The two main principles that Mendel discovered—the law of segregation and the lat of independent assortment—were the foundation for our modern understanding of genetics. But what Mendel didn’t realise was that there are exceptions to these “laws”, and that inheritance is a whole lot more complicated than that.
It turns out, Mendel’s pea plants had relatively simple genes, always completely dominant or completely recessive. But some alleles can exhibit different degrees of dominance and recessiveness. In some genes, neither allele is completely dominant—this is called incomplete dominance. In some plants, like in snapdragons, the F1 generation produced from crossing a red with a white can actually have pink petals—because the flowers have less red pigment.
We have to be careful here, because it seems to provide evidence for “blending” genes, but it’s actually not. If the blending hypothesis were true, we wouldn’t be able to “recover” the original red or white trait from the pink plant, but we can. When F1 hybrids produce F2 offspring, they can actually be red, white or pink. This tells us that the alleles maintain their identity and aren’t mixed up.
Alleles can also be co-dominant, which means they affect the phenotype in separate and unique ways. For example, there are several alleles for human blood groups, commonly known as A, B, and O. But the A and B alleles are codominant, so when they appear on adjacent loci in an offspring, that offspring doesn’t have A blood type of B blood type—they have AB blood type.
So far we’ve been talking about simple ratios, but how can we mathematically figure out the probability or the percentage that an organism will inherit a trait?
Consider a cross between YyRr and YyRr. Using a Punnett square, we can deduce that for colour, ½ the offspring will be Yy, ¼ yy, and ¼ YY. The same probabilites apply for shape: ½ Rr, ¼ rr, and ¼ RR. (Remember Y=yellow, y=green, R=round, r=wrinkled.) But how do we then figure out how many will be round and yellow, or green and wrinkled?
The rules of probability, of course.
We can determine the probabilities of the genotypes by just multiplying the traits we want to know about together. For example, what’s the probability of the pea ending up yellow and wrinkled? Well, we know that ¾ of our offspring will be yellow, and ¼ will be wrinkled. ¾ x ¼ = 0.1875. So about 18.75% of our offspring will be both yellow and wrinkled. (If you don’t like fractions, just use 0.75x0.25.)
What about green and wrinkled? ¼ x ¼ = 0.0625. So 6.25% will be green and wrinkled. We can do the same for the others:
Yellow and round: ¾ x ¾ = 0.5625 = 56.25%
Green and round: ¼ x ¾ = 0.1275 = 18.75%
Adding all of these up gets you 100%, of course. It also gives us our ratio that we’ve talked about—9:3:3:1.
But all of the above only describe what happens when we follow one particular gene through the cross. Mendel also observed the ratios of different characters as they were crossed together—such as following colour and shape, knowing that round peas are dominant (R) and wrinkly peas are recessive (r). He wanted to know whether certain genes stayed together and were more commonly found with each other, generation after generation, or whether they went their own way—whether they’re inherited independently.
To figure this out, Mendel performed a dihybrid cross, crossing YYRR with yyrr. He found that in the F1 generation, all plants are YyRr, so they’re all yellow and round. But in the F2 generation, after self-pollination, you end up with a ratio of 9:3:3:1—9 parts yellow and round, three parts yellow and wrinkled, three parts green and round, one part green and wrinkled.
If the colour and shape were inherited together, you’d end up with a 3:1 ratio, 3 parts yellow and round, one part green and wrinkled. But because Mendel ended up with the other, more complicated ratio, he realised that the alleles couldn’t be inherited together—they were independently passed down, paying no attention to any of the other alleles. This is called Mendel’s Law of Independent Assortment.
Note that this law only applies to genes on different chromosomes—those on the same chromosome tend to be inherited along with nearby genes (remember it’s more probably that far-away genes are crossed over). Their inheritance are more complex than this law can predict.
One way to easily illustrate and predict the patterns of inheritance is using a Punnett square. Usually, we use a capital letter to indicate a dominant allele and a lowercase letter to indicate a recessive allele. For example, Yy would be a pea plant with one dominant yellow allele and one recessive green allele.
If an organism has two identical alleles for a particular gene (like, a pea with two yellow alleles), then they are called homozygous for that gene (i.e. YY). If they have two different alleles, they are called heterozygous for that gene (i.e. Yy). When you cross two organisms that are both homozygous for the same gene, then their offspring will always be homozygous for that gene too. This is called purebreeding, or breeding true.
When we cross organisms that are heterozygous for that gene, we get:
When we cross organisms that are homozygous but have different alleles like yellow true bred peas and green true bred peas, we get:
Let’s say we have a plant that has a yellow phenotype, but we don’t know what its genotype is—since yellow is dominant, it could be YY or Yy. How can we figure it out? We can perform what’s called a test cross: cross is with a plant that is homozygous but only recessive, like yy. The allele contributed by the yellow plant will therefore always determine the appearance of the offspring—and if all the offspring are yellow, we know the original plant had dominant YY alleles.
If the offspring are half yellow and half green, we know the original plant had Yy alleles.
Quick, possibly dumb, question: how was Mendel sure that the P generation peas were pure-bred?
Nope, not dumb at all. Mendel knew the P generation was true-breeding because he bred it himself. Basically, he allowed a certain variety of pea plant to self-pollinate (which is what peas ordinarily do) for several generations until they were homozygous for a given trait.
He could test this—say he had a yellow pea and allowed it to self-pollinate. If it’s homozygous, it could only ever produce yellow offspring, not the ratios we’ll see later on.
In the 19th century, a European monk called Gregor Mendel performed experiments in the garden of his abbey that would forever change the course of biology. Until that point, farmers and agriculturalists had been attempting to grow hybrids of plants with mixed success, because they didn’t really know what laws dictated how genetic information is passed on. Though Mendel had never looked through a microscope and had no idea what the actual process of DNA replication and meiosis was, he still was able to determine four fundamental rules of genetics through the power of his well-designed experiments.
Mendel’s experimental subjects were peas (Pisum sativum). Not very exciting, but perfect for what he wanted: they had short generation times, a large number of offspring, can both self-pollinate or pollinate with others, and they were available in lots of varieties. Their physical characteristics like colour and shape were also very obvious, allowing him to visually track the changes through the generations. Remember that the expression of a gene is called a character, like pea colour, and the expression of an allele is called a trait, like green or yellow pea colour.
Mendel selected pure-bred pea plants with particular traits and cross-bred them in order to see what phenotypes they expressed in different generations. Using carefully planned experiments, he figured out patterns of inheritance.
In a typical experiment, Mendel would take two very different pure-bred plants and cross them together. For example, he crossed a pure-bred yellow pea plant with a pure-bred green pea plant. This mating is called hybridisation. Note: we call the first generation the P generation (for parent), the second generation the F1 generation, and the third generation the F2 generation, usually given by self-pollination.
In completing this yellow and green pea cross, Mendel found this relationship:
In the F1 generation, all plants produced yellow peas. Even though the parents were green and yellow, the F1 generation didn’t mix the colours to be greeny-yellow—they were just yellow.
Then, when Mendel crossed the F1 gen with the F1 gen (through self-pollination), he found that only three quarters of the plants had yellow peas, and one quarter mysteriously were green. This 3:1 ratio is recurring—remember it.
This happened every single time Mendel crosses plants in this way. He realised that this regularity must be the key to some underlying mechanism of inheritance.
If crossing two different genes plants could blend the genes, then we’d expect the F1 generation to be a greeny-yellow colour. However, this isn’t the case. So what happened to the green in the F1 generation? Obviously it hasn’t disappeared completely, because it crops up again in F2. Mendel reasoned that it was hidden from view, and termed the yellow colour as a dominant trait and the green colour as a recessive trait. We now know that there are dominant alleles and recessive alleles, and only one is expressed in the phenotype.
In order to come up with the law of segregation, Mendel noted four related concepts.
Offspring have different physical characteristics because genes have different “versions”, called alleles. These account for variation.
For each gene, an offspring inherits one allele from each parent.
If two alleles at a locus are different, then the dominant allele will determine what the organism looks like. The recessive allele will have no observable effect.
The two alleles for a gene of one parent separate when gametes are formed. They end up in different gametes, so the egg or sperm only get one of the two alleles present in the somatic cells of the organism. For example, if the gene has a dominant and a recessive allele—this separation means that 50% of gametes will end up with the dominant allele, and 50% will end up with the recessive one. This is called the Law of Segregation.
