The Human Genome Project took the world on a wild ride in the 1990’s. It was the culmination of years of research into human DNA and the first time that the concept of genes was being applied to the human body. In this chapter we will discuss some of the basic concepts of genetics, including the concept of a gene, its relationship with DNA, and the DNA inside of you that makes you you.
In the previous chapter of our genetic exploration, we learned about the genome, and how much of our DNA we inherit from our parents. We also discussed how your DNA is made up of different types of molecules. Today, we’ll start with the basics of how the genes in your DNA are made, and how they change over time.
If you’ve read the first chapter of our series, you know that we’re taking a look at the history of genetics and the impact it has had on human health over the last thousands of years. To do this, our number one goal is to take a deep dive into the basics of genetics. So, as you read this chapter, you’ll learn how our genes are passed from our parents, what traits they can pass on, and how we can take advantage of them to better our lives.
Chapter 2
The fundamentals of genetics
This chapter will teach you the following:
This chapter will teach you the fundamentals of:
- What genes do and how they do it;
- What is the significance of computation and biomedical engineering?
- DNA’s structure, as well as
- What our genetic code has to do with any features we have.
This chapter is a challenge (or a warning).
It’s intended to serve as a guide for the rest of the book. As a result, there’s a lot of data here.
To grasp the fundamental concepts underlying genetic testing, you don’t need to understand or remember everything.
Feel free to skim, skip, or return to this chapter… Whatever you want to do.
We recommend that you go through at least some of this information if you’re new to genetics or just want a refresher.
Go ahead and skip by if you’ve already completed your genetics graduate studies.
A quick rundown of important terms
Let’s study a few basic words before we start into this chapter.
(Any bolded term can also be found in our glossary.)
DNA is a biological molecule that contains the genetic code that allows all living things to exist.
Interesting tidbit!
Some viruses are devoid of DNA. Some viruses have single-stranded DNA genomes, such as parvovirus. Some viruses contain double-stranded DNA genomes, such as pox viruses. The majority of them have RNA genomes of some sort.
Genes are DNA segments that contain instructions for producing specific proteins.
If a gene has a name, we add italics around it, like this: FGF21. This distinguishes them from the proteins with which they are associated.
Consider the following example:
- The FGF21 gene (italicized) produces the protein fibroblast growth factor 21, or FGF21 (no italics).
- Taste receptor 2 member 38, or TAS2R38, is a protein encoded by the TAS2R38 gene.
Alleles or polymorphisms are variations of the same gene.
The type of earwax you have, for example, is determined by a single gene called ABCC11 (which is also involved, by the way, in how your sweat smells). You’ll have moist earwax if you have one of two variations / alleles of the gene; if you have a third variant / allele, your earwax will be dry.
Genetics is the study of genes, how they work, and how certain features (such eye color) are passed down from one generation to the next (known as heredity).
One gene’s expression can affect two or more seemingly unrelated processes or features. As we look at individual issues, such as metabolism, we’ll see examples of this. Pleiotropy (from the Greek pleion, which means “more,” and tropos, which means “way”) describes this phenomenon. A single gene variation can have a wide range of consequences.
Our genotype is our genetic code, but our phenotype is how that code manifests itself in our surroundings. Different phenotypes can arise from the same genotype. Different settings (for example, our activity, nutrition, toxicity exposure, and so on) can alter our observable characteristics (for instance, our physiology or behavior).
Relationship between genotype and expressed traits (Figure 2.1).
The study of how gene expression is activated and inhibited is known as epigenetics. Exercising, for example, can increase production of genes involved in the antioxidant response, and the same genetic “blueprint” can be utilized to express different things. Even if we previously have those genes, exercise has an effect on their epigenetic expression.
A genome is the whole set of genetic information for an organism. The Human Genome Project, for example, looked at the full genetic code of humans.
We’ll talk about genetic testing in this book.
This does not necessarily imply that we are testing the complete genome. As you’ll see, the quantity of information contained in a whole human genome is enormous. In our DNA strings, we have roughly 22,000 genes and about 3 billion base pairs, or nucleotide pairs. (In a moment, we’ll learn more about nucleotides.)
We normally examine a single gene or single nucleotide polymorphism (SNP), which is a single point mutation to one nucleotide inside a gene, with genetic testing. Multiple SNPs might exist in the same gene; the most common SNPs are found in noncoding areas.
Noncoding regions, often known as introns, are portions of the genetic code that do not code for any proteins. Exons are regions of the genome that code for proteins. (In Chapter 4, we’ll go over coding and noncoding regions in greater depth, and we’ll go over splicing in further depth below.)
