4.3: The Language of DNA - Biology

4.3: The Language of DNA - Biology

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In this short chapter you will learn how modern molecular biologists manipulate DNA, the blueprint for all of life. The four letter alphabet (A, G, C, and T) that makes up DNA represents a language that when transcribed and translated leads to the myriad of proteins that make us who we are as a species and as individuals. Let's continue with the metaphor that DNA is a language. To master that language, as with any other language, we need to be able to read, write, copy, and edit that language. If you were using a word processor to find one line in a hundred page document, or one article from one book out of the Library of Congress, you would also need a way to search the large print base available. You might want to compare two different copies of files to see if they differ from each other. From the lab and this online discussion and problem set, you will learn how modern scientists read, write, copy, edit, search, and compare the language of the genome. These abilities, acquired over the last twenty years, have revolutionized our understanding of life and have given us the potential to alter, for good or evil, life itself.

DNA in human chromosomes exists as one long double stranded molecule. It is too long to physically study and manipulate in the lab. Using a battery of enzymes, the DNA of chromosomes can be chemically cleaved into smaller fragments which are more readily manipulable. (Similar techniques are used to sequence proteins, which require overlapping polypeptide fragments to be made.) After the fragments have been made, they must be separated from each other in order to study them. DNA fragments can be separated on the basis of some structural feature that differentiates the fragments from each other. Polarity can not be used since all DNA fragments have negatively charged phosphates in the sugar - phosphate backbone of the molecule. Although each fragment would have a unique sequence, it would be hard to separate all the different fragments, by, for instance, attaching some molecule that binds to a unique sequence in the major groove of a given fragment to a big bead and using that bead to separate out that one unique fragment. You would need a different bead for each unique fragment! The best way to separate the fragments from each other is to base the separation on the actual size of the fragment by using electrophoresis on an agarose or polyacrylamide gel.

A carbohydrate extract called agarose is made from algae. Water is added to the extract, which is then heated. The carbohydrate extract dissolves in the water to form a viscous solution. The agarose solution is poured into a mold (like warm jello) and is allowed to solidify. A plastic comb with wide teeth was placed in the agarose when it was still liquid. When the agarose is solid, the comb can be removed, leaving in its place little wells. A solution of DNA fragments can be placed in the wells. The agarose slab with sample is covered with a buffer solution and electrodes placed at each end of the slab. The negative electrode is placed near the well end of the agarose slab while the positive electrode is placed at the other end. If a voltage is applied across the agarose slab, the negatively charged DNA fragments will move through the agarose gel toward the positive electrode. This migration of charged molecules in solution toward an oppositely charged electrode is called electrophoresis. Pretend you are one of the fragments. To you the gel looks like a tangle cobweb. You sneak your way through the openings in the web as you move straight forward to the positive electrode. The larger the fragment, the slower you move because it is hard to get through the tangled web. Conversely, the shorter the fragment, the faster you move. Using this technique and its many modifications, oligonucleotides differing by just one nucleotides can be separated from each other. In electrophoresis of DNA fragments, a fluorescent, uncharged dye, ethidium bromide, is added to the buffer solution. This dye literally intercalates in-between the base pairs of DNA, which imparts a fluorescent yellow-green color to the DNA when UV light is shown on the agarose gel.

A. Reading DNA:

We will discuss one method of reading the sequence of DNA. This method, developed by Sanger won him a second Nobel prize. To sequence a single stranded piece of DNA, the complementary strand is synthesized. Four different reaction mixtures are set up. Each contain all 4 radioactive deoxynucleotides (dATP, dCTP, dGTP, dTTP) required for the reaction and DNA polymerase. In addition, dideoxyATP (ddATP) is added to one reaction tube The dATP and ddATP attach randomly to the growing 3' end of the complementary stranded. If ddATP is added no further nucleotides can be added after since its 3' end has an H and not a OH. That's why they call it dideoxy. The new chain is terminated.. If dATP is added, the chain will continue to grow until another A needs to be added. Hence a whole series of discreet fragments of DNA chains will be made, all terminated when ddATP was added. The same scenario occurs for the other 3 tubes, which contain dCTP and ddCTP, dTTP and ddTTP, and dGTP and ddGTP respectively. All the fragments made in each tube will be placed in separate lanes for electrophoresis, where the fragments will separate by size.


