Neisseria diseases

Neisseria gonorrhoeae: Gonorrhea is an ancient disease recorded even in early Greek time. In fact, gonorrhea came from a Greek term that meant "spilled seed" because they believed that the pus dripping out of the penis was the seed necessary for fertilizing a woman.

Facts about Gonorrhea:
1. It is the second most common STD in the US after Chlamydia.
2. 400,000 cases are reported every year, with an estimated of 800,000 cases endemic in the population.
3. Infection can occur in the mouth, anus, penis, cervix, and the eye (particularly in newborn infants).
4. 95% of men exhibit symptoms, such as purulent discharge, painful urination, while 70% of women exhibit symptoms, also including purulent discharge. Left untreated in women, gonorrhea can result in pelvic inflammatory disease, infertility, and transmission to newborns.

Neisseria meningitidis: Meningitis is a disease that is known to affect people in close quarter, such as dormitory where college students interact with each other.

Facts about meningitis:
1. 3,000 cases are reported each year in the US.
2. Nasopharyngeal area can be infected without symptoms.
3. In most cases, people will develop immunity.
4. Infection can spread to the bloodstream, an event that is called meninges.

Both gonorrhea and meningitis are treatable with antibiotic.

Molecular determinants of pathogenesis:
1. lipo-oligosaccharide (LOS)
2. Sialic acid capsule (in N. meningitidis)
3. IgA protease
4. Iron acquisition proteins
5. Type IV pili
Protein components:
1. PilE = pilin is a major structural subunit
2. PilC
3. PilT

Patriot Act

Something my professor said:

Congress enacted this bill called the Patriot Act. Many of you have probably heard of the Patriot Act. Part of the Patriot Act was that, to work on these organisms, they are willing to give you millions of dollars to work on these organisms, but you have to do it under conditions of biosecurity. They're just the most onerous guidelines that you can imagine. The record-keeping has to be impeccable. Nobody from any of the seven countries that sponsor terrorism can be associated with the lab. You have to all be checked out by the FBI and have federal clearance. Nobody is allowed access to the lab without a witness. It's so onerous that I for one am not willing to do it. People have already been arrested and charged and put into jail. On one hand, they're saying, here's all the money in the world to work on it, but we're going to make you miserable. But that is the way it is, and I guess that's the reality of our times.

Neisseria diseases

Neisseria gonorrhoeae: Gonorrhea is an ancient disease recorded even in early Greek time. In fact, gonorrhea came from a Greek term that meant “spilled seed” because they believed that the pus dripping out of the penis was the seed necessary for fertilizing a woman.

Facts about Gonorrhea:
1. It is the second most common STD in the US after Chlamydia.
2. 400,000 cases are reported every year, with an estimated of 800,000 cases endemic in the population.
3. Infection can occur in the mouth, anus, penis, cervix, and the eye (particularly in newborn infants).
4. 95% of men exhibit symptoms, such as purulent discharge, painful urination, while 70% of women exhibit symptoms, also including purulent discharge. Left untreated in women, gonorrhea can result in pelvic inflammatory disease, infertility, and transmission to newborns.

Neisseria meningitidis: Meningitis is a disease that is known to affect people in close quarter, such as dormitory where college students interact with each other.

Facts about meningitis:
1. 3,000 cases are reported each year in the US.
2. Nasopharyngeal area can be infected without symptoms.
3. In most cases, people will develop immunity.
4. Infection can spread to the bloodstream, an event that is called meninges.

Both gonorrhea and meningitis are treatable with antibiotic.

Molecular determinants of pathogenesis:
1. lipo-oligosaccharide (LOS)
2. Sialic acid capsule (in N. meningitidis)
3. IgA protease
4. Iron acquisition proteins
5. Type IV pili

Protein components:
i. PilE = pilin is a major structural subunit
ii. PilC
iii. PilT

6. Opacity proteins–explains why no acquired immunity is available for Neisseria gonorrhoeae.

Public Health 150A

The Introduction to Epidemiology and Human Diseases class has two homeworks: the first deals with using PubMed as a resource, the second deals with answering questions in time for the lab session.

