# Genetics

## Variation in Traits

**Traits** are any characteristics of an organism.

An organism's **genotype** is [the genetic makeup of the organism](#user-content-fn-1)[^1], but its **phenotype** would be the actual characteristics and behaviors the organism actually expresses. Both genetic *and* environmental factors can influence the variation and distribution of traits.

{% hint style="info" icon="vial-vertical" %}
If a person has dark skin but genetics tied to lighter skin, their skin may be affected by the environment. For example, the person may have gotten a tan from being in the sun too long.

Through this, we can also conclude that *phenotype isn't permanent but genotype is*.
{% endhint %}

## DNA Structure

**Deoxyribonucleic acid** (DNA) is a [double helix](#user-content-fn-2)[^2] consisting of two long strands that wind around each other. DNA is composed of a chain of nucleotides.

DNA is also **antiparallel**, meaning the ends of its strands are opposites. Each DNA strand has a 3' end and a 5' end, which is denoted by the order in which carbons of the sugars are placed. At the 3' end, there is hydroxyl (OH) and at the 5' end, there is a phosphate.

DNA's nucleotides each consist of a deoxyribose sugar, a phosphate group, and a nitrogenous base. The sugars and phosphates make up the **phosphate-sugar backbone**. DNA's nitrogenous bases are arranged so that each of the two strands' bases meet and are connected by hydrogen bonds.

### The Nitrogenous Bases of DNA

Nucleotides in DNA can have one of four different nitrogenous bases: **adenine**, **thymine**, **cytosine**, and **guanine**. Two complementary bases are called a **complementary base-pair**.

Adenine and thymine are complementary. When there is an adenine on one strand, there is a matching thymine on the other strand. Adenine and thymine bases are connected by *two* hydrogen bonds.

Cytosine and guanine are complementary. When there is an cytosine on one strand, there is a matching guanine on the other strand. Cytosine and guanine bases are connected by *three* hydrogen bonds.

<div data-with-frame="true"><figure><img src="/files/z4qxeilYBdFRH74kaJAj" alt="" width="563"><figcaption><p><strong>Image 1</strong> — Different representations of the structure of DNA.</p></figcaption></figure></div>

## DNA Replication

When DNA replicates, it is **semiconservative**. Instead of duplicating and staying attached, it splits the two strands apart and creates a complementary strand for each of the original strands. The two resulting DNA have one original strand each like shown in Image 2.

<div data-with-frame="true"><figure><img src="/files/ASkI04JFJmzA6lTQ9hSF" alt="" width="563"><figcaption><p><strong>Image 2</strong> — DNA replication is semiconservative.</p></figcaption></figure></div>

### Steps of DNA Replication

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#### Splitting DNA

In order to replicate, DNA must split apart first. An enzyme called **helicase** breaks the hydrogen bonds between bases to separate the strands into a **replication fork** like in Image 3.

<div data-with-frame="true"><figure><img src="/files/2lWGaC8EFuOR44OKQS9e" alt="" width="563"><figcaption><p><strong>Image 3</strong> — A replication fork. The protein shown is helicase.</p></figcaption></figure></div>

The strand that is cut starting at the 3' end is called the **leading strand template**. The strand cut at the 5' end is called the **lagging strand template**. The new DNA strands made complementary to these templates are the **leading strand** and **lagging strand** respectively.
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#### Priming the Leading Strand

An enzyme called **Primase** adds a small sequence of RNA bases complementary to the leading strand template called a **primer**. This marks the starting point for the construction of the leading strand.
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#### Constructing the Leading Strand

An enzyme called **DNA Polymerase** binds to the primer. DNA Polymerase can only add bases in one direction: from the 5' end to the 3' end.

On the leading strand template, the enzyme then adds new complementary DNA bases to construct the actual leading strand continuously whilst the helicase enzyme is still splitting the DNA strands apart like in Image 4.

