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