linkages, and is highly branched. OpenStax also notes glycogen is the primary energy-storage molecule in animals and bacteria.

Flow:
extra glucose→ linked into glycogen→ stored in liver/muscle→ broken down when energy is needed→ glucose released for metabolism

why bacteria digest starch outside. why bacteria secrete amylase/maltase to digest starch outside instead of absorbing starch into the cell.

flow

Starch is a large polysaccharide, so it is too big to be transported directly into the bacterial cell. Bacteria secrete extracellular enzymes such as amylase and maltase to hydrolyze starch outside the cell into smaller sugars like maltose/glucose. Those smaller sugars can then be transported into the cell and used for energy.

Flow:
starch outside cell→ too large to enter→ bacterium secretes amylase/maltase→ starch hydrolyzed into smaller sugars→ glucose/maltose transported inside→ catabolism makes ATP.

Lipids

Lipid

Nonpolar

Hydrophobic

Fatty acid

Triglyceride / triacylglycerol

Phospholipid

Amphipathic

Sterol

Hopanoid

Ergosterol

Lipids are mostly nonpolar, hydrophobic molecules used for energy storage, membranes, insulation, pigments, and hormones.
The lecture slide says lipids are major components of cell membranes, consist of C/H/O, are nonpolar and insoluble in water, and include triglycerides, phospholipids/sphingomyelin, and sterols. OpenStax says lipids are diverse molecules that can store carbon/energy, form membranes, and act as hormones.

Term	Detailed meaning
Lipid	Hydrophobic or amphipathic biomolecule; usually rich in C-H bonds.
Nonpolar	Does not have strong charge separation; does not mix well with water.
Hydrophobic	Water-fearing; avoids interaction with water.
Fatty acid	Long hydrocarbon chain with a carboxyl group at one end.
Triglyceride / triacylglycerol	Glycerol + three fatty acids; energy storage lipid.
Phospholipid	Glycerol + two fatty acids + phosphate-containing head; membrane lipid.
Amphipathic	Has both hydrophilic and hydrophobic regions.
Sterol	Ringed lipid with an –OH group, such as cholesterol.
Hopanoid	Bacterial sterol-like molecule that strengthens membranes.
Ergosterol	Sterol-like membrane molecule in fungi and some protozoa.

Triglyceride

flow

OpenStax says a triglyceride forms when three fatty acids are linked to glycerol and functions as an efficient energy-storage molecule.

Flow:
glycerol + 3 fatty acids→ dehydration synthesis / ester bonds→ triglyceride→ long-term energy storage.

Saturated vs unsaturated fatty acids

Saturated fatty acid

Unsaturated fatty acid

Cis unsaturated

Trans unsaturated

structure, effect

OpenStax explains that saturated fatty acids have only single bonds and are saturated with hydrogen, while unsaturated fatty acids have at least one double bond and fewer hydrogens. Unsaturated fatty acids often have kinks, affecting lipid properties.

Type	Structure	Effect
Saturated fatty acid	No C=C double bonds; many hydrogens; straighter chain.	Packs tightly; more solid/less fluid.
Unsaturated fatty acid	One or more C=C double bonds; fewer hydrogens.	Kinks prevent tight packing; more fluid. Kinks in unsaturated fatty acids are permanent bends in their carbon chains caused by double bonds in the cis configuration
Cis unsaturated	Hydrogens on same side of double bond.	Creates strong kink.
Trans unsaturated	Hydrogens on opposite sides.	Straighter, behaves more like saturated fat.

how fatty acid content in high-temperature bacteria should compare with bacteria at moderate temperature.

flow

High-temperature bacteria would be expected to have more saturated fatty acids, because saturated tails pack tightly and help prevent the membrane from becoming too fluid at high temperature. Bacteria in cooler or moderate conditions can use more unsaturated fatty acids to keep membranes fluid.

flow:

high temperature→ membrane becomes too fluid→ more saturated fatty acids stabilize packing→ membrane stays functional.

