Bio 280  

operon means what?

Exam 3 Study Guide  

Genetics II  

- 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  

What is an operator in biology?

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  

What is a mutation in biology?

We also discuss several other topics like Socioeconomic means what?
We also discuss several other topics like What is media responsibility?

Mutation 

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  

Point mutations:  

- 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  

- Palindromes

- 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: 

- Metabolism  

- Energy  

- Oxidation and reduction

- Connection b/w redox and energy  

- Energy storage (ATP)

- Enzymes  

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 

- 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

Fermentation 

Anaerobic respiration 

Catabolism: 

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  

- ETC  

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  

Aerobic reparation

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 

Human skin  

- 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. -

Stomach 

- 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