Download modification of gene expression

Introduction to Genetics and Genomics
Christina Sax
Maryland University of Integrative Health
#MUIH
@MUIHealth
@CMSax
Outline
1.
2.
3.
4.
5.
Cells, DNA, Chromosomes
Genes and Gene Expression
Gene Regulation
Human Genetics
Genetic Variation
Part 1: Cells, DNA, Chromosomes
Cells, DNA, Chromosomes
• Humans composed of eukaryotic
cells
• Eukaryotic – animal cells
• Prokaryotic – bacterial cells
• Every eukaryotic cell contains a
nucleus
• Nucleus contains genetic
information (chromosomes,
DNA, and genes)
• Cells contain the same complete
set of genetic information
Cells
• Basic building block of living
organisms
• Adult human body has 10 to 100
trillion cells
• Membrane: semi-permeable,
regulatory barrier
• Ribosomes and Endoplasmic
Reticulum: protein production
• Nucleus: houses genetic
information, site of DNA & RNA
production
DNA and Chromosomes
• Human cells
• 46 chromosomes
• 46 pieces of DNA
• DNA - Deoxyribonucleic Acid
• A type of nucleic acid (DNA & RNA)
• Molecule that carries genetic information
and instructions in living cells
• Chromosome
• Physical structure of compacted DNA
• Genome – all the DNA in a cell or
organism
• Genomics – study of structure, function,
analysis, mapping of the genome
https://www.youtube.com/watch?v=dKubyIRiN84
Why twist & compact?
• Space: total length of DNA a
single cell is 6 feet
• Protection from tangles and
breakage
DNA Double Helix
• Double helix - structure of
the DNA molecule
• DNA molecule consists of 2
strands that wind around
each other like a twisted
ladder
• 3 primary components
• Nucleotides
• Sugar phosphate backbone
• Hydrogen bonds
Nucleotides
• Basic building blocks of nucleic
acids (DNA & RNA)
• 4 different nucleotides in DNA
•
•
•
•
A – adenine
C – cytosine
G – guanine
T - thymine
• Nucleotides are molecules with
3 distinct parts
• Phosphate group (common)
• Sugar (varies between DNA &
RNA)
• Nitrogenous base (varies between
nucleotide)
Nucleotides
Nucleotides
On one side of DNA ladder
nucleotides boned together
through sugar and phosphate
groups
DNA is a polymer made of long
chains of nucleotides bonded
together
Sugar-Phosphate Backbone
• Each strand has a backbone
made of alternating groups of
sugar (deoxyribose) and
phosphate groups
• Sugar-phosphate backbone is
portion of DNA double helix that
provides structural support to
the molecule
• The order of nucleotides in a
DNA molecule has meaning
• The order of nucleotides = genetic
instructions
Nucleotide Base Pairing
• Two strands of DNA are held in
close proximity by weak
hydrogen bonds
• Weak bonds allow two strands to
separate from one another for
important processes
• Hydrogen bonds form between
nucleotide bases on each side of
DNA ladder
• Human genome has:
• 6 billion individual nucleotides
• 3 billion pairs of nucleotide base
pairs
Nucleotide Base Pairing Rules
• Hydrogen bonds only form
between certain pairs of
nucleotides
• Size – uniform width of rungs of
the ladder
• Purine (large) – Pyrimidine (small)
• Chemical alignment for
hydrogen bonding
• Adenine (A) – Thymine (T)
• Cytosine (C) – Guanine (G)
• Result: stability & flexibility
Review and Questions
• What is the relationship between DNA and chromosomes?
• What is the overall structure of DNA?
• What are the nucleotide base pairing rules?
• Why are the nucleotide base pairing rules important?
• Other ????