Phospholipids and membranes

flow

OpenStax says phospholipids have a charged phosphate-containing hydrophilic head and nonpolar hydrophobic tails; this amphipathic structure allows them to form micelles, liposomes, and lipid bilayers. Cell membranes of nearly all organisms are made from lipid-bilayer sheets.

Flow:
phospholipid has hydrophilic head + hydrophobic tails→ placed in water→ heads face water→ tails avoid water and face inward→ bilayer forms→ cell membrane form

Sterols, hopanoids, ergosterol

Cholesterol

Hopanoids

Ergosterol

found in and role

OpenStax says cholesterol strengthens eukaryotic cell membranes and membranes of wall-less bacteria like Mycoplasma; most prokaryotes do not produce cholesterol, but bacteria produce similar compounds called hopanoids; fungi and some protozoa produce ergosterol.

Molecule	Found in	Role
Cholesterol	animal/eukaryotic membranes	strengthens/stabilizes membrane; precursor to steroid hormones.
Hopanoids	many bacterial membranes	sterol-like membrane stabilizers.
Ergosterol	fungi and some protozoa	membrane stabilizer; important drug target later.

Proteins

Enzyme

Transporter/carrier

Receptor

Structural protein

Movement protein

Regulatory protein

Toxin

Amino Acid

Proteins are amino-acid polymers that do most of the work in cells.
The lecture says proteins are essential for cell structure/function; enzymes speed reactions; transporter proteins move chemicals across membranes; flagella are made of proteins; some bacterial toxins are proteins.

OpenStax says amino-acid-derived molecules can act as structural components, nutrients, storage reservoirs, hormones, enzymes, receptors, and transport molecules.

Protein role	What it does	Microbiology example
Enzyme	Speeds chemical reactions.	amylase breaks starch; lactase breaks lactose.
Transporter/carrier	Moves molecules across membranes.	sugar transport proteins.
Receptor	Detects signals or binds molecules.	cell-surface sensing proteins.
Structural protein	Builds/supports cell structures.	flagellin in flagella.
Movement protein	Helps movement.	flagella proteins.
Regulatory protein	Controls cell processes/gene expression.	repressors/activators later in genetics.
Toxin	Damages host cells.	some bacterial toxins are proteins.

The lecture also lists protein roles as carriers/transporters, receptors, control/regulation molecules, enzymes, communication molecules, movement elements, and structural elements.

Amino Acid

α carbon

Amino group

Carboxyl group

Hydrogen

R group / side chain

Amino acid = protein monomer.
OpenStax says an amino acid has a central α carbon bonded to a hydrogen atom, a carboxyl group, an amino group, and a variable R group/side chain.

Part	Meaning
α carbon	Central carbon of amino acid.
Amino group	–NH₂ or –NH₃⁺ group.
Carboxyl group	–COOH or –COO⁻ group.
Hydrogen	Attached to central carbon.
R group / side chain	Variable group that makes each amino acid chemically different.

Flow:
same amino acid backbone→ different R groups→ different chemical properties→ different protein folding→ different protein function.

Peptide bonds

flow

The lecture says amino acids are connected by peptide bonds to form peptides and proteins. OpenStax says peptide bond formation occurs when the carboxyl group of one amino acid reacts with the amino group of another, forming a peptide bond and releasing water.

amino acid carboxyl group + amino acid amino group→ dehydration synthesis→ peptide bond forms→ water released→ peptide chain grows.

Peptide vs protein

Dipeptide

Tripeptide

Oligopeptide

Polypeptide

Protein

Term	Meaning
Dipeptide	2 amino acids.
Tripeptide	3 amino acids.
Oligopeptide	Short amino acid chain, up to about 20 amino acids.
Polypeptide	Longer amino acid chain, up to about 50 amino acids in OpenStax wording.
Protein	Large functional amino-acid polymer, sometimes made of multiple polypeptide subunits.

