Exam 3 Study Guide
- Structure and function of genes
- Gene expression in bacteria
- Mutation and variation
- Horizontal gene transfer in bacteria
There are three levels at which enzymes can be regulated
- In prokaryotes, expression is generally regulated at the level of transcription
- In bacteria, genes are organized into operons
- Operon- a cluster of genes whose expression is controlled by a single operator
- Operator- a specific region of the DNA at the initial end of a gene or operon, where a repressor protein binds and blocks mRNA synthesis - Repressor protein – a regulatory protein that binds to specific sites on DNA and blocks transcription
One method of gene regulation – ENZYME INDUCTION
a. Inducer binds to the repressor allowing transcription to be carried out by RNA polymerase
- The lac operon is an example of enzyme induction
- When lactose is unavailable, the repressor is active!!
- It binds to the operator region which blocks the binding of RNA polymerase to the operator region
- When lactose is present, it causes a conformational change in the repressor, which renders it unable to bind to the operator
- The lactose operon is in genetic control
Another method is: ENZYME REPRESSION
b. The corepressor binds to the repressor which keeps RNA polymerase from doing transcription
- An example of enzyme repression is the arginine operon o The repressible operon is in control
It is any permanent, heritable change in the genetic info of a cell Types:
- Point mutations – substitution, insertion, or deletion of one or a few bases
- Large insertions or deletions
- Effects of substitution
- Nonsense is the most deadly or lethal type
- Insertions and deletions result in frame shifts
- Insertions or deletions of large segments of DNA can disrupt a gene (depending on where the insertion lands)
- Transposable elements: jumping genes
- Transposons – pieces of DNA that “jump” from gene to the middle of another gene, disrupting it
- Disruption of gene due to insertion of a transposable element: We also discuss several other topics like What is the meaning of memory?
Causes of mutations Don't forget about the age old question of What is the himalayas today?
- Spontaneous – due to replication mistakes or background effects - Induced – exposure to mutagens such as radiation or chemicals - Electromagnetic radiation
- Chemical mutagenizes
Horizontal gene transfer in bacteria
- Conjugation – direct transfer between bacteria We also discuss several other topics like Are marginal cost and marginal revenue, are the same?
- Transformation – uptake of naked, extracellular DNA
- Transduction- transfer of DNA from one cell to another by a virus LECTURE 12 METABOLISM
General Aspects of metabolism:
- Oxidation and reduction
- Connection b/w redox and energy
- Energy storage (ATP)
Metabolism – process by which cells convert nutrients into energy and use that energy to grow If you want to learn more check out What is the resolution of the cuban missile crisis?
Catabolism – process of breaking nutrients into smaller molecules - Releases energy
Anabolism – process of making larger molecules from smaller molecules - Anabolism requires energy
- Energy comes from covalent bonds
- REDOX reactions – reactions that involve the movement of electrons from one atom or molecule to another
- Loss of electrons: oxidation (H-)
- Gain of electrons: reduction (H-)
- In biological systems, electrons rarely travel alone, usually travel with a proton
- Electron carriers – necessary for moving electrons around o Common H-carrying intermediates are NAD and FAD
o Energy is released when covalent bonds are broken
Enzymes and enzyme activity
- Without enzymes, rate of reactions could take years through spontaneous decomposition of bonds
- They’re catalysis’s
- Enzymes break bonds to release energy in seconds
- Rate of reaction is much quicker
REDOX: enzymatic reduction of NAD (coenzyme) using a substrate as an electron donor
- The electron DONOR – substrate
- Enzymes react with the substrate (electron donor)
- Oxidized from NAD+
REDOX: enzymatic reduction of substrate using NADH as an electron donor - Substrate is the electron ACCEPTOR
- Reduced from NADH
- Hydrogen has a negative charge (H-)
Direct control of enzyme activity
- Competitive inhibition – non-substrate “competitor” molecule binds to and blocks the active site
- Allosteric enzyme - one which contains both an active site and a regulatory site (allosteric site) where an effector molecule binds
- Allosteric (feedback) inhibition – an enzyme product (effector) binds to the enzyme itself to block its activity
METABOLISM II: SPECIFIC PATHWAYS
Aerobic respiration: glycolysis, Krebs cycle, electron transport system, ATP generation
Glycolysis, TCA cycle, and ETC
*know inputs and outputs of each
*know important intermediates like molecules
- During fermentation, NADH is recycled
- Glucose is not a product of glycolysis
- Main product of krebs is NADH and FADH
- Be able to count carbons for krebs cycle
o We do this process because of bacteria
o O2 is the final electron acceptor
o If there is no O2, then this doesn’t work all the way through the krebs cycle
o Protons are getting pumped out and form a proton motive force o Protons go back in through the ATP synthase to make ATP o ATP synthase uses the proton motive force to produce ATP o O2 is not the only possible electron acceptor
Other highly oxidized molecules like SO42- and NO3- can also receive the ‘spent’ electrons from the ETC
Biosynthesis - often uses intermediates from catabolic pathways – like glycolysis and TCA – to make new molecules like nucleic and amino acids, lipids, vitamins, etc.).
