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Remember that post about evolution as “changes in allele frequency?” It only requires a few minutes to breeze through, but I’ll give you the sparknotes version : when the alleles in a population change, so do the individuals. BOOM, evolution.  But evolution happens over many thousands of years; how do scientists compare allele changes over _smaller time scales?

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Fitness = the contribution that an individual makes to the gene pool of the next generation relative to the contributions of other individuals.

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To condense, if I have four children, and you only have one, then I’m FOUR TIMES as fit as you. It has nothing to do with strength and nothing to do with cunning or ability to do anything. In fact, it can’t even be calculated until after you’re DEAD… how physically fit can you really be then?

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Animals who are the most fit have two defining characteristics:

• They live long enough to reproduce.
• They have either lots of kids, or they have a few children that are pretty sure to survive. This is called having “viable” offspring.

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What this does for scientists is allow them to take information about all of the individuals that were able to reproduce successfully and compare that to information about individuals that were not. From this, they can find out if there are any genetic similarities between those who were successful versus those who were not. This gives scientists a good idea about what is emerging as the evolutionary changes in a small amount of time.

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Hope this helps!

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Let’s catabolize this.

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What is an allele?

You already know that an allele is a form of a gene. Much like shoes come in all different sizes and designs, genes do as well. There’s the tuxedo gene, the air force 1 gene, the stiletto gene, the flip-flop gene, the groovy platform gene… I think you get my drift.

Alleles are the different forms of THE SAME genes that are floating around in the cells of individuals. For instance, baseball and top would be alleles of the HAT gene, whereas stiletto and flip-flop would be alleles of the SHOE gene.  NOTE*: There is a difference between the number and types of alleles and the number and types of genes. Learn more about alleles HERE.

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What is “allele frequency?”

The phrase “allele frequency” is nothing more than a fancy word for a proportion, or percentage, or the total alleles in a group of individuals.

For instance, let’s assume that I have ten marbles. Three of them are red, two are yellow, and five are blue. I could say that the “frequency” of blue marbles is 5 in every 10, or one half, or 50%.

Just like that, the “allele frequency” simply establishes the percentage of alleles that are floating around for a particular gene.

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Let’s put ‘em together!

So, what then, is evolution? Evolution is the result of changes in the amount of certain alleles in a population.

Alleles are forms of genes, so we know that they code for some sort of protein. Different alleles mean different forms of the same protein. It may do essentially the same cellular job, but in a little bit of a different way. When all of these alleles add up, what we see is an organism. If those alleles change, then the organism changes as well.

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How about an example?

Andrew lives in a place that only has three hundred people. Everybody is exactly the same other than their eyes. 100 People have blue eyes, 150 have green eyes, and the other 50 have brown eyes. Eventually, over thousands of years, something happens that makes the green-eyed people move away. Now, there are only 150 people in the town. 100 have blue eyes, and 50 have brown eyes.

The brown eyes allele of the eye color gene once made up only 17% of the total alleles. Now, it’s 33%. For this population of people, it can be said that they have evolved to only have blue and brown eyes… but mainly blue.

It’s a really far stretch, but it’s supposed to be nothing more than an abstract explanation. If you’re still having any problems, post them in the forum, and I’ll try to cater to your issue specifically.

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Hope this helps!

When placing a large number into scientific notation:

1. Place the decimal point after the first integer in the number.
2. Count the number of integers after the decimal point.
3. Round to however many decimal places you’re required to.
4. Take your rounded number and write as (NUMBER x 10^integers ). You don’t have to include the parentheses.
5. Where you see the word integers, write the number that you counted in step 2.

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Here’s a quick example:

• So, we want to put the number 759865783674748 into scientific notation with two places after the decimal.

• The first thing we’re going to do is to place the decimal after the first integer like this:   7.59865783674748

• After counting the number of integers that follow the decimal point, we find that there are fourteen.

• Now, we can round the number to two places after the decimal. Since “8″ is bigger than “5,” we can round up. We end up with 7.60 as the rounded number. You may be asking why we leave that zero there when zeros after the decimal aren’t usually written. When you’re specifically asked to write the number with two decimal places, it’s necessary to fill both of those places, even when it’s just with a zero.

• So, we have all of the pieces. All that we need to do now is to put them all together. Using the formula in step 4, we can arrange the information to get this as the final answer:

• 7.60 x 10¹⁴

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Using small numbers rather than big ones:

• Now that you’ve seen how to write very large numbers in scientific notation, what about really small numbers? The whole point is to avoid writing out a lot of digits. Can’t that be used to write really small numbers too?