Part 2: Genes & Gene Expression
Genes
• Basic physical and functional
unit of heredity
• Defined segments of DNA
• Chromosome = book
• Genes = chapters
• Vary in size from a few hundred
DNA nucleotides long to more
than 2 million nucleotides long
• Human Genome Project
estimates humans have between
20,000 and 25,000 genes per cell
Genetic Coding
• Discrete instructions coded in DNA
• The order of nucleotides in a DNA molecule has meaning
• The order of nucleotides = the genetic instructions for how to make
specific proteins
Translating the Code
The Central Dogma: DNA to RNA to Proteins
• Two processes to use transfer information
and use directions coded in DNA to make
proteins
• Transcription: use info DNA to make RNA
• Translation: use info in RNA to make protein
RNA Structure
• Similar to DNA
• Nucleic acid molecule
• Nucleotide building blocks
• Nucleotides bonded together through
sugar and phosphate groups
• Different from DNA
• Single Strand
• Nucleotide differences
• Oxy (-OH) group in sugar
• Uracil (U) instead of Thymine (T)
Transcription
• Transfer information stored in
DNA to storage in RNA
• Messenger RNA (mRNA)
• Information stored in order of
nucleotides in both DNA and
RNA
• Use DNA as a template to make
RNA – the order of nucleotides
in DNA determines the order of
nucleotides in RNA
DNA
A
G
A
T
C
G
G
Coding
Strand
mRNA
T
C
T
A
G
C
C
A
G
A
U
C
G
G
Template
Strand
RNA Nucleotide Rules
A–U
C-G
Transcription: Major Players
GENE
Upstream Promoter
of Gene
Region
Coding Region
Promoter Region:
Nucleotide sequences that attract proteins and
enzymes that synthesize mRNA
Terminator Downstream
Region
of Gene
Terminator Region:
Nucleotide sequences that cause RNA polymerase to
disconnect from DNA; mRNA synthesis stops
Transcription Process
Gene expression profiling
measures amount of mRNA
produced, using PCR, microarray,
DNA chip technology
Translation: RNA to Protein
• Use information stored in RNA
to make specific proteins
• Information stored in order of
nucleotides in RNA
• The order of nucleotides in RNA
determines the order of amino
acid subunits in the protein
DNA
A
G
A
T
C
G
G
Coding
Strand
mRNA
T
C
T
A
G
C
C
Template
Strand
A
G
A
U
C
G
G
Protein
Protein Structure
• Proteins are large complex
molecules
• Built from amino acids
subunits, bonded together
in long chains
• 20 different types of amino
acids
Translation: Cracking the Code
• mRNA interacts with ribosome
complex
• Ribosome "reads" the sequence
of nucleotides in mRNA
• Each sequence of 3 nucleotides
is called a codon
• Each unique codon indicates
that a particular amino acid
should be added next to the
growing protein molecule
Translation: Cracking the Code
mRNA
CUUAGGCUG
Protein
Leucine
Leucine
Arginine
Translation Process
Review and Questions
•
•
•
•
•
•
•
•
•
•
What is a gene?
What kind of information is coded in DNA?
How is information coded in DNA?
What is the overall structure of RNA?
What is the overall structure of a gene?
What is the role of a gene’s promoter region?
What activities occur during transcription?
What is the overall structure of protein?
What activities occur during translation?
How is the order of amino acids in a protein determined?
• Other ????
