Nuclear Genome : Gene

Structure and Function

 Outcomes
•explain the terms genome, gene, pseudogene,
heredity and genetics as a basic terminology
•summarize the amplification of genetic information from
genome to proteome to gene networks and ultimately to
cellular function and phenotype
•recognize the nuclear genome, gene organization,
structure and function
•define the structural features of a typical human gene
•describe alleles, dominant and recessive traits
•calculate the probability of genotypes using Punnett square
•define homozygousity and heterozygousity
•estimate genotype-phenotype correlation
• invent your genetic traits
 Certain Characteristics are
Passed from Parent to Offspring
DIFFERENT TRAITS
Body Shape
Hair Texture Hair Color

Eye Color Skin Color

 Heredity and Genetics
• Your GENES determine whether or not you
possess certain physical traits.

• Your GENES make you blue eyed or brown

eyed, or have brown or blond hair.

• These traits are highly complex, and

involve the interaction of many genes.
Genetics is a PLAN for Life
What is genetics?
the scientific study of heredity & hereditary variations
But what does hereditary mean?
something is hereditary if it is passed from one
generation to the next generation.
Why is understanding genetics important?

It is major intellectual problem (question)

It has huge practical implications (cancer, hereditary
diseases, crop domestication, etc.)
 Molecular Genetics
Digital life information on DNA
Digital music
information on
CD
play
transcription
or
RNA
play CD
player translation
ribosome
sound protein
waves

Ear and Development and

brain metabolism

music life
 What is a GENE?
• A code made up of pairs of bases carried
on the DNA molecule.

• Each DNA molecule contains many genes

• The basic physical and functional units of

heredity
 What is a GENE?
• A specific sequence of bases
– Sequences carry the information needed
for constructing proteins
• Proteins provide the structural components
of cells and tissues as well as enzymes for
essential biochemical reactions.

• The human genome is estimated to

be made of ~ 22,000 genes.
 What is a GENE?
• Each chromosome carries a couple of
thousand genes

• Many of these are common to all human

beings.

• So, 99.9% of your DNA is identical to

everyone else's
 What is a GENE?
• The remaining 0.1% influences the
differences between us
– height, hair color and susceptibility to a
particular disease

• Environmental factors, such as lifestyle (for

example, smoking and nutrition) also
influence the way we look and our
susceptibility to disease
 What is a Gene?
• May be in several parts
– Exon – the expressed parts of the DNA
sequence
– Intron – the intervening, “junk DNA?”,
not expressed

• Parts are cut, put together and then used

to make RNA and proteins
XRTHISISGENEAUIXXVXVXVHMNTHISISGENEBMMMXYHTRPKLVXVXVH
MZMETUTHISISGENECNBUNYBLIHIUBWERJBOUWEJBRPJB
 Mitochondrial genome
16,569 bp
NUCLEAR GENOME 37 genes
24 distinct chromosomes (22
autosomal + X + Y)
3,200 Mbp
22,000 genes???
CpG islands in the regulatory areas of
human genes
 Intronless Genes;

 Interferongenes
 Histone genes
 Many ribonuclease genes
 Heat shock protein genes
 Many G-protein coupled receptors
 Various neurotransmitters receptors and
hormone receptors
 Classical gene families: members
exhibit a high degree of sequence similarity

CS = chorionic somatomammotropin

four placenta-specific genes, primates only

serum albumin alpha-albumin vitamin D-binding protein

Gene families: gene products bearing
short conservative amino acid motifs
DEAD box proteins are involved in mRNA splicing
and translation initiation; DEAD box (Asp-Glu-Ala-Asp)

WD proteins take part in a variety of regulatory functions,

GH (Gly-His) should be at 23-41 aa distance from WD (Trp-Aps)
Gene superfamily: Proteins that are
functionally related in a general sense, but
show only weak homology
 Six major types of
noncoding human DNA
have been described
 noncoding
introns

Segmental
duplications

Simple
sequence
Noncoding DNA in repeats (SSRs Long
interspersed
Eukaryotes Structural
elements
DNA
Dead
transposons
Transposable
elements
Long terminal
repeats
Pseudogenes
Short
interspersed
elements
Noncoding DNA in
Eukaryotes

