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Gene Expression & Regulation Cheat Sheet by

Gene Expression & Regulation

DNA Structure & Replic­ation

Stru­cture of DNA
Each DNA nucleotide is made up of 5-carbon sugar called deoxyr­ibose, a phosphate group, and a nitrog­enous base.
DNA uses bases A, C, G, & T. (RNA uses A, C, G, & U)
Double Helix
DNA has an antipa­rallel structure→ The 2 strands run in opposite directions of eachother.
Each strand has a 5' end and a 3' end.
DNA Replic­ation
DNA is Semi-­Con­ser­vative
→Each of the 2 strands in DNA acts as a template to produce 2 new strands.
Enzymes "­unz­ip" DNA molecules by breaking the hydrogen bonds that hold the two strands together.
Primary enzyme involved is DNA polymerase
→ Joins nucleo­tides to synthesize the new comple­mentary strand.
→Proof­reads each DNA strand to prevent errors.
Leading & Lagging Strand
Leading Strand
→runs 5' to 3' towards the fork and is made contin­uously.
Lagging Strand
→runs 5' to 3' away from the fork and is made in small pieces called Okazaki fragments.
Other Things to Know:
DNA polymerase only synthe­sizes DNA in the 5’ to 3’ direction only. The difference between the leading and lagging strands is that the leading strand is formed towards replic­ation fork, while the lagging strand is formed away from replic­ation fork.

DNA replic­ation is not the same as cell division. Replic­ation occurs before cell division, during the S phase of the cell cycle. However, replic­ation only concerns the production of new DNA strands, not of new cells.

Replic­ation

Mutations

point mutation
affects 1 nucleotide pair
1. silent mutations
do not change amino acid transl­ation
2.missense mutations
a single nucleotide change results in a codon that codes for a different amino acid
3. nonsense mutation
a regular amino acid codon is changed into a stop codon, ending transl­­ation
inse­rtion or deletion
additi­on/loss of nucleotide pairs
1. frame shift mutation
deletion or insertion in a DNA sequence that shifts the way the sequence is read
muta­­gens
forces that interact with DNA in ways that cause mutation example: xrays
 

Transc­ription

Tran­scr­iption Key Points
Involves copying a gene's DNA sequence to make an RNA molecule.
Performed by RNA polymerase
3 Stages: Initia­tion, Elonga­tion, Termin­ation.
RNA molecules are spliced and have a 5' cap and poly-A tail put on their ends. (Eukar­yotes) }
Init­iation, Elonga­tion, Termin­ation
RNA polymerase binds to a sequence of DNA called the promoter, found near the beginning of a gene. Each gene (or group of co-tra­nsc­ribed genes, in bacteria) has its own promoter. Once bound, RNA polymerase separates the DNA strands, providing the single­-st­randed template needed for transc­rip­tion.
One strand of DNA, the template strand, acts as a template for RNA polyme­rase. As it "­rea­ds" this template one base at a time, the polymerase builds an RNA molecule out of comple­mentary nucleo­tides, making a chain that grows from 5' to 3'. The RNA transcript carries the same inform­ation as the non-te­mplate (coding) strand of DNA, but it contains the base uracil (U) instead of thymine (T).
Sequences called termin­ators signal that the RNA transcript is complete. Once they are transc­ribed, they cause the transcript to be released from the RNA polyme­rase. An example of a termin­ation mechanism involving formation of a hairpin in the RNA is shown below.

DNA

Terms

DNA
Nucleic acid that transmits genetic inform­ation from parent to offspring and codes for the production of proteins
Nucleotide
Building block of nucleic acids
Double Helix
Structure of two strands, intert­wining around an axis like a twisted ladder
DNA replic­ation
Process during which a double­-st­randed DNA molecule is copied to produce two identical DNA molecules
Base Pairing
Principle in which the nitrog­enous bases of the DNA molecules bond with one another (AT, CG))

DNA vs. RNA

DNA
RNA
Double Stranded, Anti-p­arallel
Single Stranded
A+T and C+G
A+U and C+G
Mostly Found in Nucleus
Mostly Found in Cytoplasm
Deoxyribose
Ribose
Long Polymer
Much Shorter
Forms Double Helix Structure
Forms Secondary or Tertiary Structure
 

Transl­ation

Tran­sla­tion
tRNAs are molecular "­bri­dge­s" that connect mRNA codons to the amino acids they encode.
One end has an anticodon, which can bind to specific mRNA codons. (sequence of 3 nucleo­tides)
The other end carries the amino acid specified by the codons.
Init­iation, Elonga­tion, Termin­ation
The ribosome assembles around the mRNA to be read and the first tRNA (carrying the amino acid MET[AUG]). This initiation complex is needed in order for transl­ation to get started.
The mRNA is read one codon at a time, and the amino acid matching each codon is added to a growing protein chain.
Each time a new codon is exposed,
→a matching tRNA binds to the codon
→the existing amino acid chain (polyp­eptide) is linked onto the amino acid of the tRNA via a chemical reaction,
→the mRNA is shifted one codon over in the ribosome, exposing a new codon for reading.
tRNAs move through the A, P, and E sites of the ribosome. This process repeats many times as new codons are read and new amino acids are added to the chain.
The finished polype­ptide chain is released. It begins when a stop codon (UAG, UAA, or UGA) enters the ribosome, triggering a series of events that separate the chain from its tRNA and allow it to drift out of the ribosome.
The polype­ptide may still need to fold into the right 3D shape, undergo proces­sin­g,get shipped to the right place in the cell, or combine with other polype­ptides before it can do its job as a functional protein.

Transc­ription & Transl­ation

The Central Dogma of Molecular Biology

The Central Dogma (TCD)
During expression of a protei­n-c­oding gene, inform­ation flows from DNA → RNA → protein. (This process is known as CD)

The Lac Operon

The Lac Operon of E.Coli
Condit­ions: Lactose is available and Glucose is not.
More inform­ation here

3 Types of RNA

mRNA
synthe­­sized using DNA template, attaches to ribosome in cytoplasm and specifies the primary structure of protein
rRNA
molecu­­le­s...and proteins make up the ribos­omes
tRNA
translates between nucleic acid (DNA) and protein lang. by carrying specific amino acids to ribosome, where they recognize the approp­­riate codons in the mRNA

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