Mutations in the nucleotide sequences are the original source of genetic variation, causing different versions of alleles to exist. Once we have these differences, alleles can then be reshuffled, like a pack of cards, in order to produce the variation that makes each individual organism have its own unique combination of characteristics.
In sexually-reproducing organisms, most variation arises from processes that happen during meiosis and fertilisation.
Independent Assortment of Chromosomes:
When homologous pairs (with one maternal and one paternal chromosomes) line up at the metaphase plate in meiosis I, their orientation is random—there’s a 50% chance that the daughter cell will be given the maternal or the paternal chromosome of any given homologous pair.
In addition, each homologous pair orients itself independent of whatever any other chromosome is doing, i.e. independent assortment.
The daughter cells are therefore just one of many possible combinations of maternal and paternal chromosomes. Because humans have 23 chromosomes, the number of possible combinations is 2^23, or about 8.4 million.
Each individual gamete does not have only one paternal or one maternal chromosome. Rather, it actually ends up with a mix of them. This is due to recombinant chromosomes.
As we saw in our discussion of meiosis, in prophase I homologous pairs join up along their lengths, precisely aligning with corresponding alleles next to each other. Then, they essentially swap out alleles, exchanging them along their lengths—like swapping arms.
The further away alleles are from each other, the more likely they’ll be swapped. Alleles that are located close to each other are therefore more likely to be inherited together.
What results is a pair of homologous chromosomes that have been randomly mixed up.
This is incredibly important, because mutations are happening all the time. They can actually destroy the function of genes, so if no crossing over ever occurred to increase diversity, mutations would just accumulate and eventually all genes would be destroyed. Instead, crossing over helps non-mutated chromosomes to reform.
Basically, a sperm cell randomly chooses an egg cell. Because each one is already one of 8.4 million combinations, the random fusion of sperm and egg produces a zygote of 70 trillion possible combinations (2^23 x 2^23).
All somatic cells are produced through mitosis, which is the process of cell division that we’ve already talked about. But sex cells, or gametes, do not replicate and divide this way—they go through a similar but distinct process called meiosis. This is because they have to remain haploid, otherwise the next generation would have two sets of 43 chromosomes, and the next generation would have double that, and overall it would be an enormous disaster.
Meiosis only occurs in the ovaries and testes, and many of its steps are similar to mitosis. You might want to go quickly brush up on my cell division post before we go on, so you remember how it’s done for somatic cells.
Like mitosis, meiosis is preceded by chromosomes replicating, but the actual process is split into two parts—meiosis I and meiosis II, each with their own version of prophase, metaphase, anaphase, and telophase and cytokinesis. Meiosis starts with one diploid cell and results in four haploid daughter cells, as opposed to the two diploid cells that mitosis creates. The point of mitosis is to preserve identity and copy the cells’ DNA faithfully, while the purpose of meiosis is to create gametes with maximum diversity.
In this initial stage, the homologous chromosomes in the diploid parent cell replicate, forming sister chromatids. It goes from two sets of chromsomes to four sets of chromosomes (represented as 2n to 4n).
In this stage, the parent cell (4n) divides, forming two haploid cells with the replicated chromosomes (2n).
Prophase I: Chromosomes condense and form homologous pairs (i.e. composed of one paternal and one maternal chromosomes). These pairs are lined up gene for gene, so the loci for different genes are aligned. A special protein structure physically connects them along their lengths—this process is called synapsis. While they’re connected, crossing over is completed (we’ll talk about that later—basically it’s a process to boost diversity). Then, the spindle forms, the nuclear envelope breaks down, and the homologous pairs move towards the metaphase plate.
Metaphase I: The homologous pairs are aligned on the metaphase plate.
Anaphase I: Homologous pairs are allowed to separate and they move towards opposite poles, as guided by the spindle apparatus. At this point sister chromatids are still attached to each other and move together.
Telophase I & Cytokinesis I: Each half of the cell has a complete haploid set of chromosomes, each composed of two sister chromatids. Cytokinesis occurs, forming two haploid daughter cells.
Then, the two haploid cells replicate and divide again, forming four haploid daughter cells (1n).
Prophase II: Spindle apparatus forms. Chromosomes move towards metaphase plate.
Metaphase II: Chromosomes align, and because of crossing over, the sister chromatids aren’t identical.
Anaphase II: Sister chromatids are separated and more to opposite poles are individual chromosomes.
Telophase II & Cytokinesis II: The nuclei form and the chromosomes decondense. Cytokinesis splits the cells, producing four haploid daughter cells in total. Each is genetically distinct from BOTH each other and from the parent cell.
We know that DNA contains the genetic information of the cell, providing the instructions for how to build proteins. We know how DNA replicates itself and we know how somatic cells divide. But how does DNA actually determine what we look like and who we are? Why does one person have brown hair while the other has blonde? How can someone have blue eyes if both of their parents are brown-eyed?
It’s all down to the chromosomes in the cell.
Humans are diploid organisms, meaning we have two copies of every chromosome—remember, a chromosome is the condensed version of DNA. In most of our cells (all our somatic cells), we have 23 chromosome pairs, totalling 46. These cells are therefore diploid.
22 of these 23 pairs of chromosomes are called autosomes. But the last pair is the pair you’ve probably heard about the most—the X and Y chromosomes. These are called allosomes, and females have two X chromosomes while males have one X and one Y chromosome. The Y chromosome mainly carries genes specific to maleness, so it’s smaller, while the X chromosome is larger and much more important, carrying thousands of genes for all different aspects of life, and only a small number to do with determining sex.
Some cells, however, don’t have the full 46 chromosomes. They only have half that—26. These are called haploid cells, otherwise known as gametes or sex cells. Sperm and egg cells are haploid, which makes sense because they have to join up to become what’s called a haploid zygote, forming the basis for a new living being.
In this offspring, therefore, one set of chromosomes come from the father (sperm cell), and one set of chromosomes come from the mother (egg cells). Thinking about allosomes, the father could contribute an X or a Y, and the mother can only contribute an X. There’s a 50-50 chance that the offspring will receive an X or Y, so there’s a 50-50 chance a child will be male or female.
Along a chromosome, located at specific locations (called loci), are specific sequences of nucleotides called genes. Genes are the heritable units that parents pass onto their children—the nucleotides code for a specific character, which is the physical manifestation of the gene: for example, there is a gene that codes for eye colour. The different variations of genes that code are called alleles, and they are expressed as traits; for example, blue or brown eyes.
Chromosomes are called homologous chromosomes when they both carry genes that control the same traits at the same places—for example, they would both carry the gene for eye colour at exactly the same loci. The X and Y chromosomes are an exception to this; though human females carry a homologous set of XX chromosomes, in males, X and Y chromosomes are only homologous in certain places. These are therefore called sex chromosomes instead.
An offspring gets a set of alleles from both its mother and its father (on the chromosomes it receives from the egg and sperm cells). For eye colour, it might get one green and one brown allele—but the offspring will not just mix them together and have greeny-brown eyes. It either has green or brown; only one allele is expressed.
So how is it decided which one is expressed? It’s not 50-50. It’s actually because for each type of allele, one is dominant and one is recessive. The dominant allele is therefore expressed physically while the recessive one is not.
The way people look does not necessarily reflect their genetic make up. You might have red hair, but you could have alleles for both red and blonde hair, and no one would know from looking at you. We call an organism’s physical appearance its phenotype (i.e. the physical expression of its alleles), and its genetic make-up its genotype (the set of alleles that it has). Its genotype is therefore all the possible characteristics that could happen, and its phenotype is what actually happens, as determined by both the alleles and the environment.
We learnt about all the mechanisms in the last article, now let’s see how proteins are actually put together.
There are three stages of translation:
mRNA, tRNA carrying the first amino acid, and the two subunits of ribosome come together
The smaller subunit binds to both the mRNA. There are two sites: the A site where the start codon sits, and the P site where the first codon sits.
A peptide bond is formed between the amino acid carried by the tRNA and the start codon.
The amino acid slides down through the unit so a new one can be attached.
Amino acids are added, one by one.
The stop codon is reached.
A protein called a release factor binds to the stop codon. This causes a water molecule to be added to the polypeptide chain instead of an amino acid, which breaks the bond between the chain and the tRNA.
Translation is complete.
It’s important to note that proteins are synthesised in a particular “direction”, just like DNA is—proteins are synthesised from the N-terminus to the C-terminus.
It’s also important to know that there’s a difference between DNA replication in prokaryotes and eukaryotes. Prokaryotes don’t have nuclei, so it all happens in the cytoplasm—while in eukaryotes, the process is segregated: transcription happens in the nucleus, and translation happens in the cytoplasm.