Introns, exons, and mSplicing of RNA are depicted in Figure 2.2.
CNV relates to whether or not pieces of genetic information are repeated, similar to having three or more pairs of the identical socks instead of just one.
CNVs can also have an impact on how genes function. Multiple copies of genes that produce the enzyme amylase, for example, would improve our ability to break down the carbohydrate amylose. This variance could be linked to our body weight and reflect our ancestral past (for example, whether we originate from an ethnic group that has typically consumed a high-starch diet).
Figure 2.3: Genetic material duplication
Figure 2.4: Variation in copy number (CNV)
What are the functions of genes?
Information is encoded in genes.
When we use information in the actual world, we must consider the following:
- How to transmit and move data – how to get it from one location to another without losing it in the process.
- How to accurately and meticulously reproduce information.
- How to keep data without it degrading or taking up too much space.
- The manner in which humans receive and interpret informational impulses.
All of this happens inside our bodies thanks to genes and their associated products and activities.
A gene might be thought of as a piece of data or a collection of instructions for producing anything — in this example, a specific protein.
DNA is structured in chromosomes in the nucleus of eukaryotic cells (cells with a nucleus and separate organelles bound by a membrane).
Chromosomes are duplicated and DNA is replicated when cells divide. When cells divide, they each get their own complete set of chromosomes. Eukaryotes store most of their DNA in the nucleus of their cells and part of their DNA in organelles like mitochondria and chloroplasts (in plants).
In terms of genetics, we are roughly half of each of our parents. However, we are not identical to our parents. We’re also not exactly 50 percent of each. We’re more like a 49-point-something percent of each, with a few random mutations thrown in for good measure.
In a moment, we’ll learn more about mutations.
For the time being, the following are the most important points:
- Information is stored in genes.
- Information is passed down from one generation to the next.
- It isn’t always a flawless transmission.
We can witness this transmission of information when we look at our genes, or specific variations in our DNA. And we can perceive the differences between us, even within the same family.
- What causes this to happen?
- What is the mechanism behind this?
- What does all of this imply for your personal genetic code?
To explain, let’s start with an idea that you might not be familiar with.
Biology is a form of computation.
Most people think of biology as a collection of squishy, moist parts. Biology can also be thought of as a sort of computing.
Assume you’re attempting to train a computer to perform a task.
Because computers are very literal and only do what you tell them, you need to be very specific. You’ll also need to provide the computer some set parameters to work with while making decisions, otherwise they’ll become confused.
You could, for example, instruct the computer:
IF THIS IS ACTUALLY TRUE, THEN DO THIS.
If today is July 18, send a birthday card to Dr. John Berardi.
MAKE CAKE FOR DR. JB IF HE LIKES IT.
Perhaps your IF / THEN statements include conditions:
MAKE A CAKE IF DR. JB LIKES CAKE OR YOU LIKE CAKE.
If you’re on a desert island and it’s July 18, make a “Happy birthday” sign out of driftwood.
Biology follows a similar pattern.
Consider a simple communication system between a cell and the rest of the world.
On the membranes of some cells are receptors (such as a specific sort of protein). Other things, such as other proteins or smaller molecules, bind to these receptors.
Each receptor is selective and will only bind to specific chemicals (known as ligands), similar to how a key will only open one or two locks.
Receptors and binding sites are depicted in Figure 2.5.
A receptor functions similarly to a switch. When something attaches to a receptor, it sets off a chain of events, similar to turning on a light switch.
As an example, suppose the instructions for our cell’s “biological computer” were written as follows:
IF RECEPTOR A IS ACTIVE AND RECEPTOR B IS ACTIVE, PRODUCE PROTEIN FROM GENE A.
If gene A is active and gene B is available, then use gene B to create the protein.
It’s worth noting that this resembles computer code you would have learned in school:
IF xyz is true, then take action.
In comparison to biology, computers are still fairly dumb. However, the principle is identical on a fundamental level.
Like a computer program, genes encode a collection of instructions… Systems, like computer programs, accumulate difficulties.
Computers have the ability to start over. In principle, you could build a computer that thinks like no other computer has ever thought before, utilizing components that have never been utilized before.
That is not how biological systems work. They can only make use of the structures and systems they were given (along with, of course, any new mutations, which are only a small part of a much bigger whole).
This can indicate that biological processes are rather efficient — evolution may have gone to great lengths to tidy things up.
The systems can be inefficient at times. They have a lot of “cruft,” or clutter and redundant trash, such as obsolete equipment or code that sits around and either does nothing or actively clogs up the system.
