Gene structure and regulation

Chromatin has highly complex structure with

several levels of organization.

 Nature Education Adapted from Pierce, Benjamin. Genetics: A Conceptual Approach

https://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437/
 Every cell in a plant contains the same genetic information, the same set of genes.
  Yet Therefore different sets of genes are required for the various functions of different
cells or tissues, as well as for plant responses to environmental stimuli or stresses.
 This is achieved by regulating the activity of genes according to the physiological
demands of a particular cell type, developmental stage, or environmental condition.
This regulation of activity is known as gene expression.
 The expression of genes in specific plant cells, tissues, and organs and the timing of
this expression require a precise level of regulation.
 Expression, or genetic function, can potentially be regulated at any of the steps from
transcription, RNA processing, translation, through post-translational protein
modification
Promoters
 Eukaryotes use regulatory proteins to control transcription, but each eukaryotic gene has its
own set of controls.
 In addition, there are many more regulatory proteins in eukaryotes and the interactions are
much more complex.
 In eukaryotes transcription takes place within the membrane-bound nucleus, and the
initial transcript is modified before it is transported from the nucleus to the cytoplasm for
translation at the ribosomes.
 The initial transcript in eukaryotes has coding segments (exons) alternating
with non-coding segments (introns).
 Before the mRNA leaves the nucleus, the introns are removed from the
transcript by a process called RNA splicing and extra nucleotides are added to
the ends of the transcript; these non-coding "caps" and "tails" protect the
mRNA from attack by cellular enzymes and aid in recognition by the
ribosomes.
Gene Promoter
 The signals for starting and stopping transcription are located within DNA
sequences.
 Specific nucleotide segments called promoters are recognized by RNA
polymerase to start RNA synthesis.
 After the transcription of full-length RNA strand is completed, a second
segment of DNA called terminator invokes termination of RNA synthesis and
the detachment of RNA polymerases from the DNA template.
Protein-coding region
The protein-coding region of a gene is composed of the sequence of nucleotides that codes
for amino acids.
The coding region begins with an ATG start codon (AUG in RNA) and then ends with one of
three stop codons.
These sequences include only exons, but not all exonic sequences are protein coding as they
may include untranslated regions.

Figure 3. The protein-coding region of a gene contains nucleotides that codes for amino acids. The 5′ and a 3′ UTR sequences do not code
for amino acids but contain regulatory sequences that influence gene expression. In mRNA, translation start is AUG and translation stop can
be UAA, UAG, and UGA. Image by Walter Suza.
Untranslated regions (UTRs)
 Mature transcripts contain some sequences that do not code for amino acid sequences in
proteins. These are referred to as untranslated regions or UTRs.
 Most mRNA transcripts contain a 5′ and a 3′ UTR. The 5′ UTR contains sequences toward the
5′ end of the mRNA sequence, before the start codon.
 These sequences can often be important for translational regulation, and sometimes
other functions.
 The sequences following the stop codon are the 3′ UTR. The 3′ UTR may also have
important functions regulating transcript stability or directing transcript localization
within cells, or sometimes even transport (trafficking) between cells.
Figure 1. Prokaryotic transcription and translation occur simultaneously in the cytoplasm, and regulation occurs at the transcriptional level. Eukaryotic gene
expression is regulated during transcription and RNA processing, which take place in the nucleus, and during protein translation, which takes place in the
cytoplasm. Further regulation may occur through post-translational modifications of proteins.

https://courses.lumenlearning.com/wm-biology1/chapter/reading-prokaryotic-and-
eukaryotic-gene-regulation/
Transcription
 The genetic information of DNA is transferred to an intermediate molecule called
RNA that is often translated to amino acid sequences used to build proteins.
 RNA is a nucleic acid, like DNA, but with some important differences. RNA contains
a ribose sugar group instead of the deoxyribose found in DNA.
 RNA molecules are single stranded, instead of being double stranded.
 RNA contains a uridine (U) base and does not contain a thymidine base. The other
bases (A, C, G) are contained in both RNA and DNA. U has the property of base-
pairing with A.
The enzyme RNA polymerase (RNA Pol) uses the template strand to synthesize RNA in the 5′ to 3′
prime direction. The base T is replaced with U in RNA. Image by Walter Suza.
 RNA synthesis is directed by a DNA template in a process called transcription.
 A protein complex containing the enzyme RNA polymerase synthesizes an RNA
molecule by adding nucleosides to the 3′ end of a growing chain.
 The principle of base pairing is used again and each nucleotide base added is
complementary to the corresponding base on the DNA template.
 Thus, the RNA is complementary in sequence to the template strand of DNA, which
is also referred to as “antisense” or “negative” strand.
 The RNA is identical in sequence (except U replaces T) to the other strand, which is
called the “sense” or “positive” strand. Because RNA molecules are produced by
the process of transcription, they are often referred to as transcripts.
RNA processing

Coding (transcribed) region

 This is the region that is transcribed by RNA polymerase, also known as the RNA
coding region. It may include introns, sequences that are removed from the mature
RNA molecule during RNA processing.
 The transcribed region is demarcated by promoter and terminator sequences.