31
 TF – transcrition factor
heterochromatin

S – silencer P – promoter I – insulator E – enhancer

2010, 11, 439-446

o Promoters – recognition sequences for binding of RNA polymerase

o Enhancers – increase transcription of a related gene
o Silencers – decrease transcription of a related gene
o Insulators or boundary elements – block undesirable influences on
genes:

o LCR – locus control regions – activate some gene clusters

CROSS-TALK
Tandem and interspersed repeats
• Telomere is a series of short tandem repeats at
the ends of eukaryotic chromosomes; prevents
chromosomes from shortening with each
replication cycle
• Transposons  jump and interrupt the
normal functioning may increase or
decrease production of one or more
proteins

• can carry a gene that can be activated

when inserted downstream from an active
promoter and vice versa
 Alu elements
• Length = ~300 bp
• Repetitive: > 1,000,000 times in the human genome
• Constitute >10% of the human genome
• Found mostly in intergenic regions and introns
• Propagate in the genome through retroposition (RNA intermediates).
• Common source of mutations in humans
• Alu insertions have been implicated in several inherited human
diseases and in various forms of cancer.
• The study of Alu elements has also been important in elucidating
human population genetics and the evolution of primates, including
the evolution of humans.

41
Chromosomal location of repeats
Summary 1
Summary 2
 Pseudogenes
• Non-functional copy of a gene
– Non-processed pseudogene
• Nonfunctional copies of the genomic DNA sequence of a gene
• Contain exons, intron, and flanking sequences
– Processed pseudogene
• Nonfunctional copies of the exonic sequences of a gene
• Reverse-transcribed from an RNA transcript
• No 5’ promoter
• No introns
• Often includes polyA tail

– Both include events that make the gene non-functional

• Frameshift
• Stop codons

• Could be as high as 20-30% of all Genomic sequence predictions

• We assume pseudogenes have no function, but we really don’t know!
How can they arise?
 Pseudogene
DNA sequences that closely resemble
known genes but are nonfunctional

Genome
The complete DNA sequence, containing
the entire genetic information,
of a gamete, an individual, a population,
or a species

Genomics
The field of genetics concerned with
structural and functional studies of the
genome
 Dominant and Recessive
Each parent has two genes (or letters) for a trait.
These letters are called alleles.

Capital letters are called Dominant alleles.

When these alleles are present, they take
over or show. They are the “stronger”alleles

Lower case letter are Recessive alleles and

are the “weaker” of the alleles
 Dominant and Recessive

􀂋 B – brown eyes 􀂋 b – blue eyes

􀂋 T – tall 􀂋 t – short
􀂋 C – curly hair 􀂋 s – straight hair
􀂋 W – widows peak 􀂋 w – no widows peak
􀂋 F – freckles 􀂋 f – no freckles
􀂋 D – dark skin 􀂋 d – light skin
 Punnett Squares

Using Punnett Squares allow us to show what

the offspring could look like

Allows us to calculate probability of certain

genotypes and phenotypes to occur
 Let’s try all!
Hand Clasping

Clasp your hands together (without thinking about it!).

Most people place their left thumb on top of their right

and this happens to be the dominant phenotype.

Now, for fun, try clasping your hands so that the

opposite thumb is on top. Feels strange and unnatural,
doesn’t it?

Alleles: L,l
Dominant phenotype: left thumb on top
Dominant genotype: L –
Recessive genotype: ll
Bent Little Finger

A dominant allele causes the

last joint of the little finger
to dramatically bend inward
toward the 4th finger.

Lay both hands flat on a

table relax your muscles,
and note whether your have
a bent or straight little
finger.

Alleles: B, b
Dominant phenotype: bent little finger
Dominant genotype: B –
Recessive genotype: bb
Diseases: Thalassemia
Diseases: Thalassemia
Amplification of Genetic Information
Suggested Readings

Thomson and Thomson

Chapter 3
The Human Genome:
Gene Structure and Function