• Of course it can. In fact, let’s look at how to write the number 0.000000000003145 in scientific notation.

• This is really similar to what we did before. The only real difference is that in step 4, you’re going to write it as ten raised to the NEGATIVE number of integers.

• You’d think that we’d place the decimal first, just like last time, right? Not quite. If you place the decimal before you count the number of integers between where it is now and where you’re going to put it, how will you know how many integers there are!!?!?

• So, after counting the integers, we find that there are twelve between the decimal point’s start and end location.

• Now that we know this, we can move the decimal to it’s new location… AFTER THE FIRST ACTUAL NUMBER: 3.145

• Round to two places after the decimal: 3.15

• Now, we simply complete by putting all the information together: 3.15 x 10^-12

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Hope this helps!

Grey

One of my favorites, other than those amazing croissants, is his fresh bread. I can’t give away the recipe, but let’s pretend for a second. Let’s say that my friend the baker gets commissioned to cater a luncheon for 24 people. They want him to make his bread, so he decides to be generous and prepare 12 loaves. (That’s a lot of bread when you think about the fact that each person gets half of a whole loaf.) Each loaf of bread requires 7 eggs. If you do the math correctly, you should find that the total number of eggs he’s going to need comes to 168 eggs… aaaaand ACTION!

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Scenario 1 – Before the mole.

Back in his kitchen, my friend the baker has set aside ten extra minutes to check and recheck that he has the correct number of eggs. Why so much time? Because he has to COUNT THEM ALL BY HAND. They come in buckets with to set number in each bucket. He has to sit there and count eggs to 168… and hope that he doesn’t get distracted or lose count. By the time he get’s up to 76, the phone rings for the third time, and he loses count again… there HAS to be a better way…

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Scenario 2 – Mole to the rescue.

Thankfully, eggs come in cute little packages of ONE DOZEN EGGS. There’s not much thinking involved. He knows that every time he reaches for a package of eggs, he’s getting 12. In his head, it only takes a second or two to calculate that he’s going to need 14 packages of eggs. It’s so much easier when there’s a system to make the counting easier. HINT HINT.

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The mole in chemistry is pretty much the exact same thing. It’s just a way of grouping molecules together just like eggs. The only real difference is the size. Since molecules are so small and we are so big, we tend to use measurements that are humongous… try 6.0221415 x 10²³ items in a mole compared to the 12 items that are in a dozen.

It’s a good thing we don’t buy moles of eggs!!

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1. Water is the most abundant chemical compound on the planet.

There are more water molecules in the breath you just took than there are people who you will EVER MEET IN YOUR LIFETIME. I can prove it.

There is one mole of water in every 22.4 liters of air at normal conditions. That means that there is approximately 5% of a mole in every liter of air. A normal human breathes about one half of a liter of air in every breath. That means that there is approximately 2.5% of a mole in every breath. Since one mole is 602,200,000,000,000,000,000,000 molecules, there are 15,100,000,000,000,000,000,000 little waters in every breath. There aren’t even half that many people alive right now.

2. Water can serve as a source of both Hydrogen and Oxygen.

If you know anything about biology, you know that without either of those elements, you wouldn’t last another hour. Both oxygen and hydrogen are necessary for running some of the most foundational cellular processes that keep you alive. A molecule that can give you both of those elements at the SAME TIME is a winner.

3. Water is a medium for almost all biological reactions.

If it happens, it happens in water. Water is just the “in” place among the cool chemicals.

But on a more serious note, water is a wonderful medium for chemical reactions because it allows solutions to be very dense. Much more dense than in air. If your body was to use air for a biological medium in the same way that it uses water, you would either be very very very large or you would always be in danger of EXPLOSION from the high pressure!

4. Water is usually inert/stable at normal Earth conditions.

Water is just smooth… and cool. It doesn’t need to go exploding all the time in order to make friends. It’s smarter than that.

For whatever reason, water has become the perfect conditions for water to exist at a fairly stable state. This means that it is possible for living organisms to use it without much risk of danger.

5. Water can hold tightly to large amounts of heat energy.

It takes a lot to get water all steamed up, but when he’s hot, he STAYS that way. Rawrr!

Water has a ginormous heat capacity, so it doesn’t change temperature very easily. It takes a lot of energy to heat water up, and water releases that heat very slowly. This is advantageous for animals especially because animals (humans included) are composed of mostly water… around 60%. The heat capacity of water makes it easier to control body heat because the water in your body doesn’t allow for rapid temperature changes.

6. Water was the habitat for life on Earth before land was.

Many scientists believe that there was a point, many millions of years ago, that all living creatures lived underwater. Of course, this was long before the Earth looked anything like it does today. Scientists think that the earth was once completely covered in water; eventually geological activity forced the sea-bottom up to the top, and land was formed.