Figure: Didexoynucleotides

PROBLEM: You will pretend to sequence a single stranded piece of DNA as shown below. The new nucleotides are added by the enzyme DNA polymerase to the primer, GACT, in the 5' to 3' direction. You will set up 4 reaction tubes, Each tube contains all the dXTP's. In addition, add ddATP to tube 1, ddTTP to tube 2, ddCTP to tube 3, and ddGTP to tube 4. For each separate reaction mixture, determine all the possible sequences made by writing the possible sequences on one of the unfinished complementary sequences below. Cut the completed sequences from the page, determine the size of the polynucleotide sequences made, and place them as they would migrate (based on size) in the appropriate lane of a imaginary gel which you have drawn on a piece of paper. Lane 1 will contain the nucleotides made in tube 1, etc. Then draw lines under the positions of the cutout nucleotides to represent DNA bands in the gel. Read the sequence of the complementary DNA synthesized. Then write the sequence of the ssDNA that was to be sequenced.

3' G A C T 5' (primer)

3' G A C T 5' (primer)

3' G A C T 5' (primer)

3' G A C T 5' (primer)

3' G A C T 5' (primer)

3' G A C T 5' (primer)

3' G A C T 5' (primer)

3' G A C T 5' (primer)

Since the DNA fragments have no detectable color, they can not be directly visualized in the gel. Alternative methods are used. In the one described above, radiolabeled ddXTP's where used. Once the sequencing gel is run, it can be dried and the bands visualized by radioautography (also called autoradiography). A place of x-ray film is placed over the dried gel in a dark environment. The radiolabeled bands will emit radiation which will expose the x-ray film directly over the bands. The film can be developed to detect the bands. In a newer technique, the primer can be labeled with a flourescent dye. If a different dye is used for each reaction mixture, all the reaction mixtures can be run in one lane of a gel. (Actually only one reaction mix containing all the ddXTP's together need be performed.) The gel can then be scanned by a laser, which detects fluorescence from the dyes, each at a different wavelength.

Figure: DNA sequencing using different fluorescent primers for each ddXTP reaction

One recent advance in sequencing allows for real-time determination of a sequence. The four deoxynucleotides are each labeled with a different fluorphore on the 5' phosphate (not the base as above). A tethered DNA polymerase elongates the DNA on a template, releasing the fluorophore into solution (i.e. the fluorophore is not incorporated into the DNA chain). The reaction takes place in a visualization chamber called a zero mode waveguide which is a cylindrical metallic chamber with a width of 70 nm and a volume of 20 zeptoliters (20 x 10-21 L). It sits on a glass support through which laser illumination of the sample is achieved. Given the small volume, non-incorporated fluorescently tagged deoxynucleotides diffuse in and out in the microsecond timescale. When a deoxynucleotide is incorporated into the DNA, its residence time is in the millisecond time scale. This allows for prolonged detection of fluorescence which give a high signal to noise ratio. Newer technology in which sequence is done by moving DNA through pores in membranes could bring sequencing down to $1000/genome or less.

Animation of Sanger Sequencing

Nanopore sequencing

B. Writing DNA:

Oligonucleotide can be synthesized on a solid bead. By adding one nucleotide at a time, the sequence and length of the oligonucleotide can be controlled.

C. Copying DNA:

Several methods exists for copying a sequence of DNA millions of times. Most methods make use of plasmids (which are found in bacteria) and viruses (which can infect any cell). The DNA of the plasmid or virus is engineered to contain a copy of a specific DNA sequence of interest. The plasmid or virus is then reintroduced into the cell where amplification occurs.

Initially, a DNA containing a gene or regulatory sequence of interest is cut at specific places with an enzyme called a restriction endonuclease, or restriction enzyme for short. The enzyme doesn't cleave DNA any old place, but rather at "restricted" places in the sequence, much as an endoprotease cleaves a protein after a given amino acid within a protein chain. Instead of cleaving one strand, as in proteins, the restriction endonuclease must cleave both strands of dsDNA. It can cut the strands cleanly to leave blunt ends, or in a staggered fashion, to leave small tails of ssDNA. Multiple such sites exist at random in the genome. The gene of interest must be flanked on either side by such a sequence. The same enzyme is used to cleave the plasmid or virus DNA.

Figure: Cleaving DNA with the Restriction Enzyme EcoR1

The foreign fragment of DNA can then be added to the plasmid or viral DNA as shown to make a recombinant DNA molecule. This technique of DNA cloning is the basis for the entire field of recombinant DNA technology.

