Week 3 - Eukaryotic and prokaryotic genome. Flashcards
Genetic code
Genetic code : set of DNA and RNA = determines aminoacid sequence when synthesizing proteins for an organism.
Biochemical basis for hereditary
Hereditary = ärftlighet
nearly universal in all organism.
Set of 64 codons (building block of 3 nucleotides) - correspondant to
the 20 aminoacids- protein synthesis and + signals for starting and stopping proteins. 4x4x4 nt = 64
Codes are nonoverlapping
One code = 1 aminoacid.
not meaning of 2 or 3.
Each code is dedicated to 1 aminoacid. Code is triplets of nucleotides.
Explain how you should read this image
By not reading it!
Start codon?
Stop codon?
Other aminoacids are specified by more than one codon…
Start codon AUG - codes for methosine
Stop codon are UAA, UAG, UGA. They encode no aminoacid
Usually difference in 3rd part, called degenerate code
What to understand from this picture
Different sequences for same protein.
Why is there sometimes improper use of the term genetic code
Found fossils with their “genetic code” but should be found genome
What information to extract from this slide?
Nearly universal means not, difference in e.g. stop codon for different species etc.
Definition of the gene in plain terms and in molecular terms
Short answer to the terms the parts of the gene?
What do genes encode?
Fundamental, physical and functional unit of heredity
In molecular terms
a gene is a chromosomal DNA sequence
required for synthesis of functional protein or RNA molecule
A gene has
- coding regions a.k.a exons
- transcription- control regions
- introns
Majority of genes encode proteins, some encode different types of RNA (e.g tRNA and rRNA
Draw an overview of the gene structure transcription
No acces to internet? Draw a mental image homie dont be lazy
Promoter region
Located at 5’ end
- has sequences responsible for proper initation of transcription
What exists in the 5’ end
What does numbers on the sequence mean? e.g -25
Several DNA elements, whose sequence is conserved among different genes
e.g.
- CpG regions
- TATA box
- CpG island
- Locus control region
Conserved meaning = they barely havent changed evolutionary, find in many parts in all sort of species. High similarity of regulatory sequences. Important evoloutionary throughout time.
Numbers meaning: Everything downstream after start of transcription is positive and everything before is negative
TATA box
Located?
25-30 bp upstream from transcription (before yani)
Important: determine start of transcription
1/4 of human genes contain TATA box regulatory sequence
Tissue-specific genes
More robust genes dont have these?
What does this image show
Shows how TATA protein is able to bind into specific DNA sequence.
By binding to this sequence → protein will initiate bending and unwinding of DNA sequence = what we need to start DNA transcription
OBS KOLLA UPP
Another part of the 5’ region is CpG islands
Area rich with C and G
Found in 70% of genes:
- including housekeeping
- tissue-specific
- development regulator genes
Stretches 20-50 nucleotides within 100 base pairs upstream from start
Important for switching on & off genes.
→ can be connected to faculative heterochromatin which had CpG-islands methylated → methylated CpG islands can “silence the gene”
Dvs repression of gene expression function
HENNES LECTURE:
Binds transcription functions and are targeted for DNA methylation → repression of gene expression
5’ untranslated region
Explain where it lies
Explain what exists there
5’ untranslated region - look at the name
= Transcription to mRNA
((((NOT translated to DNA))))) = wrong????
Dvs this untranslated region will be copied into mRNA molecule but NOT translated into protein sequence
Most common: residue at
C = -1
A = +1
Has a initiator codon
Topic: reading dna sequence
Sequence from start to stop is called…? - and how many of them are possible in every DNA region.
How many are used when translating a gene?
1st codon from start is called? and from what direction does it go between 5’ and 3’
ORF - open reading frame
1st codon is ATG
Last is stop codon; TAG, TAA, TGA
6 possible reading frames
3 in every direction
In translation there is usually 1 ORF and it is typically only 1 that is used
Start and stop codons?
How to find ORF
A complete guide by prof. Adam Kareem
-
Write the complementary strand of DNA
If you have from 5’ to 3’ then write 3’ to 5’ - Start reading on the strand above. Read 3 nucleotides until you find ATG.
