Genomes
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Genomes of most bacteria and archaea range from 1 to 6 million base pairs (Mb); genomes of eukaryotes
are usually larger
Most plants and animals have genomes greater than 100 Mb; humans have 3,000 Mb
Within each domain there is no systematic relationship between genome size and phenotype
Humans and other mammals have the lowest gene density, or number of genes, in a given length of DNA
Multicellular eukaryotes have many introns within genes and noncoding DNA between genes
Multicellular eukaryotes have much noncoding DNA and many multigene families
 The bulk of most eukaryotic genomes neither encodes proteins nor functional RNAs
 Much evidence indicates that noncoding DNA (previously called “junk DNA”) plays important roles in the
cell
 For example, genomes of humans, rats, and mice show high sequence conservation for about 500 noncoding
regions
 Sequencing of the human genome reveals that 98.5% does not code for proteins, rRNAs, or tRNAs
 About a quarter of the human genome codes for introns and gene-related regulatory sequences
 Number of genes is not correlated to genome size
 For example, it is estimated that the nematode
C. elegans has 100 Mb and 20,000 genes, while Drosophila has 165 Mb and 13,700 genes
 Vertebrate genomes can produce more than one polypeptide per gene because of alternative splicing of
RNA transcripts
 Intergenic DNA is noncoding DNA found between genes
 Pseudogenes are former genes that have accumulated mutations and are nonfunctional
 Repetitive DNA is present in multiple copies in the genome
 About three-fourths of repetitive DNA is made up of transposable elements and sequences related to them
Transposable Elements and Related Sequences
 The first evidence for mobile DNA segments came from geneticist Barbara McClintock’s breeding
experiments with Indian corn
 McClintock identified changes in the color of corn kernels that made sense only by postulating that some
genetic elements move from other genome locations into the genes for kernel color
 These transposable elements move from one site to another in a cell’s DNA; they are present in both
prokaryotes and eukaryotes. Eukaryotic transposable elements are of two types
Transposons, which move by means of a DNA intermediate
Retrotransposons, which move by means of an RNA intermediate
Sequences Related to Transposable Elements
Multiple copies of transposable elements and related sequences are scattered throughout the eukaryotic genome
In primates, a large portion of transposable element–related DNA consists of a family of similar sequences called Alu
element.Many Alu elements are transcribed into RNA molecules; however their function, if any, is unknown
The human genome also contains many sequences of a type of retrotransposon called LINE-1 (L1)
L1 sequences have a low rate of transposition and may help regulate gene expression
Other Repetitive DNA, Including Simple Sequence DNA
About 15% of the human genome consists of duplication of long sequences of DNA from one location to another
In contrast, simple sequence DNA contains many copies of tandemly repeated short sequences
A series of repeating units of 2 to 5 nucleotides is called a short tandem repeat (STR)
The repeat number for STRs can vary among sites (within a genome) or individuals.Simple sequence DNA is
common in centromeres and telomeres, where it probably plays structural roles in the chromosome
DNA packaging
DNA is wound around histone protein which forms a nucleosome (10 nm fiber). The nucleosome is composed of a
core of eight histone proteins and the DNA wrapped around them. The DNA between each nucleosome is called a
linker DNA.
The types of interphase chromatin
Chromatin is found in two varieties:
- heterochromatin highly condensed
- euchromatin loosely packed chromatin
REPLICATION
Replication is semiconservative
Watson and Crick hypothesized that during DNA replication, the double helix is unwound and each parental DNA
strand is used as a template to generate a new daughter duplex conserves only one strandand of parental DNA and
the other strand is completly new. DNA polymerases can extend DNA only in the 5’ – 3’ direction, but the two
parental strands are antiparallel.
Atiparallel elongation
Because strands in a DNA double helix run in opposite directions, the new strands must be made in different ways.
Therefore, one daughter strand ( leading strand) is synthesized continuously, in the direction of fork movement,
while the strand synthesized in the opposite direction ( the lagging strand) must be replicated discontinuously as a
series of Okazaki fragments.
Components of Replication
Template- strand that directs the polymerization reaction according to Watson-Crick base pairing rule
Topoisomerases -are enzymes that regulate the underwinding of DNA during DNA replication DNA becomes
overwound ahead of a replication fork. If left unabated, this tension would eventually halt DNA replication. to help
overcome these types of topological problems topoisomerases bind to either single-stranded or double-stranded DNA
and cut the phosphate backbone of the DNA. This intermediate break allows the DNA to be unwound, and, at the end
of these processes, the DNA backbone is resealed again.
