BIOL 3000 Gene Complexity and Gene Structure

Complexity

The state of having many parts and being difficult to understand or find an answer to

Biological complexity

The result of hierarchical organization of cells

1960’s

The discovery of repetitive DNA sequences

“Junk DNA”

DNA that we do not know what function it has

What defines complexity?

The number and type of cells

The degree of cellular organization

Gene value

The amount of DNA that you have in an organism

C value Paradox

Comes from junk DNA

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

T or F

Genome size correlates with organismal complexity

True

The Onion Test (T. Ryan Gregory 2007)

Ask the audience who has more complex DNA and see what they say

The onion has more DNA than us

G-value Paradox

The number of genes does not correlate with organismal complexity.

The number of genes because most of the organism has the same number of genes.

Percent of coding DNA sequences in the human genome

2-5% of the human genome (~20,000 protein coding genes)

Eukaryotic advancements

-Alternative splicing

-Transcription factors

Are you more advanced than an onion?

We don’t really know!a

Three classes of nucleotide sequence

1. Highly repetitive DNA sequence (HR)

2. Moderately repetitive DNA sequence (MR)

   1. Single copy DNA sequence (Unique)

Highly repetitive DNA sequence (HR)

Comprises of about 10% of the human genome

Most is located in the heterochromatin regions around the centromere/telomere (“non-coding DNA regions”)

Occurs as variable length motifs (5-100 bp), in long tracks of up to 100Mb; there are repeats of certain bases and have long tracks

Present at >10⁶ copies per genome

Postulated functions include structural and organization role to nothing more than junk

e.g. - alpha satellite DNA

Alpha satellite DNA

Two to more then 30 repeats of 171 bp tandem repeats

Moderately repetitive DNA sequence (MR)

Comprises of about 30% of the human genome

Found mostly throughout the euchromatin

Average 300 bp in size

Present between 10-10⁵ copies per genome

Also includes ‘redundant’ genes for histones, and ribosomal RNA and proteins, (gene-products present in cell in large numbers)

Functions in length mutability, modulation of transcription, factor binding spanning between promoter elements, and alternates splicing

e.g. Microsatellite DNA, interspersed repetitive DNA

Microsatellite DNA

Repeating sequences of 2-30 bp of DNA

Variable number of tandem repeats typically occurring in non-coding regions of the genomes

Ranging in size of the repeating

Occurs through a mutation process known as “slippage recognition”

Useful genetic markers that tend to be highly polymorphic

Slippage recognition

Happens in DNA replication

The repeats causes the DNA to slip forwards or backwards

Interspersed repetitive DNA

Transposable elements

Single copy DNA sequence (Unique)

Comprises about 1-5% of the human genome

Found throughout the euchromatin

~20,000 protein coding genes

“Coding DNA regions = GENES”

Present at single or low copy number per genome

Percentage of HR, MR, and unique DNA

10% (HR) + 30% (MR) + 5% (Unique) = 45%

Giemsa Stain

Highly repetitive: Heterochromatin (tightly coiled)

Moderately repetitive: scattered throughout Euchromatin

Unique: Euchromatin - genes

Gene

The basic physical and functional unit of heredity

How one person passes along traits

A sequence of unique nucleotides (genotype) that carry the genetic information which is to be expressed (phenotype)

What are the instruction manuals for our bodies?

Genes

Molecular level “gene”

DNA sequence that gives rise to an RNA molecule

“Transcriptional unit”

The template for the RNA

Transcribed region

DNA to RNA

Part of this region contains the information that specifies an amino acid sequence

Exon

“Coding sequences” = phenotype

Intron

“Intervening sequences” = areas of genes that generally don’t code for phenotype

5’ Untranslated Region

mRNA that is directly upstream from the initiation codon, before the start codon

3’ Untranslated Region

Section of the messenger mRNA that immediately follows the translation termination codon

Promoter

DNA sequence onto which the transcription machinery binds and initiates transcription

Signals the beginning of transcription

TATA Box

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

Allows transcription to be turned off or on (on a basal level)

Core DNA sequence is ^5’-TATAAA-^3'

“ON/OFF” for transcription

Regulatory Sequences- Enhancers

They enhance or inhibit and affect the rate of transcription

CAAT Box

^5’-GGCCAATCT-^3’ consensus sequence that occurs upstream by 60-100 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

Regulator proteins

Proteins bind to them to modify their speeds

“Ramped up” level of transcription

Termination

“The end of the gene”

Tells the DNA polymerase to leave

No one else can turn off transcription, only terminator

Terminator

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

Regulatory sequence

Site for the binding of regulatory proteins. The role of regulatory proteins is to influence the rate of transcription. Regulatory sequences can be found in a variety of locations. Controls the mechanism

Types of Genes

1. Solitary genes

2. Duplicated genes

3. Multigene families

4. Pseudogenes

   1. Repeated genes

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 original 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

Many copies of a single gene (management)

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 different times

One class/family genes but they have different functions

Pseudogenes

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

Often the 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