Gene Expression and regulation

Introduction to Gene Expression

The discovery of the structure of DNA also provided a glimpse into understanding how a cell uses its genes to make proteins. The process, known as gene expression, requires not only DNA but also RNA.

Some properties of DNA and RNA

DNA (Deoxyribonucleic Acid)	RNA (Ribonucleic Acid)
Large double-stranded molecule	Small single-stranded molecule
In Bacteria and Archaea, found in the nucleoid and plasmids; in Eukarya, found in the nucleus, mitochondria, and chloroplasts	In all organisms, found in the cytosol and in ribosomes; in Eukarya, also found in the nucleolus
Always associated with chromosome (genes); each chromosome has a fixed amount of DNA	Found mainly in combinations with proteins in ribosomes (ribosomal RNA), as messenger RNA, and as transfer RNA
Contains a 5-carbon sugar called deoxyribose	Contains a 5-carbon sugar called ribose
Contains bases adenine, guanine, cytosine, and thymine	Contains bases adenine, guanine, cytosine, and uracil
Contains phosphorus (in phosphate groups) that connects deoxyribose sugars with one another	Contains phosphorus (in phosphate groups) that connects ribose sugars with one another
Functions as the molecule of inheritance	Functions in gene expression and gene regulation

The Central Dogma — **The flow of genetic information proceeds from DNA to RNA to protein (polypeptide)**

The process of manufacturing a protein starts when a particular gene is copied into a complementary RNA through a process known as transcription.
In the cytoplasm, the RNA carrying the gene message, along with other types of RNA, is transformed into a growing protein molecule or polypeptide by linking amino acids altogether.
This reading of the RNA bases is called translation, and the polypeptide produced reflects the genetic information that was originally coded in the DNA.
The expression of genes through transcription and translation is known as the central dogma (dogma = “truth”).

Transcription Copies Genetic Information into Complementary RNA

Transcription is the first, and perhaps most regulated, step in gene expression.
The large enzyme responsible for transcription is RNA polymerase.

Transcription Process During Elongation — For transcription to occur, a gene must be unwound and the base pairs separated. The enzyme RNA polymerase does this as it moves along the template strand of the DNA and adds complementary RNA nucleotides. Note that the other DNA strand of the gene is not transcribed.

In prokaryotes, there is but one RNA polymerase with the archaeal enzyme being much more equivalent to the eukaryotic polymerases.
Like DNA polymerases, RNA polymerase “reads” the DNA template strand in the 3 to 5 direction. However, unlike DNA replication, only one of the two DNA strands within a gene is transcribed.
Transcription begins when RNA polymerase acknowledges a sequence of bases called the promoter.
The sequence is found on only one of the gene’s two strands, this represents the DNA template strand recognized by the RNA polymerase.
The enzyme binds to the promoter (initiation step), unwinds the helix, and separates the two strands within the gene.
As the enzyme moves along the DNA template strand (elongation step), complementary pairing brings RNA triphosphate nucleotides to the template strand—guanine (G) and cytosine (C) pair with each other and thymine (T) in the DNA template pairs with adenine (A) in the RNA.
However, an adenine base on the DNA template pairs with a uracil (U) base in the RNA because RNA nucleotides contain no thymine bases.
Termination of transcription occurs at a specific base sequence, called the terminator, on the DNA template strand.
The RNA transcription product released represents a complementary base sequence to the base sequence in the DNA template strand.
Transcription produces three types of RNA that are needed for translation. In addition, a number of other types of RNA are used to regulate gene expression. Here, we focus on the three closely involved with translation.

Messenger RNA

This RNA carries the genetic information (message) that ribosomes “read” to manufacture a polypeptide.
Each messenger RNA (mRNA) transcribed from a different gene carries a different message, that is, a different sequence of nucleotides coding for a different polypeptide.
The message is encoded in a series of three-base combinations called codons that are found along the length of the mRNA.
Each codon specifies an individual amino acid to be slotted into position during translation.

Ribosomal RNA

Three ribosomal RNA (rRNA) molecules are transcribed from specific regions of the DNA.
Together with more than 50 proteins, these RNAs serve a structural and functional role as the framework of the ribosomes, which are the sites at which amino acids assemble into a polypeptide.

Transfer RNA

The conventional drawing for a transfer RNA (tRNA) is in a shape roughly like a cloverleaf.
One region consists of three bases, which functions as an anticodon, that is, a sequence that complementary binds to an mRNA codon.
The tRNAs have a transport role in delivering amino acids to the ribosome for assembly into a polypeptide.
Each tRNA has a specific amino acid attached to it. For example, the amino acid alanine binds only to the tRNA specialized to transport alanine; glycine is transported by a different tRNA.
There is one important difference between microbial RNAs. In most bacterial and some archaeal cells, all of the bases in a gene are transcribed and used to specify a particular polypeptide or RNA.

RNA Processing and Gene Activity — **(A)** In bacterial cells, gene DNA is almost entirely protein-coding information that is transcribed and translated into a protein having structural or functional roles in the cytoplasm, or gene regulation roles. **(B)** **In eukaryotic cells, some of the intron RNA may be degraded, used to regulate gene function, or be associated with other RNAs or proteins in the cytoplasm.**

However, in other archaeal cells, and all eukaryotic cells, certain portions of the RNA coding sequence of a gene are not part of the final RNA and are removed from the RNA before the molecule can function.
These intervening DNA segments removed after transcription are called introns, whereas the remaining, amino acid-coding segments that are reattached are called exons.

Reference and Sources

https://www.flashcardmachine.com/chapter-8218.html
https://en.wikipedia.org/wiki/Gene
https://quizlet.com/157243724/microbiology-chapter-8-microbial-genetics-flash-cards/
https://findanyanswer.com/what-enzyme-unwinds-dna-during-transcription
https://quizlet.com/77504365/chapter-8-microbial-genetics-flash-cards/
https://courses.lumenlearning.com/microbiology/chapter/rna-transcription/
https://www.coursehero.com/tutors-problems/Biology/9648276-i-need-help-with-following-questions-anyhelpers/
https://quizlet.com/125209263/microbiology-exam-2-flash-cards/
https://en.wikipedia.org/wiki/DNA_sequencing

What is Gene Expression?