Biology is a form of engineering.
Remember when you were in high school and had to memorize chemical graphs like this?
Figure 2.6 shows a basic H20 molecule.
(That’s water, by the way.)
Or these?
Caffeine and nicotine molecules are shown in Figure 2.7.
(Those are caffeine and nicotine, two of your high school best pals, you rebel.)
You could have gotten the notion that “molecules” are nothing more than flat polygons and lines.
Molecules, on the other hand, are three-dimensional.
As a result, water looks more like this:
Figure 2.8: H20 molecule in three dimensions
Nicotine appears to be more like this:
Figure 2.9: A three-dimensional representation of the nicotine molecule
The same is true for cellular structures in the body.
For example, our co-author Alaina printed a three-dimensional protein (a Cas9 nuclease, in case you were curious) in her lab:
Figure 2.10: A three-dimensional protein
Proteins aren’t just abstract line drawings; they’re real, concrete objects.
If you magnified the nicotine protein, it would look somewhat like this:
Figure 2.11: Nicotine protein in three dimensions
The protein’s physical shape would have an impact on how you may interact with it. At the molecular level, the same phenomenon occurs.
As an example, suppose you have a protein that looks like this:
Figure 2.12: A protein with a hook-like structure.
It has two ends, one straight and the other hooked.
Consider the movement of a three-dimensional J-shaped protein in your body.
Then it comes upon a protein that looks something like this:
Figure 2.13: A protein in the shape of an eye bolt.
So, what happens next? If the circumstances are correct, the hook-shaped portion of the first protein might latch on to the eye-shaped portion of the other protein and stay there.
Hook and eye proteins are linked in Figure 2.14.
Protein interactions are determined by their physical forms.
If all you have is this:
Column-shaped protein (Figure 2.15).
…then there’s nothing for the J-hook to connect to.
To put it another way, form is important. Molecules’ physical properties influence whether and how they interact (or react) with other molecules. After all, biology is essentially a series of reactions with the end effect of generating something living.
DNA is a three-dimensional molecule.
To begin, what does the abbreviation “DNA” mean?
Yes, eager student in the front with your hand raised, deoxyribonucleic acid is the answer.
Knowing the complete name of DNA gives you clues about how DNA is formed and how genetics works, in addition to making you the team champion at trivia night. Part of it has to do with DNA’s physical form and how the molecules interact.
A DNA strand is made up of two sections that are shaped like a ladder:
- A deoxyribose “backbone,” or the DNA ladder’s side rails. (Ribose is present in RNA.)
- Bases, also known as nucleotides, are the rungs of the ladder.
Figure 2.16: The “ladder” of DNA
Ribose is a simple sugar. Because “deoxy” implies “without oxygen,” “deoxyribose” is a ribose that lacks oxygen.
Now picture that the deoxyribose sugar is a T-shaped Lego brick, like this:
Deoxyribose “Lego” (Figure 2.17).
Consider stacking a few of those Legos on top of one another like this:
Deoxyribose “Lego” stack (Figure 2.18).
Then pretend you’re getting very fancy with the Lego stack and you’re trying to figure out which way is up.
As a result, you draw an arrow like this along the stack.
Deoxyribose “Lego” stack with arrows (Figure 2.19).
Congratulations. You’ve just finished constructing DNA’s deoxyribose backbone.
You’ve also laid the groundwork for a specific unit of DNA known as a codon, because you have three pokey-outy parts to which other things can connect (aka a sequence of three nucleotides).
Computation is used by DNA.
Imagine instead of numbers, we’re dealing with amino acids in DNA computing.
Do you recall our Lego structure? Bases, or nucleotides, can be stuck on it. Nucleic acids are made up of bases, which are the building blocks.
Figure 2.20: Nucleotides on the “backbone” of deoxyribose
We have four nucleotide possibilities with DNA:
- Adenine is a kind of adenine (A)
- Cytosine is a kind of cytosine (C)
- Guanine is a kind of guanine that (G)
- Thymine is a kind of thymine (T)
One more comes from RNA (which we’ll look at in a minute): uracil (U), which takes the place of thymine.
The nucleotides A and G are both long. Two of them (C and T) are very short. Short nucleotides pair with long nucleotides in a whole strand of DNA, and vice versa.
As an example:
Figure 2.21: Nucleotide pairings that are short and lengthy.
The protein nucleotide formula
Imagine that each nucleotide is a box with one of four potential nucleic acids inside: an A, a C, a G, or a T, as shown below:
Nucleotides in boxes (Figure 2.22).
We obtain 4 x 4 values = 16 potential possibilities with two boxes.
