Bio week 8 – Cell Time

On By patrickledouxbiologyIn Big Idea 2, Big Idea 3

Image result for cell art

Summary

This week we focused heavily on the mechanics of cells. This included how cells “eat” and “drink,” as well as what makes up the borders of cells and how materials flow through and across these boundaries, aka cell membranes.

Terms

Phospholipid Bilayer– the backbone of the cell membrane, making up most of its surface and structure. It is comprised of two layers of lipids aligned with their hydrophobic fatty acid tails facing each other and their hydrophilic heads facing each other. This provides an effect boundary for the cell, through which only small nonpolar molecules can pass without the help of proteins.Image result for phospholipid bilayer

Extra Cellular Matrix- Wire like in appearance, strands of proteins that attach to cells and hold them to each other.

Image result for extracellular matrix

Passive Transport- The action of molecules moving across the bilayer with no effort done by the cell. This happens when there are varying concentrations of molecules inside vs outside the bilayer, so molecules flow on their own from high concentration areas to low concentration areas.

Image result for Passive transport vs active transport

Active Transport- The action of cells using ATP and protein pumps to ship molecules across the membrane, especially from low concentration to high concentration.

Tonicity- A relative measurement of the combined concentration of all solutes in solution.

Endocytosis- The process by which a cell will “eat” a mass of food (or something like a plastid or mitochondria) by wrapping its cell membrane around the item then enveloping it inside the cell to be digested.

Image result for endocytosis

Exocytosis- The reverse of Endocytosis.

Questions Going Forward:

This past week has made me more excited to learn about specific cell mechanics, and to better understand how my own body functions. That being said, how do ribosomes actually work? Why don’t ribosomes read DNA instead of RNA? Can cells merge? How do cells recognize other cells as part of the same whole? How is food and minerals delivered to cells?

Weekly Reflection #6

On By patrickledouxbiologyIn Big Idea 1

Tundra_Biome_600

This week we began learning some biochemistry, focusing on the properties of water. To start, we reviewed and defined the three subatomic parrticles we will need to know:

  • protons: positively charged particles found in the atom’s nucleus. Have a mass of 1 amu and a charge of +1
  • neutrons: neutrally charged nucleus particles, mass of 1 amu
  • electrons: negatively charged particles that orbit the nucleus. Basically massless and have a charge or -1

These are all what makes up an atom. An element is a type of atom with a specific number of protons, and is the smallest unit of a substance that still retains its properties. (ex. carbon, 6 protons). There are about 120 different elements represented on the periodic table, of which biology uses CHONPS (carbon, hydrogen, oxygen, nitrogen, phosphorous, silicon) most of the time.

We also learned about how atoms interact, i.e. different types of atomic bonds.

  • Bio Covalent
  • Covalent Bonds- bonds created by atoms ‘sharing’ an electron. Ex. O=O bonds or C-H bonds. These bonds are relatively strong.
  • Ionic bonds- created when one atom gives an electron to another atom. This usually happens to complete the outer shell(s) of one or both atoms. This creates an attraction between the atoms as one atom is now negatively charged while the other is positive. In general these bonds are relatively strong.
  • Hydrogen Bonds- Intermolecular bonds that form between the positively charged hydrogen of a polar molecule and the partially negatively charged oxygen or nitrogen end of another polar molecule (ex. H — O bonds between water molecules)

Next, we learned about why water is so important to human bodies. The primary reason for this is that water has a high specific heat (4.184 J/g*C). This means that it takes a lot of energy to change the temperature of an organism containing lots of water, so it is easier for said organism to maintain homeostasis.

Next we had a discussion of the pH scale and what it measures.  We read an interesting set of stories that explained how a lower pH (0-7) indicates an acidic solution, while a high pH (7-14) indicates a basic solution. An acid is a substance that donates protons to solution, like HCl, while a base is a substance that accepts protons (like bleach). The pH of a solution is the -log[H+].

Questions Going Forward

Will we need to memorize the body’s buffer compounds? How much chemistry will we need to know for the AP test? Will we do a lab regarding pH or specific heat?

 

Weekly Reflection #5

On By patrickledouxbiologyIn Uncategorized

This week we moved on from Hardy-Weinberg and focused on the process of speciation. Speciation can be defined as “reproductive isolation,” or the inability of two populations of organisms to interbreed and/or produce fertile offspring. But what would cause a population to split? And what would cause these groups to become so different they can no longer interbreed?

There are several ways this can happen. These fall into two general types of speciation: Allopatric and Sympatric speciation.

Image result for allopatric vs sympatric

In Allopatric speciation, two populations of the same species become physically separated, usually by geographic means. This can include a river, canyon, mountain range, separating continents, etc. This is the more common type of speciation.

In Sympatric speciation, two distinct groups emerge within a population without a physical/geographic barrier between them. This type of speciation is more complicated and less common.

