Human Genome and Karyotype Flashcards
Genome size/C-value:
- amount of DNA in one copy of the genome.
- Humans have 3.2 x 109 base pairs of DNA in each somatic cell of our bodies.
Humans have _____ base pairs of DNA in each somatic cell of our bodies.
3.2 x 109 base pairs
How many genes are in the human genome?
about 22,000
Humans have ____ pairs of autosomal chromosomes and ____ sex chromosomes (X or Y).
- 22 pairs of autosomal chromosomes
- 2 sex chromosomes (X or Y).
What cell phase does condensation of chromatin into chromosomes occur?
prophase of mitotic cell division
Genome size generally ______ with an organisms complexity.
increases
The C-value enigma:
- Wide variations exist between genome size and organism complexity.
- e.g., some single-celled protists have genomes much larger than that of humans.
Ploidy is:
the number of chromosomes in an organism
Does chromosome number (ploidy) increase with organism complexity?
NO
The two basic mechanisms by which genome complexity/size arises:
- duplication: partial or whole
-
incorporation: of other specie’s DNA
- “lateral transfer”
- mitochondria
The three models of human genome make-up:
- Mostly junk, some useful parts.
- due to incorporation; “littered”
- Highly complicated, each part has specific function and everything works together.
- Highly complicated machine, with a simple function.
Five regions of genomic DNA:
- Protein coding
- Regulatory (promoters, enhancers, etc).
- Long non-coding (RNA; no protein)
- Short non-coding (RNA; no protein)
- Unknown function (RNA; no protein)
Goal of ENCODE project:
- map the human genome in about 80 different human cell types
What criteria were used by the ENCODE project to determine what was “functional” DNA?
- Transcripts and protein-encoding exons.
- Chromatin (histone) modification and DNA methylation.
- DNAse hypersensitivity.
- Binding of ~100 known transcription factors, RNA Pol II/III, and other proteins.
The ENCODE project determined that chromatin exists in how many functional states?
7
The ENCODE project determined that ____% of our DNA is transcribed into RNA?
60-75%
What was the main conclusion of the ENCODE project?
- At least 80% of the genome is likely to be functional, implying thatnon-coding regions may be as, or more important than, protein-encoding regions (as determinants of health and disease).
Single-nucleotide polymorphisms (SNPs) definition and prevalence:
- A:T vs G:C (single nucleotide swap out)
- about SNPs 3,000,000 per genome
Insertions and deletions definition and prevalence:
- GCATT vs. GT
- about 800,000 indels per genome
Block substitutions definition and prevalence:
- GCATT vs. GTTAT
- about 50,000 per genome
Inversions definition and prevalence:
- GCATT vs GTACT (sequence reversed)
- about 100 per genome
Copy number variations definition and prevalence:
- GCATT vs. GCATCATT (sequence repeated)
- about 50-100 per genome; small and large
Three types of repetitive sequences present in the human genome:
- tandem repeats (of genes of blocks of genes)
- short repeats
-
retrotransposons
- repeats that are the products of reverse transcriptases
How to determine the age of a tandem repeat:
- the more recent the incorporation of the repeat, the more sequence identity it will share with the original sequence
- more divergent = older
- older = much different encoded proteins
What kinds of genome changes form “hot spots” for recombination?
tandem repeats
- increases the chance of structural change in chromosomes and the frequency of some genetic conditions.
Tandom repeats are substrates for recombination because:
- they are similar or identical in nucleotide sequence.
- If sequence identity exist in more than 2 places, recombination can occur between these regions.
Recombination between repeats may cause:
- inversion, duplication, or deletion, depending on the position and orientation of the repeats.
- occurs during meiosis.
Red-green color blindness is caused by:
- recombination between duplicated genes with almost identical sequence identity on the X chromosome (tandem repeats).
- occurs during meiosis - misalignment of chromosomes.
Contiguous gene syndromes are due to:
(a.k.a. microdeletions)
- Recombination occurs between large repeats deletes a block of DNA which contains multiple genes.
- ex:
- diGeorge syndrome
- prader-willis
- angelman
- ex:
Satellite sequences:
- short repeat
- tandem repeats of sequences of a few hundred base pairs long
- hundreds to thousands of copies, mostly at centromeres and telomeres.
Microsatellites:
- short repeats of a few nucleotides.
- relatively common.
- copy number highly variable.
- widely used to identify specific chromosomes in genetic counseling, because often each of the four parental copies will be different.
The two types of short repeat sequences:
- satellites
- microsatellites
Where are satellite sequences normally found?
centromeres and telomeres
Retrotransposon process:
- ds-DNA transcribed into mRNA by RNA polymerase.
- mRNA transcribed back into ds-cDNA by reverse transcriptase.
- ds-cDNA randomly incorporated back into ds-DNA. This reintegration can disrupt normal gene function.