Human Genome Organization - Sikela

Question 0

Of the _________ base pairs in the human genome, only ___% code for proteins and ___% are regulatory.

Answer 0

3 billion
1.5%
5%

Question 1

Inheritance pattern of mitochondrial DNA?

How many genes does mitoch. DNA code for?

Answer 1

Maternal inheritance

codes for 37 genes

Question 2

What is single-copy DNA?

Answer 2

DNA whose nucleotide sequence appears once (or only a few times) in the genome.

Question 3

What is repetitive DNA?

Answer 3

DNA whose nucleotide sequence is repeated (exactly or very nearly so) hundreds to millions of times in the genome.

Question 4

Normal human chromosomes:

_____ autosomal pairs
_____ pair of sex chromosomes ____

Answer 4

22

1, XX or XY

Question 5

Typical vs. Retroposed gene?

Answer 5

typical = intron-containing
retroposed = intronless

Question 6

Give two types of repetitive DNA.

Answer 6

1. Tandem repeats (head-to-tail)

2. Interspersed throughout the genome

Question 7

What / Where is the alpha-satellite family of DNA?

Answer 7

Composed of tandem arrays of a 171-bp repeat located at the centromere of each chromosome.

Critical for attachment of centromeres to the microtubules of the spindle apparatus during cell division.

Question 8

LINE and Alu sequences?

Answer 8

dispersed repeats making up a significant portion of the genome (Alu 10%, LINE 20%).
implicated in some hereditary diseases

Question 9

About _____ new mutations occur in each individual.

Genotype + ______ = phenotype.

Answer 9

30

environment

Question 10

Why might it be the case that trisomy of chromosomes 13, 18 and 21 are the ones where the fetus survives to live birth?

Answer 10

These genes are the three most “gene poor” of all the autosomal chromosomes. Only the Y chromosome has fewer genes.

Question 11

Does the human genome has more A-T rich regions or more C-G rich regions?

Answer 11

A-T

54% A-T rich
38% C-G rich

Question 12

Euchromatic regions of the genome are more __________ while Heterochromatic regions are more _______ and _______.

Answer 12

relaxed

condensed and repeat-rich

Question 13

Medically important genes: beta-globin, BRCA1 and MYH7 (beta-myosin heavy chain).

How many exons in each and what diseases are each linked to?

Answer 13

beta-globin: 3 exons, hemoglobin disorders
BRCA1: 24 exons, breast and ovarian cancer
MYH7: 40 exons, inherited hypertrophic cardiomyopathy

Question 14

Beta-like globin genes on chromosome 11. What are they and in what order are they turned on?

Answer 14

Beta-like globin genes code for hemoglobin subunits and are positioned along the chromosome and turned on in the following order (5’ to 3’)

1. Epsilon; embryonic yolk sac
2. G_gamma, A_gamma; fetal liver, spleen and bone marrow
3. Delta, Beta; birth –> adulthood

Question 15

In general, two individuals’ genomes will be ______% identical and differ by ________ base pairs.

Answer 15

99.9%

3,000,000

Question 16

What is special about the repeats found on the long arms of chromosomes 1, 9, 16 and Y

Answer 16

These contain a pentaneucleotide repeat and are hotspots for human-specific evolutionary changes

Question 17

What is a retrotransposition product?

Answer 17

when RNA –> cDNA and this cDNA gets inserted into the genome.
may inactivate genes

Question 18

What is NAHR?

Answer 18

non-allelic homologous recombination
as a result of repeats, non-allelic repeats line up (incorrectly) and undergo recombination at the wrong spot.

–> microdeletions / microduplications

Question 19

What are copy number variations? (CNV’s)

What percentage of the genome do they cover?

Answer 19

a form of structural variation:
variation in segments of the genome (200bp - 2Mb) that can range from one add’l copy to many or in a deletion of a segment.

may cover 12% of the loci in the genome

Question 20

Gene families arise through _____________ and are a major mechanism behind _____________.

Answer 20

gene duplication

evolutionary change

Question 21

Between any to human genomes there is roughly one SNP every _________ base pairs.

Answer 21

1000

Question 22

Give two examples of intronless genes.

Answer 22

Histones

Interferon

Question 23

What is a gene family?

Answer 23

A set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions.

Question 24

Describe the Alu gene family

Answer 24

a family of dispersed repetitive elements
about 300 bp in length (similar but not identical to each other)
about a million of them in the total genome (10% of the DNA)

Question 25

Describe the LINE gene family

Answer 25

LINE = Long Interspersed Nuclear Element
up to 6 kb in length
about 850,000 copies per genome (20% of the genome)

Question 26

The OR family of genes is really a part of what “super-family” of genes?

Answer 26

The G protein gene superfamily.

G protein-coupled receptors, characterized by a conserved membrane-spanning protein motif, are critical for the function of a diverse repertoire of receptors. (see ch. 12)

Question 27

What is a pseudogene?

What are the two main types of pseudogenes?

Answer 27

DNA sequences that closely resemble known genes (e.g. globin family or OR family) but are non-functional.

1. Non-processed pseudogenes are thought to be byproducts of evolution & are perhaps “dead” genes (vestigial)
2. Processed pseudogenes are formed by retrotransposition (incorporation of cDNA into the genome)

Question 28

What is unique about processed pseudogenes?

Answer 28

Since processed pseudogenes are retrotransposed (RNA –> cDNA –> incorporated back into the genome) they lack introns and may not be on the same chromosome as their progenitor gene.

Question 29

What is an important class of non-coding RNA genes.

Answer 29

Non-coding RNA genes for microRNA (miRNA).

miRNA’s are short (22-bp) that (often) control expression or repression of other genes throughout development.

Question 30

What are micro and mini satellite genes?

Answer 30

Two different types of multi-allelic insertion / deletion (indels) polymorphisms

Question 31

What is a microsatellite?

Answer 31

di-, tri-, or tetra-nucleotide repeats. Repeated one to a few dozen times.
5 x 10^4 per genome
a.k.a. Short Tandem Repeat Polymorphisms (STRP’s)

Question 32

What is a minisatellite?

Answer 32

10-100 bp, tandem repeat blocks of DNA
a.k.a. Variable Number Tandem Repeats (VNTR’s)

Used in Southern Blot DNA fingerprinting. Only identical twins will have identical versions of their VNTR’s

Question 33

What is the missing heritability problem?

Answer 33

Many regions of the genome remain unexamined.

The currently implicated loci for genetic contribution (to complex diseases) do not seem “sufficient” to account for the observed variability and number of diseases.