- The molecules used in anabolism are made during catabolism - The raw materials that are then used to make stuff
Lecture 14 Human Microbiome
Infection and Disease I
Humans as Habitats
- Bodies are great places to be!
o Warm, stable, lots of nutrients available, constant pH & osmotic pressure, etc.
- Our bodies are not uniform environments, though
o Each region or organ differs; skin, GI tract, respiratory tract, etc. provide different conditions
- Animals possess great defense mechanisms
o The successful colonizers (and the successful pathogens -- more on this next lecture) are those that can deal with these defense - “Normal” doesn’t mean non-pathogenic; we often have pathogens (S. pyogenes, S. aureus, etc.) in low numbers in and on us
- Colonization (and infection) frequently begin at mucous membranes o These are found throughout the body. Consist of single or multiple layers of epithelial cells, tightly packed cells in direct contact with the external environment.
- Breaches in the mucosal barrier can result in infection
(pathogenesis)by opportunistic pathogen
- Bacteria may associate loosely or firmly
- The ones that penetrate or go between the cells are usually pathogens How do we get indigenous microflora?
- Normally, a human fetus has NO resident microorganisms - Initial colonization comes during breaking of fetal membranes and, especially, birth itself.
- Environment in general is colonization source: mother, father, doctor, etc. Can vary by maternity wards.
- Initial microflora depends on whether infant is breastfed or not. Bifidobacterium vs. others.
Effects of breastfeeding vs bottle feeding on indigenous microflora - Large effect seen -- breastfed infants develop primarily Bifidobacterium populations, bottle-fed get a mixture of various species of coliforms, Clostridium, Staphylococcus, Streptococcus, Lactobacillus, etc.
- Breastfed infants have __lower pH__ and less buffering capacity in large intestine. This disfavors enterobacteria and favors Bifidobacteria. - Bifidobacterium seem to compete with potential pathogens like Clostridium difficile and some enterobacteria
- Which has a more diverse microbiota?
- Which is less acidic?
Microbiota of specific regions
- Skin surface is unfavorable habitat.
o Mainly populated by transient microbes
o Exceptions are moister areas: scalp, face, ears, underarms, genitourinary, palms, toes.
- Most resident skin microorganisms inhabit _deeper_ layers of the epidermis, sweat glands, and follicles.
- Most of the residents are Gram-_positives_, especially Staphylococcus andPropionibacterium
- Dermis and subcutaneous tissue are normally sterile
- Microorganisms cover the surface and reside deep in hair and glands - Bacteria and fungi form _communities_ on the skin surface - Commensal fungi form hyphae or exist as individual cells. - virus particles live freely and within bacterial cells
- Skin mites live in and near hair follicles
- Eccrine glands
o Widely distributed
o Main glands for perspiration; secrete a hypertonic saline solution with a variety of organic and inorganic substances
o Relatively devoid of microorganisms, probably due to salinity and low pH
- Apocrine glands
o Restricted to underarms, genitals, etc.
o Don’t develop before puberty
o Apocrine sweat has higher pH than eccrine sweat
o Population numbers can be high
- Sebaceous glands -- associated with hair follicles
- Produce _sebum_, chief component of skin lipids
- These lipids have antibacterial activity, esp. against Gram-positive cocci.
- The skin microbiome is highly dependent on the microenvironment of the sampled site
Microbiota of the human mouth
- A great place to live! (in contrast to the skin)
o The only negatives: salivary enzymes (lysozyme and
lactoperoxidase), and constant need to re-attach
- Initially (i.e. at birth), there are only a limited number of bacterial types (aerotolerant anaerobes like Lactobacillus and Streptococcus), o as teeth erupt there are more anaerobes and bacteria adapted to living in crevices and on smooth surfaces
- biofilm / plaque formation
o Begins as thin film of glycoproteins in saliva
o This is colonized (quickly) by individual Streptococcus (S. mutans, etc.) cells, which grow to microcolonies
o Extensive growth of these results in formation of a thick biofilm. Further colonization can include filamentous forms, spirochetes, and various anaerobes
Microbiota of the Human GI tract
- The body is like a donut, with the alimentary canal the ‘inside’ of the donut.
- Things inside the alimentary canal are not truly ‘inside’ the body - where do you think the most bacteria are found??
- What causes ulcers?
- The upper portions of the small intestine are acidic and resemble the stomach.
- The lower portions have increasing numbers of bacteria, from 105 to 107 per gram.
- The large intestine has enormous numbers of bacteria, >10____ cells/gram! (There are approx. 3 X 1011 stars in the galaxy). - The large intestine is essentially a fermentation vessel. -
- pH of stomach is low, around 2
- acts as a microbiological barrier
- Example: Infectious dose of Vibrio cholerae dropped 3-4 logs when it was administered with bicarbonate (like Tums). Foods had similar effect.
- Bacterial count of stomach contents is low, but walls can be heavily colonized.
- Bicarbonate soda changes the pH and makes it easier for them to survive
- Empty stomach- acidic, more bacteria is needed for infection