With three boxes, we can create 4 x 4 x 4 values, for a total of 64 potential possibilities.
Proteins are coded by DNA. Amino acids are the building blocks of proteins. As a result, a portion of that DNA must code for a specific amino acid.
We’ll need roughly 20 amino acids to get started.
We can’t achieve it with just one box (which can only contain one of four nucleotides) or even two boxes (which only gives us 16 possible combinations). We’ll need three boxes.
As a result, a codon is three units long. MATH IN BIOLOGY!!
To code for these 20 amino acids, we require a variety of 3-nucleotide codons. It can be difficult to keep everything straight. As a result, academics have devised several tools to aid in the cataloging and interpretation of codons, such as a codon wheel (shown below).
We may use a codon wheel to figure out what amino acid a specific codon codes for, as well as which codons code for which amino acid.
Begin by reading the wheel from the center. It’s a single nucleotide. Then travel outdoors and choose another of the four options. And then outwards again, selecting another of the four options.
Consider the following example:
- The amino acid leucine is obtained by starting with C in the middle, going outwards and picking another C, then moving outwards and picking a U, C, A, or G.
- You get glutamine by starting with G in the middle, moving outwards and picking an A, then moving outwards again and picking an A or a G.
You may also observe that some amino acids can be produced from many nucleotide combinations.
The DNA codon wheel is shown in Figure 2.23.
Later, we’ll learn more about codons and how they function.
For the time being, only recall the DNA structure:
Figure 2.24: DNA’s basic structure
Genes have a geographical location.
DNA does not have a random shape.
To return to the idea of genes storing information, the shape is not by chance. Because of how the DNA Lego blocks interlock:
- The molecule has a high level of stability.
- Our bodies can replicate it with a great degree of fidelity and precision.
This is beneficial because, as we’ll see later, we don’t want things to fall apart or get sloppy in terms of reproduction. Errors abound, but we have biological proofreaders on hand to catch them.
Do you recall our ribose Lego? Deoxyribose is a carbohydrate, meaning it is made up of carbon. The carbons are counted in biochemistry. One carbon is called the 5-prime (written as 5′) and the other is called the 3-prime (written as 3′) in each miniature Lego block.
Our bodies interpret DNA in a specific order (thus the arrow): from 5-prime to 3-prime, in opposing orientations. One side will read 5′ to 3′ up, while the other will read 5′ to 3′ down.
Figure 2.25: DNA Piece Directionality
The directionality of each DNA strand is critical.
Consider how you read. If you can read English, you can:
FROM LEFT TO RIGHT, YOU READ.
.TFEL OT THGIR MORF DAER T’NOD UOY.TFEL OT THGIR MORF DAER T’NOD UOY
The same principle applies to DNA reading. It must travel in a specific direction.
Assume you’re building a DNA-reading machine. Because it’s a rudimentary machine, it can only read one nucleotide at a time. It reads the names of each nucleotide as it scans along the strand from 5′ to 3′, as follows:
A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A
and so forth. It had to go that way because the opposite (reading from 3′ to 5′) would be completely different:
G T T C A G T T C A G T T C A G T T C A G T T C A G T T C A G T T
Distinct “letters” have different connotations.
In cells, DNA does not just float around aimlessly. Massive amounts of genetic material are packed into highly ordered structures, tightly wrapped around proteins called histones like beads on a string, to fit into the limited space of a cell’s nucleus.
Your DNA strands would be about two meters long if they weren’t spooled. Despite this, they only take up around 1/1,000 of a millimeter of space.
The protein-DNA combination that makes up your body’s chromosomes is known as chromatin.
Figure 2.26: Chromosome structure
Our chromosomes’ spatial folding and physical organization in the nucleus can have a big impact on how genes are expressed.
Consider the following scenario:
- Enhancers, which improve the likelihood of a gene being transcribed, must be adjacent to the areas on which they affect.
- Histone modification, or changes to the physical configuration of the histone proteins that DNA wraps around, is central to epigenetics (which we’ll look at briefly below), or the regulation of gene expression.
We can now see how chromatin is arranged in a living cell, according to recent revolutionary research from the Salk Institute for Biological Studies. (Before, we had to dissect the cell to view this, so we couldn’t see how chromatin functioned in the wild.)
The way chromatin was packed into the nucleus — both its form and density — had an effect on its function, according to this study.
This entails the following:
- It is critical to consider the form of molecules. The shape of molecules has an impact on how they function and interact with one another.
- As a result, genetic expression is determined not only by the genes we possess, but also by their location.
