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What is bacterial metabolism?

The total of all chemical reactions in the cell that results in energy and synthesis of new macromolecules.

Why do we study bacterial metabolism?

1.) Pathogens acquire energy and nutrients at the expense of their host.
2.) Metabolic enzymes are targets for antimicrobials.
3.) Biochemical testing is used to help identify pathogens in clinical specimens.

What is catabolism?

The converging of nutrients to waste producing energy (ATP) - tearing apart

What is anabolism?

The converging of nutrients to macromolecules to allow growth - reconstructing.

Catabolism + Anabolism = ?


All living organisms need a source of ____ and _____.

Energy & carbon

Life forms can be categorized based on they obtain their _____ and _____.

Carbon and energy

Organisms that utilize organic compounds as their energy and carbon source are _______

Chemoheterotrophs (humans)

Organisms that acquire energy from sunlight and carbon from carbon dioxide are _______

Photoautotrophs (plants)

Organisms that acquire energy from sunlight and carbon from organic compounds are ________


Organisms that acquire energy from oxidation of inorganic compounds and carbon from carbon dioxide are ______

Lithoautotrophs (only bacteria will do this)

Heterotrophic organisms oxidize organic chemicals to:

1) release energy to fuel anabolism
2) provide raw material for biosynthesis of new macromolecules

Energy from organic chemicals can be obtained by bacteria through:

1) aerobic respiration
2) anaerobic respiration
3) fermentation (anaerobic)

Glucose are oxidized, releasing energy that is then stored as:

high energy phosphate bonds of ATP

There are _____ stages of heterotrophic catabolism


What is Stage 1?

Macromolecules are broken down (eg. proteins > peptides > amino acids)

Because of their rigid cell walls, bacteria can't _________

engulf nutrient particles so they break them down outside of the cell then transport them across their plasma membrane.

What is an exoenzyme?

enzymes excreted by the plasma membrane to begin digestion of nutrients outside of cell.

Glycolysis is Stage ____


What is glycolysis?

The breaking apart of amino acids, fatty acids, glycerol etc., into simpler molecules that can enter the tricarboxylic acid cycle (TCA, Krebs, Citric acid cycle).

Where does glycolysis take place?

In the cytoplasm

Is oxygen required for glycolysis?


What is the overall rxn of glycolysis?

6-carbon glucose > 3-carbon molecules of pyruvic acid (pyruvate) + ATP

Glycolysis yields a net of how many ATP molecules?


What is stage three?

The Krebs cycle (pyruvate oxidized to carbon dioxide and water)

What is included in the Krebs Cycle?

Tricarboxylic acid cycle (TCA) and the electron transport chain

What is the transition reaction?

pyruvate (3-carbon) > Acetyl CoA + Carbon dioxide (2-carbon)

Where does TCA take place in the cell?

Prokaryotes: Inner surface of the plasma membrane
Eukaryotes: Mitochondria

What two purposes does the 3rd State facilitate?

1) supplies intermediates for biosynthesis
2) generates large numbers of electrons to enter the electron transport chain.

What is ETS?

Electron Transport Sysem

What is the ETS composted of?

Membrane-bound carrier protiens

Membrane-bound carrier protiens transfer...

electrons from donors like NADH adn FADH2 through reduction-oxidization reactions to O2 (final acceptor).

What is the maximum yield from ETS with O2 as electron acceptor?

34 (Eukaryotes)
32 (Prokaryotes) (36 ATP total)

What ist he terminal electron acceptor for Anaerobic respiration?

Inorganic molecule

Why are fewer ATP generated?

ETC is shorter and less efficient

Fermentation is the partial oxidation of glucose when...

no external electron acceptor is available.

ATP is generated only from?

Glycolysis (2 ATP)

Dental caries are created by?

Lactic acid fermentation

Infectious outcomes are determined by?

Host factors
Microbe factors

Innate defense mechanisms

Present at birth
React immediately (don't need sensitization)
First & second lines of defense

Innate defense mechanisms have two lines of defense

First and Second

First line of Defense (innate) prevent pathogens from entering the body through:

Physical barriers (skin)
Chemical defences
Microbial antagonism (role of normal flora)

Intact skin and mucous membranes are forms of what?

Physical barriers

What are 3 characteristics of intact skin?

thick, several layers
composed of mainly keratin
dry surface

What are 3 characteristics of mucous membranes?

thinner, less efficient
lined with mucous, cilia that trap microbes
line body cavities that are open to the environment (respiratory, digestive, urinary tracts)

Lysozymes and acids are forms of what?

Chemical defences

Lysozymes are found in _________ and target gram ___ organisms.

tears, saliva, sweat and mucous
gram positive

Lysozymes decrade what?