So that’s the way it happens: DNA to RNA to PROTEIN. That’s how everything is made. Because this is absolutely fundamental—this process is the basis of everything that we are. Building proteins from DNA instructions is essential to living beings, and it’s happening inside of me and you right now—every second, billions of tiny enzymes and ribosomes and RNA molecules are swarming around inside of you, making copies of the most fundamental part of you: your literal identity.
DNA is the genetic information of the cell—the blueprints for how every protein in your body is built, dictating the sequences of amino acids. However, although our genes provide the blueprints, they don’t directly build the proteins. That job is delegated to the ribosomes, the cell’s protein-synthesising machinery.
But in eukaryotes, the DNA never leaves the nucleus, and ribosomes are in the cytoplasm. There needs to be some mechanism for getting DNA’s information to the ribosome—and mRNA (messenger RNA) does the job.
Messenger RNA (mRNA) is a strand of RNA that holds the faithful translation of the protein-building instructions of DNA. Remember that RNA is a nucleic acid just like DNA, but it differs in three man ways:
Its main sugar is ribose, not deoxyribose.
It only has one strand, not two.
Its nucleotides are Adenine, Uracil, Cytosine and Guanine—so A pairs with U instead of T, and C pairs with G like in DNA.
mRNA is created by an enzyme called RNA polymerase, which uses a strand of DNA as a template. This process is called transcription, and there are three stages.
RNA polymerase binds to the DNA strand at a very specific sequence of nucleotides, called the promoter. RNA polymerase can’t actually recognise the promoter sequence by itself, so it uses the help of something called the TATA box.
RNA polymerase begins to move along the DNA strand, unwinding the helix by breaking the hydrogen bonds between the DNA’s nucleotides. The base pairs are exposed and are paired with RNA nucleotides: A with U, T with A, G with C, C with G.
Behind RNA polymerase, the freshly synthesised RNA strand peels away from the template, and the DNA double helix reforms (hydrogen bonds are usually pretty keen to snap back together).
The RNA polymerase has to be given a signal to stop transcription. In prokaryotes, there’s a terminator sequence in the DNA just like the promoter sequence, and the RNA polymerase recognises it and detaches.
In eukaryotes, however, there’s this extra step where pre-mRNA is created—almost like a draft of the real mRNA. RNA polymerase transcribes a signal sequence on the RNA, which cause associate proteins to cut the pre-mRNA free. The polymerase, however, keeps on transcribing for a few hundred nucleotides—bit of a waste, really, because the RNA it creates is usually just digested by an enzyme.
So, what’s up with this pre-mRNA business in eukaryotes? Basically, before it’s sent out as a genetic message to the cytoplasm (where all the ribosomes are), enzymes modify the pre-mRNA. This is called RNAprocessing. The ends are given a “cap” and a “tail” to protect them and aid with attachment later, and bits from the transcript are cut out and the remaining bits are spliced together.
Imagine your friend has just given you a copy of their short story to edit. There are some parts you really like, but there are other parts that are utterly unnecessary to the plot. So before you give it back to them, you make some edits—you delete the side-adventure about the runaway cat, you remove the misogynistic old uncle, and then bridge the gap between the scenes. The story is a whole lot cleaner and more efficient now.
That’s basically what happens in RNA processing. There are sections of a DNA sequence called introns that are non-coding—they don’t actually code for any amino acid sequence, they’re just there, scattered amongst the rest. Whatever they say is not expressed in protein building. The other regions are called exons, which are coding and are expressed. In RNA processing, enzymes do some editing, splicing out those useless intron sequences and stitching the exons up seamlessly.
So the mRNA that is sent out into the cytoplasm,all grown up and off to synthesise proteins, is an abridged version of the original DNA sequence: a continuous coding sequence.
Next, we’ll learn about how proteins are assembled: translation.
Now let’s take a look at the movers and the shakers of DNA replication, the enzymes.
Enzymes and their functions:
These untwist the double helix at the replication fork, breaking the hydrogen bonds between the nitrogenous bases (A, T, C, G) in order to unzip the strands. This then makes them available as template strands.
Single stranded binding proteins:
These bind to the unpaired DNA strands, keeping them separated—if you’ve gone to all the trouble of prying them apart, you don’t want the hydrogen bonds snapping back together.
When the double helix untwists, it causes strain on the whole system—this enzyme relieves the stress by breaking, swivelling, and rejoining the DNA strands.
After topoisomerase does its work, the strands are ready to serve as templates for the synthesis of complementary DNA strands. But although enzymes can perform this synthesis, they can’t initiate it—only add to the end of an existing chain.
The initiation job is up to the RNA primase, which makes a short, initial chain of nucleotides called an RNA primer from 5’ to 3’.
These enzymes use the RNA primer as a starting point from which to synthesise DNA, then they go along and add nucleotides to the template strand. They also have proofreading abilities, able to check the nucleotide they just synthesised against its template.
There are three types of DNA polymerase, which differ mainly in how long they can work before they call off the template.
I and II are mainly repair enzymes that can only proofread ahead of themselves (from 5’ to 3’); I can also remove the RNA primers from the Okazaki fragments, ripping them up like railroads, and put down nucleotides instead.
II can make far more phosphodiester bonds than I before falling off. III, on the other hand, basically has to synthesise the entire chromosome, so it stays on for a long time—they can make about half a million bonds.
III are fast, accurate little proteins, and they have the unique ability proofread backwards, from 3’ to 5’, basically meaning they can back up and remove nucleotides it put down wrong. These guys are so good at their job that on average, there’s only 1 error in every billion nucleotides. When DNA polymerase finds one, it removes it and resumes synthesis. When it misses one, a mutation can occur.
Since the polymerase can only synthesise in a 5’ to 3’ direction, they have no way to complete the bit at the 5’ end of the daughter cell where RNA was originally put as a starting point. Therefore, as we go through successive rounds of replication, the ends become shorter and shorter.
But there’s a way to fix this. At the end of a strand is a telomere, a region where nucleotides are repeated like a little cap to help protect the chromosome from deterioration or fusion with a nearby chromosome. When these are shortened, the enzyme telomerase adds nucleotides to the ends, lengthening it again so they don’t become shorter in the next round of replication. It’s been proposed that this process of shortening is linked to the aging process.
This enzyme joins up the sugar-phosphate backbones of the Okazaki fragments, making them into a continuous DNA strand.
Hopefully you now have a basic idea of how DNA replication works. It can take a while to get your head around all these enzymes, though, so check out the videos I’ve linked to below to see it in a different light. Next time, we’ll talk about how the information in DNA can actually be used to build useful things like proteins.
This process is the foundation of who we are—without it, our cells could not reproduce, and we wouldn’t be able to live. I’ll run through the basic process, then let the proteins do the talking for me.
Essentially, in replication, the double helix is unwound in two separate strands by the enzyme helicases, which break the hydrogen bonds between the base pairs. The base pairs are explained, ready to serve as a template for the synthesis of new strands. The place where the helix is being unwound is called the replication fork. The replication fork has a bunch of enzymes swarming all over it, including DNA polymerase which synthesises new nucleotides to whack down like train tracks as the helix unwinds.
However, DNA polymerase can only add new nucleotides in a 5’ to 3’ direction, so one strand is going to get left out. An enzyme can just zip over the top strand and synthesise a matching one since it’s facing the right direction, and it’ll keep going as the strand keeps unwinding because the enzyme is moving left. But the bottom strand has to be synthesised in a 3’ to 5’ direction too, which is in the opposite direction to the way the helix is unwinding, away from the replication fork. So we’ve got these bits constantly being exposed at the fork.
Instead of synthesising continuously like the top strand, the bottom strand has to be synthesised discontinuously—little bits at a time, starting at the replication fork and moving until they reach the last fragment. These fragments are called Okazakifragments, and in humans, they’re only made in stretches of 100-200 nucleotides. These fragments then have to be stitched together by an enzyme called ligase, creating one long continuous strand.
Because the bottom strand has to wait for the replication fork to open up a bit before it can start synthesising fragments, the process takes slightly longer—so it’s called the lagging strand, while the top strand is called the leading strand.
Another problem faced by the lagging strand is the creation of RNA. See, DNA polymerase, which synthesises new nucleotides and thus creates the new strands, actually lacks the ability to initiate the process. It can’t start strands out of nothing—it needs to have something to build off of. So, an enzyme called RNA primase is given the job of creating a short, initial stretch of nucleotides. Then DNA polymerase latches on and happily zips off.