- Commercial genetic testing can tell us about some of the genes we have, but not how they’re arranged physically. A commercial test will not reveal the geographic location of our genes, which means we won’t learn much about how those genes are expressed.
How do genes become proteins?
Molecular biology’s core tenet
All of this adds up to what is sometimes referred to as molecular biology’s basic dogma: DNA to RNA to proteins.
- Codons are three-nucleotide groupings that are read from DNA.
- These DNA codons are transcribed to messenger ribonucleic acid, a “in-between” molecule (mRNA). (In a moment, we’ll go over this in further depth.)
- Each mRNA codon is translated into one amino acid after the mRNA is read.
- Proteins are made up of amino acids bonded together.
As a result, DNA’s function is to store the information needed to produce proteins.
This fundamental idea underpins all of molecular biology.
DNA to RNA to Protein (Figure 2.27).
Protein synthesis and gene expression
To produce a protein, there are two basic processes. They’re referred to as gene expression when they’re combined.
- RNA synthesis (transcription) is the process of producing RNA from DNA instructions. In this phase, enzymes called polymerases unzip double-stranded DNA into single, complementary strands of RNA, much like a zipper.
- Protein synthesis (translation) is the process of making proteins from RNA instructions.
RNA serves a variety of functions, and there are various varieties, which we’ll discuss shortly.
For the time being, we’ll concentrate on messenger RNA (mRNA). mRNA serves as a link between DNA and proteins.
For a long time, scientists believed that one gene coded for one mRNA, which then coded for one protein: if you had 100 genes, you’d end up with 100 separate mRNAs, which would then result in 100 different proteins. If you knew all of the genes, you’d also know all of the proteins.
It’s a little more complex than that. (Warning: This is something we’re going to mention a lot.) Quite a bit.)
Splicing of RNA
Through RNA splicing, a single gene can code for a large number of related proteins.
Think of director’s edits, alternate endings, 20th anniversary edition cuts, and what-have-you-done-to-my-favorite-movie?? cuts as examples of RNA splicing in action.
Some of the cuts may be small. Some people have the ability to entirely alter the movie (i.e., the protein that is expressed).
DNA to RNA to splicing to proteins (Figure 2.28).
Now assume that your movie also has a lot of adverts in it. You must watch the movie in segments. This is infuriating. Assume you re-cut the movie, removing the advertisements and reassembling all of the movie segments to create one continuous full-length feature.
Introns (sometimes known as “intervening sequences”) might be compared to advertising. Keep in mind that introns do not code for proteins.
Exons (also known as “expressing sequences”) can be compared to the movie itself. Exons are like the “narrative” of what will happen genetically because they code for proteins.
mRNA is spliced so that all introns are eliminated, leaving only the exons, or expressing sequences, just like a movie without the annoying and pointless commercials.
Now and again, there’s a minor snag: our editor is outstanding, but not flawless.
So, during the RNA splicing process, our “mRNA movie” gets “re-cut”:
- It’s possible that we’ll wind up with a perfect, commercial-free remake of the original film. Just a bunch of good exons spliced together in a continuous, faithfully duplicated sequence.
- Alternatively, if alternate splicing occurs, we may find that a few sections from our film are missing. It’s possible that a few exons will be removed.
Splicing of RNA (Figure 2.29).
mRNA transport into and out of the nucleus
Keep in mind that DNA and RNA are mostly found in the nucleus. (We’ll talk about another type of DNA, mitochondrial DNA, in Chapter 6, which doesn’t.)
mRNA must overcome a few more obstacles before it may be used to code for protein. This is where mRNA export comes in.
- mRNA must travel from the nucleus to ribosomes, the cytoplasm’s protein-making factories.
- It must also prevent itself from deteriorating. It can’t be used if it’s been broken down (degraded).
You don’t want RNA to escape the nucleus at random, any more than you don’t want drunken texts to your ex or boss to escape your phone at 3 a.m.
As a result, you must control mRNA breakdown and stability in order for it to reach the ribosome and be translated into a protein.
Nuclear export involves nuclear transport receptors that chaperone the mRNA via a nuclear pore, making it a bit of a bottleneck to get the mRNA out of the nucleus.
RNA migration through the nuclear pore (Figure 2:30).
When precursor mRNA matures (through splicing and the addition of some accessories for stability), it is picked and transferred out of the nucleus.
Mature mRNA has a number of additional nucleotides (a 3′ poly-A tail) on one end that behaves like the small plastic ends on your shoelaces that keep them from fraying. It has a cap on the other end of the mRNA (the 5′ end) (a 7-methylguanosine cap).