<div data-with-frame="true"><figure><img src="/files/cqCfxjpDS6ID5kq87fhV" alt="" width="563"><figcaption><p><strong>Image 4</strong> — The creation of the leading strand on top by DNA Polymerase. Helicase, to the far<br>left, is still splitting DNA as this goes on.</p></figcaption></figure></div>
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#### Priming and Constructing the Lagging Strand

Since the lagging strand template runs in the opposite direction, DNA Polymerase can't continuously create the lagging strand. It instead creates them in chunks called **Okazaki fragments**.

A primer is first created. Then, a short row of DNA bases are created in the 3' to 5' direction. Another primer is added further down and the process repeats like in Image 5.

<div data-with-frame="true"><figure><img src="/files/FpxqFPGue4S0Z6xjhe7I" alt="" width="563"><figcaption><p><strong>Image 5</strong> — Primase priming the lagging strand. The gap is where the Okazaki fragment will be.</p></figcaption></figure></div>
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{% step %}

#### Cleaning Up and Resealing

An enzyme called **exonuclease** removes all the RNA primers from both of the new DNA strands. Then, DNA Polymerase fills in the gaps.

Finally, an enzyme called **DNA Ligase** seals both DNA strands up.
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{% endstepper %}

## Organization of DNA

A **genome** is an organism's complete set of genetic material. Different organisms have different genomes.

DNA is condensed into a structure called the **chromosome**. An organized package of DNA, chromosomes are how DNA can fit inside the nucleus of every cell.

Chromosomes are in an x-shape like in Image 6, with the center called the **centromere**, four **arms**, and four **telomeres**. When uncondensed, chromosomes are called **chromatin**.

<div data-with-frame="true"><figure><img src="/files/xGwcCNzwmjN85o5jYBRv" alt="" width="386"><figcaption><p><strong>Image 6</strong> — The structure of chromosomes.</p></figcaption></figure></div>

The **karyotype** is an individual's collection of chromosomes.

{% hint style="success" icon="lightbulb" %}
Humans have a karyotype of 46 chromosomes.
{% endhint %}

**Genes** are sequences of DNA that encode for RNA and proteins. Different genes code for different proteins and some genes don't even have to code for proteins.

### DNA Arrangement

The area on the chromosome where a specific gene is located is called the **locus**.

All organisms have a set number of chromosomes in every cell, yet they are grouped into chromosome pairs. The two chromosomes of a pair are homologous, meaning each gene in both chromosomes code for the same purpose. This is why each chromosome pair is also called **homologous chromosomes**.

Formally, homologous chromosomes are a pair of chromosomes of the same length and pattern that possess genes for the same traits.

Homologous pairs are not identical, however. Though every gene on one chromosome in a homologous pair is matched with the corresponding gene of the other, they can have different variants of the gene. A variant of a gene is called an **allele**.

{% hint style="info" icon="vial-vertical" %}
A homologous pair for a flower can have different alleles for the gene that heavily determines petal color. This means one of the chromosomes in the pair can code for white petals, but the other could code for purple petals.
{% endhint %}

When a homologous pair has a gene with the same allele, it is considered as **homozygous**. When a homologous pair has a gene with two different alleles, it is considered as **heterozygous**.

## The Central Dogma

### The Product of Genes

Genes' DNA codes for different proteins that can help provide structure and function to the organism. Despite this, only about 1.5% of genes code for proteins and RNA. The rest of the DNA *regulates* **gene expression**, the process of going from DNA to a [functional product](#user-content-fn-3)[^3].

In order to actually get to proteins from DNA, there is a process requiring RNA.

<div data-with-frame="true"><figure><img src="/files/VSD77JWOqhhG4ouf2rW0" alt="" width="495"><figcaption><p><strong>Image 7</strong> — Comparison between RNA and DNA.</p></figcaption></figure></div>

The major differences between RNA and DNA are that RNA is single-stranded and uses a different nitrogenous base in the place of thymine: **uracil**. Uracil is also complementary to adenine.

### Protein Synthesis

If you remember, proteins are created within the [ribosomes](/learn/sci/fundamental/biology/cells.md#organelle-list) of a cell.

DNA, being long and complex, is to large to leave the nucleus as is. To transfer the gene outside of the nucleus, an RNA sequence is constructed for just the gene needed.