If you’re living in water, fighting every other creature there just to stay alive or competing with everybody else to get access to food, you would have a much easier life if you could live on land. It is believed that some plants and animals were able to make the transition from water to land. Because land creatures were once aquatic, though, we still possess true needs for water as well as the ability to use water for biological reactions.

7. Water can act as both a base and an acid.

In most circles, the definition of an acid is any molecule that releases a lone hydrogen atom into solution, and the definition of a base is usually anything that can release a hydroxide ion. Since every reader of this article isn’t a biochem major, I’ll anabolize this for you.

You know that water is H2O, but that also means that it’s H-O-H. There are two hydrogen atoms and an oxygen atom. A lone hydrogen atom (H+) carries a positive charge that makes it very reactive; this charge causes the lone atom to be called an ion. Likewise, the other half of the water molecule (termed a “hydroxide ion”), carries a negative charge and is also very reactive. When either of these are very concentrated in a solution, they tend to make things happen… as far as reactions go. It gets much more complicated than I can really efficiently describe here, but trust me, the fact that water can do all of that is really significant.

8. Water is the Universal Solvent.

Ok, so everything in the universe can’t dissolve in water. In fact just today in chem class, I learned of a little trick chemists use to describe how much of a “non soluble” compound will actually dissolve. But that’s an idea for another post… and takes that idea in a completely opposite direction.

As far as animals are concerned, all of the necessary molecules are soluble. Water is the medium for ALL major body processes. It is used to regulate temperature and to be the medium for reactions throughout the body. It’s pretty darn significant… if you ask me.

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But there’s not really any surprise there… water is Chuck Norris.

Apparently only the “in crowd” among the bird people know this… but birds have this uncanny ability to see a larger range of colors than humans do. This wider range includes some wavelengths of ultraviolet – that sunlight stuff that you try so hard to avoid. But here’s the real kicker: birds of prey like hawks can use this ability to see trails of urine glowing in sunlight. This leads them straight to those poor little buggers scurrying through the fields. I’ll bet you didn’t know THAT!

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2. That gold you wear is actually bacteria poop.

Well, technically it is. Just like OUR poop, gold is something that the bacteria Pedomicrobium cannot digest, so it is passed right out of their systems… in 24 carat purity. It was a scientist named John R. Watterson who first discovered that many huge lumps of the shiny stuff were plagued with bacteria… they were dead, of course, having been entombed in pure gold for around 200 million years. What a sad way to go… entombed in your own… gold.

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3. Shrub Bombs. Fear Them.

Before I go on, I have to come clean and admit that the picture you see above is not of the amazing burning bush. It’s simply a picture of Adesmia pinifolia… a simple boring shrub. HOWEVER, in some rocky areas of the middle east, there exists a shrub of the genus Cystus that is known for it’s release of flammable gasses. Pretty much all creatures release gases other than just oxygen and carbon dioxide, but this bush is VERY special. On hot, non-windy days, when the plant’s metabolism it at its peak, it becomes enshrouded in a cloud of flammable gas and oxygen – a deadly combination. Even the small sparks made by rocks rolling downhill can be enough to set them ablaze. Crazy, right?

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4. Not all creatures run AWAY from the forest fire.

from palestrina55 (flikr)

Did you really think that the world worked that smoothly? HAH! Puny human.  These beetles are the most hardcore of any that I’ve ever read about… they even beat out the dung beetle. Fire Beetles, as they’re known, can actually smell the charring wood and it causes them to become aroused. They can smell the flames from hundreds of miles away, and they converge on the area to mate. If you’re scratching your head and wondering what could possibly be the advantage to that, think about it this way: if your apartment was just fumigated, and everybody either ran away or died, who would be around to hunt you and your babies? Or to stop you from eating all the food they left behind? Nobody. Likewise, the Fire Beetles take advantage of the area full of rotting wood to deposit their young.

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5. Your perfume angers your house plants.

I really wish I was a good enough writer to make this stuff up. This really isn’t that crazy, but I’m almost positive you’re never thought about it like this. I’m sure you remember at some point in your science education, somebody has told you that organisms need all the energy they can get… so they spend their entire lives doing whatever is necessary to get nutrients. More important, however, is the fact that the “body” of a plant or animal doesn’t WASTE energy once it acquires some. So, do you really think that those “floral scents” that you like so much are JUST TO SMELL PRETTY? No. As it turns out, many of the molecules that COINCIDENTALLY smell good to us are meant to signal other plants about insects in the area. These molecules are sensed by other plants that then start to create anti-bug toxins. Your perfume, air freshener, laundry detergent… in plant language, “them’s fightin’ words.”