Figure: Cloning a Restriction Fragment into a Plasmid

Animation of Gene Splicing

The plasmid can be added to bacteria, which take it up in a process called transformation. The plasmid can be replicated in the bacteria which will copy the DNA fragment of interest. Typically the plasmid carries a gene that can make the bacteria resistant to an antibiotic. Only bacteria that carry the plasmid (and presumably the insert) will grow. To isolate the desired fragment, the plasmids are isolated from bacteria, and cleaved with the same restriction enzyme to remove the desired fragment, after which it can be purified. In addition, the bacteria can be induced to express the protein from the foreign gene. In lab 4, we will transform bacteria with a plasmid containing the gene for human adipoctye acid phosphatase beta, HAAP-B, and induce expression of the gene.

A similar method can be used to copy DNA in which the foreign fragment is recombined with the DNA of bacteriophage , a virus which infects bacteria like E. Coli. The recombinant DNA can be packaged into actual viruses, as shown below. When the virus infects the bacteria, it instructs the cells to make millions of new viruses, hence copying the foreign fragment of interest.

Sometimes, "cloning" or copying a fragment of DNA is not what an investigator really wants. If the genomic DNA comes from a human cell, for instance, the gene will contain introns. If you put this DNA into a plasmid or bacteriophage, the introns go with it. Bacteria can replicate this DNA, but often one wants not to just copy (amplify) the DNA but also transcribe it into RNA and then translate it into protein. Bacteria, however, can not splice out the intron RNA, so mature mRNA can not be made. If one could clone into the bacteria DNA without the introns, this problem would not exist. One such possible method exists in which you start with the actual mRNA for a protein of interest. In this technique, a dsDNA copy is made from a ss-mRNA molecule. Such dsDNA is called cDNA, for complementary or copy DNA. This can then be cloned into a plasmid or bacteriophage vector and amplified as described above.


In the mid 80's a new method was developed to copy (amplify) DNA in a test tube. It doesn't require a plasmid or a virus. It just requires a DNA fragment, some primers (small polynucleotides complementary to sections of DNA on each strand and straddling the section of DNA to be amplified. Just add to this mixture dATP, dCTP, dGTP, dTTP, and a heat stable DNA polymerase from the organism Thermophilus aquaticus (which lives in hot springs), and off you go. The mixture is first heated to a temperature which will cause the DsDNA strands to separate. The temperature is cooled allowing a large stoichimetric excess of the primers to anneal to the ssDNA. The heat stable Taq polymerase (from Thermophilus aquaticus) polymerizes DNA from the primers. The temperature is raised again, allowing dsDNA strand separation. On cooling the primers anneal again to the original and newly synthesized DNA from the last cycle and synthesis of DNA occurs again. This cycle is repeated as shown in the diagram. This chain reaction is called the polymerase chain reaction (PCR). The target DNA synthesized is amplified a million times in 20 cycles, or a billion times in 30 cycles, which can be done in a few hours.

Figure: Copying DNA in the test tube - the polymerase chain reaction (PCR)

Animation of PCR

D. Editing DNA

During our studies of protein structure, we spent much time discussing how specific amino acids could be covalently modified to either identify the presence of the amino acid, or in an attempt to modify the activity of the protein. A newer and revolutionary technique has emerged in the last 15 years. Using recombinant DNA technology, the gene that encodes the protein can be altered at one or more nucleotide, in a way which would either change one or more amino acids, or add or delete one or more amino acids. This technique, called site-specific mutagenesis, is used extensively by protein chemist to determine the importance of a given amino acid in the folding, structure, and activity of a protein. The techniques is described in the diagram below;

Figure: Site Specific Mutagenesis

E. Searching DNA

Where on a chromosome is the gene that codes for a given protein? One way to find the gene is to synthesize a small oligonucleotide "probe" which is complementary to part of the actual DNA sequence of the gene (determined from previous experiments). Attach a fluorescent molecule to the DNA probe. Then take a cell preparation in which the chromosomes can be seen under the microscope. To the cell add base which unwinds the double stranded DNA helix, add the fluorescent probe to the cell, and allow double stranded DNA to reform. The fluorescent probe will bind to the chromosome at the site of the gene to which the DNA is complementary. Hybridization is the process whereby a single-stranded nucleotide sequence (the target) binds through H-bonds to another complementary nucleotide sequence (the probe).