Part 3: Gene Regulation
Gene Expression and Regulation
• Gene Expression - process by which information from a gene is used
in the synthesis of a functional gene product
• Regulation of Gene Expression - mechanisms used by cells to increase
or decrease the production of specific gene products
• When combined, determine the characteristics of cells and organisms
• Together, determine the complement of proteins and relative
amounts of proteins in cells and organisms
• Proteins do most of the work in cells - required for the structure,
function, and regulation of cells, tissues, organs
Cell Differentiation
• All cells in the body contain the same
complete set of genes
• Some genes are active (and make
protein) in all cell types
• Some genes are only active in specific
cell types, and only make protein in that
cell type
• Each cell expresses only a fraction of its
genes
• Unique sets of proteins differentiates
cell types from one another and gives
them their unique characteristics &
functions
MUSCLE
NEURON
Differential Gene Expression
MUSCLE
Ferritin
(stores & release iron in a
controlled manner)
On
Myosin
(fibrous & contractile)
Off
Dopamine
(transmits signals)
Off
On
MUSCLE
NEURON
On
On
Off
Off
On
Protein Function determined by Structure
The order of amino acids determines each protein’s
unique 3D structure, shape, and specific function
Gene Regulation
Genes differentially turned on and off …
• During various stages of organismal development
• During various stages of a cell’s lifecycle
• In response to environmental changes (e.g. metabolism, infection)
• As a result of variation and modification of a gene’s nucleotide sequence
• As a result of modification of transcriptional regulatory proteins
Gene Regulation
Gene Regulation
Epigenetics
Genetic Variation
Epigenetics
Common minor changes in an Changes in an organism
organism caused by
caused by modification of
modification of the gene
gene expression
For example, single nucleotide
polymorphisms
Change in protein structure
Change in production of
and function
protein
Nutritional Genomics
Nutrigenomics
• NUTRITIONAL GENETICS: combination
of nutrigenomics and nutrigenetics
• NUTRIGENOMICS: effects of nutrients
on genome, gene expression, gene
regulation, proteome, and
metabolome
• NUTRIGENETICS: identifies how genetic
makeup of a particular individual coordinates his or her response to various
dietary nutrients
Nutrigenetics
Review and Questions
• What is gene expression?
• What is gene regulation?
• What is the general role of proteins in cells and organisms?
• How do DNA and proteins contribute to cell differentiation?
• What are the factors that regulate the expression of a gene?
• What is epigenetics? How does it relate to DNA?
• What is neutrogenomics? How does is relate to DNA?
• Other ????
Part 4: Human Genetics
Human Chromosomes
• 46 chromosomes per cell
• 23 pairs of chromosomes per cell
• 22 pairs autosomal chromosomes
• 1 “pair” sex chromosomes (X and Y)
• 1 chromosome in each pair
inherited from mother, 1 from
father
• Since there are genes on each
chromosome, each cell has 2
copies of each gene
Genotype and Phenotype
• Genotype – the genetic makeup
of an organism
• Phenotype – observable
characteristics of an individual
resulting from (physical &
chemical):
• Expression of its genes and the
production of proteins
• Interaction of genotype and
proteins with environment
Inherited Human Traits (Phenotypes)
• Single gene traits
• Mendelian inheritance
• Dominant traits
• Recessive traits
• Autosomal and X-linked traits
• Complex traits
• Many genes involved in
determining the trait
• Polygenic, multifactorial
• Specific degree of expression
and resulting phenotype
difficult to predict
Autosomal Dominant Traits
• Require only one copy of a gene
to express the trait
• Two alleles (variants) for the
gene
• A: autosomal dominant
• a: autosomal recessive
Affected
Parent
A
a
Unaffected
Parent
a
a
Aa
Aa
aa
aa
Autosomal Recessive Traits
• Recessive traits require two
copies of a gene to express the
trait
• A 'carrier' has only one copy of
the gene for the recessive trait,
so the carrier does not express
the trait
• Two alleles (variants) for the
gene
• R: autosomal dominant
• r: autosomal recessive
Carrier Father
R
r
Carrier Mother
R
r
RR
Rr
Rr
rr
Review and Questions
• What is the composition of chromosomes in human cells?
• What are genotype and phenotype? How are they related to one another?
• How are genes inherited?
• Other ????
Part 5: Genetic Variation
Genetic Variation
• Human genome is 99.9% identical among individuals
• Most genes have small sequence differences that vary among
individuals – polymorphisms
• ALLELES - Alternative forms of a gene with small differences in their
sequence of DNA bases.
• SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) - Single nucleotide
change at a specific location in DNA
• These small differences in DNA result in small differences in the
proteins made by cells, and contribute to each person’s unique
physical features.