Introns and exons

 Introns are sequences that are removed from transcripts during RNA processing.
Sequences that are retained in mature transcripts are called exons.
 Introns are commonly found in genes of eukaryotes but are rare in prokaryotic
organisms.
Intron splicing
 The process of transcription produces pre-mRNA that contains both introns and
exons.
 The process of splicing involves removal of introns from pre-mRNA and joining
together the exons. A complex group of proteins that form a spliceosome perform
the splicing reaction.
 Introns sometimes serve as boundaries for sequences encoding functional protein
domains, leading to possibility for new and variant proteins by exon shuffling.
Also, introns can provide possibility for productions of variant RNA forms through
alternate splicing allowing more than one gene product from a single gene.
 Some introns result from the insertion of transposable elements and may be spliced
perfectly of imperfectly, offering more possibility for new genetic diversity.
DNA (gene) transcription produces precursor-mRNA (pre-mRNA) that contains both introns and exons. The 5′ cap is 7-methyl guanidine. The
enzyme poly(A) polymerase adds the poly(A) tail. The process of splicing involves removal of introns from pre-mRNA and joining together the
exons to form mature mRNA. Image by Walter Suza
5′ Capping
 The 5’ capping is the addition of a 7-methyl guanidine to the first nucleotide of mRNA molecule,
usually and adenine or guanidine.
 The phosphodiester linkage between 7-methyl guanidine and the target nucleotide is 5′-5′ instead
of 5′-3′, and 3 phosphates rather than 1 are retained in the linkage.
 The cap stabilizes the 5′ end of the mRNA and plays a role in translation initiation.

Poly adenylation
 The transcription of a gene may proceed beyond what ends up as 3′ end of mature mRNA. Thus
the 3′ end of mRNA is formed after transcription. The enzyme poly(A) polymerase adds numerous
adenosines to the 3′ end to result in what is called the poly(A) tail.
 The poly(A) tail is necessary for proper processing and transport of mRNA to the cytoplasm.
The poly(A) tail is also important for the stability of mRNA, and initiation of translation in eukaryotic
organisms.
Translation (Peptide chain formation)
 Protein synthesis is initiated by the 40s subunit through attachment it’s to the mRNA,
and recognition of the AUG codon.
 This is followed by the attachment of the 60s subunit to the 40s-mRNA complex to
provide the structure necessary to align each successive aminoacyl-charged tRNA for
transfer of its amino acid to the growing polypeptide.
 Successive amino acids are attached to the growing polypeptide by the formation
of peptide bonds that form between the carboxyl group of one amino acid and the
amino group of the next.
 Like nucleic acids, polypeptides also have molecular directionality.
 One end of a polypeptide chain will have a free amino group and the opposite end
will have a free carboxy group.
 As such, these ends are referred to as the amino-terminus or carboxy-terminus,
respectively.
 During translation, mRNA templates are read from the 5’ end toward the 3’ end.
Proteins are synthesized beginning at the amino terminal end going toward the
carboxy terminus.
 Proteins are polypeptides of different amino acids. Adapted from 
NIH-NHGRI.
Ribosomes, tRNA and Anti-codons

 The ribosomes are a large molecular complexes containing an assembly of several

ribosomal RNAs (rRNA) and many proteins.
 Ribosomes are the machinery of protein synthesis, facilitating the ordered addition of
amino acids to a nascent polypeptide chain under the guidance of an mRNA template.
 The meaning of a codon for a specific amino acid is determined by the tRNA (transfer
RNA).
 Each tRNA contains a triplet of nucleotides referred to as an anticodon, which is
complementary to a specific codon.
 For each of the 20 amino acids, a specific enzyme (aminoacyl-tRNA synthetase)
catalyzes its linkage to the 3′ end of its specific tRNA adapter.
 The function of aminoacyl-tRNA synthetase is critical as it provides a check for
accuracy in protein synthesis by adding a specific amino acid to a specific tRNA
molecule.
 In this way, one particular amino acid is targeted to each codon triplet of mRNAs.
The key molecules needed for translation are the
mRNA, ribosome, tRNA, and amino acids. Illustration
by NIH-NHGRI.
 Take-home message

 Protein synthesis is the process in which cells make proteins. It occurs in two stages:

transcription and translation.
 Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus. It
includes three steps: initiation, elongation, and termination. After the mRNA is
processed, it carries the instructions to a ribosome in the cytoplasm.
 Translation occurs at the ribosome, which consists of rRNA and proteins. In
translation, the instructions in mRNA are read, and tRNA brings the correct sequence
of amino acids to the ribosome. Then, rRNA helps bonds form between the amino
acids, producing a polypeptide chain.
 After a polypeptide chain is synthesized, it may undergo additional processing to form
the finished protein.
Different levels of Levels of protein
structure
https://iastate.pressbooks.pub/genagbiotech/chapter/transcription/#pb-interactive-content

https://humanbiology.pressbooks.tru.ca/chapter/5-6-protein-synthesis/

https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/#