Learning Outline

Mini Lesson:
DNA

Deoxyribonucleic acid—the information molecule

Structure of DNA

Nucleotides

Nucleotide is the subunit, made of three components:

Sugar (ribose in RNA; deoxyribose in DNA)
Phosphate
Nitrogen base
- Different types of nitrogen base: cytosine, guanine, adenine, thymine (DNA only), uracil (RNA only)
- First letters are used as abbreviations: C, G, A, T, U
- Bases may link C-G or G-C and T-A or A-T (in RNA, U-A or A-U)
  - This rule is complementary or obligatory "base-pairing"

Nucleotides combine to form a double helix structure

Sugar and phosphate groups link together to form the "backbones" of the double helix
The nitrogen bases link in pairs to connect the two backbones

Nucleotides link to form DNA.
Sugars and phosphates link to form the backbones and bases link in pairs to hold both helices together.
(Click image to enlarge it and view source)

DNA double helix model.
(click image for larger view)

watson and crick This classic photo of James Watson (l) and Francis Crick (r) shows them in 1953 with their original model for the double helix model of the DNA molecule.

Maurice Wilkins and Rosalind Franklin have also been given credit for participating in the discovery of this vitally important molecule's structure and essential function. (Wilkins shared the 1962 Nobel Prize in Medicine/Physiology with Watson & Crick)

Researchers continue to unravel the many complexities and mysteries of what Watson called, "the most golden of all molecules."

Genetish—language of genetics

Genetish is a made-up word introduced by author Matt Ridley to describe the coding used by cells in DNA/RNA

Codon

Every three bases make up one "word" or codon in genetish
Each different codon represents a different amino acid
- Amino acids combine to form polypeptides or proteins

Gene

A sequence of codons containing the information needed to make one polypeptide/protein is called a gene (gene = "recipe" for one protein)
- A gene could also make more than one type of polypeptide
- A gene could instead make a functional RNA molecule
Genes are found at various locations along a DNA molecule (chromatin/chromosome)
All genes on all chromosomes is a set of information called the genome

Codon table. This table is a type of "phrasebook" for the language of "genetish" —-showing the meaning of different possible codons.

Codon wheel. This is another type of "decoder" for determining which amino acid is represented by any codon. (clickimage to enlarge it and view source)

Click here to see Ben Fry's easier-to-read version of this classic table!
Ben constructed this as a student at MIT.
This version is similar to that found in our Anatomy & Physiology textbook.

Function of DNA

The information molecule

Master code for proteins made by the cell

Proteins perform functions that regulate the cell, make up parts of the cell, and regulate the synthesis (and breakdown) of other types of molecules (lipids, carbohydrates, so on)

In humans, temporary "working copies" of specific genes from DNA are in the form of RNA (review Cell Structure & Function)

Information "between the genes" formerly called "junk DNA" may also have functions in regulating gene expression, etc.

Acronym Table
rRNA ribosomal RNA	Forms ribosomes
mRNA messenger RNA	Unfolded strand contains gene (code for one polypeptide); temporarily folds when leaving nucleus
tRNA transfer RNA	Brings specific amino acids to ribosome and places them according to code on mRNA
nuclear DNA	"Master" genetic code in the nucleus
mDNA or mtDNA mitochondrial DNA	Additional "master" genetic code in the mitochondrion

Optional: Click here for another helpful outline Making Proteins from the Foundations in Science course.

Replication of DNA

DNA helix "unzips" and nucleotides with bases complementary to those in each exposed DNA strand "fill in" and make a new side

Results in two identical "daughter molecules" of DNA
Semiconservative (half is new; half is old)

Facilitated by enzymes (isn't everything?)

DNA replication.
(click image for source and attribution)

Transcription of RNA

Transcription

mRNA is a "transcribed" copy of one gene in DNA

DNA unzips at one gene, and other side "fills in" with RNA nucleotides with bases that complement the exposed bases of the DNA strand

Promoter — sequence of bases that tells the cell where to start transcribing the gene
RNA polymerase — enzyme that facilitates formation of mRNA strand

Transcription
(click image to enlarge)

Editing

mRNA transcript is edited before leaving nucleus

Introns — parts of sequence that are deleted ("nonsense")
Exons — parts of sequence the remain in the final mRNA molecule
A structure called the spliceosome forms on the mRNA, facilitating the splicing of transcript (removal of introns, gluing together of exons)

DNA editing (simplified)
(click image for larger view)

Other forms of RNA (tRNA, mRNA) produced in a similar manner

The edited transcript then usually folds into a complex shape, unlike the simple strand of mRNA

mRNA leaves nucleus via nuclear pores

Translation of RNA (protein synthesis)

Location

Translation occurs in the cytoplasm outside the nucleus

Process

Initiation — mRNA associates with rRNA of ribosome
Elongation — tRNA brings amino acids into place (anticodons on tRNA complement codons on mRNA) elongating string of amino acids
Termination — protein is released

Translation.
EAch tRNA (blue) brings a specific amino acid to ribosome (green) and links to the complementary codon on mRNA strand. As amino acids link together with peptide bonds, a polypeptide grows in length.

Mutations

Definition

Chromosomal mutations — additions, deletions to chromosome
Point mutations — change in one or few nucleotides in a gene sequence

Cause

Mutations can be spontaneous (no known cause)
Can be caused by radiation (x-ray, UV, etc.), chemicals, mechanical damage, extreme temperature, and other factors

Regulation of gene expression

Chromosome level

Packing — DNA wraps around histone proteins, forming "beads" called nucleosomes
Packing can prevent certain genes from being activated (transcribed)

Transcription level

Master genes turn on a group of other genes
Enhancer genes change the rate of transcription of other genes
Regulatory chemicals, such as steroid hormones, may activate certain genes
mRNA can be edited in different ways (exons can be linked in different ways)
mRNA can be "made ahead of time" and then "masked" until needed later

Translation level

Translation can be halted by regulatory mechanisms in the cell
Interferon released by nearby virus-infected cells can trigger the activation of genes that produce translation-inhibiting proteins
- This causes the cell to be more careful in checking mRNA and will halt translation of viral RNA that has infected the cell
RNA interference (RNAi)
- Mechanism by which translation of mRNA can be disrupted (interference)
- May help regulate gene expression
- May help defend against mutations and viral RNA infection
- Also called gene silencing

Location of DNA

Nucleus

46 chromosomes (diploid number) within nucleus (except during cell division)

DNA location and structure.

Mitochondrion

Single, ringlike strand of DNA comprising one chromosome

Mitochondrial DNA (mtDNA). This ringlike strand of DNA, similar to that seen in bacteria, contains genes that code for enzymes needed in mitochondrial function. Click on image to see larger source image, which is labeled with gene locations.

Genomic cartography is the study of methods to map out the genome of humans an other species in a way that makes the information easy to interpret and therefore more useful to everyone. Click here for an optional discussion from genomic cartographer Ben Fry.

If you think about it, DNA is kind of like a cookbook, with genes being the individual recipes used to "cook up" the proteins of the body!

Kevin's Mom's Hot Milk Cake Recipe