The cap and tail safeguard and stabilize the mRNA by preventing it from being broken down. The more protein the mRNA can produce, the more stable it is.
RNA of different types
There are various forms of RNA that we need to create proteins in addition to pre-mRNA and mRNA.
- RNA transfer (tRNA). The RNA molecules known as tRNAs transport certain amino acids to the ribosome. They match mRNA codons to their amino acid counterparts.
- The RNA enzyme ribosomal RNA (rRNA) joins amino acids in the ribosome to form a polypeptide chain. Remember that ribosomes are where mRNA is read and paired with tRNA, which carries amino acids, and then the protein is formed.
Small nuclear RNA (snRNA), microRNA (miRNA), and small interfering RNA (siRNA) are examples of RNAs that control how much and what sort of protein is produced.
There will be no exam.
Just keep in mind:
There’s a lot more to it than “one gene, one protein.”
| The RNA type | The primary function |
|---|---|
| mRNA | Proteomic codes |
| rRNA | An RNA enzyme that connects amino acids. |
| tRNA | mRNA codons and the amino acids they code for are linked by bridges. |
| snRNA | RNA splicing |
| miRNA | Generally prevents certain mRNA from being translated, although it can also upregulate (raise) it. |
| siRNA | Degrade certain mRNAs on a selective basis |
Gene expression regulation: from DNA to protein
From DNA to protein, there are five processes that are controlled by mRNA production, processing, and transport.
- Transcription is the process of converting DNA into RNA.
- Splicing RNA is a type of RNA processing.
- RNA export is the process of mRNA leaving the nucleus.
- Making protein from mRNA is a translation.
- Post-translational processing is the process of removing unneeded or damaging mRNA before proteins are produced (kind of like a quality control mechanism)
Your body does not produce RNA from DNA on a regular basis. It’s a highly controlled procedure. Only particular genes, and only at specific times, are transcribed.
Three control areas exist in each gene:
- promoters
- enhancers
- terminators
For all genes, the promoters and terminators (essentially the starts and stoppers) are the same.
Enhancer regions, on the other hand, are unique. Their differences allow them to more precisely match transcription factors, allowing systems to activate or deactivate transcription of specific genes based on the presence or absence of their transcription factor (s).
What causes mutations?
Consider nucleotide pairs as a pair of coordinating socks. After doing laundry, you should have all of your socks correctly sorted and paired. That happens from time to time. Not all of the time.
You may lose or mismatch one sock, a pair of socks, or several pairs of socks from time to time. You may even find yourself with new socks… socks that aren’t even yours.
The similar thing can happen with DNA nucleotide pairs. This is referred to as a mutation, which is a change in the nucleotide pairing sequence that is permanent. This can happen in a variety of ways and for a variety of causes.
Antioxidants and reactive oxygen species are two examples.
You’ve probably heard the phrase “antioxidant” before (for example, as a component of “superfoods” or vitamins C and E).
But why are antioxidants required in the first place?
We produce reactive oxygen species as part of our normal metabolism (ROS). ROS are oxygen-containing molecules that are produced naturally as a consequence of cellular respiration. Oxidative damage occurs naturally during cell metabolism, according to some estimates, 10,000 times each day per cell.
Normally, our cells’ antioxidant systems are able to counteract oxidative damage.
Under certain conditions, such as when a cell is exposed to toxins, ROS can build up faster than the cell can discharge them. Mutations can occur when the nucleotides are chemically modified to form a slightly different molecule.
Mutation types and causes
One source of mutations is the presence of a large amount of reactive oxygen species (ROS).
Oxidative alterations can occur in a variety of ways, including:
- ionizing radiation exposure (e.g., X-rays or radioactive substances);
- particular compounds (for example, heavy metals or herbicides);
- ultraviolet radiation (UV light is particularly sensitive to two nucleotides, cytosine and thymine); and
- Errors in the DNA replication/copying process that occur spontaneously (and are not repaired).
Mutations can influence anything from a single nucleotide to chromosome changes on a vast scale. They have the ability to alter gene structure and function.
Small alterations can have a substantial impact on the amino acid makeup of a protein:
- Substitution mutations occur when one nucleotide in a codon is replaced by another (for instance, an A for a G or a C for a T). These could include:
- Mutations that code for the same or a similar-enough amino acid are known as silent mutations (e.g., both CCA and CCT result in proline)
- Mutations that code for a different amino acid are known as missense mutations (e.g., CCA results in proline, but CTA results in leucine).