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If any of this has sparked your interest and you would like to learn more, check out a BBC documentary series called “Supernatural – The Unseen Powers of Animals.” You can view them all online by clicking here.

Great Danes ruled the world, followed closely by Pit Bulls. There were no laws or languages. Any poor puppy that was unlucky enough to be born had to fight to remain alive 47 hours a day. (Their planet spun more slowly than ours.) Life for them was constant warfare. Anything that COULD be used as protection or as a weapon WAS.

Many dogs found that chewing on the bones of their prey could sharpen their teeth. Some other dogs found that if they didn’t eat a lot, they would lose weight, and they could move much faster. K-9 was an awful place to live… ESPECIALLY for the small dogs – those dogs that couldn’t run quickly and didn’t have sharp teeth or claws. They became very very good at hiding, though.

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One Glorious Day…

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A toy poodle found a teacup chihuahua. Stepping very lightly, so as not to be heard, the poodle creeped up behind the poor chihuahua. The poodle hadn’t eaten in WEEKS, so when he arrived close enough to the chihuahua, he GRABBED it by the tail, THREW it high into the air, and SWALLOWED it whole.

But there was something… ehh, different… about this chihuahua. This awesome little yippy dog passed into the stomach of the poodle and was UNHARMED. (Scientists are still trying to figure that one out.) While passing through the intestine of the now-uncomfortable poodle, the chihuahua became lodged in the cecum. And it STAYED THERE.

One would predict that this would cause problems for both the poodle and the chihuahua, however it benefit both parties. The chihuahua no longer had to fight a losing battle for food on K-9, and because it could digest things that the poodle could not, it helped the poodle get more nutrient from the food. Win-win situation.

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Ok, Ok, Ok, so that analogy isn’t great…

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Let’s see YOU do better. The endosymbiotic hypothesis (the fancy name for this whole shendig), is the most popular scientific theory about how mitochondria and chloroplasts came to exist for the first time.

Scientists think that at one point, they were once unique cells. They think that waaaaaaay back in the day, millions of years ago, the only creatures on the planet were single celled organisms. Germs. They ate each other. So if a cell wanted to survive being eaten, it had to figure out ways to neutralize the the predator’s attacks.

Scientists think that eventually, it just so happened that a cell ate another cell… but there was something special about this cell (*chihuahua*). The prey cell could avoid being digested by the predator cell somehow, but the prey cell could also do something that the predator cell could not. The predator cell couldn’t eat the prey cell, but it could give it nutrients and protection in exchange for whatever the prey cell could do.

When we put this in terms of mitochondria and chloroplasts, we can see that the mitochondria prey-cells had the ability to use air along with sugar to make energy molecules. (Scientists think that this was a lot more efficient than whatever the predator cells had been doing.) As for chloroplast prey-cells, can you imagine how helpful it would be for the predator cell to eat a prey-cell than could make energy from air and light… all the predator cell had to do was give it water! EASY!

SO, let’s recap:

• Mitochondria and Chloroplasts were once feeely-living cells.
• They were eaten by another cell, but they could survive digestion.
• Both cells (predator/prey) had something that the other could use.
• Eventually, the cells came to rely on each other, which lead to the birth of eukaryotic cells as we know them.
  

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Hope this helps,

Grey

One day last month, his mother came home after working a 57.5 hour shift at the factory that makes those metal bands that hold pencil erasers to wooden pencils. Thankfully, it just so happened that Jimmy’s dad was dropping Jimmy off at home before leaving for work at that very moment. (So Jimmy wasn’t left home alone at that age. We don’t want you thinking that we condone leaving children unattended.)

Mrs. Jimmy’s-Mom-Lady was exhausted. Wouldn’t you be? She wasn’t the kind of person that would take out her aggression on her child, but like any human being, she had her buttons for pushing. And like any 8-year-old coming home from school, Jimmy was easily influenced by the song of the ice-creram-truck down the street.

“Mommy, will you please take me to the corner so I can get an ice cream?” Jimmy asked, very politely.

“Mommy is very tired, Jimmy. Why don’t you sit on the porch, and the ice cream man will eventually come past the house.”

At this point, Jimmy stopped being polite and threw a tantrum. His mommy, already at the end of her string, grabbed him by the ear and locked him in the tower until his hair grew long and he decided to change his name to Rapunzel.

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Take Two

Rimmy is the eight year old alternate identity of Jimmy, who lives in a parallel universe.

