Genome Complexity and Gene Structure

biological complexity

the result of hierarchal organization of nested levels of cells, and higher order parts acitng together

junk DNA

DNA that we don’t know what it does

sometimes thought to be more structural

C value paradox

excess DNA is present in the genome that does not seem to be essential for the development or evolutionary divergence of an organism

The Onion Test

made by T. Ryan Gregory

asked which was more complex? onion or human

onions tend to have ~5x more DNA so are onions more complex than us?

how much of the human genome do coding DNA sequences take up?

2-5%

~20000 protein coding genes

G-value paradox

the number of genes does not correlate with organismal complexity

What are the three classes of nucleotide sequences?

1. highly repetitive DNA sequence (HR)

2. moderately repetitive DNA sequence (MR)

3. single copy DNA sequence (unique)

Highly repetitive DNA sequence (HR)

comprises about 10% of human genome

most is located in heterochromatic regions around the centromere/telomere

vary in length

what are some postulated functions of HR DNA sequence?

structural and organizational role to nothing more than junk

what is an example of HR DNA sequence?

alpha satellite DNA

alpha satellite DNA

HR

from 2 to more than 30 repeats of 171 bp tandem repeats

moderately repetitive DNA sequence (MR)

comprises about 30% of the human genome

found mostly throughout the euchromatin

average 300 bp in size

includes redundant genes for histones, and ribosomal RNA and proteins

MR DNA sequence example

microsatellite DNA and interspersed repetitive DNA

what are the functions of MR DNA sequences?

length mutability

modulation of transcription factor binding

spacing between promoter elements

cytosine methylation

alternative splicing

mRNA stability

transcriptiondstart and termination sites

Microsatellites

variable number of tandem repeats typically occurring in non-coding regions of the genome

how do microsatellites occur?

a mutation process known as slippage recognition

in DNA replication when polymerase is reading down the strand and slips on these regions

if it slips forwards, it can forget to read things

if it slips backwards it can copy things multiple times

what are some examples of microsatellites being useful genetic markers?

used to sequence human genome

markers for certain disease conditions

primary markers for DNA testing in forensic cases

what do microsatellites tend to be?

highly polymorphic (several different forms)

Single copy DNA sequence (unique)

comprises about 1-5% of the human genome

found throughout euchromatin

present at single or low copy number per genome

what percent of genes are the same in all people?

99%

what percent of genes contribute to each persons unique physical characterisitcs?

<1%

molecular level gene

DNA sequence that gives rise to an RNA molecule

regulatory sequence

site for the binding of regulatory proteins

their role is to influence the rate of transcription

can be found in a variety of locations

promoter

signals the beginning of transcription

transcribed region

part of this region contains the information that specifies am amino acid sequence

terminator

signals the end of transcription

exon

coding sequences=phenotype

intron

intervening sequences= areas of genes that generally dont code for phenotype

mRNA

RNA that only consists of exons

what are the flanking regions of the transcribed region of DNA?

the 5’ untranslated region and the 3’ untranslated region

the promoter (TATA BOX)

5’ untranslated region

mRNA that is directly upstream from an initiation codon

3’ untranslated region

section of mRNA that immediately follows the translation termination codon

what is the promoter characterized by?

the TATA box

TATA box

highly conserved sequence in DNA serving as the binding site for transcription factor binding

core DNA sequence: 5’-TATAAA-3’

ON/OFF for transcription

what are the regulatory sequences of the gene?

CAAT box

GC box

terminator

CAAT box

5’-GGCCAATCT-3’

consensus sequence that occurs upstream by 60 to 100 bases to the initial transcription site

typically required for inducible genes to be produced in sufficient amounts

GC box

region of DNA that can be bound with proteins (activators) to activate transcription of a gene or genes

terminator sequence

section of nucleic acid sequence that marks the end of gene or operon in genomic DNA during transcription

STOP CODONS DONT END TRANSCRIPTION TERMINATORS DO

solitary genes (unique)

a single copy of a gene (haploid situation); two copies in diploid

comprises the bulk of euchromatin

duplicated genes

process by which a portion of a chromosome is duplicated resulting in an additional copy of a gene

results in a copy of the OG gene called a paralog gene

either of the two genes may mutate and change the original function of the gene

usually occurs due to an error during meiosis

multigene families

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

most often located in similar regions of the chromosome

most often used or synthesized at a different time

Psuedogenes

dysfunctional relatives of genes that have lost their protein-coding ability

often result of multiple mutations within a gene

repeated genes

multiple copies of small genes clustered throughout the genome at specific sites

present in high copy number

many times present in a head to tail configuration