What if you don't know the nucleotide sequence of the gene, but you know the amino acid sequence of the protein, as in the example shown below? From the genetic code table, you could predict the possible sequence of all possible RNA molecule which are complementary to the DNA in the gene. Since some of the amino acids have more than one codon, there are many possible sequences of DNA which could code for the protein fragment. The link below shows all possible corresponding mRNA sequences that could code for a short amino acid sequence. The 20 mer sequence of minimal degeneracy in the nucleotide sequence should be used as possible genomic probe .


The DNA sequence of each individual must be different from every other individual in the world (with the exception of identical twins). The difference must be less than the difference between a human and a chimp, which are 98.5 % identical. Let us say that each of have DNA sequences that are 99.9 % identical as compared to some "normal human". Given that we have about 4 billion base pairs of DNA, that means we are all different in about 0.001 x 4,000,000,000 which is about 4 million base pairs different. This means that on the average we have one nucleotide difference for each 1000 base pairs of DNA. Some of these are in genes, but most are probably in between DNA, and many have been shown to be clustered in areas of highly repetitive DNA at the ends of chromosomes (called the telomeres) and in the middle (called the centromeres).

Now remember that their are restriction enzyme sites interspersed randomly along the DNA as well. If some of the differences in the DNA among individuals occurs within the sequences where the DNA is cleaved by restriction enzymes, then in some individuals a particular enzyme won't cleave at the usual site, but at a more distal site. Hence, the size of the restriction enzyme fragments should differ for each person. Each persons DNA, when cut by a battery of restriction enzymes, should give rise to a unique set of DNA fragments of sizes unique to that individual. Each persons DNA has a unique Restriction Fragment Length Polymorphism (RFLP). How could you detect such polymorphism?

You already know how to cut sample DNA with restriction enzymes, and then separate the fragments on an agarose gel. An additional step is required, however, since thousands of fragments could appear on the gel, which would be observed as one large continuous smear. If however, each fragment could be reacted with a set of small, radioactive DNA probes which are complementary to certain highly polymorphic sections of DNA (like teleomeric DNA) and then visualized, only a few sets of discrete bands would be observed in the agarose gel. These discrete bands would be different from the DNA bands seen in another individual's gene treated the same way. This technique is called Southern Blotting and works as shown below. DNA fragments are electrophoresed in an agarose gel. The ds DNA fragments are unwound by heating, and then a piece of nitrocellulose filter paper is placed on top of the gel. The DNA from the gel transfers to the filter paper. Then a small radioactive oligonucleotide probe, complementary to a polymorphic site on the DNA, is added to the paper. It binds only to the fragment containing DNA complementary to the probe. The filter paper is dried, and a piece of x-ray film is placed over the sheet. Also run on the gel, and transferred to the sheet, are a set of radioactive fragments (which are not complementary to the probe), which serve as a set of markers to ensure that the gel electrophoresis and transfer to the filter paper was correct. This technique is shown on the next page, along with a RFLP analysis from a particular family.

When this technique is used in forensic cases (such as the OJ Simpson trial) or in paternity cases, it is called DNA fingerprinting. With present techniques, investigators can state unequivocally that the odds of a particular pattern not belong to a suspect are in the range of one million to one. The x-ray film shown below is a copy of real forensic evidence obtained from a rape case. Shown are the Southern blot results from suspect 1, suspect 2, the victim, and the forensic evidence. Analyze the data.


Recent References

  1. Avise. Evolving Genomic Metaphors: A New Look at the Language of DNA. Science. 294, pg 86 (2001)

Поиск скрытых сообщений в ДНК (Биоинформатика I)

This course begins a series of classes illustrating the power of computing in modern biology. Please join us on the frontier of bioinformatics to look for hidden messages in DNA without ever needing to put on a lab coat. In the first half of the course, we investigate DNA replication, and ask the question, where in the genome does DNA replication begin? We will see that we can answer this question for many bacteria using only some straightforward algorithms to look for hidden messages in the genome. In the second half of the course, we examine a different biological question, when we ask which DNA patterns play the role of molecular clocks. The cells in your body manage to maintain a circadian rhythm, but how is this achieved on the level of DNA? Once again, we will see that by knowing which hidden messages to look for, we can start to understand the amazingly complex language of DNA. Perhaps surprisingly, we will apply randomized algorithms, which roll dice and flip coins in order to solve problems. Finally, you will get your hands dirty and apply existing software tools to find recurring biological motifs within genes that are responsible for helping Mycobacterium tuberculosis go "dormant" within a host for many years before causing an active infection.