Using PubMed is necessary for researching on certain diseases and composing Fact Sheet, which contains enough information that you can show to another person, allowing them to have a gist of what a disease does, where it comes from, whom it affects, when its symptoms appear, how to treat it, and why you should worry.

I don’t know what kind of lab the Public Health class will be, because the only lab experience I had was in Chemistry and Biology. In Chemistry, I had to focus on doing experiments, while in Biology, I had to dissect animals and to look at specimens.

how muscle cell contracts

Demonstration of regulation of skeletal muscle contraction: http://www.sci.sdsu.edu/movies/actin_myosin.htmlHow does muscle cell contract?

The basic level of contraction is that myosin is needed to bind with pure actin and hydrolize ATP. However, thin actin filament has two proteins called tropomyosin and troponin that prevent myosin binding in the absence of Ca++.  Multiple tropomyosin molecules bind head to tail to form a continuous chain wrapping around the thin filament. It blocks the movement of myosin along the thin filament. When Ca++ is released from the sarcoplasmic reticulum after a signaling from motor nerve tells the muscle to contract, it binds to troponin, which moves tropomyosin out of the way, allowing myosin to move along the thin filament employing the cross-bridge cycle. Such a freedom of movement causes a contraction.

It seems like too many steps to take, but I understand the necessity to prevent unnecessary contraction.

Molecular and Cell Biology

I don’t think I have the stamina to keep studying molecular and cell biology. It is so boring. No, not really boring. It is just so many things to memorize.

I wish that I had focused on math, or just studied history or political science. Math doesn’t require memorization beyond formulas, but I didn’t like the pressure and difficulty of figuring out answers. Surprisingly, I haven’t explored History or Political Science in my years of higher-education studies: Yes, I did take a US History class for fulfilling the requirements, but I haven’t taken one for an elective, for my own pleasure.

I shall soon see what comes of this major. I think that I will be a science writer. Researching hasn’t been appealing to me since I received a low grade on my midterms. Medical school is even less considered, and has become rather an embarrassing entertaining artifact of a dreamer.

jargon

Cdk activating kinase (CAK) and Cdc25 phosphatase antagonize the activity of Wee1.

16-9 to 16-11 (working on it)

16-9. (b) is true. If a protein that binds to DNA in the region upstream of the promoter sequence of the sys gene is a positive regulator, then loss-of-function mutations in the gene encoding the DNA-binding protein would result in no expression because positive regulation enhances binding of protein, not suppressing of it. Without this positive regulator, transcription cannot be encouraged.
16-10.

a) 1 (given)
b) 6, lac O^c
c) 2, lacZ missense mutation
d) 4, lac operon inversion (excluding lacI), still work because lacI protein work in trans.
e) 5? might be a superrepressor.
f) 3, it doesn’t grow, but it can repress

 

16-11.

a) Genotypes 1 & 2 show that arabinose is necessary to start expression because expression is off without the presence of arabinose.
b) Without araC, as shown in genotypes 3 & 4, the araBAD gene is not expressed, indicating that araC helps to promote expression.

16-12. For each of the growth conditions listed, what proteins would be bound to lac operon DNA? (Do not include RNA polymerase.

a) glucose: lacI repressor
b) glucose + lactose: no proteins
c) lactose: CRP (cAMP receptor protein)

16-13. Assume that each of the seven mutations is one and only one of the genetic lesions in the following list. Identify the type of alteration each mutation represents.

a) superrepressor—cannot induce: 4
b) operator deletion—cannot start: 3 6
c) nonsense (amber) supressor tRNA gene: 7
d) defective CRP-cAMP binding site: 2
e) nonsense (amber) mutation in beta-galactosidase gene: 6 3
f) nonsense (amber) mutation in repressor gene: 5
g) defective CRP gene (encoding CRP protein): 1

problem sets

Now to solve some problems:

Chapter 16: #1, 4-6, 8-15, 18, 19, 21, 22

16-1. a. induction, (4) stimulation of protein synthesis by a specific molecule

b. repressor, (8) negative regulator

c. operator, (5) site to which repressor binds

d. allostery, (2) protein undergoes a reversible conformational change

e. operon, (7) group of genes transcribed into one mRNA

f. catabolite repression, (1) glucose prevents expression of catabolic operons

g. reporter gene, (3) often fused to regulatory regions of genes whose expression is being monitored

h. attenuation, (6) gene regulation involving premature termination of transcription

16-4. Question: Would you expect mutations in the promoter that prevent binding of RNA polymerase to act in trans on another copy of the operon on a plasmid in the cell or in cis on the copy immediately adjacent to the mutated site?