- No ATG? Start from 2nd nucleotide
- Still no ATG? Start from 3rd nucleotide
OBS to later start by 4th nucleotide doesn’t make sense as it would be the same as - GO TO ANOTHER STRAND and read from 5’ to 3’
- If no ATG still → Same as before
; start with 2nd and 3rd - FOUND IT? = Read the open frame aka from start to stop
- Identify the sense and the antisense
Sense = coding strand
Antisense = noncoding strand of DNA
= COPY of mRNA will be representation of the genetic code of the sense strand
Exons and introns
Where they are located in schematic repr. of gene structure
Exons:
- coding sequence
- Will be translated to the protein
Introns: interuppted parts with - -
- no coding sequence,
- not translated into protein
Will be removed from mRNA after synthesis of it and not translated into protein
3’ untranslated region
(trailer)
- Where it is located
- What it contains
- Location shown in image below
- Consists of regulatory sequence which promotes degradation of mRNA when synthesis of proteins are finished.
- Regulate levels of translation
Will be copied to mRNA but not translated into proteins
Polyadenation signal
- location?
- exists only in what?
- Main sequence?
- Its function?
Location: 3’ untranslated region
Specific to eukaryotic protein-coding genes
Main sequence is AAUAAA
2xA U 3xA
Needed for cleavage signal at the end of the end of pre- mRNA
Promotes downstream transcriptional termination
How control of gene activity works
Balance between transcriptional activators and repressors
Gene flanking regions contain enhancers and silencers.
Enhancers and silencers are like on/off switches in the upstream regulatory sequences of DNA that control whether a gene is “turned on” or “turned off”—kind of like light switches for a gene!
Schematic rep. of gene that codes for protein Albumin
21.00 lecture 3 part 2
Every cell in human body contain same DNA but not in all cells all genes are active
= have a certain number of genes called housekeeping genes that are active in all cells and ensure homeostasis of organism, necessary for basic survival of organism
→ need to have variations in gene expressions in different genes to ensure different way of how our tissues and organs work
What does the Locus control region (LCR) do
Has the ability to enhance the expression of linked genes
What does this image show
OBS cont. 25.00 lect. 3 pt.2
Example of LCR of globin coding genes
Erytrocytes contain hemoglobin - built up of 2alphaprotein and 2 chains of the betaglobin
Can see that the genes coding for hemoglobin is located on different chromosomes! (11 and 16)
Explain this image!
LCR will bind to promoter regions in different genes throughout our lifetime.
Bind to different regulatory factors (proteins)
Will help promote: bending of DNA and provide ability to bind LCR to the promoter region of a gene
OBS lägg i ps och markera en grön nere och en tad region
Why LCR can activate genes within a certain topological domain but not with antoher gene in antohwr topological domain
28.11 lect 3 pt 2
Tells us how one regulatory sequence upstream is able to activate certain genes.
Regulatory regions work only within 1 TAD.
What is this an example of
globin coding genes = example of the gene family
coding for similar proteins with simillar function and located close within the chromosomes, regulated by the same LCR
Constitutive heterochromatin
details
Facultative genes details
What does this image show and what conclusion can be drawn from it?
What does this image show?
Proportion of the coding and noncoding parts of the genome. Shows nuclear and mitochondrial genome seperately.
How does the organisation of human nuclear genome look like?
Comparison LINE vs SINE without looking at the picture
LINE has 2 ORF/coding areas
- RNA binding protein
- Endonuclease and reverse transcriptase
SINE
No enzymes coded, uses only enzymes that are already coded / hijacks functions of different functions
Reliant on enzymes that are involved in synthesis of tRNA or ribosomal RNA
Where does the transposones fit in this image?
In RNA when going back to DNA via reverse transcriptas
Transposable elements functions
OBSSS DELA UPP OCH FÖRENKLA SVARET- VAD FAN SKA DE BETYDA???
What daaaa heeeeeelll is this
Schematic rep. of human mitochondrial genome
25.40 contin.
What is H and L in this image?
What is the base composition in mtDNA
Distribution of the 37 genes in mtDNA between the 2 strands?
44% (C+G)
H is heavy strand and L is light strand
H: rich in G
L: rich in C
28 genes by H and 9 by L
Prokaryotic genome
(similar to mitochondrial genome)
Simple compared to eukaryotes:
- Does not contain introns
promoter region: 2 regulatory sequences.
OBS UNDERSTAND IMAGE BELOW……!!!!
The lac operon in E.coli:
Function?
Name the 2 components and the 3 functional genes
What is the lac operon an example of?
To remember lac think
lac zorro, lac ylmir, lac adomi
What does this image show?
32.40
lect. 3 pt. 3
Schematic rep. of lac operon
Understand what the hell she is yapping about
38.45