SNPs
• Single nucleotide change at a
specific location in DNA
• Most simple form of genetic
polymorphism
• Represent 90% of human
polymorphisms
• Four possible SNPs per spot in DNA
• Each variant (version) = Allele
• Occurs 1 in every 100-300
nucleotides
Mutations
• Changes in the structure of DNA, resulting in a variant form that may be
transmitted to subsequent generations
• Types of changes
• Alteration of a single nucleotide
• Deletion, insertion, rearrangement of larger sections of DNA
• Result of changes
•
•
•
•
Changes to the production, structure, function of the coded protein
Non viability
Disease
Normal variation
• SNPs vs Single Nucleotide Mutations
• SNPs present in 1% or more of population
• Mutations present in <1% of population
Types of SNPs and Consequences
Non-Coding Region
of DNA (in between genes)
Coding Region
of DNA (in the gene)
Non-Synonymous SNP
Missense SNP
Change of codon results in a
change of 1 amino acid in the
protein
Synonymous SNP
Silent change. Change of
codon, but no change
of amino acid in the protein
Nonsense SNP
Creates a stop codon in the
gene and results in premature
truncation of the protein
(incomplete protein made)
SNPs and Codon Changes (example)
SNP Variant
Variant 1
Variant 2 (synonymous SNP)
Codon
UGU
UGC
Amino Acid
Cysteine
Cysteine
Variant 3 (missense SNP)
Variant 4 (nonsense SNP)
UGC
UGC
Tryptophan
Stop codon
SNPs and Protein Changes
• SNPs can change the structure
and function of protein … can
change cell and organismal
function
SNP variant 1 protein
SNP variant 2 protein
MTHFR Gene and Enzyme
MTHFR = methylene tetrahydrofolate reductase enzyme
(rate-limiting enzyme in methyl cycle)
Supports:
• Processing of
dietary folic acid
• Production of DNA,
RNA, proteins,
lipids
• DNA methylation
DNA Methylation
• Methyl groups added to adenine (A) and cytosine
(C) nucleotides in DNA
• DNA methylation typically represses gene
expression – blocks mRNA and protein production
Epigenetics
Epigenetics
Changes in an
organism caused by
modification of
gene expression
Change in
production of
protein
SNP - MTHFR 677T
GCC = Alanine
Alanine
Valine
GTC = Valine
thermolabile
MTHFR enzyme
MTHFR 677T SNP
Impaired function of MTHFR leads
to blocks completion of folate
cycle and entry into methylation
cycle …
• Sensitive to folic acid intake
• Blocks DNA, RNA, protein, lipid
synthesis
• Blocks DNA methylation
Genetic Variation
Common minor changes in an
organism caused by
modification of the gene
Change in protein structure
and function
Nutritional Genomics
Nutrigenomics
• NUTRITIONAL GENETICS: combination
of nutrigenomics and nutrigenetics
• NUTRIGENOMICS: effects of nutrients
on genome, gene expression, gene
regulation, proteome, and metabolome
• NUTRIGENETICS: identifies how genetic
makeup of a particular individual
coordinates his or her response to
various dietary nutrients
Nutrigenetics
MTHFR and Methylation
MTHFR
MTHFR
677T SNP
Methylation cycle
proceeds
Methylation cycle
slows
DNA methylation
occurs
DNA methylation
occurs at a lesser rate
Gene expression
repressed
Gene expression
more active
Specific set of proteins
made/not made
New and different set
of proteins made
Genetic Variation vs Epigenetics
MTHFR
Epigenetics
Changes in an
organism caused by
modification of gene
expression
Change in production
of protein
MTHFR
677T SNP
Methylation cycle
proceeds
Methylation cycle
slows
DNA methylation
occurs
DNA methylation
occurs at a lesser rate
Gene expression
repressed
Gene expression
more active
Specific set of proteins
made/not made
New and different set
of proteins made
Genetic Variation
Common minor
changes in an
organism caused by
modification of the
gene
Change in protein
structure and
function
Review and Questions
• What are single nucleotide polymorphisms (SNPs)?
• What is their impact on genetic variation in the human population?
• What is their potential impact on protein production, structure, and
function?
• What is the role of DNA methylation in cells?
• How is DNA methylation and the MTHFR gene/protein an example of both
epigenetics and genetic variation?
• How is MTHFR an example of nutrigenetics?
• Other ????