We also learned about the barriers of species, aka the reasons why a giraffe doesn’t mate with a pine tree. These include pre-zygotic (before fertilization) and post-zygotic (after fertilization) barriers. Mechanical isolation and gametic isolation are prezygotic because they make is mechanically impossible for organisms to mate, and for the sperm to fertilize an egg. Habitat isolation, temporal isolation and behavioral isolation are also prezygotic as they prevent organisms from even trying to mate. Postzygotic barriers include hybrid viability, reduced hybrid fertility and hybrid breakdown. These make hybrid offspring of two species either die during birth or are so unsuited to their environment they die anyways. Hybrid Breakdown indicates that the first generation of hybrid offspring are perfectly fine and viable, however after 2 or more generations severe problems begin to arise.

 

Image result for prezygotic vs postzygotic species barriers

Questions Going Forward:

Will these species barriers relate to HWE in any way? How often do hybrid offspring become their own species? How many of the earth’s species are a product of hybrid reproduction?

Weekly Reflection #4 – HWE

On By patrickledouxbiologyIn Big Idea 1

This week’s focus was all Hardy-Weinberg Equilibrium.

Image result for hardy-weinberg equilibrium

We learned the history behind the HWEQ equation, who discovered it, and how to properly use it. We also focused on the conditions necessary for HWEQ. We started out with defining some terms as they relate to Hardy-Weinberg:

  • Gene-  DNA that determines a trait
  • Allele – A variant of a trait (DNA)
  • Dominant Allele – Shows a trait/phenotype, regardless of the other allele.
  • Recessive Allele – An allele that only shows when paired with another recessive.
  • Homozygous – A matching allele pair (PP, dd, hh, KK, etc.)
  • Heterozygous – An unmatched allele pair (Pp, Dd, Hh, Kk, etc.)
  • Evolution – Change in allele frequencies over time.
  • Population – a localized group of interbreeding individuals.
  • Gene Pool – The collection of all the alleles present in a population.
  • Mutation – Creates variation/ new and novel traits. Always happening.
  • Gene Flow – Movement of organisms into/out of a population, changes allele frequencies.
  • Non-Random Mating – Causes sexual selection and sexual dimorphism.
  • Genetic Drift – Random, chance events that change the gene pool.

After learning these terms, we went over the conditions necessary for a population to in HWE, listed below.

  1. Random Mating
  2. No Mutations
  3. No Gene Flow
  4. No Natural Selection
  5. No Genetic Drift

As you can see, very few real-world populations are actually in HWE. What is the purpose of HWE then, if it fails to describe reality? This was an important question this week. Turns out HWE is best used as a null model- a control group.  If you calculate the allele frequencies for a population if it stopped evolving and changing altogether, you can then see how that population has evolved over time compared to the null model. We did a lab to try this technique out on Friday to see if we could achieve HWEQ amongst ourselves. No surprises, we couldnt.

HWE Equation: p^2 + 2pq + Q^2 = 1,     p + q = 1

Synthesis/Questions Going Forward

HWE seems to pull together everything we’ve been learning the past few weeks. It brings all the vocab and methods of evolution and types of alleles into play. This feels like the first relatively powerful tool we’ve received, akin to M1V1 = M2V2 in Chemistry. But how will we better mathematically describe populations and allele frequencies in the future? How will we better simulate reality? Are there ways to account for the things HWE must hold constant?

Big Idea #1

Image result for six fingered amish

 ^ Polydactyly ^

 

 

 

Weekly Reflection #3

On By patrickledouxbiologyIn Big Idea 1

9/23 – 9/28

This week we covered many topics related to evidence for evolution. We began by defining several terms, as to avoid confusion with the way they are used in common speaking.

  • Falsifiability: the idea that scientific thoughts can never be 100% proven, only supported by evidence.
  • Hypothesis: A testable Statement
  • Theory: A major unifying framework supported by all evidence currently known.
  • Law: A deduced fact that will always hold true.

We then discussed the names for the various structures used in comparative anatomy that suggest evolution. Comparative anatomy is a method of deducing organism’s evolutionary relationships by comparing similar structures in their bodies.Image result for comparative anatomy structures

  • Homologous Structures: similar structures in related organisms that serve independent purposes. These suggest that organisms share a common ancestor that had this structure.

 

  • Image result for comparative anatomy structures Structures: Similar adaptations to similar situations and problems (these serve as evidence for convergent evolution)
  • Vestigial Structures: Structures that no longer serve any or very little function, but don’t cause the organism to be selected against (Like the human appendix or the pelvic bones and femurs of whales).

Another topic we covered was the development of phylogenetic (or evolutionary) trees. We learned how modern DNA sequencing results have helped scientists build more expansive and accurate trees, as comparing DNA sequences can reveal evolutionary histories often better than comparative anatomy.Image result for phylogenetic tree

Ongoing Questions:

How is DNA actually collected and read? Can we recreate synthetic DNA? If so, could we design our own synthetic organism? Would that organism be in its own synthetic domain?