In the leading strand, the RNA primase needs to do its job just once, and DNA polymerase chugs along continuously. But in the lagging strand, RNA primase constantly has to create new initial chains of nucleotides—one for each fragment. As you can probably imagine, this is a nightmare—because it means that between every Okazaki fragment, there are bits of RNA, disrupting your DNA strand.
So, before the Okazaki fragments can be stitched together by ligase, these RNA bits have to be removed.
Finally, once all this is done and the lagging strand has been patched up, we have two DNA molecules: each one with one parent strand, and one daughter strand, as per the semi-conservative model. Pretty neat, huh?
Next time: the super-long explanation of the mechanisms behind it all.
In 1958, Meselson and Stahl performed what has been called the most beautiful experiment in biology in order to figure out which model of DNA distribution is correct. It really is dazzlingly simple.
They knew that nitrogen is a key component in DNA—the nucleotides are made up of nitrogen, hence being called “nitrogenous bases”. Almost all of the nitrogen in DNA is nitrogen-14 as it’s the most common isotope in nature. An isotope is an atom that is the same element but has a different numbers of neutrons, making it either heavier or lighter, and sometimes making it unstable and thus radioactive.
While nitrogen-14 makes up about 99.6% of all nitrogen, there are some rarer isotopes like the non-radioactive nitrogen-15 (0.04%). It’s rare enough to be distinctive, which is why Meselson and Stahl chose to use it in their experiment.
Firstly, they took E. coli cells (bacteria that usually live in our gut and divide every 20 minutes) and grew them in a medium that contained nitrogen-15 isotopes. This meant that the nitrogenous bases of the E. coli’s DNA was now being made out of the heavier N15 instead of the normal N14. After several generations, until their DNA was saturated with 15N, and there was no 14N left.
As a control, an ultracentrifuge was used to extract DNA from the E. coli. A centrifuge is used to separate material by density, so it separated out the 15N DNA and allowed Meselson and Stahl to see the “level” of density of the 100% 15N DNA in a solution.
The lighter the sample is, the higher the band will be—the heaviest band, the 100% 15N DNA, will always be the lowest.
Afterwards, the 15N E. coli was placed into an environment that had regular 14N, and they were allowed to divide and reproduce and have all the fun they wanted. After one generation (20 minutes!) DNA was extracted again using the centrifuge—and this time, Meselson and Stahl saw something different. The density of the new DNA molecules had decreased. They realised they were seeing hybrid DNA, containing both the heavier 15N parent strand and lighter 14N daughter strand.
This ruled out the conservative model—if it were correct, they would have seen two distinct bands: one lighter all 14N band, and one heavier all 15N band, because parent and daughter strands stick to their own kind.
But still, at this point, they couldn’t tell whether the DNA molecules were half daughter and half parent like the semi-conservative model suggests, or had bits and pieces distributed throughout like the dispersive model suggests.
So, the E. coli were allowed to replicate again. After another generation, they extracted the DNA yet again with their ultra-cool ultracentrifuge. Now, there were two bands: one heavier band that was still a hybrid (half 15N, half 14N) and one lighter band that was all 14N. If the dispersive model was correct, then we would have seen a band that was neither pure 14N or exactly hybrid—its density would have been somewhere in the middle, since the original 15N would’ve been split (dispersed) randomly among all the strands.
So that had to mean the semiconservative model of DNA replication is correct. When DNA replicates, the resulting molecule is made up of one parent strand and one daughter stand—in this case, one heavier strand and one lighter strand.
If the experiment kept going onto successive generations, we’d see the 14N getting progressively more and more predominant, essentially phasing out the 15N—the opposite of what Meselson and Stahl did at the very beginning to get their E. coli specimens ready.
So to recap: separate DNA out by density, and voila, you’ve proved something that is fundamental to every living being!
Don’t worry if you have no idea how DNA actually physically replicates—that’s coming up next.
So: for the next few articles, we’ll be talking about DNA replication, which has to happen in order for cells to grow and divide. Remember when I told you the somatic cell cycle was all about preserving identity? When cells split, they need the exact same DNA as the original cell so they can carry out the same functions perfectly, so all of the original DNA has to make an exact copy of itself.
To do this, the DNA double helix peels apart into two strands, and each strand then serves as a template for new strands to be synthesised. This makes sense—base pairing rules dictate that Adenine must be paired with Thymine, and Guanine with Cytosine. When the double helix splits, the base pairs are exposed and they are able to dictate which nucleotide must be synthesised to match. The “daughter” strands that are produced are exact replicas of the “parent” strands.
This process involves a whole bunch of enzymes, and we’ll go through that in more detail next article.
But for now, let me just ask: what happens to the strands after replication? We’ve got a separated double helix with two parent strands, and two synthesised daughter strands. We know they’ve got to become two double helixes, but are they shuffled around? Which goes where?
In the 1950s, when Watson and Crick first proposed the double helix structure ased on Rosalind Franklin’s data, there were three prevailing theories for how DNA was distributed after replication.
Conservative model: This model suggested that the two parent strands split, served as templates for daughter strands, and then returned to their original pairing with themselves. The two daughter strands, meanwhile, paired up too. So, the parent DNA molecule is “conserved”.
Semi-conservative model: This is the model that Watson and Crick proposed, though they had no evidence. It suggests that each new DNA molecule will have one parent strand and one daughter strand. That is, they don’t return to their original states like in the conservative model; they stay where they are synthesised.
Dispersive model: This model suggests that the DNA is synthesised in short pieces as the double helix unwinds bit by bit. This means that both the parent and daughter molecule have a mixture of old and new parts, dispersed throughout the molecules.
To figure out which model is the correct one, we did what we always do in science when we don’t know the answer: an experiment. Wait with baited breath til the next article, kids.
Rubisco is the most abundant protein on Earth. It’s used to recognise carbon dioxide in the Calvin Cycle of photosynthesis and fix it to RuBP, so it’s incredibly important to the food chain on Earth—but it’s actually incredibly bad at its job.
It only correctly recognises CO2 about 80% of the time, making the two 3-phosphoglycerate molecules it’s supposed to. This process is called carbon fixation. The other 20% of the time, Rubisco mistakenly grabs up oxygen and attempts to fix it to RuBP, instead producing only one 3-phosphoglycerate and one phosphoglycerate plus a CO2 molecule. This process is called photorespiration. Although Rubisco can make 3-phosphoglycerate with oxygen, it’s far less efficient.
Rubisco does this because carbon dioxide and oxygen are fairly similar-looking molecules, as they both have two oxygens. The percentages above are a rough estimate at 25 degrees Celsius—when the environment is hotter and the ratio of O2 to CO2 in the environment increases, the inefficiency increases too.
To make photosynthesis more efficient, some plants in hot or arid environments have developed alternative methods of carbon fixation, which focus on concentrating carbon dioxide. Plants that just use the Calvin Cycle method are known as C3 method, but while the plants that use specialised methods are called C4 and CAM.
The C4 method is used by plants that live in hot, dry, intense-light conditions, like sugar cane, corn, and tropical grasses. C4 plants aim to keep the concentration of CO2 high and the concentration of O2 low in the chloroplast. They have two special mechanisms that help them do this: a specialised lead anatomy, and a more efficient enzyme to “fix” the CO2 that comes into the chloroplast.
First of all, CO2 molecules that enter through the leaves’ stomata are transported into thin-walled mesophyll cells. Here, the enzyme PEP carboxylase is used to fix CO2 into a temporary 4-carbon compound (hence the name of the method). PEP carboxylase is pretty good at discriminating between CO2 and O2, so we say that it has a highaffinity for CO2. Because it can bring in CO2 quicker, the stomata have to be open for less time, and so less water is lost through them.
Then, the mesophyll cells pump the carbon compound across to specialised bundle sheath cells, which have much thicker walls that don’t allow CO2 to leave or O2 to enter. Here, the carbon compound is split into CO2 and a 3-carbon compound, and the Calvin Cycle takes place in the bundle sheath cell’s chloroplast, where CO2 is much more highly concentrated than in the chloroplast of C3 plants. Thus, the CO2 is delivered “directly” to Rubisco, so it basically has less opportunity to screw up.
This process is much more efficient than C3 (from 10 to 120 times more efficient!), but the main drawback is that it costs quite a bit of ATP in order to pump the organic acid into the bundle sheath cells. Because of this, C3 plants often outperform C4 plants if they have sufficient water and sunlight. About 0.4% of plant species use the C2 mechanism.