What are the normal pH of the skin, stomach and vagina/

Skin: ph 4
Stomach: pH 1.5
Vagina: pH 4


To live together

What are the three types of symbiosis?

1.) mutualsim
2.) commensalism
3.) parasitism


both organs benefit (colon)


one organism benefits, other unaffected (Staph. epidermis)


lives at expense of host

What microbes colonize on surfaces of the body without causing disease?

Normal microbiota (mutualistic or commensal)

Are microbes normally found in organs, blood, or internal cavities?


When is normal flora acquired?

within first few months of life

How does normal microbiota benefit host?

1.) provides nutrients (Vit. K, B12)
2.) Stimulate immune system
3.) Compete with pathogens by:
Occupying receptor sites, consuming nutrients, producing antimicrobial chemical

Opportunistic Pathogens become pathogenic when:

1) Immune system suppressed
2) Normal flora altered (hormones, pregnancy, stress)
3) Enter normally sterile sites (heart valves)

2 types of normal microbiota

Resident - remain throughout life, change over time
Transient - remain for hours/days/months (can transfer if hands aren't washed)

Second line of defense

cells, processes and antimicrobial chemicals that operate against any microbe that's evaded the body's 1st line of defense. (Inflammation, phagocytosis, defense components of blood, antimicrobial chemicals and fever)

2 purposes of inflammation

1) remove or contain invading microbes
2) repair tissue damage

Process of inflammation

1) Damaged cells release chemicals (histamine)
2) Vasodilation:
Increased blood flow (redness, heat)
Increased BV permeability (swelling, pain, migration of phagocytes)
3) Fibrin clot formation (prevents spread)
4) Phagocytosis of bacteria and damaged cells
5) Tissue repair (fibroblasts)

2 types of inflammation

Actue & Chronic-> tissue damage (heart disease, arthritis, gingivitis & periodontitis)

Ingestion of foreign material ic?

In tissue-macrophages
In blood-neutrophils

Process of phagocytosis

1) Chemotaxis-directed migration (phagocytes to microbe via chemical attractants)
2) Attachment-mediated by antibodies
3) Ingestion-pseudopodia surrounds microbe (endocytosis). Forms PHAGOSOME
4) Digestion-phagosome fuses with lysosome = PHAGOLYSOSOME
5) Elimination-done by exocytosis. Remaining bits may remain to help immune system.

What is the purpose of adaptive immune response?

1) differentiate between 'self' and 'non-self'
2) distroy or disable non-self

Vaccination is a form of

Adaptive immune response

What are characteristics of an adaptive immune system

1) specific: recognizes 'non-self' (T-cells)
2) self-tolerant: unresponsive to self
3) Memory: rapid response to second exposure

Dual system

Humoral Antibody response (B cells)
Cell mediated (T cells)

Hymoral antibody response

Formation of specific circulating antibody that tags microbes. Acts as extracellular antigen (most bacteria)


any foreign substance that stimulates host immune response


serum protein (immunoglobulin) made in response to antigen. Specific.

Antibodies are produced by

lymphocytes called activated B cells

T cells

recognize and attack:
*intracellular pathogens (viruses)
*Abnormal host cells (cancer)
*Transplanted cells

What are the 3 types of T cells?

Cytotoxic - act against intracellular pathogens (effector cells)
Helper - regulate B cells and cytotoxic cells, secrete cytokines (communication method)
Suppressor T cells - repress immune response

What are the ultimate parasites?


Viruses depend on hosts for

protein synthesis and nucleic acid production. They cannot replicate on their own.

Virus particles are composed of:

a) Genome (DNA or RNA)
b) Capsid (protein coat)
c) Envelope (may or may not have one)


1 type of nucleic acid (DNA or RNA)
Single, double-stranded, circular or linear

Small amount of Viral genetic material codes for:

Structural proteins (for capsid or envelop)
Enzymes (genome replication or infective process)


-made up of proteins that repeat = CAPSOMERES (symmetrical shape)

Genome + Capid =


Common capsid shapes are

-Polyhedral (20 triangles - herpes virus)
-Helical (hollow cylindrical rod - rabies)
-Complex (T4 bacteriophage)


-phospholipic membrane taken from host cell's plasma membrane or nuclear membrane
-altered by addition of viral glyoprotein spikes, knobs, fibres that allow the cell to bind to host cell receptors
-Eveloped viruses are more susceptible to antimicrobial chemicals than 'naked' viruses (envelopes are antimicrobial targets, can't live w/e envelope)

Classification of viruses depends on:

type of host cell (plant, animal, bacteria)

Viral subgroups are based on:

-presence of envelope (unenveloped=non-lipid, naked; enveloped=lipid virus)
-capsid shape
-type of genetic material

