The Biology and Genetics of Cells and Organisms

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.title[
# The Biology and Genetics of Cells and Organisms
]
.subtitle[
## DNA, Deoxyribonucleic Acid
]
.author[
### Mikhail Dozmorov
]
.institute[
### Virginia Commonwealth University
]
.date[
### 2025-09-03
]

---

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.large { font-size: 130%; }
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## Genes and genome

* **Genes** are discrete hereditary units located on chromosomes (DNA).

* Each gene provides specific instructions for producing a particular trait or function in the organism.

* The complete set of genes in an organism is called its **genome**.

---
## Building blocks of DNA

* The basic unit, a **nucleotide**, consists of an organic **base** attached to a deoxyribose **sugar**.

* A **phosphate** group is also attached to the sugar.

* The **base** can be one of four types: **cytosine (C), thymine (T), adenine (A), or guanine (G)**.

---
## Nucleotide structure

---
## Nucleotide structure

.pull-left[
.center[Ribose Sugar]
<img src="img/Ribose.png" width="385" height="40%" style="display: block; margin: auto;" />
.center[**RNA** - **Ribo**_nucleic_ acid]
]
.pull-right[
.center[ Deoxyribose Sugar ]
<img src="img/Deoxyribose.png" width="385" height="40%" style="display: block; margin: auto;" />
.center[**DNA** - **Deoxyribo**_nucleic_ acid]
]

---
## Bases

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## Getting to know DNA: Gel electrophoresis

* In the mid-1900s, methods were developed to separate and visualize DNA using an electrically charged gel (originally made from sugar).

* DNA samples are loaded into “lanes” at the top of the gel, and an electric field is applied.

* Smaller DNA fragments migrate faster and move farther down the gel, while larger fragments remain closer to the top.

* This allows detection of DNA and comparison of relative fragment lengths.

* One lane is often reserved for a **DNA ladder**, a set of fragments of known sizes.

---
## Getting to know DNA: Gel electrophoresis

<img src="img/gel_electrophoresis_dna_bands_yourgenome.png" width="40%" style="display: block; margin: auto;" />
.small[ https://www.yourgenome.org/theme/what-is-gel-electrophoresis/ ]

---
## Discovery of double helix, 1953

- James Watson and Francis Crick

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## Genomic DNA

* DNA is a **double helix**, with bases oriented inward (like rungs of a ladder) and sugar-phosphate backbones forming the outer sides (like the rails of a twisted ladder).

* The two strands are **complementary**, following Watson-Crick base-pairing rules.

* **A** (a purine) pairs with **T** (a pyrimidine), and **C** (a pyrimidine) pairs with **G** (a purine).

* Base pairs are held together by **hydrogen bonds**, and the twisting of the helix results from the geometry of these interactions.

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## Before the discovery

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## Genomic DNA
<img src="img/watsoncrick.png" width="37%" height="37%" style="display: block; margin: auto;" />
.small[ WATSON, J., CRICK, F. Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature 171, 737–738 (25 April 1953). https://doi.org/10.1038/171737a0 ]

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## Nucleic acid strand

- Strand synthesis - from 5' to 3' end: (5') TACG (3')
<img src="img/strand.png" width="40%" height="40%" style="display: block; margin: auto;" />

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## Double strand: DNA base pairing

- The two strands are held together by hydrogen bonds between bases

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## Rules of base pairing

- Rules of base pairing: A-T(U), C-G (and G-U in RNA)

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## Base pairing

* Base pairs are held together by weak **hydrogen bonds**.

* While each bond is weak individually, their cumulative effect across the strands provides strong overall stability.

* This makes DNA chemically stable and an effective carrier of genetic information.

<!--
## Helixes conformation

<center>
![](img/Helixes.png)
</center>

- A: B-form: Right-handed, 3.4 nm between bases, 10 bases per turn
- B: A-form: Right-handed, 2.3 nm between bases, 11 bases per turn
- C: Z-form: Left-handed
-->

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## Helixes conformation

<img src="img/Helixes2.png" width="40%" height="40%" style="display: block; margin: auto;" />
- A: B-form: Right-handed, 3.4 nm between bases, 10 bases per turn
- B: A-form: Right-handed, 2.3 nm between bases, 11 bases per turn
- C: Z-form: Left-handed

---
## Eukaryotic DNA packaging

<img src="img/packaging.png" width="40%" height="40%" style="display: block; margin: auto;" />
.small[ https://www.biointeractive.org/classroom-resources/how-dna-packaged ]

---
## The central dogma of molecular biology

.pull-left[
<img src="img/Central_Dogma2.png" width="80%" height="80%" style="display: block; margin: auto;" />
]
.pull-right[
- Formulated by Francis Crick in 1953

- **DNA makes RNA and RNA makes protein**

- **Transcription** is the making of an RNA molecule off a DNA template.

- **Translation** is the making of a protein off an RNA template.
]