CAM plants are even more water efficient than C4 plants, and mainly include succulents like Cacti, as well as some orchids, pinapples, and ferns.
CAM plants keep their stomata closed all day in order to conserve water, but during the night—when there’s no sunlight and the temperature is lower—the stomata open to let CO2 in and let O2 out. But if there’s no sunlight, the light reactions can’t take place and so neither can the Calvin Cycle. Photosynthesis can’t go ahead.
So instead of going straight into the Calvin Cycle, the CO2 that comes in is fixed into an organic acid called malic acid (by PEP carboxylase again), and stored away. Then, in the heat of the day, the stomata close, the acid is broken down, and the CO2 is passed onto Rubisco to be used in photosynthesis. This process all takes place in the same cell, rather than shuttling the CO2 between cells as in C4 plants.
Hi! I saw your reply to someone who failed grade 12 from health issues. I'm not sure this would mean much, but I just wanted to say that I had been in a similar situation too- not a whole grade, but I did fail some classes and my disease is incurable so I thought that was it, and I'd given up. A few years & many drs. appointments later, I've found some treatment and I just wanted to say that even though I'll still always be sick, that things can get better unexpectedly, even if it cant be fixed.
Thanks so much for messaging and sharing your situation! It’s such good news that things are getting better for you xx
Photosynthesis is sometimes described as the opposite of cellular respiration, but that’s not really accurate. Quick recap: in cellular respiration, energy is released from sugars when electrons (from hydrogen) are transported through the electron transport chain to an oxygen molecule, where they form water. As these electrons and protons “fall” down the ETC, their energy is harnessed to make ATP.
Photosynthesis, however, reverses the direction of the electron flow. Water is split up and electrons are taken from it. These electrons and their associated hydrogen protons are transferred to carbon dioxide, and they reduce the carbon into a sugar. Sugars are the endgame of photosynthesis; they’re the organic compounds we use to get energy for our bodies. The process of moving the electrons requires energy—which is supplied by light.
This is the equation always quoted when explaining photosynthesis, but it doesn’t do very good job at illustrating the processes going on—the reactants and products don’t actually occur at the same time, like equation suggests.
There are two different stages of photosynthesis: the light reactions (the “photo” part) and the Calvin Cycle (the “synthesis” part). The light reactions take place in the the thylakoid membranes, and the Calvin Cycle takes place in the stroma (the dense fluid inside the chloroplast around the thylakoids). They’re often called the light-dependent reactions and the light-independent reactions, because only the light reaction needs light directly in order to proceed.
Let’s talk about the light reactions first.
Remember that there are two protein complexes in the thylakoid membrane called photosystem II and I. In the heart of each photosystem is a reaction centre: an enzyme that uses light energy to reduce (give electrons to) molecules. The reaction centre is surrounded by light harvesting complexes that transfer light energy from pigments down to the centre.
When a photon of light strikes photosystem II, it excites an electron in a chlorophyll pigment. In this excited state, chlorophyll becomes unstable—it wants to get back to its stable ground state. When the electron “falls” back down to its normal state, its energy excites another pigment, and then that excites another, and so un until the energy reaches the reaction center. Here, the energetic electrons are given to a primary electron carrier called plastoquinone. Plastoquinone then transports these electrons through an electron transport chain into photosystem I.
Back in PS II, these electrons are replenished by splitting up water into its components: H2O became electrons, protons (hydrogen ions), and oxygen. The oxygen pairs up with another oxygen and is released as O2, a byproduct. The electrons and protons are used to replenish the electrons and protons that are constantly moving onto PS I.
So, back to the electron transport chain. While the electrons get carted into PS I, the protons are being pumped into the hydrogen space. This creates a gradient, which can be used to generate ATP via chemiosmosis—just like in cellular respiration in the mitochondria. But while the mitochondria use it to turn chemical energy into ATP, chloroplasts use it to turn light energy into ATP.
Meanwhile, the electrons in PS I are passed through to the reaction centre, where an electron carrier is waiting for them. A pair of electrons and a hydrogen ion are transferred to NADP+, reducing it to NADPH. This carrier is the endgame of the light reactions. It’s what all this fuss has been about.
After it’s reduced, NADPH+ leaves the photosystems and ventures out into the stroma, ready for the Calvin Cycle, where it will become a sugar.
So, a quick round up: H2O, NADP+ and light go into the light reactions, and O2, ATP and NADPH come out.
However, what I’ve explained above is called non-cyclic electron flow. This is only one of two possible pathway that electrons can travel in the light reactions. The other pathway is called cyclic electron flow.
Cyclic electron flow only uses photosystem I, and it doesn’t give any electrons to NADP+—so it doesn’t create NADPH. Instead, electrons are just passed from PS I through an electron transport chain, causing protons to be pumped across the membrane to create ATP, and then the electrons get put straight back in PS I. The main goal of cyclic electron flow is simply to create a bit more ATP—because the next step, the Calvin Cycle, needs more ATP than NADPH, so the light reactions need to make a bit extra.
Obligate aerobes: require oxygen for cellular respiration and can’t live without it.
Facultative anaerobes: make ATP by aerobic respiration if oxygen is present, but can also switch to fermentation or anerobic respiration when it isn’t.
Obligate aneorobes: only carries out fermentation or aerobic respiration. Can’t use oxygen—may, in fact, be poisoned by it.
Glycolysis can occur without oxygen, but at some point in aerobic respiration, there’s a point where oxygen is essential to continue on.
The electron transport chain in aerobic respiration uses oxygen as its final electron acceptor, so when oxygen isn’t available, it can’t pass on its electrons. This means it can’t take electrons from NADH and FADH2 because it’s got nothing to give them to, and the whole cycle gets blocked up. Normally, the ETC and the citric acid cycle are intricately linked, because when the ETC oxidises the electron carriers to NAD+ and FAD+, it just passes them back to the citric acid cycle to get recycled all over again. So when oxygen isn’t available and the electron transport train stalls, it stops the citric acid cycle too.
The electron transport chain could use some other atom accept its electrons, like sulfate or nitrate. These aren’t as efficient as oxygen, because they have smaller reduction potentials (i.e., not as good at accepting electrons), but they manage. It just means that fewer ATP are produced in comparison to aerobic respiration.
This process, where oxygen is not the final electron acceptor, is called anaerobic respiration (i.e., without oxygen).
Anaerobic respiration is sometimes used interchangeably with the term fermentation, but there’s a difference. Anaerobic respiration doesn’t use the citric acid cycle (which doesn’t produce oxygen but is an aerobic process), but it still uses the electron transport chain to create a proton gradient across membranes to power ATP synthase.
Fermentation, on the other hand, creates ATP through substrate-level phosphorylation. It doesn’t use the electron transport chain or a proton gradient—it attaches phosphate groups directly to ATP without the help of ATP synthase. Fermentation doesn’t produce much ATP, though. It doesn’t use the citric acid cycle or the ETC—it occurs directly after glycolysis. Remember that glycolysis produces NADH, so fermentation only has one NADH to take an electron from and make energy. Its endgame is actually to oxidise NADH to NAD+ again, because that will allow glycolysis to continue in the absence of oxygen. The hydrogens that are taken from NADH are given to the pyruvate molecules from glycolysis, and one of two things happens: they form either ethanol (alcohol) or lactate, which forms lactic acid.
Humans are not entirely obligate aerobes—fermentation can actually occur in our muscles, forming lactate. When we’re exercising and we can’t get oxygen to our cells quick enough, fermentation occurs, which is what causes muscle fatigue.
Ethanol is formed when a carbon dioxide molecule is removed from pyruvate, and a hydrogen is removed from NADH. The result is NAD+, ethanol, and CO2. The enzyme that facilitates this reaction isn’t found in humans, though, which is a relief or else we’d be walking around drunk all the time.
There are a variety of ways that pyruvate can be broken down to extract energy, but by far the most efficient is aerobic respiration—with oxygen as its final electron acceptor, you just can’t beat the output of dozens of ATP.
From the mitochondrial matrix, the products of the citric acid cycle—NADH and FADH2—move into the mitochondrial membrane. Thanks to endosymbiosis, the mitochondria has two membranes, and the electron transport chain (ETC) takes place in the inner membrane and the inter-membrane space.
So, we’ve got these two electron carriers, NADH and FADH2, and we know they contain energy because we know that every hydrogen atom has one electron. These molecules pass into the membrane, which contains four special protein complexes that span the membrane.