Answer: I would expect it to act in cis because the promoter is the DNA sequence. Therefore, it cannot affect another cell

16-5. Question: Indicate whether the strain is inducible, constitutive, or unable to express beta-galactosidase and permease. Below are merodiploid strains containing lac operon alleles.

a. I+ O+ Z- Y+ / I+ Oc Z+ Y+

b. I+ O+ Z+ Y+ / I- Oc Z+ Y-

c. I+ O+ Z- Y+ / I- O+ Z+ Y-

d. I- P- O+ Z+ Y- / I+ P+ Oc Z- Y+

e. Is O+ Z+ Y+ / I- O+ Z+ Y-

Answer:

Permease Beta-galactosidase

a. constitutive constitutive

b. inducible constitutive

c. inducible inducible

d. constitutive no expression

e. no expression no expression

16-6. Question: Mutants were isolated in which the constitutive phenotype of a missense lacI mutation was suppressed. The operon was now inducible. These mapped to the operon but were not in the lacI gene. What could these mutations be?

Answer: The mutations could be the operator, which allows the missense mutation of the lacI gene to bind and thus repress the gene.

16-8. a. The DNA-binding protein is a negative regulator of gene expression because it suppresses transcription. Without this, the gene becomes constitutively expressed.

b. I should see that reg1 works in cis while reg2 works in trans because regulatory protein of reg2 is able to diffuse throughout the cytoplasm and act at target DNA sites on any DNA molecule in the cell. In contrast, the reg1 is a regulatory site that can influence only the expression of adjacent genes on the same DNA molecule that it is in. Reg2 should be dominant and makes all emu operon inducible, while Reg1 should affect only one operon, the operon that it is on.

I will work on the rest of the problems later. Now I must eat dinner.

Regulation of Gene Transcription

There are negative regulation and positive regulation. Negative refers to inhibition of RNA polymerase activity, while positive refers to enhancement of RNA polyemerase activity.

The gene for degrading the sugar lactose (found in milk) is comprised of lac permease and beta-galactosidase. The lac permease permits the lactose sugar to enter the cell, while the beta-galactosidase is necessary for cleaving the sugar bond. The lac gene is usually not active when the bacteria are in a medium that doesn’t have lactose. Adding lactose will induce the bacteria to express the lac gene.

The Operon Theory

The Operon Theory proposes to explain how repressors, promoters, inducers and other players work to achieve regulation of the gene for lactose utilization. The promoter (P) and the operator (O) are two regulatory elements that make up the lac operon: a single DNA unit enabling the simultaneous regulation of the three structure genes (lacZ, lacY, and lacA) in response to environmental changes.

In the negative regulation model, there is a repressor that binds to the operator and prevents RNA polymerase from binding to the promoter and begin transcription. However, an inducer in the form of lactose can bind to the repressor, inducing a conformational change that prevent the repressor from binding to the DNA. This then allows the RNA polymerase to bind to the promoter and begins transcription.

After the Operon Theory, a landmark in the field of genetics and biology, was proposed, people believed that negative regulation was the only regulative control available.

There was a key question, however, that brought up the idea of positive regulation. When bacteria grow in the presence of glucose and lactose, they do not express the lac gene. It is only when glucose is not available as an alternative source of fuel that bacteria start utilizing the lactose gene.

Positive control helps increase the transcription of lacZ, lacY, and lacA by enhancing the ability of RNA polymerase to bind and initiate transcription. CRP (catabolite activator protein), when bound to cAMP, enables CRP to bind to DNA in the regulatory region of the lac operon, increasing the ability of RNA polymerase to initiate transcription.

Glucose, however, regulates the level of cAMP by decreasing the availability of adenyl cyclase, which cleaves pyrophosphate from ATP to produce cAMP. It is only in the absence of glucose, therefore, that cAMP level rises.