DNA helicase- binds to the DNA at the replication fork untwist (“unzips”) DNA using energy from ATP.Breaks
hydrogen bonds between base pairs.
SSBs stabilize the single-stranded template and prevent ssDNA from reannealing to form dsDNA
Primer- short fragment of RNA that is complementary to the template
Primase the primase is a protein complex that synthesizes short RNA primers that are complementary to the
template strand and from which DNA polymerase initiates the synthesis of DNA.
DNA ligase -“seals” the gaps in DNA .Connects DNA pieces by making phosphodiester bonds
DNA polymerase adds nucleotides to RNA primer .
Final product: two identical DNA molecules
Flow of genetic information
The information content of DNA is in the form of specific sequences of nucleotides.The DNA inherited by an
organism leads to specific traits by dictating the synthesis of proteins.Proteins are the links between genotype and
phenotype. Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription
and translation
Transcription
Components of transcription
RNA polymerases (5’ → 3’ direction)-RNA polymerase also known as DNA-dependent RNA polymerase, is an
enzyme that produces RNA. RNA polymerase enzymes are essential to life and are found in all organisms
RNA polymerase is necessary for constructing RNA chains using DNA genes as templates, a process called
transcription. RNA polymerase doesn’t need primers. Three distinct RNA polymerases carry out DNA-dependent
synthesis of RNA
 RNA polymerase I
 RNA polymerase II
 RNA polymerase III
Template- DNA The coding (nontemplate) strand of the DNA is identical in base sequence to the RNA transcribed
from the gene, with U in the RNA in place of T in the DNA.The template strand is used to direct RNA synthesis by
RNA polymerase .
Free ribonucleotides ATP, GTP, CTP,UTP
Promoters- is a region of DNA that initiates transcription and is recognized by the RNA polymerase
Transcription factors- General transcription factors (GTFs) are essential for the transcription of all protein-coding
genes. The most common GTFs are
 TFII A
 TFII B
 TFII D
 TFII E
 TFII F
 TFII H
Final product; mRNA, rRNA, tRNA, snRNA
RNA processing include:
splicing
5′ methylguanosine cap (5’- Capping) -four functions
1. Ensures proper splicing
2. Facilitates transport
3. Protects from degradation by 5’exonucleases
4. Hhelps the transcription bind to the ribosome
3’- Polyadenylation (3′ poly-A tail ) - four functions
1. Transcription termination
2. Splicing
3. RNA stability
4. Transport to cytoplasm
Translation
Translation
During translation, the mRNA is read in the 5 to 3 direction. The flow of information from gene to protein is based
on a triplet code. These triplets are the smallest units of uniform length that can code for all the amino acids.There
are 20 amino acids, but there are only four nucleotide bases in DNA
The Genetic Code
• Universality- the genetic code is virtually universal, the specificity has been conserved from very early
stages of evolution
• Degeneracy - some amino acids are specified by more than one codon
• Amino acids are coded by groups of 3 nucleotides, called codons. 64 possible codons, and only 20
amino acids. Each amino acid is coded for by more than one codon
• Specificity- the genetic code is specific (unambigous), a particular codon always codes for the same amino
acid
• Nonoverlapping and commaless- the code is read from a fixed starting point without any „punctuation”
between the codons
• Four codons have special functions in the genetic code
–
one start codon AUG,
also codes for methionine
–
three stop codons
UGA*,UAA, UAG
These codons determine the beginning and end of the genetic code in an mRNA molecule (and so the beginning and
end of a polypeptide)
Components of Translation
Template - mRNA
tRNA - Picks up the appropriate amino acid floating in the cytoplasm and transports amino acids to the mRNA.
tRNAs are transcribed in nucleous by RNA Pol III.Each carries a specific amino acid on one end.Each has an
anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA. A tRNA molecule
consists of a single RNA strand that is only about 80 nucleotides long
Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf
Free amino acids- 20 amino acids
Aminoacylo-tRNA synthetase- attaches amino acids to tRNAs. Each cell must have 20 different species of these
enzymes
Ribosomal subunits - Ribosomes are organelles facilitate the specific coupling of tRNA anticodons with mRNA
codons during translation. Ribosomes are multi-subunits particles present in cell in large numbers. Ribosomes
consists of two subunits which are made up of proteins and ribosomal RNAs (rRNAs). The ribosomal subunits in
ekaryotes are made in the nucleous. The resulting ribosomal subunits are translocated into cytoplasm
Protein factors
Sources of energy
Final product: protein