Family name ends in _____, genus/species ends in _______

Viridae; virus

Virus Replication Cycle:

1) Attachment/absorption: specific (protein or glycoprotein molecules on envelope/capsid attach to host cell receptors
2) Penetration: 1 of 3 ways - a) direct penetration b) Fusion c) Receptor Mediated Endocytosis
3) Release of nucleid acid - capsid removed>into cytoplasm (RNA virus) or nucleus (DNA virus)
4) Transcription & Translation - host cell organelles/enzymes replicate virus genetic material and create new protiens
5) Assembly - capsids form, enclosing viral nucleic acid
6) Release - virus particles escape via a) ruptures (release mature particles) b) bud out (nuclear or plasma membrane creating envelope, take host membrane as envelope c) exocytosis

Direct Penetration

Genome enters host (naked viruses)
Rare in animals


viral envelope fuses with host's membrane > nucleocapsid enters host
(HIV, measles, mumps)

Receptor Mediated Endocytosis

-Most common in animals
-Host cell absorbs entire virus

Types of virus infections

a) acute: rapid onset, short duration
b) latent infection:
c) transformation

Acute Viral Infection

rapid onset, short duration

Latent Infection

short w/ symptoms, long w/o symptoms, may reactivate later (Herpes virus)

Transformation (Oncogenic)

Oncogenic virus infection of normal cell to cancer cell (20% of cancers); "onco" = cancer causing
Eg. Papillomaviruses: chronic infection of skin or mucosal epithelium leading to carcinoma. (oral cancer)

Causes upper and lower respiratory illness in humans and other mammals and birds?


Influenza infects ________- eliminating lung's __________. Host more susceptible to secondary bacterial infections

Respiratory epithelial cells (they die); first line of defense

Influenza effects _____ % of population

10-20% each flu season
-1,200 deaths/year in BC
-Most common viral infection
-40 million died with Spanish flu epidemic (1918-1919)

What is the structure of the influenza virus?

-ssRNA virus with 8 linear segments
-envelope with glycoprotein spikes composed of hemaglutini or neuaminidase (virulence)
-Type A strains are subtyped according to NA/HA (H1N1)


attaches to host cells triggering endocytosis
-mutations of hemagglutinin code for new strains of flu


-an enzyme that aids the virus in penetrating mucous
-facilitates release of viruses from host cell
-mutations of hemagglutinin code for new strains of flu

Reproductive cycle of influenzavirus

1) Inhale; 36-48 hours later
2) attach to epithelial cells of lung via hemagglutinin>endocytosis
3) Viral envelope fuses w/ membrane of endocytic vesicles
4) viral genome directs production of viral protein (capsid, HA, NA) in cytoplasm & new copies of viral RNA in nucleus.
5) gene segments enclosed in random 'full head' manner
6) envelope proteins transported to cytoplasmic membrane via ER and Golgi apparatus
7) virus particles exit via budding, eventually destroying the infected epithelial cell.

New strains of influenza are developed

Due to mutations in the genes that code for HA and NA.
-Antigenic Drift
-Antigenic Shift

Antigenic drift

small changes in HA and NA > small antigenic changes, immune system fails to recognize completely > localized influenza outbreaks (every 2 years)
=> Thus, new formulations of flu vaccine are needed every year

Antigenic Shift

(Major quick change, rare)
Gene reassortment due to change in HA and NA
-2 differente viruses co-infect one cell > new strain > no immunity > MAJOR epidemic or pandemic (every 10 years)

Where is major site of antigenic shift?

Asia. Epicentre for emergence of novel influenza viruses.

Asia is epicenter for antigenic shift because:

1) humans live in close proximity to domestic birds/animals
2) Live poultry markets with many bird species

What are prerequisits to start pandemic?

a) new virus with no immunity
b) can replicate in humans causing disease (60% human mortality rate with avian flue)
c) can transmit from human to human

Annual immunization with ____

multivalent vaccine
-WHO decides in February which strains will be included

Treatment for influenza includes:

1) annual immunization
2) Antiviral agents/profilaxis (in first 48 hours) Blocks release of viral particles from infected cells = limits spread
3) hand washing
4) staying at home if sick

Microbe incluences of infection:

1) Dose, varies with ea. pathogen
2) Suitable entry site
3) Virulance


Ability to cause disease in host


Degree of pathogenicity (of particular organism in host under defined conditions) Factors include: structures that help a pathogen be virulent resulting in disease.



What determines virulence?

a) spread from host to host (transmissible)
b) gain entry to host
c) attach to host
d) invade and spread
e) evade host defenses
f) damage host tissue to cause disease

What are modes of infection transmission?

