Thursday, January 31, 2013

Metabolic pathways

Overview
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Energy from Carbohydrates
1. Glycolysis (breaks 1 glucose into 2 pyruvate)
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2. Pyruvate to Aceytl co-A
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3. Acetyl co-A into the Kreb's cycle
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4. FADH2 and NADH go into electron transport chain for oxidative phosphorylation (see post on this topic)

Energy from Proteins
1. Break into Amino Acids (hydrolysis)
2. Transamination: transfering the amino group to a carrier (amino acceptor)
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3. Deamination: take the amino group OFF and send it to be made into urea.  What's left over can be put into the Krebs cycle (alpha-ketoglutarate is one of the steps of Krebs).
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4. Can go straight from Amino Acids to Acetyl co-A then put that into Kreb's cycle
5. Can synthesize glucose out of amino acids when needed, which can then be used or stored as above in the section on carbs


Energy from Fats
1. Triglycerides can be broken down into glycerol and fatty acids
2. Glycerol can be used to make glucose (gluconeogenesis) in the liver
3. Fatty acids can be oxidized into Acetyl-coA (fatty acid oxidation) to go into the Krebs cycle, and harvest energy from there
 
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Wednesday, January 30, 2013

Membrane Transport and Osmotic Pressure

This is a good video giving an overview of all the different kinds of membrane transport.  It also includes an explanation of the sodium-potassium pump which is important in membrane potentials, and it would be great to watch this to help prepare for that section! :)



Overview of types of transport:

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Simple Diffusion
Dissolved stuff wants to get evenly spread out.
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Facilitated Diffusion
This shows all again, but notice the 2 in the middle:

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Osmosis
If the membrane isn't permeable to the solute (ions etc), water (the solvent) is what moves to try to get things evenly distributed.  This is called osmosis.
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Tonicity

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Due to the differences in tonicity, osmotic pressure can cause cells to change because the water moves trying to equalize the solute-solvent ratios.  Here is the classic example of red blood cells in plasma.  The hypertonic/ isotonic/ hypotonic is referring to the plasma or solution, in relation to the inside of the RBC.
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Primary Active Transport
Something is pumped against its concentration gradient, using ATP as the energy source
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Secondary Active Transport
Something is pumped against its concentration gradient, using something besides ATP as the energy source.  In these examples, one ion is pumped with its gradient, and that energy is used to pump something else against its gradient.  Here are a few examples:
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Electron Transport Chain & Oxidative Phosphorylation

This process is really confusing when not understood, and really phenomenal and awesome when understood.  Learn and geek out with me, if you will. :)
First, the electron transport chain (done by Virtual Cell):


Next, the explanation of ATP Synthase:



And a beautiful animation of these processes (see if you can point out the players):


I am so grateful that Virtual Cell and BioVisions have made these awesome videos!

Wednesday, January 23, 2013

Protein Synthesis

As a quick overview, you can see the processes of transcription, translation, protein synthesis and exocytosis in this video.  It's detailed and labelled, the pertinent parts for this post are at minute 4:30 to 5:30, roughly:

DNA --> mRNA --> tRNA --> Amino Acids

Transcription
Source: wikipedia
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Translation

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Here's a great video of this process:

Cell Organelles

Here are some various drawings of an idealized animal cell, showing all the different types of organelles.  Different artists depict them slightly differently, so looking at many versions should be helpful.  If you click the "source" link under each picture, you will find many great websites with further information.  In some cases this will be necessary to be able to see the image.  My black background is messing some of these up, sorry about that.
Look at these to orient yourself, we will then go into detail on each organelle, and then have some unlabeled cell drawings so you can quiz yourself.  Enjoy!