The first protein complex strips the electrons from NADH, and actually separates the electrons from their hydrogens atom too. Hydrogen only had one electron in the first place, so basically all that’s left are protons (these are called hydrogen ions). The protein complex then chucks the NAD+ molecules away as a byproduct and pumps the protons up into the inter-membrane space. Electron carriers pass the electrons across to the next protein complex.
In this next protein, the same thing happens to FADH2. Hydrogen ions are pushed up into the intermembrane space, FAD+ is cast off, and the electrons are passed into the next complex. This one does something a bit different—it gives the electrons away, passing them down into the mitochondria, where they’re grabbed up by an oxygen atom (this atom is called the final electron acceptor, for obvious reasons). This oxygen atom is paired with a hydrogen ion (just a proton) to form our good friend H2O.
But remember our endgame here—we’re trying to churn out ATP, not water. And anyway, where did we get that hydrogen ion if they’re all swarming about up between the membranes?
Here’s the deal: protons are positively charged, and there are a whole bunch of them up in the inter-membrane space. This creates something called a proton gradient, which means there’s this imbalance of charges from one side of the gradient to the other. Those hydrogen ions are keen as hell to balance out the charges—they want to cross back through the membrane and join the mitochondrial party. But the electron transport chain pumped them up there for a reason, and it’s not going to let them get back down without making them pay a toll.
So, in order to come down, the hydrogen ions have to force their way through the last protein complex in the chain: ATP synthase. The name gives it away—essentially, the kinetic energy of the hydrogen ions pushing back down turns a kind of turbine in the protein, which creates enough energy to smuch an ADP molecule and a phosphate group together, forming ATP. This process is called chemiosmosis and is part of a bigger process called oxidative phosphorylation. (Chemiosmosis is specifically using the diffusion of hydrogen ions to generate ATP, and oxidative phosphorylation is the overall metabolic pathway that uses energy released by oxidation to make ATP.)
These processes are pretty efficient. For each glucose molecule, glycolysis makes 2 ATP, the citric acid cycle makes 1 ATP, and the electron transport chain makes about 32–34.
Man, this is exciting because I finally get to say it—THIS is where the majority of the energy gets made. THIS IS THE POWERHOUSE OF THE CELL.
So wait, what about those hydrogen ions that shove their way down through that turbine? These are those same ions that join up with oxygen, the final electron acceptor, to form water. Tidies the whole thing up nicely.
Here’s a diagram that may or may not make this less complicated:
3 NADH and 1 FADH2 come in from the citric acid cycle and are stripped of their hydrogens by the protein complexes. 3 NAD+ and 1 FAD+ are released, and passed back to the citric acid cycle to be recycled.
The hydrogen atoms are split; the hydrogen protons are pushed up into the intermembrane space, and the electrons are passed through the complexes and are attached to oxygen, which grabs up some hydrogen ions and forms H2O.
Hydrogen ions do work down their concentration gradient to power a turbine that generates ATP from ADP + Pi. Approximately 32–34 ATP are produced for each glucose molecule.
Note that because oxygen is the final electron acceptor, this process can only happen if oxygen is present. If not, anaerobic respiration or fermentation occurs.
The citric acid cycle (sometimes called the Krebs cycle) occurs in the mitochondrial matrix and is the third stage in the aerobic breakdown of glucose. The first, of course, is glycolysis, which creates pyruvate, NADH, and ATP. The second—which isn’t long enough to get its own post—is the linking reaction in which pyruvate is converted to Acetyl CoA. This is a coenzyme that the citric acid cycle breaks down to use later in energy production. Basically, the purpose of the linking reaction is to make pyruvate into something the cycle can use.
The main goal of the citric acid cycle is to convert bond energy (in the form of Acetyl CoA) into its reducing equivalents: i.e., to make some more NADH and FADH2, which are electron carriers. These then go through the electron transport chain and use their electron energy to create ATP. Remember, to reduce a compound is to add electrons to it—think of the mnemonic OILRIG.
So, how does the citric acid cycle do this?
Some diagrams get pretty complicated, especially when you include the enzymes responsible and the carbon compounds formed at every stage, but I’m going to break it into relatively simple steps.
An enzyme joins acetyl-CoA to oxaloacetate in order to form citric acid, which is where the cycle gets its name. Then, a water molecule “attacks” the acetyl, and CoA is ejected from the cycle.
Next, water is ejected and then put back in to help facilitate the reduction of NAD+ into NADH. For every turn of the cycle, 3 NADH molecules are created, and 2 molecules of CO2 are released.
ADP plus a free phosphate group (denoted as “Pi”) is put into the cycle, and these are smushed together to form an ATP.
Finally, FAD+ is reduced to FADH2. (FAD and NAD are both very similar coenzymes, performing the same oxidative and reductive roles in a reaction, but they’re different because they work on different classes of molecules: FAD oxidises carbon-carbon bonds, and NAD oxidises carbon-oxygen bonds)
A diagram might make it a little clearer:
So, let’s do a quick round-up of what’s happened:
Acetyl-CoA has been released as two CO2 molecules
3 NAD+ were reduced to 3 NADH
1 FAD+ was reduced to 1 FADH2
1 ADP+Pi formed 1 ATP molecule
This isn’t the end—the main goal of citric acid cycle is to prepare the electron carriers NADH and FADH2 for the electron transport chain, where much more ATP will be made.
The name “glycolysis” is delightfully fitting: glyco means “carbohydrate”, and lysis means “splitting”. That’s exactly what this first step in cellular respiration does: split a carbohydrate. Glycolysis occurs in the cytoplasm so it doesn’t need any special organelle, which means that every living organism can do it. It also doesn’t require oxygen—remember that, because it’ll be important later on.
Here’s what happens: 1 glucose molecule (a six-carbon sugar) is split into two three-carbon sugars, which are oxidised and arranged to form 2 molecules of pyruvate, 2 NADH, and 4 ATP.
Really, there are six steps in glycolysis, but they involve a whole bunch of enzymes that we don’t need to worry about (if you study further biochemistry, you’ll have to worry about it, so good luck with that). What we need to know is that the whole process can be split into two short phases: energy investment and energy payoff. Glycolysis can’t just create ATP from nothing—it actually invests two ATP molecules in order to run the processes to get more back.
In the energy investment phase, a phosphate group is taken from each ATP molecule and attached to the 6-carbon glucose molecule. This process is called phosphorylation, and causes the ATP molecules to become ADP. The glucose molecule is then split in half, forming two 3-carbon sugars with a phosphate attached to each. These are called Glyceraldehyde-3-Phosphate (G3P).
In the energy pay-off stage, the G3P molecules are given an inorganic phosphate group each, and simultaneously transfer one hydrogen atom each to two molecules of NAD+, creating two molecules of NADH (a coenzyme that carries electrons). The G3P molecules are therefore oxidised (because they lose electrons) and the NAD+ is reduced (because they gain electrons).
Four ATP molecules are then produced by substrate-level phosphorylation, which is a process where phosphate groups are given directly to ATP. (Note: Be aware that there’s a difference between substrate-level phosphorylation and oxidative phosphorylation; we’ll talk about it soon).
So, the debt of the investment phase is paid off—glycolysis used up two molecules of ATP and got four back, giving us a net profit of 2 ATP.
These phosphate groups were taken from our G3P molecules, and once they’re gone, our 3-carbon sugars rearrange to become two 3-carbon molecules of pyruvate. The carbon bonds of pyruvate have a lot of chemical energy stored in them, and in the next few stages of cellular respiration, I’ll show you how this energy is extracted.
Here’s a breakdown of what we’ve done:
6-carbon glucose is broken down into two 3-carbon pyruvate molecules.
2 NAD+ have been reduced to 2 NADH.
2 ATP have been invested, yielding 4 ATP—with a net gain of 2 ATP.
At this stage, we come to a crossroads. Up until this point, we haven’t needed oxygen to do anything, but now there are two options: if oxygen is present, we can go onto the citric acid cycle and complete aerobic respiration. If oxygen isn’t present, we can go onto fermentation.
Further resources:Khan Academy: Glycolysis (Khan Academy literally got me through my bio class so excuse me if I link it a lot)
Can anyone recommend interesting lectures or special talks on YouTube? I listened to Feynman’s ‘Los Alamos From Below' today and it was hauntingly fantastic. I need some more compelling sciencey stuff to pass time on my way to work - suggest some?
So, this is where it gets relatively exciting: this is where the energy that runs every one of your cells comes from. The process is called cellular respiration, and it uses oxidative and reductive reactions (known as redox reactions) in order to release energy stored in the bonds of glucose molecules. It does this through four distinct stages: glycolysis, link reaction, the citric acid cycle, and the electron transport chain.
