What's in our Genomes Flashcards
What percent of the human genome is completed of protein coding genes?
1-2% – 1.5% codes for proteins
***It feels like there should be a lot more of genome BUT protein coding genes is really a small portion of the genome
- genome has very few protein coding sequences
- Very few genes in genome
- Small fraction of genome that makes proteins (surprising we think it should be more)
Gene
Segment of DNA that actually codes for proteoms
Central Dogma
Flow of information from DNA –> RNA –> Protein
Transcription
DNA –> RNA
Translation
RNA –> Protein
Genes in genome
Gene make up a small portion of our genome – 2% of genome
***26,500 genes in human genome – there are a lot of genes BUT they make up a small portion of the genome
What Makes up the genome
2% genes
26% Introns
44% Transposable Elements
16% Repetative Sequences
12% Unknown
Amount of Introns in genome
26% – higher volume than genes
Introns
Parts of DNA that are transcribed THEN removed from RNA transcription to make mature RNA
**Part of RNA that is removed
**After removed = get mature RNA
What is the purpose of Introns?
- Alternative Splicing (Especially in higher Eukrayotes)
- Regulation
- To give extra space to protein genes (protects protein coding genes because it makes it less likely that a mutation will be in the protein coding genes
Introns protection
Give extra space to protein genes (protects protein coding genes because it makes it less likely that a mutation will be in the protein coding genes
Introns Regulation
Control of Intron splicing rates can regulate gene expression
- If have transcription ready and hold back on splicing = makes different rates of when genes are expressed
Where is alternative splicing found
Especially used for higher Eukaryotes
Alternative Splicing
Reuse DNA – 1 gene = encodes different proteins that can do different things -
***Can create different proteins from one gene
Alternative Splicing (process)
Body can choose which introns to remove – removes different introns/exons = get similar proteins BUT different
***Can keep some exons or remove others = creates different proteins during splicing process
When in process does splicing occur
Between transcription and translation
Transcription –> Splicing –> Translation
What makes up majority of genome?
Transposable elements = held together by Transposable elements
Transposable Elements (overall)
Selfish Jumping genes – copy themselves and jump to another part of the genome
- Selfish genetic elements OR genomic parasites
***Discovered by Barbra
Purpose of Transposable elements
Unknown BUT likely NOT junk DNA
***Before they thought it was Junk BUT professor does not think that they are junk
Possibilities:
1. Regulatory
2. Evolutionary
***NOT JUNK – we adapted them over time for a purpose
Common Types of Transposable elements
SINEs/LINE
Regulatory Transposable elements
SINE TE – found upstream if ISL1 alters gene expression
SINE TE
Regulatory Transposable elements – found upstream of ISL1 – alters gene expression
***As SINE TE moves = allows gene to be expressed or not
Upstream
In front
Evolutionary Purpose of Transposable elements
Idea = Transposable elements have evolutionary purposes – helps us evolve
Example – During splicing you might have Transposable elements as part of exon that is then translated to proteins = get novel proteins
Why should Transposable elements be Junk
Why would we still have them after evolution –> why would we keep them in and have to replicate more fo DNA than we need
Repetitive Sequences
Sequences that are repeated
Heterochromatin
Dark band on chromsome –> tightly packed together – HELPS packing
- Typically full of repetitive sequences
Purpose of Heterochromatin
Helps packing DNA into cell
Where can repetative sequences be found?
Found in Heterochromatin regions –> manes that repative MUST be important for condensing DNA
Types of repetative sequences
- Short and Sequential
- Long and Segmented
Short and Sequential Repetitive Sequences
Short and sequential nucleotides that repeats
Example – trinucleotode repeat such as CAGCAGCAG –
Other names:
1. Simple repeats SSRs
2. Simple Tandem Repeats (STRs)
3. Microsatalites
***Can include 1, 2, or 3 nucleotide repeats
Long and Segmented Repetitive Sequences (overall)
- Can be 10,000 BP long
- can repeat within same chromsome or between two chromsomes
Affect of Long and Segmented Repetitive Sequences
Can affect recombination
Importance of Long and Segmented Repetitive Sequences
Important for condesning DNA – we know this because they are found in Heterochromatin (which is used for condensing DNA)
Long and Segmented Repetitive Sequences in Heterochromatin
Helps condensing DNA – the Heterochromatin has lots of repetitive sequences + proteins that bind to repetitive sequence that helps condense DNA
Genome variation between people
ONLY 0.1% is variable between people
***Most of DNA is identical
Where is variation found in the genome (in coding or non-coding regions)?