**Transcription** is the process in which mRNA is constructed from DNA. **Translation** is the process where mRNA codes for amino acids, which then chain into a protein.

{% stepper %}
{% step %}

#### Transcription

To start, the enzyme **RNA Polymerase** attaches onto the DNA where the gene is located. RNA Polymerase—like DNA Polymerase—can also only read from the 3' end to the 5' end. The strand that RNA Polymerase reads is called the **coding strand**. The other strand is called the **noncoding strand**.

RNA Polymerase then reads the coding strand and creates the RNA sequence complementary to the gene. This sequence of RNA is called **messenger RNA** (mRNA).

mRNA can now leave the nucleus in order to reach a ribosome.
{% endstep %}

{% step %}

#### Translation

Once mRNA reaches the ribosome, it feeds into it.

More RNA called **transfer RNA** (tRNA) reside within the cytoplasm. tRNA molecules read the mRNA strand in units called **codons**, which are snippets of *three consecutive* nitrogenous bases. Each codon corrsponds to a specific amino acid (or stop codon). The tRNA then takes the amino acid coding for the **anticodon** of the codon it read.

{% hint style="info" icon="circle-info" %}
Note that a ribosome won't start making a protein until it reads a start codon. Conversely, it won't stop reading and release the mRNA until it reaches a stop codon.
{% endhint %}

<div data-with-frame="true"><figure><img src="https://microbenotes.com/wp-content/uploads/2023/09/Amino-Acid-Codon-Wheel-scaled.jpeg" alt="" width="563"><figcaption><p><strong>Image 8</strong> — Amino acid codon wheel.</p></figcaption></figure></div>

{% hint style="info" icon="circle-question" %}
The anticodon is the set of three base pairs that is complementary to the codon.
{% endhint %}

The tRNA carries the amino acid over to the mRNA and places the first amino acid. The mRNA then feeds through and the next amino acids are placed by more tRNA. As codons are read and amino acids are chained, previously used tRNA detaches from the mRNA in order to be reused.

Once the ribosome reaches a stop codon (refer to Image 8), it releases the mRNA and **ribosomal RNA** (rRNA) inside the ribosome creates peptide bonds to fully connect the amino acids into a polypeptide chain.

The protein has now been created.
{% endstep %}
{% endstepper %}

## Mutations

A **mutation** is a permanent change in the DNA sequence. This is done when there is a mistake in DNA replication, though external factors (like radiation) can also cause mutation.

### Insertion and Deletion

There are exactly as they seem; **insertion** adds a base to the sequance, while **deletion** removes a base from the sequence.

Because of the way they alter the DNA sequence, insertion and deletion are considered as **frameshift mutations**. These mutations completely change which amino acids are chained from the mutation and onward.

### Substitution

**Substitution** is when a base is switched for a different base. There are three types of substitution mutation...

**Silent substitution mutations** are when the mutation has no effect on the amino acid. This means that the correct amino acid is used and the protein still functions as normal.

**Missense substitution mutations** are when the mutation changes one amino acid into another. This changes a single amino acid in the sequence and can cause the protein to work differently or not function properly.

**Nonsense substitution mutations** are when the mutation changes the amino acid into a stop codon, prematurely ending the amino acid chain. This can cause proteins to not function properly.

### Mutations Transferring During Reproduction

Sometimes, a mutation may be present in a [**gamete**](#user-content-fn-4)[^4]. This mutation would then carry on to the offspring, when it fuses with the other gamete, making it highly likely that the offspring has the mutation. This is called a **germline mutation**.

If the mutation happens in any other cell, it is a **somatic mutation**, making it non-heritable.

[^1]: The set of genes of the organism.

[^2]: Which resembles a twisted ladder.

[^3]: In most cases, it's a protein.

[^4]: A gamete is a reproductive cell of an organism. For humans, women have eggs and men have <mark style="color:red;">s</mark><mark style="color:orange;">p</mark><mark style="color:yellow;">e</mark><mark style="color:green;">r</mark><mark style="color:blue;">m</mark>.


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