It sounds daunting, but friends we are going to OWN cellular respiration by the time I’m done.
First of all, you need to know what oxidation and reduction mean, because they’re terms that are going to be used a lot. My saving grace is the mnemonic OIL RIG.
OIL: Oxidation is losing electrons.
RIG: Reduction is gaining electrons.
In biology, it can sometimes get confusing because biologists like to talk about oxidation as losing hydrogen, and reduction as gaining hydrogen. This took me weeks to figure out, but basically, they do this because hydrogen only has one electron and one proton. So, if a molecule gains one hydrogen atom, it gains one electron (and is reduced). If a molecule loses one hydrogen atom, it loses one electron (and is oxidised). For the purposes of cellular respiration, we can use hydrogen and electron interchangeably when talking about redox reactions.
Quick example: if NAD+ becomes NADH, it has been reduced. If NADH becomes NAD+, is has been oxidised. The little + signs on diagrams are really handy; obviously, if something has a positive charge, it’s lost an electron.
Redox reactions are just the transfer of electrons. Certain compounds in cellular respiration such as NADH and FADH2 act as electron carriers, taking electrons from glycolysis to the electron transport chain, where they’re used to make ATP, the cell’s energy currency. Think of them as like tiny shuttle buses. The first few stages of cellular respiration aim to make these little guys, and the last stage aims to extract energy from them.
Enzymes need to be regulated, otherwise they might make too much of one thing or too little of another. Activators and inhibitors are used to moderate the interactions between the enzyme and the substrate. Activators help increase the activity of an enzyme, like green lights, while inhibitors do the opposite, like red lights. There are two types of inhibitors:
Competitive inhibition: This is when another molecule binds to the active site that the enzyme wanted. The enzyme now can’t fit—they literally have to compete to get the active site first.
Non-competitive inhibition: A non-competitive inhibitor doesn’t bind to the active site—it binds to a different spot on the substrate. This can actually distort the substrate, which sometimes makes the active site change shape—so the enzyme might not fit, and the reaction can’t take place.
These inhibitions are often reversible—inhibitors might only bind temporarily, freeing up the substrate after a little while. But irreversible inhibitors bind permanently, completely blocking active sites and thus significantly reducing reaction rates.
Hi. Last year you happened to give an speech as part of a year 12 graduation ceremony at your old school. I would just like to thank you for doing that. I happened to fail year 12 due to a of slew health issues, but your speech showed me that was okay and that I should still try to pursue my passions. I would just like to thank you for that.
I’m sorry to publish this publicly but I really wanted to reply:
I am so, so touched to get this message. I’m so glad that my talk made even one person feel okay about where they’re at, because I really meant every word—you do not have to be defined by any grade that anyone ever gives you. High school is never the limit.
I hope you’re doing much better than you were health-wise.
Please feel free to keep in touch and let me know how you’re doing, if you’re comfortable with doing so!
Sciencesoup I absolutely love and adore your work that you put in for each post. As much as I love cells and Biology, can we get a little more of the Astronomy again or possibly just small fun fact posts to read about in between the biology ones?
Hey bud, I’m actually studying for exams right now and writing up these biology posts is past of my revision. Otherwise, I’m flat out studying+working+interning so I don’t have time to write anything else. When the biology series finishes, then we’ll be back to a broad range of posts.
I just realised that I haven’t yet explained what enzymes are, even though I’ve mentioned them like five times.
Enzymes are a special kind of protein that are really good at causing and carrying out chemical reactions—they’re catalysts. A catalyst is something that speeds up a chemical reaction without being consumed by the reaction; all enzymes are catalysts, but not all catalysts are enzymes. These reactions are responsible for breaking molecules apart and building molecules back up again, so essentially enzymes are the workforce of the cell. Without them, your food wouldn’t be broken down into usable energy, and you’d starve.
Enzymes can act as catalysts because each chemical reaction has an activation energy—i.e., an amount of energy that has to be put in before the reaction goes ahead. Enzymes lower this activation energy, so it takes less energy to cause the same reaction.
Imagine trying to push a boulder across a flat plain. It’s heavy and you’ve got to overcome friction, so you’re finding it hard to budge. But then your friend helps you push—and suddenly you’ve got to expend a lot less energy to get it to move. Your friend, in a way, has lowered the activation energy of the boulder.
Because they’re proteins, enzymes are made up of a string of amino acid monomers joined together in a specific order. We know that the 3D structure of proteins determines their function, and the amino acid sequence determines the 3D structure, so the sequence is especially important when making up enzymes—it essentially makes the enzyme an efficient catalyst for a specific chemical reaction.
Each enzyme has only one function, and every substrate (the substance upon which an enzyme acts) has its own enzyme. Because of this, enzymes have to “fit” with their substrate, like a key in a lock. A reaction occurs only when the enzyme slots into the substrate at a place called the active site. Enzymes bind there using temporary hydrogen bonds.
Like living workers, enzymes have optimal work conditions. Temperature and pH have especially big effects. Cold temperatures will slow the reaction rate down, and as the temperature increases, molecules will have more kinetic energy so they’ll moving around faster, increasing the probability that they’ll collide and thus cause a reaction. Each enzyme has a specific optimum temperature where the reaction rate is at a maximum. Very hot temperatures can distort the enzyme up, lowering the reaction rate again to the point where it’s denatured and it can no longer work.
Enzymes are also affected by pH, interfering with their bonds and active site. Like temperature, each enzyme has an optimum pH—for example, an enzyme that has developed to work really well in the acidic environment of your stomach might be completely useless elsewhere in your body.
Reactions can also be sped up if enzymes use cofactors, which act like helper molecules, temporarily binding to the enzyme’s active site in order to help recognise the right substrate. Cofactors can either be inorganic molecules, like metal or zinc ions (called prosthetic groups), or organic molecules (called coenzymes). Prosthetic groups bind tightly, while coenzymes bind loosely.
Lastly, a little trick: if the name of a substance ends in –ase, you can assume it’s enzyme. It’s not a rule, but it’s a good guide—lactase, maltase, polymerase, helicase, and ligase are all enzymes.
Eukaryotic Cell Cycle: Stages of Mitosis and Cell Division
Finally, the cell cycle, where one cell becomes two and cell growth occurs. For any multicellular organism, cell division is a vital part of life—otherwise, we wouldn’t be able to maintain our bodies.
Just a note before we start: in the previous post, I wrote up the definitions of a bunch of important terms, because otherwise this post would be complex and cluttered. It might be helpful to have that post up in a separate tab to refer to when you’re reading through this.
First, here’s an overview of the stages of the cell cycle:
Interphase is where the preparatory work happens, and mitosis is where the interesting stuff goes down. Interphase is further broken down into three stages:
G1 (Gap 1) phase, where the cell grows, ready for DNA synthesis.
S (synthesis) phase, where DNA is replicated—i.e., the chromosomes duplicate.
G2 (Gap 2) phase, where the cell continues to grow until it’s ready to enter mitosis. There’s a checkpoint between G2 and mitosis—if something goes wrong, the cell will undergo programmed cell death (apoptosis: essentially, cell suicide). If everything goes fine, it will continue onto mitosis.
Mitosis looks like a small part in a larger cycle, but it’s perhaps the most important bit. This is where the duplicated genetic material is divided equally (pretty much the most important goal of cell division), and the two daughter cells are created. The basic steps are as follows: chromosomes condense, the mitotic spindle is formed, the nuclear envelope is broken down, the chromosomes are aligned, and then chromatids are condensed. After that, the cell is divided into two and the process is done.
But to understand all of what I just said, we need to look at the process in more detail. For that, we can break mitosis down into four main phases: prophase, metaphase, anaphase and telephase (PMAT). Cytokinesis (the division of the cell) is tacked onto the end of this. It’s important to note that these phases are arbitraty—mitosis is a continuum, and creating these phases just helps us understand the sequence.
In this stage, chromatin condenses into neat chromosomes that are about 10,000 times more compact than DNA in its initial state. There’s a good reason this is necessary: DNA is huge. If you wanted to stretch out all the DNA of a single cell into a straight line, you’d end up with a molecule that’s two metres long. Condensing the DNA into chromesomes is a pretty smart move—if you think it’s the end of the world when your headphones get tangled, imagine the chaos when your DNA gets tangled.
The rest of prophase is essentially just preparatory work: in order for chromatin to become chromosomes, DNA first needs to form chromatids, which each get a kinetochore, and then sister chromatids join up at the centromere to finally form chromosomes.