Карьерные результаты учащихся

4.3: The Language of DNA - Biology

  1. The genetic code is not a true code it is more of a cypher. DNA is a sequence of four different bases (denoted A, C, G, and T) along a backbone. When DNA gets translated to protein, triplets of bases (codons) get converted sequentially to the amino acids that make up the protein, with some codons acting as a "stop" marker. The mapping from codon to amino acid is arbitrary (not completely arbitrary, but close enough for purposes of argument). However, that one mapping step -- from 64 possible codons to 20 amino acids and a stop signal -- is the only arbitrariness in the genetic code. The protein itself is a physical object whose function is determined by its physical properties.

Furthermore, DNA gets used for more than making proteins. Much DNA is transcribed directly to functional RNA. Other DNA acts to regulate genetic processes. The physical properties of the DNA and RNA, not any arbitrary meanings, determine how they act.

An essential property of language is that any word can refer to any object. That is not true in genetics. The genetic code which maps codons to proteins could be changed, but doing so would change the meaning of all sequences that code for proteins, and it could not create arbitrary new meanings for all DNA sequences. Genetics is not true language.

Genetic Code: 8 Important Properties of Genetic Code

(1) Code is a Triplet (2) The Code is Degenerate (3) The Code is Non-overlapping (4) The Code is Comma Less (5) The Code is Unambiguous (6) The Code is Universal (7) Co-linearity and (8) Gene-polypeptide Parity.

Genetic Code refers to the relationship between the sequence of nitrogenous bases (UCAG) in mRNA and the sequence of amino acids in a polypeptide chain. In other words, the relationship between the 4 letters language of nucleotides and twenty letters language of amino acids is known as genetic code.

DNA (or RNA) carries all the genetic information and it is expressed in the form of proteins. Proteins are made of 20 different amino acids. The information about the number and sequence of these amino acids forming protein is present in DNA, and during transcription is passed over to mRNA. The form in which it is transferred was not understood for long.

Sugar (pentose) and phosphate of DNA could not perform this job of passing on the genetic message to mRNA because sugar is only of one type and so also the phosphate. This leaves only four nucleotides to form the message for 20 amino acids, but 4 nucleotides are too few for twenty amino acids.

This difficult problem was solved with the discovery that a codon (hereditary unit of a gene) containing coded information for one amino acid consists three nucleotides (i.e., a triplet code). Thus for twenty amino acids, 64 (4 x 4 x 4 or 4 3 = 64) possible permutation are available. This break through resulted into 64 codons dictionary — the Genetic Code.

According to Bark (1970) the genetic code is a code for amino acids, specifically it is concerned with as to what codons specify what amino acids. Genetic code is the outcome of experiments performed by M. Nirenberg, S. Ochoa, H. Khorana, F. Crick and Mathaei. Professor M. Nirenberg was awarded Nobel Prize in 1961 for this outstanding work.

The dictionary of genetic code employs the letters in RNA (U, C, A, G, i.e., A = Adenine, U = Uracil, C = Cytosine, G = Guanine)

The codon for the amino acids, which are the same in all known life forms, have been determined experimentally. They are given in Fig. 7.3.

In Fig. 7.3 note that more than one codon can signal a particular amino acid to be incorporated into a protein. In addition, some codons serve special functions.

For example, the codon AUG serves two functions:

(1) As an initiator codon signaling for the start of synthesis of a peptide, and

(2) For the incorporation of methionine into the growing chain of a peptide. Other special-purpose codons are UAA (Ochre), UAG (Amber), and UGA (Umber), all of which signal STOP.

When the ribosomal synthesis site encounters one of these stop codons, the peptide chain is released and assumes its secondary and tertiary structures. Since UAA (Ochre), UAG (Amber) and UGA (Umber) do not specify any amino acid they are also called nonsense codons.

“When preceded by an initiator region, the codon AUG signals: “Start a new peptide molecule beginning with N-formylmethionine, or fMet.” The codons UAA, UAG and UGA signal termination of the protein synthesis.”