- Nonsense mutations can truncate proteins by creating stop codons (e.g., TAC generates tyrosine, whereas TAA signals “halt”). This means that before a protein has all of its amino acids, the ribosome (the protein-making factory) in a cell will cease generating it. As a result, the protein’s function may be affected.
- Frameshift mutations: The DNA copying process can occasionally insert or delete one or more nucleotides, causing the entire reading frame to shift. It’s possible that everything beyond the frame is now nonsense, or that the gene is merely missing some amino acids.
- Insertions are when one or more additional nucleotides are added to the DNA.
- Deletions are changes in the DNA that eliminate one or more nucleotides.
Insertions and deletions are shown in Figure 2.31.
The following are examples of more serious mutations that can affect one or more whole genes:
- Amplifications or duplications of genes or parts of a chromosome, or more than one copy of a gene or region of a chromosome.
- Large sections of a chromosome are deleted, resulting in the loss of some genes in those areas.
- Bringing together previously isolated pieces of DNA, possibly resulting in the formation of new genes (known as fusion genes). The unique seaweed-digesting bacterial enzyme found in the gut bacteria of people of Japanese heritage, which researchers believe may have originated from the DNA of marine bacteria that thrive on seaweed, is an example of this. Horizontal gene transfer refers to the transfer of DNA from unicellular species (such as bacteria) to multicellular creatures (such as humans).
- Translocations of chromosomes, which occur when unrelated chromosomes swap portions.
- When a fragment of DNA is removed from a single chromosome, it is referred to as a terminal or interstitial deletion. Large deletions can be harmful to an organism, even fatal. An interstitial deletion causes Prader-Willi Syndrome, which disrupts many areas of normal growth, development, and metabolism.
- Inversions of chromosome segments, which “flip” the order of a chromosome segment. The majority of these mutations are harmless.
- Heterozygosity loss, or the loss of an allele from the (potentially distinct) pair of genes you receive from your parents, leaving you with only one “regular” allele.
Other mutations (Figure 2.32).
Sometimes mutations have visible consequences, and sometimes they don’t.
Consider the following example:
- Genes can be partially or completely turned off. These are known as inactivating mutations or loss-of-function mutations. A mutation inactivates the androgen receptor in androgen insensitivity syndrome (AIS), causing chromosomally XY people to develop physically as females.
- Genes have the potential to become more powerful. There are more copies of a gene to be transcribed if there are more copies of a gene in a genome (copy number variation, or CNV), and the effect can be more dramatic.
- Genes have the ability to change their function. For example, a mutation in HBB, the -globin gene (which alters the amino acid coding from glutamic acid to valine) can cause hemoglobin to be less oxygen-carrying. This mutation is known as sickle-cell anemia.
- Sometimes mutations are beneficial, providing us with a competitive advantage in our surroundings. They can be hazardous at times. They may have no impact at all at times.
- Mutations that provided us an advantage in one environment (for example, the ability to store energy when food was scarce and required a lot of effort to obtain) may not give us an advantage in another (e.g., now that food is abundant, cheap, and energy-dense).
Mutations, on the other hand, can sometimes lead to the death of an organism. These mutations are referred to as fatal mutations. With a few exceptions, if you’ve made it to maturity, you’ve probably avoided the majority of the main deadly mutations.
Repairing damage to DNA
How does the body achieve the aforementioned great fidelity? By promptly detecting and fixing some of the most prevalent mutations.
At several “checkpoints” throughout the cell cycle, our bodies carefully check for DNA damage and quality, much like the Quality Assurance process in industrial production.
If damage is discovered, the “QA testers” should (ideally) stop the “production line,” halt cell division, and repair the problem.
Given the number of components in our genome, it’s incredible how effective and efficient our DNA copying process is — with only one big error per 1010 (or 10,000,000,000) nucleotides. You’ll have a hard time finding a factory with that degree of perfection!
Our bodies have numerous mechanisms for repairing DNA damage:
- When a set of genes “notices” defects in DNA replication and recombination, mismatch repair (MMR) occurs.
- We know of seven DNA MMR proteins (MLH1, MLH3, MSH2, MSH3, MSH6, PMS1, and PMS2) that work together to discover and fix problems.
- When MMR fails, we may develop microsatellite instability (MSI), which means that small, changeable, and highly mutation-prone portions of DNA (known as microsatellites) become part of our genetic material. Many cancers have been related to MSI.
- The processes of base excision repair (BER) and nucleotide excision repair (NER) repair lesions and physical damage that can cause DNA mispairing or breakage during replication. BER / NER deficiencies have been linked to cancer and neurodegeneration.
