Topic 1: Nucleic Acid structure & Gene Expression
The nucleic acid
made by the nucleotide polymers (to build DNA)
Primary concerns in molecular genetics
DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)
2 carbon w/ H
2 carbon w/ OH
Polypeptides (the basic components of all proteins)
Building blocks & chemical bonds in DNA & RNA
DNA & RNA
are large polymers defined by a linear sequence of sample repeated units
Base
Purine
Adenine (A)
Guanine (G)
Pyrimidines
thymine (T)
Cytosine(C)
Uracil (U)
2 ring structures
1 ring stuctures
number of H bond
(A)-(T) = 2 H bonds
(G)-(C) = 3 H bonds
Difference in Nucleoside & Nucleotide
Nucleoside
Base + sugar(ribose)
Nucleotide
Base + sugar(ribose) + phosphate
aka (nucleoside + phosphate)
Nucleotides are linked by phosphate bonds in nucleic acid (covalent bond)
H bond b/w nucleotides
DNA
double helix
WHAT FORCES HELP DNA TO STAY HELICAL?
hydrophobic stacking of bases
Watson-crick base paring
base pairing through hydrogen bonds
(A)-(T)= 2 H bonds
(G)-(C)= 3 H bonds
Higher G-C content = higher melting point
Two chains are anti-parallel orientation
5' end = phosphate
3' end = a nucleotide with a free OH (hydroxyl group)
the forces that stabilize the double helix are hydrophobic stacking interaction & base paring
DNA replication
Semi-conservative
in new molecule have the DNA is replicated
one stand form parental DNA & the other strand is newly synthesized
AKA Semi-discontinues
bc the newly deep synthesis the DNA strand always go through the 5' prime to 3' direction
so this way the leading strand is always continues; and the synthesis in the lagging strand is discontinuous
In lagging strand their will always see fragments called Okazaki fragments
There are 3 types of double helix structures (could be in different organisms or the same organism)
A Form-DNA
B Form-DNA
Z Form-DNA
Biological significance = TATA box transcription
Biological significance= DNA/ RNA hybrids
Those hybrids are being transcribed (gene coding sequence area)
Also (not as important): degree of hydration VERY LOW,Right handed,11 mean base pairs, purine rich
that area is the promoter sequence
Biological significance = methylated CpG islands
in human genome the CpG are actually in shortage & when a lot are present they will form the Z form of the DNA
CG islands
In human genome when CG islands ((CG)n) repeated for many times often time down stream there is a functioning gene
very easily methylated bc the Cytosine is very easy target by the enzyme & and a methyl group will be added
this will still pair with (G),
allowing the complementary C to also get methylated = fully methylated called epigenetics
called epigenetics bc this kind of methylated C can be inherited (not changing DNA sequence ); but can cause very easy gene mutation
methylation at CpG islands inhibit gene expression (meaning it causes gene silencing)
Gene expression
Central Dogma
gene expression can mean gene mutation & gene translation
gene expression can be expressed in RNA level = transcription &
DNA --(transcription)--> RNA --(translation)--> Protein
gene expression can be expressed in Protein level = translation
(cDNA) DNA <--(reverse transcription)-- RNA
Enzyme involved in Reverse transcription= (reverse transcriptase)
DNA ---Replication--->DNA
The rate limiting steps in gene expression is TRANSCRIPTION!
RNA transcription
(1). the gene promoter (cis) elements:
CAAT box ----
GC box ---- SPI
(2). transcription factors binds to these gene promoters elements
(3). RNA polymerase is recruited to the transcription starter site
(4). Primary (premature mRNA, pre-mRNA) mRNA is made
(5). Intron sequences in pre-mRNAs are spliced out
splice donor site: GU
Branch site: A
splicer acceptor site: AG
SnRNPs U1, U2, U4, U5, U6 (small nuclear RNA-binding proteins) are required
TATA box ---- TFIID
Gene expression in Animal Cell
Nucleus ---transcription---> then processing RNA--->
main place to watch expression happen is NUCLEUS! (bc more then 99.99% of genes are located in nucleus.)
-->then mature RNA will get inside of cytoplasm---
-->to preform translation
Gene expression can also occur in the MITOCHONDRIA (since mitochondria DNA also have functioning genes)
mtDNA---transcription---> primary transcription---> translation
they can do translation bc they have their own ribosomes
main step in controlling gene expression is in the Transcriptions
making or not making RNA molecules
(first). a lot of TF (transcription factors) will bind to the promoter sequence, so it can recruit RNA polymerase
once RNA pol. binds to the promoter sequence, it will start transcription to make an RNA molecule
Template strand: is a template strand to be used as a template to make RNA during transcription (contains (U))
Coding stand (aka SENSE strand): bc these DNA sequence is identical to the RNA sequence but it has (T)
TFIID is the transcription factor (involved be involved in making histone proteins) ; will make mRNA or microRNA
different genes will have different promoter sequences
tRNA: A box & B box
do not contain TATA box, GC box, CAAT box
Eukaryote cell gene transcription
click to edit
Tf binds to the promoter, then will recruit RNA pol. for transcription to occur creating an initiation site where transcription initiates
@ initiation site (1+ site):
transcription will happen creating a PRIMARY RNA TRANSCRIPT (AKA: pre-mature RNA transcript)
Primary RNA transcript contains both exon sequence & Intron sequence
the INTRONS need to be removed
next step is to process the PIMARY RNA TRANSCRIPT to get Mature RNA
so the introns are removed & then the exons are ligated (splice) together
the place in the nucleus where SPLICING occurs is called SPLICEOSOME (spliceosome will help the splicing process)
more info about SPLICING:
occurs & located in the nucleus like transcription
have conservative sequence in the intron
happens to the RNA ( not the DNA)
Intron gene sequence: for many introns it starts w/ GT & ends with AG! in the middle always an A (very very conservative); GT (splicing donor site)--- A (branch site)---- AG (splice acceptor site)
In mRNA level : GU --- A --- AG