Properties of Genetic Code:

The properties of genetic code determined by extensive experimental evidences may be summarized as follows:

1. Code is a Triplet:

As pointed out earlier, the coding units or codons for amino acids comprise three letter words, 4 x 4 x 4 or 4 3 = 64. 64 codons are quite adequate to specify 20 proteinous amino acids.

2. The Code is Degenerate:

The occurrence of more than one codon for a single amino acid is referred to as degenerate. A review of genetic code dictionary will reveal that most of the amino acids have more than one codon. Out of 61 functional codons, AUG and UGG code to one amino acid each. But remaining 18 amino acids are coded by 59 codons.

3. The Code is Non-overlapping:

4. The Code is Comma Less:

A comma less code means that no nucleotide or comma (or punctuation) is present in between two codons. Therefore, code is continuous and comma less and no letter is wasted between two words or codons.

5. The Code is Unambiguous:

There is no ambiguity in the genetic code. A given codon always codes for a particular amino acid, wherever it is present.

6. The Code is Universal:

The genetic code has been found to be universal in all kinds of living organisms — prokaryotes and eukaryotes.

7. Co-linearity:

DNA is a linear polynucleotide chain and a protein is a linear polypeptide chain. The sequence of amino acids in a polypeptide chain corresponds to the sequence of nucleotide bases in the gene (DNA) that codes for it. Change in a specific codon in DNA produces a change of amino acid in the corresponding position in the polypeptide. The gene and the polypeptide it codes for are said to be co-linear.

8. Gene-polypeptide Parity:

A specific gene transcribes a specific mRNA that produces a specific polypeptide. On this basis, a cell can have only as many types of polypeptides as it has types of genes. However, this does not apply to certain viruses which have overlapping genes.

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4.3: The Language of DNA - Biology

So what does it mean to be a woman? We all have XX chromosomes, right? Actually, that's not true. Some women are mosaics. They have a mix of chromosome types with X, with XY or with XXX. If it's not just about our chromosomes, then what is being a woman about? Being feminine? Getting married? Having kids? You don't have to look far to find fantastic exceptions to these rules, but we all share something that makes us women. Maybe that something is in our brains.

You might have heard theories from last century about how men are better at math than women because they have bigger brains. These theories have been debunked. The average man has a brain about three times smaller than the average elephant, but that doesn't mean the average man is three times dumber than an elephant . or does it?

There's a new wave of female neuroscientists that are finding important differences between female and male brains in neuron connectivity, in brain structure, in brain activity. They're finding that the brain is like a patchwork mosaic — a mixture. Women have mostly female patches and a few male patches.

With all this new data, what does it mean to be a woman? This is something that I've been thinking about almost my entire life. When people learn that I'm a woman who happens to be transgender, they always ask, "How do you know you're a woman?" As a scientist, I'm searching for a biological basis of gender. I want to understand what makes me me. New discoveries at the front edge of science are shedding light on the biomarkers that define gender. My colleagues and I in genetics, neuroscience, physiology and psychology, we're trying to figure out exactly how gender works. These vastly different fields share a common connection — epigenetics. In epigenetics, we're studying how DNA activity can actually radically and permanently change, even though the sequence stays the same.

DNA is the long, string-like molecule that winds up inside our cells. There's so much DNA that it actually gets tangled into these knot-like things — we'll just call them knots. So external factors change how those DNA knots are formed. You can think of it like this: inside our cells, there's different contraptions building things, connecting circuits, doing all the things they need to make life happen. Here's one that's sort of reading the DNA and making RNA. And then this one is carrying a huge sac of neurotransmitters from one end of the brain cell to the other. Don't they get hazard pay for this kind of work?

This one is an entire molecular factory — some say it's the secret to life. It's call the ribosome. I've been studying this since 2001.

One of the stunning things about our cells is that the components inside them are actually biodegradable. They dissolve, and then they're rebuilt each day, kind of like a traveling carnival where the rides are taken down and then rebuilt every single day. A big difference between our cells and the traveling carnival is that in the carnival, there are skilled craftsmen that rebuild the rides each day. In our cells, there are no such skilled craftsmen, only dumb builder machines that build whatever's written in the plans, no matter what those plans say. Those plans are the DNA. The instructions for every nook and cranny inside our cells.

If everything in, say, our brain cells dissolves almost every day, then how can the brain remember anything past one day? That's where DNA comes in. DNA is one of the those things that does not dissolve. But for DNA to remember that something happened, it has to change somehow. We know the change can't be in the sequence if it changed sequence all the time, then we might be growing like, a new ear or a new eyeball every single day.