- The processes of nonhomologous end-joining (NHEJ) and homologous recombination repair (HRR) repair double-strand lesions or breaks. Double-strand breaks are similar to your DNA “ladder” being cut between the rails. These are some of the most serious DNA damage kinds. A single double-strand break is enough to kill a cell or compromise its genome’s integrity.
- TLS DNA polymerases allow unrepaired lesions to pass through the DNA replication process and be repaired later.
Critical mutations can occur in genes that are engaged in discovering and fixing faults rather than genes that do things like produce bodily parts. As a result, diseases of hereditary origin arise as a result of a lack of a capable “repair crew.”
You may devote your entire life to learning about genetics. (In fact, we struggled to keep this “basics” chapter under 10,000 words.)
If you just want to understand the basics of genetic testing, you don’t need to know all the specifics.
Just to give you an idea, here’s what I’m talking about:
Variations and mutations are complicated.
Mutations can sometimes knock an organism out of the game before it has a chance to reproduce. Alternatively, if the organism reproduces, the mutation is not passed on to the offspring.
Sometimes mutations have no effect on reproduction (for example, it only affects those over 60, or it gives you a funny-shaped nose, but someone still loves you).
Mutations and genetic variants are frequently passed down through generations, and as a result, they can have an impact on our health, nutrition, and fitness.
During the early stages of genetic study, scientists frequently asked if a single gene could cause specific disorders. Is it possible, for example, that a “cancer gene” exists?
Most diseases, we now know, are caused by a mix of causes.
The BRCA1 and BRCA2 gene variations, for example, play a significant role in the development of breast and ovarian malignancies. Many other genes, such as those involved in DNA repair, do as well.
Breast cancer genes are depicted in Figure 2.33.
Ovarian cancer comes in a variety of forms.
| Type 1 | Type 2 | |
|---|---|---|
| Mutations | PTEN, KRAS, BRAF, PIK3CA, ERBB2, CTNNB1, ARID1A, PPP2R1A, and microsatellite instability are all genes that have been linked to cancer. | BRCA1 BRCA2 TP53 |
| Prevalence | About 30% | About 70% |
| Type of tumor | Tumors that are serous, endometrioid, mucinous, or clear-cell | Carcinosarcomas, serous, mixed malignant mesodermal tumors, and undifferentiated tumors |
| Grade & progression | Low and borderline, sluggish, and frequently confined to the ovary | High-pitched and combative |
These differences have an impact on not only the origins, but also the locations, clinical course, and prognosis of various forms of ovarian cancer.
Cancer, for example, is not a single “thing.”
They are a wide range of events caused by complicated genetic and environmental interactions.
This will be emphasized throughout the text:
There are many complex, linked aspects in most preferences, health risks, and hereditary features.
There is almost never a single gene that causes a specific outcome.
Any genetic information we provide is merely a starting point for further investigation.
Environment has an impact on epigenetics.
Have you ever met identical twins who were diametrically opposed? Despite having the same genetic makeup, do they have different personalities, behaviors, and possibly even physical characteristics?
Researchers have looked at what occurs when one identical twin exercises or eats a healthy diet while the other does not. One study compared ten pairs of twins, for example. Each set of twins had one who exercised regularly and the other who was sedentary.
The researchers discovered that the more active twins were thinner and had a better metabolic profile. They also have greater grey matter in their brains than their inactive but genetically similar peers. Similar findings have been seen in other investigations.
Why aren’t two persons who share the same genetic blueprint identical twins?
Epigenetics, or the regulation of whether or not our genes are expressed, is the answer.
Gene expression is influenced by our surroundings (such as what we eat, what is around us, our exercise routines, what happened to us as children, and so on).
This can happen in a variety of ways, including histone modification. Histones are proteins that are part of the DNA package and can alter how sections of the DNA are active or repressed, as you may recall.
A comprehensive explanation of epigenetics would be interesting, but it is beyond the scope of this work.
Just have a look at the following to get a sense of what’s going on:
- More than only the genetic blueprint we were given at conception influences our genetic expression.
- Knowing our genotype isn’t enough to completely comprehend what it signifies or how it could influence our phenotype (for instance, our health, our risk of disease, our physical characteristics like height, and so forth).
- A variety of different factors can influence how and whether certain genes are expressed.
What’s next?
Now that you’ve mastered the fundamentals, let’s look at how genetic tests work and what they check for.
Once you understand what 2 the basics are, then you are ready to dive into the world of genetics. Genetics is the science of genetics. More accurately, it is the science of our genetic material — the DNA molecules that are carried by every cell of our body.. Read more about precision nutrition guidelines and let us know what you think.
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