HHMI Activity Link: https://www.hhmi.org/biointeractive/creating-phylogenetic-trees-dna-sequences

 

Weekly Reflection #2

On By patrickledouxbiologyIn Uncategorized

Image result for RNA world

This week we reviewed more about evolution and then focused on the origin of life. We learned about two prominent theories of how life first arose on earth, the reproduction-first and the metabolism-first theories. We used these worksheets to read about them. After reading about these theories, I couldn’t help but wonder if we could replicate this process artificially. If we can figure out how life first evolved on earth, could we give rise to an entirely new tree of life that nothing on earth has relation to?

We also joked about how a large percentage of people still do not accept evolution as the source of all species. How do they believe this? Do they deny the existence of evolution purely on religious grounds or do they not believe the evidence for it? Or is it that they were never taught the concept of evolution correctly and they don’t have a good understanding of it?

Sept 10-14 Weekly Reflection

On By patrickledouxbiologyIn Big Idea 1

What we learned this week

This week we learned the difference between and how to calculate standard deviation and standard error. I struggled a bit at first to really understand what these two numbers meant in the context of a data set, but made sure I at least somewhat knew what they were before Friday’s quiz. We then discussed the five pathways of evolution, and looked at examples of evolution in galapagos finches and desert pocket rock mice. We watched clips of a documentary and completed worksheets for each. Finally, we took notes on how the theory of evolution was developed and who contributed to it. Most of the scientists and ideas sounded familiar from freshman-year biology, but a refresher never hurt anyone. Most of these notes and the topics covered this week related to Big Idea #1.

Five Types of Evolution

These categories are how we learned to classify types of evolution, or a change in a population over time. I thought it was interesting that evolution could be influenced in so many unique ways, not limited to natural selection and mutations.

  • Natural Selection
    • The process by which those organisms with traits best fit to the environment survive and reproduce more than those with less suitable traits. This causes a change in the population over time that favors the fitter traits.
  • Mutation
    • Errors that occur while reproducing genetic material. Mutations can either be positive, negative, or most commonly, neutral. The most visible kind of mutation are positives, as neutral mutations do not usually have any effect and organisms with negative mutations wont be able to compete as well and will die out. Positive mutations will cause a change in a population as their organisms will have a competitive advantage over their brethren.
  • Preferential Mating
    • Change in a population caused by organisms preferring to choose mates with certain favorable traits.
  • Migration/Gene Flow
    • When populations of organisms move from one area to another, this causes change in the  makeup of the populations of both the old and new areas. If there is a population of 50 geese with red feathers on a lake, and 25 more geese with blue feathers are forced to move to the lake, the population of the lake has changed from 100% red to 2/3 red, 1/3 blue.
  • Genetic Drift
    • Chance changes to a population. If all the blue geese from above happen to be struck by meteors, the population makeup has changed, but only by chance.

Beaks of Finches, Shades of Mice

Image result for galapagos finches

The primary examples of evolution we focused on this week were in galapagos finches and rock pocket mice populations. For the finches, we observed how different beak sizes in differing situations performed better or worse, like in the drought of 1976. The effects of the drought caused large seeds, the food of big-beaked-birds, to become scarce. This forced the BBB’s to eat smaller seeds, which their large beaks were not very good at. Here we can see that the birds with smaller beaks have become more competitive as the environment changed, and the surviving proportion of birds with smaller beaks was accordingly larger than before the drought. In the documentary we were introduced to the scientists who had dedicated much of their life’s work to catching, tagging and tracking hundreds of finches in order to observe this. This was a good example of evolution caused by natural selection.Image result for rock pocket mice

We were presented with a similar story in the case of the rocket pocket mice. These mice lived in the deserts of Arizona, and were well camouflaged to blend in to the light-colored ground. This changed when a few thousand years ago volcanic eruptions took place nearby, spreading great lava flows out over the desert which cooled into slabs of black rock. The brown-colored mice now stood out in high contrast with the black earth, and so were easy picked off by predators like hawks and owls. The mice did not go extinct on the lava flows, however, as a few were born with a mutation that would have been a disadvantage back in the desert. This mutation effected the gene that controlled the mouse’s production of melanin, the protein that causes the dark color in mammal fur and skin. The mutated mice were dark in color, blending in to the dark lava flows. Sure enough, after several generations nearly all mice living on the flows were black. This was another simple example of natural selection, but also displayed how beneficial mutations can quickly change a population.

Keratin – Summer Item #25

On By patrickledouxbiologyIn Uncategorized

IMG_2406.jpg

Keratin is an extremely tough fibrous structural protein produced by cells. Keratin is essential in holding together an animal’s hair, nails, hooves, horns, beaks, and feathers. In humans, it forms the outer layer of our skin and hair like that pictured above. Another helpful trait of Keratin is that it is very insoluble in water.

List #62

Genetically Modified Organism – Summer Item #24

On By patrickledouxbiologyIn Uncategorized

IMG_2420img_2421-e1536122570231.jpg

A genetically modified organism, or GMO, is any organism that has had its genetic code tampered with or altered by people with modern technology. GMO’s are useful for producing large quantities of food and other goods as they can be configured to provide higher crop yields, resist pesticides or have other favorable traits. The Doritos featured above are one such product that includes these modified crops.

List #53