Levels of protein

Primary structure

Secondary structure

Tertiary structure

Quaternary structure

A protein’s shape determines its function. The lecture slide says proteins fold into three-dimensional structures and the correct structure allows normal function. OpenStax says the amino acid sequence determines shape, and shape is critical for function. Even slight active-site changes can weaken or prevent substrate binding.

Level	Meaning	Main stabilizing features
Primary structure	Sequence/order of amino acids.	Peptide bonds.
Secondary structure	Local folding into α-helices or β-pleated sheets.	Hydrogen bonding in peptide backbone.
Tertiary structure	Overall 3D shape of one polypeptide chain.	R-group interactions: hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bridges.
Quaternary structure	Multiple polypeptide subunits assembled together.	Interactions between subunits.

penStax describes these four levels and explains that tertiary structure depends on interactions between amino acid residues far apart in the chain, while quaternary structure involves multiple subunits.

protein folding flow

DNA sequence→ amino acid sequence→ primary structure
→ local hydrogen bonding→ α-helices / β-sheets→ R-group interactions→ tertiary 3D shape→ possible subunit assembly→ functional protein

Denaturation

flow

Denaturation = loss of normal 3D protein shape, causing loss of function.
OpenStax says denaturation means loss of secondary/tertiary/quaternary structure without losing primary structure.

Flow:
heat / pH change / chemical stress→ weak interactions disrupted→ protein unfolds→ active site shape changes→ protein stops working.

why many water-soluble proteins have hydrophobic interiors but hydrophilic outside layers.

Hydrophobic amino acids cluster inside the protein away from water, which stabilizes the folded shape. Hydrophilic amino acids face outward and interact with water, making the protein soluble.

Flow:
protein folds in water→ hydrophobic R groups avoid water and pack inside→ hydrophilic R groups face water outside→ stable folded interior + water-soluble exterior→ protein functions normally.

I clicker questions

Bond between O and H in one water molecule?

Bond between two water molecules?

What kind of molecule is glucose?

What kind of molecule is cellulose?

Lipids store energy / form structures / may function as hormones?

What kind of molecule is an amino acid?

What kind of molecule is a protein?

α-helices and β-pleated sheets diagram?

Full folded single chain diagram?

Slide question	Correct answer	Why
Bond between O and H in one water molecule?	Covalent bond	Electrons are shared within the molecule.
Bond between two water molecules?	Hydrogen bond	Slightly positive H attracts slightly negative O of another water molecule.
What kind of molecule is glucose?	Monomer	It is one sugar unit.
What kind of molecule is cellulose?	Polymer	It is many glucose monomers linked together.
Lipids store energy / form structures / may function as hormones?	All of the above	Lipids have all these roles.
What kind of molecule is an amino acid?	Monomer	Amino acids build proteins.
What kind of molecule is a protein?	Polymer	Proteins are amino acid polymers.
α-helices and β-pleated sheets diagram?	Secondary structure	These are local folding patterns.
Full folded single chain diagram?	Tertiary structure	This is the 3D shape of one polypeptide.

comparison table carbohydrate vs lipids vs proteins

main atoms

monomer/ building blocks

polymer or large form

main functions

key bonds/ structures

Category	Main atoms	Monomer/building block	Polymer or large form	Main functions	Key bonds/structures
Carbohydrates	C, H, O	monosaccharides	disaccharides, oligosaccharides, polysaccharides	energy, energy storage, structure, cell recognition	glycosidic bonds
Lipids	mostly C, H, O; sometimes P/N/S	not true repeating monomers like carbs/proteins (they are built from a few different smaller parts rather than a long chain of identical building blocks)	triglycerides, phospholipids, sterols	membranes, energy storage, hormones, insulation triglyuceride (A standard dietary fat is made of one glycerol molecule attached to three fatty acid tails. The glycerol and the fatty acids are completely different molecules, not repeating copies of a single unit.)	hydrophobic tails; amphipathic phospholipids
Proteins	C, H, O, N, often S	amino acids	peptides, polypeptides, proteins	enzymes, transport, structure, movement, toxins, receptors	peptide bonds; folding interactions