1L. Introduction to human genetics and genomics Flashcards
DNA: structure
- Composed of deoxyribose + purine/pyrimidine base + phosphoric acid = nucleotide
- Nucleoside: without phosphoric acid
- 1 DNA molecule = 2 polynucleotide chains
- Purine: Adenine & Guanine
- Pyrimidine: Thymine/Uracil & Cytosine
DNA: function
- Code for RNAs and proteins
- Lipids and carbohydrates are non-templated
DNA: amount
- 2* 3*10^9 bp/somatic cell (human)
- 2m/cell nucleus
DNA: organisation (chromatin, chromosome)
1) “Beads on a string”
- DNA is wrapped around histone octamers
- Octamer: 2x(H2A, H2B, H3 & H4) = nucleosome “bead”
2) Chromatin filament (interphase - G1, S G2)
- Spiral of 5/6 histone octamers connected by H1 histone
- 30nm diameter
3) Chromosome (cell division)
- Chromatin filament attached to scaffold of proteins -> further spiralized and condensed
DNA: replication
Cell cycle:
- G1: growth phase (organelles, centromeres) - 2n DNA
- S: DNA replication - 2-4n DNA
- G2: growth phase (enzymes, proteins, centromere replication completed) - 4n DNA
- M: Mitosis+cytokinesis
- Euchromatin: active, heterochromatin: packed/inactive
Genome definition
“The complete genetic material of the cell”
- 99,5 % identity of 2 people if considering CNVs
Genetics definition
“Science focusing on individual genes, the inheritance and variability”
Genomics definition
“Science focusing on the entire genome and interaction of genes”
Epigenetics definition
“Science focusing on inherited, however not DNA sequence encoded, changes og gene expression”
Gene definition
Locus definition
Allele definition + Wild type allele definition
- Gene: the unit of inheritance, part of the DNA or RNA
- Locus: location of a given gene on a chromosome
- Allele: gene variant at a given locus
- Wild type allele: most frequent variant of a given gene in nature
Genotype definition
Phenotype definition
- Genotype: genetic composition characteristic for an individual or a locus (AA, Aa, aa)
- Phenotype: Measurable and observable features of a cell or an individual
Homozygote definition
Heterozygote definition
Hemizygote definition
- Homozygote: identical alleles at the same loci of the chromosome pair (AA or aa)
- Heterozygote: different -||- (Aa)
- Hemizygote: carries only a single copy of the gene (A)
Dominant definition
Recessive definition
- Dominant allele: a gene variant that phenotypically always results in a given characteristics (also in heterozygotes (A)
- Recessive allele: a gene variant that manifests phenotypically in homo- and hemizygotes only (a)
Ploidy definition
“The number of homologous chromosomes of a cell”
- If a cell only contains a single set of chromosomes = haploid (n)
- 2 sets of chromosomes = diploid (2n)
Model organisms in genetics
- Short reproduction time
- High offpring number
- Examples: E.coli, baker’s yeast, flower, fly, mouse++
Mendel’s laws
Mendel laws (1865)
1) Law of dominance
- Pairing AA with aa will always give offspring with the dominant phenotype (Aa)
2) Law of segregation
- A pair of homologous chromosomes (the two alleles) segregate during meiosis and are distributed to different gametes
3) Law of independent assortment
- Alleles of genes on nonhomologous chromosomes assort independently (!) during gamete formation
Human genome: nuclear and mitochondrial
Nuclear
- Passed on from both mother and father
- 30 000 genes
- Introns
- Mendelian inheritance
Mitochondrial
- Only passed on from mother
- 37 genes
- No introns
- 100-10000 copies/cell
- Non-mendelian inheritance
- No histones
- 10x rate of mutations compared to nuclear
Specific sequences of nuclear genome.