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Organelles
Here are some closeups! :D

Cell membrane


Here is a good depiction of the various things embedded into a cell's plasma membrane (also referred to as the phospholipid bilayer):

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Nucleus

Notice the pores, which is where the mRNA (post-transcription) would emerge to go to a ribosome for translation.
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Mitochondria

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mitochondria
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Here is a labelled mitochondria.  Please note, Matrix and Cristae will come into play when you learn about metabolism.
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And, here is a really sweet video of a mitochondrion, showing some metabolism processes.  FYI Mitochondrion is singular, Mitochondria is plural.  (Link to the animator's website, for better quality, and links to other really cool videos: http://www.xvivo.net/powering-the-cell-mitochondria/)



Golgi

golgi body
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Cytoskeleton

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Identification Practice

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Source: wikipedia

Key for wikipedia image (includes links to wiki pages of each):

Organelles:
1 Nucleolus
2 Nucleus
3 Ribosomes (little dots)
4 Vesicle
5 Rough endoplasmic reticulum
6 Golgi apparatus
7 Cytoskeleton
8 Smooth endoplasmic reticulum
9 Mitochondria
10 Vacuole
11 Cytosol
12 Lysosome
13 Centrioles within Centrosome
14 Cell membrane

The end

Thursday, January 17, 2013

Learning Style

I promised I would post this so students can determine their learning style to help improve study strategies.
It's hard to find any one good test, so here are a few and you can see what meshes with you.

Separates into 3 categories, pretty short, 9 questions:
http://homeworktips.about.com/library/quizzes/bl_lstylequiz1.htm

Multiple Intelligences (longer survey, divides into about 6 categories)

http://www.edutopia.org/multiple-intelligences-learning-styles-quiz

This may be the best mix of simple, not too terribly long, and has 4 learning styles with some tips you can click on afterward:
http://www.vark-learn.com/english/page.asp?p=questionnaire

If I find any better ones I will add them.


Study Skills
Here is a survey about study skills.  I really love this one because when you are done, it gives lots of ideas and resources on how to improve in specific ways based on what your answers indicate you may need to work on.
http://www.angelo.edu/dept/aadvising/study_skills/


Wednesday, January 16, 2013

Homeostasis and Negative Feedback

Homeostasis is very important for life.  Many factors need to stay within certain parameters, or an organism will die.  Temperature, pH, blood pressure, concentrations of nutrients and wastes, etc. all have levels that are optimal and necessary.  Staying within these parameters is homeostasis.

In order to maintain the proper levels, many negative feedback loops are utilized.  Something triggers the release of something, which then inhibits the release of more.  The classic example is a thermostat.  When the temperature drops down below a set level, the furnace kicks on and puts out heat.  Once the temperature has reached the proper level, that shuts the furnace off.  If it didn't have the negative feedback, the furnace would never shut off.

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In the thermostat example, the factor would be temperature, the sensor is the thermometer, the integrating center is the thermostat, and the effector is the furnace (the thing that does the action to make the change to get you back to homeostasis).  The looped red arrow indicates that when the effector (furnace) does its job, that has an effect on the factor (temperature), which then causes it to stop the loop and turn the furnace off once it's reached the right level.

Here is an example in the body, with blood pressure.
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When blood pressure (factor) increases, it is sensed in the baroreceptors in the carotid arteries (sensor), which sends the signal to the brain (integrating center), which sends signals to the heart (effector) to decrease the heart rate.  This will lower the blood pressure so that the stimulus is not continued, and the loop stops.


Just FYI, there are some positive feedback loops in the body as well, which do not contribute to homeostasis, but have different functions.  Eventually the stimulus resolves itself so the positive feedback goes away.  An example is birth.  Stretching of the cervix releases oxytocin which increases contractions, which makes cervix stretch more, which increases oxytocin, and so on, until the baby is born and that stimulus is resolved.

Tuesday, January 15, 2013

pH

 

Water molecules can dissociate into Hydrogen ions (H+) and Hydroxide ions (OH-).  Even pure water will have some of these, but in pretty much equal amounts.
Unequal amounts make a liquid acidic or basic/ alkaline.

Acids are substances that donate H+ ions to the solution:

Bases are substances that donate OH- ions to the solution:


The pH scale is a logarithmic scale.  So, for every "1" on the scale, it's really a power of 10.  A four is 10 times more acidic than a 5, 100 times more than 6, and 1,000 times more than 7.
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 Equations graphics used from: www.all-about-ph.com
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