1. How Genes Work Ch. 12

2. RNA and Protein Synthesis
The double helix structure explains how DNA can be replicated but it doesn’t explain how a gene works.
Genes are coded DNA instructions that control the production of proteins within a cell.
The first step in decoding these genetic messages is to copy part of the nucleotide sequence from DNA to RNA (ribonucleic acid)
These RNA molecules will carry out the process of making proteins.

3. The Structure of RNA
Like DNA, RNA consists of a long chain of nucleotides.
There are 3 main difference between DNA and RNA:
The sugar in RNA is ribose, instead of deoxyribose.
RNA is generally single-stranded.
RNA contains the base uracil instead of thymine.

4. Types of RNA
In the majority of cells, most RNA molecules are involved in protein synthesis.
RNA controls the assembly of amino acids into proteins.
There are 3 main types of RNA:
messenger RNA (mRNA): RNA molecules that carry copies of the instructions for assembling amino acids into proteins from the DNA to the rest of the cell.
ribosomal RNA (rRNA): a form of RNA made up of several dozen proteins.
transfer RNA (tRNA): RNA molecules that transfer each amino acid to the ribosome as it is specified by the coded messages in mRNA.

5. Transcription
The information contained in DNA is stored in blocks called genes
the genes code for proteins
the proteins determine what a cell will be like
The DNA stores this information safely in the nucleus where it never leaves
instructions are copied from the DNA into messages comprised of RNA
these messages are sent out into the cell to direct the assembly of proteins

6. Transcription
The path of information is often referred to as the central dogma
DNA  RNA  protein
The use of information in DNA to direct the production of particular proteins is called gene expression, which takes place in two stages
transcription is the process when a messenger RNA (mRNA) is made from a gene within the DNA
translation is the process of using the mRNA to direct the production of a protein

7. Transcription
A protein called RNA polymerase produces the mRNA copy of DNA during transcription
it first binds to one strand of the DNA at a site called the promoter and then moves down the DNA molecule and assembles a complementary copy of RNA
RNA uses uracil (U) in place of thymine (T)

8. Transcription

9. Gene Expression in Prokaryotes and Eukaryotes
The prokaryotic gene is an uninterrupted stretch of DNA nucleotides that corresponds to proteins
In eukaryotes, the coding portions of the DNA nucleotide sequence are interrupted by non-coding sections of DNA
the coding portions are known as exons while the non-coding portions are known as introns

10. Gene Expression in Prokaryotes and Eukaryotes
When a eukaryotic cell first transcribes a gene, it produces a primary RNA transcript of the entire gene
the primary transcript is then processed in the nucleus
enzyme-RNA complexes cut out the introns and join together the exons to form a shorter mRNA transcript
the sequences of the introns (90% of typical human gene) are not translated
a 5’ cap and a 3’ poly-A tail are also added

11. Processing eukaryotic RNA

12. Translation
To correctly read a gene, a cell must translate the information encoded in the DNA (nucleotides) into the language of proteins (amino acids)
translation follows rules set out by the genetic code
the mRNA is “read” in three-nucleotide units called codons
each codon corresponds to a particular amino acid

13. Translation
The genetic code was determined from trial-and-error experiments to work out which codons matched with which amino acids
The genetic code is universal and employed by all living things

14. The genetic code (RNA codons)
There are 64 different codons in the genetic code.

16. Translation
Translation occurs in ribosomes, which are the protein-making factories of the cell
each ribosome is a complex of proteins and several segments of ribosomal RNA (rRNA)
ribosomes are comprised of two subunits
small subunit
large subunit
the small subunit has a short sequence of rRNA exposed that is identical to a leader sequence that begins all genes
mRNA binds to the small subunit

17. A ribosome is composed of two subunits

18. Translation
The structure of a tRNA molecule is important to its function
it has an amino acid attachment site at one end and a three-nucleotide sequence at the other end
this three-nucleotide sequence is called the anticodon and is complementary to 1 of the 64 codons of the genetic code
activating enzymes match amino acids with their proper tRNAs

19. The structure of tRNA.

20. How translation works

21. Translation
Translation continues until a “stop” codon is encountered that signals the end of the protein
The ribosome then falls apart and the newly made protein is released into the cell

22. Ribosomes guide the translation process

23. How protein synthesis works in eukaryotes

24. Transcriptional Control in Eukaryotes
Gene regulation in eukaryotes is geared toward the whole organism, not the individual cell
Eukaryotic DNA is packaged around histone proteins to form nucleosomes, which are further packaged into higher-order chromosome structures
This structure of the chromosomal material (chromatin) affects the availability of DNA for transcription

25. DNA coils around histones

26. Transcriptional Control in Eukaryotes
Chromatin structure can be altered in several ways that affect transcription
histones can be modified to result in greater condensation of the chromatin
this makes promoters less accessible for gene transcription
methylation of the DNA can ensure that “turned-off” genes stay off
proteins called coactivators can methylate histones and disrupt chromatin coiling, making the DNA more accessible
corepressors can remove methyl groups from histones and cause tighter coiling of chromatin and less accessibility to the DNA

27. Controlling Transcription from a Distance
Transcription is much more complex in eukaryotes than in prokaryotes
eukaryotic transcription requires proteins called transcription factors
basal transcription factors come together to form an initiation complex and recruit RNA polymerase to the promoter
specific transcription factors can also bind and will affect the rate at which genes are transcribed

28. Formation of a eukaryotic initiation complex

29. Controlling Transcription from a Distance
eukaryotic genes have special sequences, called enhancers, which can bind transcription factors called activators
even if this regulatory sequence is located far away from the gene it influences, the enhancer can have an effect because the DNA can bend to bring the activator near the RNA polymerase/initiation complex
in addition, coactivator and mediator proteins can bind and affect transcription
the many factors together form a transcription complex and allow for flexibility in the control of gene expression in eukaryotes

30. How enhancers work

31. RNA-Level Control
Some controls of gene expression in eukaryotes act after transcription
Researchers noted that double-stranded RNA molecules could block the transcription of genes whose sequence was complimentary to that of the double-stranded RNA, called RNA interference or gene silencing.

32. RNA-Level Control
Double-stranded RNA can form when complementary sections of single stranded RNA fold back into hairpin loops
In RNA interference
an enzyme called dicer cuts double-stranded RNA into smaller bits called siRNA
siRNA and proteins form a complex called RISC
the siRNA is unwound to be single-stranded and is then able to bind mRNAs complementary to it
genes are silenced because the translation of mRNAs is blocked or mRNAs are destroyed

33. How RNA interference works

34. Complex Regulation of Gene Expression
Gene expression in eukaryotes is controlled in many ways
Chromatin structure
Initiation of transcription
Alternative splicing
RNA interference
Availability of translational proteins
Post-translation modification of protein products