So, instead it changes shape, and that's where those DNA knots come in. You can think of them like DNA memory. When something big in our life happens, like a traumatic childhood event, stress hormones flood our brain. The stress hormones don't affect the sequence of DNA, but they do change the shape. They affect that part of DNA with the instructions for molecular machines that reduce stress. That piece of DNA gets wound up into a knot, and now the dumb builder machines can't read the plans they need to build the machines that reduce stress. That's a mouthful, but it's what's happening on the microscale. On the macroscale, you practically lose the ability to deal with stress, and that's bad. And that's how DNA can remember what happens in the past.

This is what I think was happening to me when I first started my gender transition. I knew I was a woman on the inside, and I wore women's clothes on the outside, but everyone saw me as a man in a dress. I felt like no matter how many things I try, no one would ever really see me as a woman. In science, your credibility is everything, and people were snickering in the hallways, giving me stares, looks of disgust — afraid to be near me. I remember my first big talk after transition. It was in Italy. I'd given prestigious talks before, but this one, I was terrified. I looked out into the audience, and the whispers started — the stares, the smirks, the chuckles. To this day, I still have social anxiety around my experience eight years ago. I lost hope. Don't worry, I've had therapy so I'm OK — I'm OK now.

Genomics: Decoding the Universal Language of Life

What is a genome? A genome contains all of the information that a cell needs to develop, function, and reproduce itself, and all the information needed for those cells to come together to form a person, plant, or animal. Genomes contain an organism’s complete set of genes, and also the even tinier genetic structures that help regulate when and how those genes are used.

The ability to regrow a torn ligament, the clues that might predict the onset of mental illness, the nutritional potential of crops, and even the history of life itself, are all encoded in genomes. By taking this course, you will discover how scientists are deciphering the language of genomes to learn how to develop sustainable food and fuel supplies, improve disease treatment and prevention, and protect our environment. Professor Robinson is the main instructor for this course. In addition, each module features several guest instructors. These guest instructors come from diverse fields of study—biology, physics, computer science, and many others—and pursue diverse research goals, yet they share a common interest in genomic approaches and technologies. The guest instructors include: - Elizabeth (Lisa) Ainsworth, Associate Professor of Plant Biology - Mark Band, Director of the Functional Genomics Facility - Alison Bell, Associate Professor of Animal Biology - Jenny Drnevich, Functional Genomics Bioinformatics Specialist with High-Performance Biological Computing - Christopher Fields, Associate Director of High-Performance Biological Computing - Bruce Fouke, Director of the Roy J. Carver Biotechnology Center - Glenn Fried, Director of the Carl R. Woese Institute for Genomic Biology Core Facilities - Nigel Goldenfeld, Professor of Physics - Brendan Harley, Assistant Professor of Chemical and Biomolecular Engineering - Alvaro Hernandez, Director of the High-Throughput Sequencing and Genotyping Facility - Victor Jongeneel, former NCSA Director of Bioinformatics and former Director of High-Performance Biological Computing - Kingsley Boateng, Senior Research Specialist with the Carl R. Woese Institute for Genomic Biology Core Facilities - Stephen Long, Professor of Plant Biology and Crop Sciences - Ruby Mendenhall, Associate Professor of African American Studies - William Metcalf, Professor of Microbiology - Karen Sears, Assistant Professor of Animal Biology - Saurabh Sinha, Associate Professor of Computer Science - Lisa Stubbs, Professor of Cell and Developmental Biology - Rachel Whitaker, Associate Professor of Microbiology - Derek Wildman, Professor of Molecular and Integrative Physiology - Peter Yau, Director of the Protein Sciences Facility

1902 - Sir Archibald Edward Garrod is the first to associate Mendel's theories with a human disease

In 1902, Sir Archibald Edward Garrod became the first person to associate Mendel's theories with a human disease. Garrod had studied medicine at Oxford University before following in his father's footsteps and becoming a physician.

Whilst studying the human disorder alkaptonuria, he collected family history information from his patients. Through discussions with Mendelian advocate William Bateson, he concluded that alkaptonuria was a recessive disorder and, in 1902, he published The Incidence of Alkaptonuria: A Study in Chemical Individuality. This was the first published account of recessive inheritance in humans.