Repetitive sequences
Human genome: 3000 Mb
1) Genes and gene-related sequences: 1000 Mb
- Genes (coding): ca 22000 genes (55 Mb)
- Gene-related sequences: 945 Mb (Introns, UTRs and pseudogenes)
2) DNA outside genes: 2000 Mb
* Mb = megabase (1 million bases)
Repetitive sequences in genome
1) Tandem: på rad-og-rekke
2) interspersed: her-og-der
Most of human genome is repetitive DNA (45 % transposons)
Structure of eukaryotic gene
Consists of (from internet):
- Exons (coding)
- Introns (noncoding)
- Promoter sequences (CAAT and TATA box)
- Terminator sequences (recognized by RNA polymerase)
- Enhancers or silencers regulatory sequences which may be upstream or downstream, near or far from the gene
- For mature mRNA modification:
- Up stream sequence signal for addition of Cap (5’end)
- Down stream sequence signal for addition of poly A tail (3’end)
Transcription definition
Making mRNA from DNA
- Transciption of antisense DNA strand -> sense mRNA
- Antisense strand is read 3’ -> 5’, which gives a mRNA growth in the 5’ -> 3’ direction
mRNA maturation (splicing, alternative splicing)
- Splicing: The process by which introns are removed from pre-mRNA to produce mature mRNA that contains only exons.
- “Spliced out” introns (mirtrons) -> miRNA -> RNAi
- Alternative splicing: a single gene is coding for many proteins, by excluding or including different exons, to give different final mRNAs -> different proteins
- Most common is exon skipping
Types of RNA
- mRNA: codes for protein
- rRNA: translation
- tRNA: translation
- snRNA: splicing and other functions
- miRNA: gene regulation
- Many others, but these are probably most important
Features of genetic code
1) Consists of triplets (= 1 codon = 1 AA)
2) Degenerated (redundant = overflødig)
- 64 triplet combinations/codons -> 20 AA
- 1 AA can be coded for by > 1 codon**
- E.g TAA, TAG, TGA are all stop codon
3) Comma-free, non-overlapping
4) Almost completely universal
5) Wobble effect
- The third letter in the triplet code is least important
- tRNA can do “wobble pairing” with the last letter
- “Wobble pairing”: U and C may be read by G in the anticodon, A and G may be read by a U or y (pseudouridine) in the anticodon.
6) Unambigous (= entydig)
- **Each codon codes for ONLY 1 amino acid
Translation and posttranslational modifications
- Translation: mRNA -> protein by ribosomal tRNA (moves along mRNA 5’->3’)
- Posttranslational modifications: induces complexity to the proteome (by phosphorylation, glycosylation, acetylation ++++)
Homolog DNA sequence
From common ancestral gene.
Ortholog DNA sequence
A common ancestral gene in different species that has conserved its function during evolution.
(Så ish samme gen funnet i forskjellige dyrearter som har stammet fra samme forfar)
Paralog DNA sequence
Generated by duplication within the same genome. Often evolve new functions.
“Same species have different gene due to duplication” (still originating from the same homolog sequence)
SNP
Single nucleotide polymorphism
- When a single nucleotide in an individual is different than in general population AND this difference exist in more than 1 % of the population
- Nucleotide mutations are rare, so often passed unchanged on to next generation - but still not much used in forensic medicine due to > 1% (1/100 - common variation, must test many SNPs to find genomic fingerprint
SNV
Single nucleotide variant
- Variation in a single nucleotide WITHOUT limitations of frequency
- May arise in somatic cells (e.g cancer) - also called single nucleotide alteration
CpG islands
“Regions of DNA of 200 bp or more with a C+G content above 50 %”
- Often found in or near promoters
Is the DNA sequence identical in all somatic cells?
No, because of gene rearrangement.
F.ex in T and B cells it is different (somatic gene rearrangement)
Transposons + transposases
1) Class I: “Copy and paste” retrotransposons
- Original transposon kept, while copy in at another place in DNA
2) Class II: “Cut and paste” DNA retrotransposons
- Original transposon moved to another place in DNA
3) Transposases: RAG1 and RAG2
2 major projects concerning human genome
1) Human genome project (completed 2003)
2) ENCODE: Encyclopedia for DNA Elements
- Shows more active DNA than thought
- Majority of noncoding regions help regulate coding region
What is a gene (after ENCODE)?
1) Genomic sequence (DNA or RNA) directly encoding functional product molecules, either RNA or protein
2) If there are several functional products sharing overlapping regions, the union of all overlapping genomic sequences are coding for them
3) This union must be coherent (sammenhengende), but does not require that all products share a common sub-sequence
Tools to study genetics
- PCR: amplification of DNA
- Restriction endonucleases: targeted cleavage of DNA and generation of recombinant DNA
- CRISPR CAS9: genome editing