One day last month, his mother came into his room after working for fifteen minutes from home. She runs a tutoring website and is very successful working from home. :) Jimmy was folding the clothes that he had earlier put through the laundry and was about to begin making dinner.

“Son,” his mother asked using a sparkling set of pure white teeth,” would you like to go for an invigorating jog and then stop by the corner at exactly the same moment that the ice cream truck ALWAYS drives past it.. without fail?”

“Why yes, mother. That would be lovely. Thank you. I shall simply finish these chores, and we shall be off!”

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What the heck does any of this have to do with transport?

How wonderful of you to ask. Jimmy and Rimmy, in these cases, are the substrates (remember that word from the enzyme article?). Their mothers played the role of the transport proteins.

In the second scene, Rimmy’s mother ACTIVELY took a role in ASSISTING her young son in MOVING to the area of some action. In this case, the acquisition of a yummy ice cream treat. Because, his mother USED SOME OF HER ENERGY to play an ACTIVE part in her son’s life, this would be an example of active transport. In a cell, this would be the movement of solutes in and out of the cell using proteins that require energy to pump these molecules across some sort of membrane wall. (Just like in enzymes, they make the movement faster).

In the first scene, however, Jimmy’s mom did NOT take her son to get ice cream. Instead, this scene was set up to highlight one specific aspect. Rather than expending energy to make the action happen (getting ice cream), Jimmy’s mom required him to wait for the action to happen naturally…. WITHOUT ANY INTERVENTION OR MANIPULATION TO MAKE IT HAPPEN FASTER. This is what we call passive transport in cells.

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SO, let’s recap:

1. Active transport: uses energy.
2. Passive transport: does not use energy.

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I hope this helps,

Grey

If you prove me wrong, I’ll be happy to give you the four large… I’ll make four million after I study you and figure out how you work.

For the rest of you, enzymes are one of a bazillion reasons you’re living. But they are the only reason that all the chemical reactions in your body can happen so fast. How fast? A few thousand times or more. For example: when your nerves send signals through your body, they release molecules that carry that signal between nerve cells. In order to set up for the next signal, any extra molecules floating around between the nerve cells have to be eradicated. Neurotransmitter-ase can completely clear out that space in fewer than one hundred milliseconds. (That’s about the same amount of time it took you to read the word “milliseconds.” )

Enzymes are so helpful because they’re so specialized. Each enzyme protein (most of them are proteins, btw) can only bind to one or only a few different molecules. They help to make reactions go faster by changing the amount of energy required to make the reaction take place. (The fancy name for something like this is a “catalyst.”)

Think about it like this. There’s a graham cracker on the table in front of you. For some reason or another, that gracker (that was actually a typo, but I think “gracker” is a good new name for it) needs to be broken apart. Nobody really knows why. Now, there’s a VERY small possibility that you could walk away and not return for 10 years, and that gracker may or may not be broken. In that time, someone else may come along and break it, an earthquake could knock it off the table, aliens with lasers could cut the entire building in half and happen to slice the gracker, or the gracker could spontaneously break all by itself…. although that last one is pretty unlikely.

Regardless, that gracker needs to be broken NOW. Maybe it’ll break without you, but maybe it wont. So, you pick it up, one side of the gracker in each hand. You twist your hands, and the gracker breaks into two pieces. GREAT JOB.

What you just did was to manipulate the mechanism of the reaction. Somehow, you figured out that if you use your hands, you can break the gracker. How smart you are! In much the same way, enzymes manipulate the way a reaction happens. By binding to the enzyme, molecules can be bent, twisted, sliced up, smooshed together, and changed in lots of different ways. BUT each enzyme can only do one thing. Just like genes, those “stupid little dumb ugly gremlins that only do what they’re told,” enzymes have only been trained in one job.

And they are SO PISSY! They will only work under certain conditions. If it’s too hot, they stop working. If it’s too acidic or too basic or too cold or if there isn’t enough substrate (the fancy word that means molecules that bind to the enzyme) they won’t work. They just sit there and complain and then fall apart. Ungrateful little… *grumblemumble…

SO, LET’S RECAP:

1. Enzymes are proteins… usually.
2. Enzymes are catalysts – They make reactions go by faster without actually being changed by the reaction.
3. They manipulate the way a reaction happens.
4. Enzymes are VERY specific – They can only bind one or a few molecules, and they only do ONE job each. (That’s why there are so many of them)
5. Enzymes have evolved to work best in very specific environments – If conditions are too (hot/cold, acidic/basic, etc.), the bonds that hold the enzyme together start to break apart and the enzyme won’t be able to work properly anymore.

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Anyway, I hope this helps!

Grey