Then the nuclear envelope breaks down into smaller vesicles, and the mitotic spindle begins to assemble, its fibres stretching across the cell.
Next, the kinetochores attach the centromere of each chromosome to the spindle fibres and move them towards the middle of the spindle. Since the kinetochore microtubules on either side have equal pulling force, the spindle pulls back and forth, and the chromosomes move until the tension at either side of them is equal—and thus, they line up at the metaphase plate, right in the middle of the spindle and equidistant from the poles. Think of it as cellular tug-of-war.
The binding kinetochore proteins break down, the centromere divides, and the sister chromatids separate. They move to either side of the spindle poles. The cells then start to elongate, ready for division.
This is almost the reverse of prophase. The chromosomes decondense, becoming chromatin again, and the mitotic spindle disassembles. Two new nuclear envelopes form at either end of the cell, around each new set of chromosomes—so two daughter nuclei are formed. Now, mitosis is complete.
This is the last stage (not technically in mitosis). Here, the cytoplasm divides and the two daughter cells are officially formed. In animal cells, thin filaments form a “cleavage furrow”, like a fibrous rubber band around the middle of the cell, which is pinched tight until the cell separate into two. In plants, a cell plate forms where the metaphase plate was, which connects with the plasma membrane and eventually splits the cells.
Note: mitosis is the replication of somatic cells, which are all of the cells except for sex cells (gametes). Sex cells undergo meiosis, which we’ll discuss later. The aim of the mitotic/somatic cell cycle is to preserve identity, so the daughter cells are identical to each other and to the parent cell, while the aim of meiosis is to increase genetic variation.
Okay, so we learned pretty much all we need to know about osmosis in the last two articles, but there are some pretty important things to keep in mind when thinking about how water moves.
A quick example: imagine we’ve got a single cell inside a large bathing solution (i.e., the extracellular fluid). Let’s say that inside the cell, we have 1 Mole of sucrose and 2M of glucose, and outside the cell, we have 1M fructose, 1M glucose, and 2M sucrose (Note: one mole is a lot. We’d never have this high a concentration inside a cell, but it’s easier to use whole numbers).
The cell membrane is permeant to fructose and glucose, but impermeant to sucrose, meaning sucrose can’t move anywhere.
How can we figure out how water will move? We follow a few intuitive rules:
Molecules that are polar, charged, or large generally cannot cross the membrane.
We assume that if a cell is in a very large volume of bathing solution, then that volume is infinite.
Because of this, internal solutes do not affect the concentration of the outside solution.
Water does not care about individual concentration of solutes, only TOTAL concentration.
Individual solutes do not care about the concentrations of other solutes, only about their OWN concentrations.
So let’s apply this. First, we work out total concentrations. Inside the cell, 1+2=3M concentration. Outside the cell, 1+1+2=4M concentration. We know water will move from low water potential (hypotonic) to high water potential (hypotonic), so it’s going to move out of the cell.
But the problem tells us that fructose and glucose can also move. The aim of this system is to get into a state of equilibrium, so the solutes are going to try and even out. So:
Glucose will move out of the cell. The intuitive reaction is that glucose will keep moving until there is 1.5M either side of the membrane, but it won’t. We have to remember that the bathing solution is INFINITE, so any glucose the moves out of a tiny cell won’t have any effect on the total concentration of the bathing solution. So, the concentration of glucose in the bathing solution will remain at 1M, and glucose will just move out of the cell until its concentration inside is 1M too.
Fructose is going to move in, and again we have to remember that the bathing solution is infinite. Fructose will remain at 1M outside the cell, and there will now be 1M inside the cell too.
Finally, sucrose can’t move at all. It remains at 2M outside and 1M inside.
So let’s tally up again: Inside the cell, our concentration is 1+1+1=3M. Outside the cell, our concentration is 1+1+2=4M.
SO water is going to move out to try and dilute that higher concentration.
But of course, as I’m trying to drill into you, the amount of water inside the cell can’t make any change whatsoever in the concentration of the bathing solution. So water will just keep moving and moving until the cell shrivels up and dies.
One more thing to keep in mind: sometimes, molecules will dissociate when they move across the membrane, which will increase the total concentration even more.
This is a particular definition that you’ve got to know if you want to talk about osmosis: tonicity.
First it’s important to know that membranes are sometimes permeant to certain solutes—say you had a cell with 1M glucose inside it and no glucose outside of it, and the membrane is permeant to glucose. Glucose will therefore pass through the membrane until the concentration is equal on both sides.
So because permeant solutions equalise themselves on either side of the membrane, they don’t affect create a concentration gradient and therefore don’t drive osmosis. Sometimes, though, cell membranes are impermeant to certain solutes, so they have to stay where they are—and if the concentration is unequal on other side of the membrane, they cause water to move. We call these impermeant solutes.
A cell’s tonicity depends on the concentration of impermeant solutes. Basically, tonicity is a solution’s ability to make a cell lose or gain water.
To describe a cell’s tonicity, we use the terms hypotonic, isotonic and hypertonic.
Water therefore moves from hypotonic to hypertonic, until the two solutions become isotonic, and the water potential is equal on both sides of the membrane.
But practically, how does tonicity affect the volume of water within a cell?
In animal cells
Animal cells want to be in isotonic solutions, where the concentrations of impermeant solutions are equal on either side of the membrane—both in the cell and in the extracellular fluid. This way, there’s no pressure on the cell. In isotonic solutions, there’s no net movement of water.
But if an animal cell was placed into a hypertonic solution where the concentration of solute outside is lower than the concentration inside the cell, water will move into the cell. This is pretty bad news—imagine if water just kept moving into you. The cell basically swells up, and sometimes it bursts. (We call this lysing.)
On the other hand, if an animal cell is placed into a hypertonic solution where the concentration of solute outside the cell is higher than inside the cell, water will move out of the cell. So, the cell’s going to shrink and often it shrivels up (crenate).
In plant cells
Animal cells want to be isotonic, but plant cells are like nah man, we want hypotonic solutions. We want the solution inside of us to be greater than the solution outside, because then water comes in and puts a bit of pressure on our cell walls and we can be all happy and bloated. (This is because the cell wall of a plant is a bit different to the softer membrane of animal cells.)
This pressure is called turgor pressure and it’s basically the reason plants can chill vertically, and the reason they wilt when they’re thirsty in hot weather. Having lots of water inside of them is normal.
If they’re put in an isotonic solution, there’s no turgor pressure, and the plant looks flaccid (this is called incipient plasmolysis).
If plant cells are put in a hypertonic solution, water seeps out of the cell. The pressure decreases, and though the rigid cell wall goes nowhere, the protoplast—the soft living bit inside the cell wall—shrinks away from the wall and shrivels (i.e., is plasmolyzed).
So basically, plants use pressure for support instead of spines, which I think is incredibly metal.
160,000,000% yes for the bio series being compiled into a pdf, please. So the way I understand it is that you will be compiling them (if you choose to, please choose to) in terms of subjects/topics? Like cellular biology, genetics (if there was, sorry I'm a new follower), microbiology, etc., will all have their own pdf file?
I’ll compile it however you guys want it compiled :)
I was thinking all in one, with a chapter for each topic, but if you want it available another way, just let me know. Crowd-sourcin’ this decision—come at me with ideas.
And FYI, genetics is the last topic, so you’ll see that in the next couple of weeks!
I'm taking summer classes at UMich right now and my microbio exam is Tuesday. Your past like 5 posts explain key concepts for my exam so much better than my text book does. I just thought I'd let you know how awesome you are.
HELL YEAH ACE THAT FINAL, FRIEND
also would anyone be interested in me compiling my bio series into a downloadable pdf, like a supplementary textbook?
You don't understand, man. Every time I read one of your posts a tear drops from the left corner of my eye, everything you write is so easy to understand. You sound like you care about what you're talking about. This 'science-in-a-can' concept is probably the most beautiful thing I've ever encountered. Amazing job, please don't stop. I love you.
This is the sweetest thing, you’re making me tear up a bit too. I love you too man.
I recently got the xkit extension where you can see what tags people have added to your posts when they reblog them
A few examples: “proteins are the bomb” and “science is so frickin cool” and “I heart DNA” and “way cool science shit” and ”I WILL SHOVE BIOCHEMISTRY DOWN YOUR THROATS” and my personal favourite “WHERE WAS THIS WHEN I WAS STUDYING FOR FINALS”
The sheer level of nerdery amongst you guys gives me strength