1) Direct host to host
2) Indirect

Direct host to host

-usually organism with poor survivability
-skin to skin (ringworm, staph, strep)
-mucous membrane to mucous membrane (oral herpes, mono, STI)

Indirect Vehicle Contamination (inanimate)

a) airborn droplets: respiratory pathogens, fungal spores
b) food/water: fecal contamination
c) fomites: inanimate objects (instruments)
d) bodily fluids (blood donations)

Idirect Via Vector (living)

a) biological vectors (living agents that transmit disease, insects)
b) mechanical vectors (on insect bodies, don't bite but spread)

How can an infection entre body?

a) break in skin/mucous membrane (surgery, injury, STIs, inoculation, etc.)
b) Inhalation (usually respiratory tract pathogens, Pneumonia, influenza)
c) Ingestion (GI tract pathogens, Cholera, intestinal parasites, hep A)


ability to attach to a target tissue.
-specific and selective
-determines specificity for host and tissue

Adhesins found on:

-Fimbriae/pili (Actin. viscosus attaches to pellicle of tooth surface)
-Glycocalyx/capsule/s layer/biofilm formation
-cell wall or membrane components


bacterial chemicals that invate the host cell's cytoskeletal machinery allowing bateria to enter by phagocytosis which are not normally phagocytic.

Infections invade/spread via

1) invasins
2) capsules
3) antiphagocytic chemicals
4) flagella
5) invasive exoenzymes (hyaluronidase, collagenase, hemolycins, coagulase, exotoxin b)


don't stimulate immune system
retard digestion inside phagocyte (strep mutans)

Antiphagocytic chemicals

leukocidins destroy phagocytic white blood cells (Aa)
-chemicals that prevent fusion of lysosome with phagosome (salmonella)


allow bacteria to invade aqueous areas of body and evade phagocytes

Invasive exoenzymes

-cause damage to host tissue in immediate vicinity of organism
-allow spread of pathogen away from initial site of infection
-typical of periopathogens


digests hyaluronic acid (tissue cement)
eg. Staph. aureus, Porph. gingivalis


digests collagen (connective tissue)
eg. P. gingivalis


-lyse RBC
-supplies iron to pathogen
-weakens host
eg. Streptococcuc


Pomotes fibrin clot formation
Protects pathogen from host defense mechanisms
eg. Staph. aureus

Exotoxin B

protease produced by certain strains of invasive strep
eg. flesh eating

Bacterio evade host defense mechanisms by:

a) antigenic variation
b) molecular mimicry

Antigenic variation

pathogen varies its antigenic expression so immune system never 'catches up'

Molecular Mimicry (ninja)

Microbe is not recognized as foreign by immune system because it covers its membrane with host proteins (syphilis)

Bacteria damage host cells by:

1) invasive exoenzymes
2) Bacterial metabolites
3) Toxin production

Damage via Bacterial metabolites

end-products of bacterial metabolism can damage host tissue (acid production by Strep. mutans)

Damage via Toxin production

Chemicals that damage tissue directly or trigger host immune response (inflammation) that causes damage
(periodonatl disease)
1) endotoxin
2) exotoxin


Part of outer membrane of gram - bacteria.
Lipid A of lipopolysaccharide
*released only when cells die
*cause fever, inflammation, diarrhea, septic shock
*heat stable (not destroyed by heat)


proteins produced by gram + bacteria.
Released from living bacterial cell
Soluable in body fluids
Can act far from site of infection
*Heat labile (destroyed above 60 degrees C)
*More toxic than endotoxin
*stimulate Ab production

3 types of exotoxins

Type I: Superantigen (toxic shock syndrome)
Type II: Damage host cell membrane (gas gangrene)
Type III: A-B Toxins - composed of 2 subunits (Active fragment and Binding fragment) (Anthrax)

Oral cavity is continuous culture incubator with:

Supply of nutrients
removal of waste products
moisture, temperature (35-38), pH (6.8-7.2), oxygen controlled
non-homogenous environment (both soft and hard surfaces for colonization)

Microbe numbers

10 (8) bacteria/mg plaque
> 10 (6) baceria/mL saliva
700 microbial species
largest components: Streptococcus spp and various anaerobes

WHy is actual sampling and culturing of oral flora difficult?

-Many strict anaerobes
-Obligate intracellular parasites
-interdependent, grow only in communities (biofilm)

How is microbial diversity determined?

Molecular methods
Gene probes

Most bacterial diseases are caused by?

normal oral flora that increase in # under certainc onditions. Leads to caries or periodontal disease (opportunisitic pathogens)

Factors that influence number and type of bacteria in oral cavity

-saliva : flow rate, buffering capacity
oral hygiene
genetic predisposition
time of day
immune system

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