More likley in non-coding regions because most of genome is Non-coding BUT variation can be found in both
- Genetic variation is scattered throughout the genome – sometimes it occurs in genes BUT often not
- Often in non-coding because most of DNA is non-coding
Where are genes + variation in genome
Genes are scattered throughout genome + variation is also scattered
Where do phenotypic differences come from?
Phenotypic difference = mostly due to difference in coding genes
Types of variation between individuals
- SNPs
- CNVs
Single Nucleotide Polymorphism
SNPs – Single nucleotide base change
Amount of SNPs between 2 humans
Between any 2 humans have 1 SNO/1000 bp –> means that there are 3-5 Million SNPs/genome (Means that there are many SNP differences between us)
NOTE: 3-5 millions SNPs/genome – genomes is 3 billion BP
Where are SNPs found
Can be found in coding and non-coding
Trend with SNPs
Often Bi-allelic – means that there are usually only 2 nucleotides possible
***Makes it easy to talk about population genetics
Allele
Version of a gene – Non-identical regions
**Can be at ANY locus (Any position) = means that it doesn’t NEED to be coding (Can be in non-coding)
**Non-identical regions = allele
***Relative position might change
Non-coding SNPs
Very important
Copy Number Variations
CNVs – means that you have different amounts of nucleotide repeats (
Example: Trinucleotide repeates
Importance of CNVs
- Diseases can occur in Tandem Number repetas occur within important genes
Example – Huntington’s dieases - Disease can occur if have CNVs at structurally important regions of a chromsome
Example – Fragile X
What causes Huntington’s disease?
CAG repeate in gene = get change in protein coding sequence = get phenotypes associated with Huntingtons
What causes Fragile X
Have CNVs at structurally important regions of the chromosome –> causes region of X chromsome to be unstable = break of peice of X chromsome = lose lots of DNA = disease
Where can CNVs occur?
Can happen in whole genome –> CAN have no phenotipic affect – often does not cause a problem espcially because most of genome is not protein coding genes
Affect of CNV
Often does not cause a problem because most of DNA is NOT protein coding genes
CNVs between individuals
Between ANY 2 humans = have 1500 CNVs
Average size of CNVs
20,000 bp (20 Kbp)
Possible affects CNVs and SNPs on phenotypes
- Disease –> if in important genes or in important sturctural region
- Different proteins being made
- Different Phenotypes
- Might not be able to make a protein – lack of protein being
- Might be adaptive
Example of Lack of protein being made
Might have lack of protein being made IF have SNP that changes start codon
Usual affect of CNVs and SNPs
Most CNVs and SNPs are not in protein coding regions (not in genes) = mostly have no affect
Example adaptation from CNV
Copper resistance in yeast – A lot of yeast live with grapes and pestscides that contain copper are often sprayed on the grapes –> the yeast have evoloved to tolerate higher levels of Copper by repeating copies of copper transporter chain
***CNV that helps YEAST
What differs between species?
- Number of chromsomes
- Chromosome size
- Types of Introns
- Number of genes
- Types of genes – there is a lot of homology BUT usually some genes are species specific
***CAN have the same between species BUT these are ALL the same within species
Genes between species
Usually there is a LOT of homology but usually there are some genes that are species specific
Differences within species (differences between humans)
Difference is made by SNPs and CNVs
Genomes between species
Many genome features are shared across species
Homology between species
- Between humans = 100%
- Humans and Chimpanzee = 98%
- Human and mouse = 92&
- Human and fruit fly = 44%
- Human and yeast = 26%
- Human and a weed = 18%
***We are more alike that we might suspect
Use of homology between species
Model organisms – because we are more alike we can use model organisms
***Model organism are important for genetic studies
Homologous genes between organisms
Genes from one organism can often replace the function of homologous genes in another organism
