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.
protein coding genes:
Solitary genes and duplicated genes
Solitary: one copy in haploid genome
Duplicated: genes with close but NOT identical sequences.
5-50 kb located within one and another
Set of duplicated genes is called a gene family
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
Pseudogene
tandemly repeated genes
32.00 3-2 more?
Genes by sequences are similar to active genes but are nonfunctional copies. Contain multiple exons of the functional gene, can find ORF. Footsteps of evoloutionary progress in our genome, genes were active by our ancestroers but after mutations etc changed to inactive but doesnt affect us.
Tandemly repeated genes
Codes rRNA, tRNA, snRNA, and histones
multiple tandemly repeated genes encode identical or nearly identical proteins or functional RNAs.
Cant risk only encoding histones from only one gene… makes sense
Constitutive heterochromatin
details
Facultative genes details
Genome, in eukaryotes and prokaryotes? The total genetic content contains what? General about size of genome?
In Eukaryots: haploid set of chromosomes
In bacteria/aerchea: In a single chromosome
In viruses: DNA or RNA
Genome size generally related to size of organism with some exceptions
What does this image show and what conclusion can be drawn from it?
What is a genome?
Human genome consists of… ?
Complete set of genetic information that is needed for the organism in order to function
Nuclear genome and mitochondrial genome
What does this image show?
Proportion of the coding and noncoding parts of the genome. Shows nuclear and mitochondrial genome seperately.
Explain gene density:
- The more complex an organism is the more…?
- How are genes spread across genome?
It has decreased gene density (just look at eukary. vs prokary.)
Genes are not spread randomly, instead they tend to be clustered together in groups that share similar characteristis or organisation, replication and expression
(can be linked to chromosomal terroritories and topological domains
= In the metaphase chromosome shit is not random!!!
Some chromosome regions are gene- rich and some are gene-poor
How does the organisation of human nuclear genome look like?
How many protein coding genes and number of RNA coding genes?
Protein coding genes = 20 500
RNA coding genes = 31 500
What does the simple repetitive region consist of?
How size is measured?
Satellite DNA:
Longest
171 bp alphasatellite and 68 bp betasatellite
Heterochromatic region of chromosome
Non coding DNA regions
Minisatellite
6-64 bp
Telomeric and subtelomeric regions of all chromosomes
Microsatelitte DNA
Shortest, 1-4 bp
Dispersed throughout the chromosome
(Can be found in regulatory sequences of the gene + in introns and exons)
Size is measured by number of bp that is afterwards repeated. E.g. 1-4 bp are repeated many times.
Intergenic regions
What other group other than simple repetitive DNA are there in intergenic regions? Explain what it is
Transposones
(transposable elements)
Mobile DNA, jump DNA, migrate to different regions of our genome.
Name of the 3/4 groups in Transposones?
What do they have in common?
Explain mechanism in 17.47
Retrotransposones
SINE, LINE, LTR
Common feature: they migrate similarly using copy and paste mechanism
Meaning: copies info from DNA, reverts/pastes it back
- Retrotransposon reads itself: It’s like the retrotransposon takes out a photocopier and makes a copy of its own instructions (called RNA).
- Turns copy into DNA: The RNA copy is then turned back into DNA using a special tool (like a reverse photocopier). This step is called “reverse transcription.”
- Pastes itself somewhere new: The new DNA copy then gets inserted (pasted) into another part of your genome. Now, there are more copies of the retrotransposon, and they can keep jumping around.
What is LINE?
Long interspersed nuclear elements (LINEs)
3 LINE families
full length LINE = more than 6kb long & encode 2 enzymes: RNA binding enzyme & enzyme with both reverse transcriptas and endonuclease activity
may cause changes in DNA sequence.
80% of human genes has at least one segment of LINE-1 (typically in an intron)
What is SINE?
Short interspersed nuclear elements (SINEs)
100-400 bp in length
Do not encode protein = need assistance to transport/move around aka transpose
Alu family = most prominent
What is LTR
Retrovirus-like elements
contain long terminal repeats
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
DNA transposones
UNDERSTAND MORE
Mobile elements
transpose through a DNA
using “cut and paste mechanism” → increase in copy number of transposone (during S-phase of cell cycle)
Unique DNA (sequences)
Unclassified, non coding DNA sequences.
What does the word transposable mean in the context of DNA
Can juuuump
Transposable elements functions
OBSSS DELA UPP OCH FÖRENKLA SVARET- VAD FAN SKA DE BETYDA???
Human mitochondrial genome
- Consists of? and how long in length?
- Amount of genes?
Double stranded DNA
16.6 kb in length
37 genes in the genome
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……!!!!
Prokaryotes genome:
- Does NOT have simple repetitive DNA
- Few transposable sequences (IS)
- Genes grouped together by functionality into units called operons; many genes regulated together
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
Example on change in genome and how it affects human pathology
Fragile X syndrome (FXS)
causes autism
Name came from scientists looking at microscope and they noticed fragile tip of chromosome X that was breaking off from the chromosome.
How? Expansion of tandem CGG repeats in 5’ UTR region of FMR1 gene
= CGG is in microsatellites, 5’ untranslated region
Or fragile X tremor syndrome = same molecular mechanism
Understand what the hell she is yapping about
38.45
Kinetochore????
multi protein comoplex that link sister chromatin together to the myotic spindle
How many unique outcomes does genetic code encode?
20 + 1stop codon
= 21
Human nuclear genome codes for protein and functional RNA? True/False
true!!!!!!
Not always protein