It was also the first time that a genetic disorder had been attributed to "inborn errors of metabolism", which referred to his belief that certain diseases were the result of errors or missing steps in the body's chemical pathways. These discoveries were some of the first milestones in scientists developing an understanding of the molecular basis of inheritance.

Animal Genetics

Does our growing understanding of animal genetics support evolutionary principles or special creation by a caring, intelligent Designer as the Bible proclaims?

DNA Similarities

Do similarities in DNA between organisms suggest a common ancestor or a common Designer? Are chimps and humans actually 98% similar?

DNA Structure

The iconic, complex double-helix structure of DNA displays the masterful design and creativity of the all-wise Creator.


Our physical makeup is determined by our genes, not our environment—right? The science of epigenetics is forcing scientists to rethink their assumptions.

Human Genome

The exhaustive project of mapping the human genome has provided further evidence of biblical truths as presented in Genesis.

Information Theory

Information only comes from other information. DNA is a complex information system, so it must have come from an information source—the mind of the Creator God!

“Junk” DNA

Using evolutionary assumptions about life’s history, geneticists have branded vast sums of DNA as junk, but research is showing this DNA is far from useless.

Mitochondrial DNA

Mitochondrial DNA research confirms that all humans alive today share common ancestors just a few thousand years ago as the Bible teaches.


Are mutations—copying errors in DNA—the driving force for biological evolution? Or do they represent the sad reality of a sin-cursed world?

Natural Selection

Is natural selection, which uses existing information leading to varations in organisms, proof of information-adding, molecules-to-man evolution?

Concept 22 DNA words are three letters long.

The genetic code had to be a "language" &mdash using the DNA alphabet of A, T, C, and G &mdash that produced enough DNA "words" to specify each of the 20 known amino acids. Simple math showed that only 16 words are possible from a two-letter combination, but a three-letter code produces 64 words. Operating on the principle that the simplest solution is often correct, researchers assumed a three-letter code called a codon.

Research teams at University of British Columbia and the National Institutes of Health laboriously synthesized different RNA molecules, each a long strand composed of a single repeated codon. Then, each type of synthetic RNA was added to a cell-free translation system containing ribosomes, transfer RNAs, and amino acids. As predicted, each type of synthetic RNA produced a polypeptide chain composed of repeated units of a single amino acid. Several codons are "stop" signals and many amino acids are specified by several different codons, accounting for all 64 three-letter combinations.

Structural differences

Even though languages are not inborn, a specific genetic predisposition within a group of genetically similar individuals might influence the evolution of particular structural features of a language. Tonal languages, for example, like Chinese, are different from non-tonal languages (like German).

© Chinesin: Getty Images / Guang Niu Cafe: Getty Images / National Geographic / Jodi Cobb

Languages are not inborn. There are approximately 7,000 languages in the world today, and learning any one of them is a lengthy process that takes around a decade. There is no reason why a Chinese child growing up in Germany should learn to speak German any worse than a German child or a child of any other nationality. A specific genetic predisposition, however, might influence the evolution of particular structural features of a language within a group of genetically similar individuals, for example whether the language is tonal or non-tonal.

Chinese is perhaps the most well-known of the tonal languages, in which a single syllable can convey different meanings according to whether it is spoken in a consistent tone or a rising, rising–falling or falling tone. The distribution of tonal and non-tonal languages corresponds closely with the distribution of two alleles, or forms, of the abnormal spindle-like microcephaly-associated (ASPM) and microcephalin genes 9,10 . Of course, alleles by themselves do not directly lead to the evolution and use of tonal languages children with different forms of the genes will still be able to learn tonal languages. A particular genetic predisposition in a population, however, might favour the emergence of languages with particular structural characteristics. It is now possible to study whether there might also be a genetic predisposition to other structural properties, like poverty or richness of inflexion.

Science historians are familiar with the power of new technologies to revolutionize science. We are standing before an advance that will feel particularly close to home. Over the next decade or so, we can expect new genomics technologies to further our understanding of one quintessential aspect of being human: language.

The languages of the world, which form part of and are the main bearers of cultures, are highly diverse. The capacity to develop, learn and use them, however, belongs to our shared genetic heritage. These aspects of language are researched intensively at the Max Planck Institutes for Psycholinguistics, Evolutionary Anthropology, and Human Cognitive and Brain Sciences.

Watch the video: DNA Structure IB Biology SL (July 2022).


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