Genes and Genomes

CHAPTER 2
An Introduction
to Genes and
Genomes
PowerPoint® Lecture by:

Melissa Rowland-Goldsmith
Chapman University
An Introduction to Genes and Genomes
Encoded with DNA are genes that provide instructions controlling the activities of all
cells. Genes influence our behaviour; determine our physical appearances such as skin,
hair, and eye colour; and affect our susceptibility to genetic disease conditions.
© 2013 Pearson Education, Inc.
Chapter Contents
• 2.1 A Review of Cell Structure

• 2.2 The Molecule of Life
• 2.3 Chromosome Structure, DNA
Replication, and Genomes
• 2.4 RNA and Protein Synthesis
• 2.5 Mutations: Causes and Consequences

2.1 A Review of Cell Structure
• All cells have these structures:

• Plasma Membrane – double-layer structure
of lipids and proteins that surrounds its
outer surface
• Cytoplasm – inner contents of a cell
between the nucleus and plasma
membrane
• Organelles – structures in the cell that
perform specific functions

• Comparison of Prokaryotic and

Eukaryotic Cells
Insert table 2.1

• Prokaryotic Cells

• Eukaryotic cells (include plant and animal

cells)
Insert figure 2.2

• Plasma membrane: fluid, dynamic, complex

double-layered barrier made of what
macromolecules?
– Roles include cell adhesion, cell-cell communication,
cell shape, transport molecules in and out of cell, is
selective barrier
• Cytosol: nutrient-rich, gel like fluid that makes up
cytoplasm
• Organelle: compartment where chemical rxns
and cell processes take place
– Each organelle has its own biochem rxns
– Allows coordination of chem rxns within a cell



Identify the structures of a liver cell from an electron micrograph


2.2 The Molecule of Life
• DNA Structure
– Building block of DNA is the nucleotide
– Each nucleotide is composed of
• Pentose (5-carbon) sugar called deoxyribose
• Phosphate molecule
• A nitrogenous base
– The nitrogenous bases are the interchangeable
component of a nucleotide
• Each nucleotide contains one base
– Adenine (A), thymine (T), guanine (G) or cytosine (C)

• Building block of DNA = nucleotide
• What is the difference between deoxyribose and

ribose sugar?
• DNA Structure
– Nucleotides are joined together to form long strands of
DNA and each DNA molecule consists of two strands
that join together and wrap around each other to form a
double helix
– Nucleotides in a strand are held together by
phosphodiester bonds
– What part of a nucleotide and adjacent nucleotide
does the phosphodiester bond connect?
– Each strand has a polarity – a 5' end and a 3' end
– Polarity refers to the carbons on what part of a
nucleotide?

• DNA Structure
– The two strands of a DNA molecule are held
together by hydrogen bonds
• Formed between complementary base pairs
• Adenine (A) pairs with thymine (T)
• Guanine (G) pairs with cytosine (C)
– The two strands are antiparallel because their
polarity is reversed relative to each other
– DNA resembles a twisted ladder

• What are the rungs of the ladder?

• What is the backbone or sides of the ladder?
• What is a gene?
• Sequence of nucleotides that provides cells with
instructions to synthesize a protein or type of RNA
• On average genes are 1000–4000 nucleotides
long
• Genes influence how cells, tissues and organs
appear
– Define the term trait:
– *not all genes are used to produce a protein
• (example) State the function of genes involved in making
tRNA.

2.3 Chromosome Structure, DNA
• Chromosome Structure
– Chromosomes – where cells package DNA
– Chromatin – strings of DNA and DNA-binding
proteins called histones
• State of DNA inside the nucleus when the cell is
NOT dividing
• During cell division chromatin is coiled into fibers
that wrap around each other so chromosomes are
highly coiled
• Why would chromatin be condensed during cell
division based on what you know about the
number of bases in every cell?
• Most human cells have two sets (pairs) of 23
chromosomes (paternal and maternal), or 46
chromosomes total
– Called homologous pairs
– Autosomes – chromosomes 1-22
– Sex chromosomes – chromosome pair # 23
• X and Y chromosomes
• Gametes (sex cells) contain a single set of 23
chromosomes (haploid number, n)
• All other cell in body are somatic cells
• What type of cell is a kidney cell?
• Characteristics common to eukaryotic chromosomes
• Chromosome consists of two thin, rodlike structures of
DNA called sister chromatids
– Exact replicas of each other copied during DNA replication
– During cell division, each sister chromatid is separated
– Each chromosome has a single centromere – region consisting of
intertwined DNA and protein that join sister chromatids together
and also contain proteins that attach chromosomes to microtubules
• Centromere delineates each sister chromatid into 2 arms – p
and q
• Each arm of chromosome ends with a telomere- highly
conserved repetitive nucleotide sequence that attach
chromosomes to nuclear envelope
– telomeres allow cells to divide without losing genes) but
during aging and cancer progression telomeres become
© 2013 Pearson Education, Inc. shortened
• Chromosome Organization
• What is a potential consequence of shortening of telomeres

during the aging process?
• Karyotype- way to study chromosome number and basic
aspects of chromosome structure
– Spread cells on microscope
slide and treat with chemicals
to release and stain
chromosomes
– Chromosomes can be
aligned and paired based
on staining pattern and size
• Based on the karyotype, which chromosome is the largest?

Explain how you came up with your answer (work in groups).
• What would a karyotype for Trisomy 21 (Down Syndrome) look
like? Explain.
• DNA Replication
– Somatic cells divide by a process called mitosis
– Mitosis
• One cell divides to form two daughter cells, each with
an identical copy of the parent cell DNA
• A single skin cell would produce how many cells

and how many chromosomes/cell?
• In order to accomplish this, the DNA of the parent cell

must be copied prior to mitosis

• DNA replication
• Sex cells divide by a process called meiosis – parent cell
divides to create 4 daughter cells which can be sperm or
egg cells
• The DNA in each daughter cell is not an identical copy of
the parent cell
• Chromosome number is cut in half to the haploid number
• How many sets of chromosomes does each daughter
cell have?
• Through sexual reproduction a fertilized egg called zygote
is formed and zygote divides by mitosis to form an
embryo = complete set of 46 chromosomes

• Semiconservative Replication
– DNA replication occurs in such a manner that, after
replication, each helix contains one original (parental)
DNA strand and one newly synthesized DNA strand


• Steps in DNA Replication
1. Unwinding the DNA
– Helicase enzyme breaks the hydrogen bonds between
complimentary base pairs that hold the two DNA strands
together; "unzips" DNA
– Single strand DNA binding proteins bind to each strand and
prevent them from base pairing and reforming a double helix
– Separation of strands occurs in regions called origins of
replication
2. Adding short segments of RNA 10–15 nucleotides long
called RNA primers
– Primase enzyme synthesizes RNA primers
– RNA primers start the replication process because they serve as
binding sites for DNA Polymerase – enzyme that synthesizes
new strands of DNA

• Steps in DNA Replication
3. Copying the DNA
– DNA polymerase enzyme binds to the
RNA primers
– Uses nucleotides to synthesize
complementary strands of DNA
– Always works in one direction – 5' to 3'
direction
– What kind of bond is formed between the
phosphate in one nucleotide and sugar in
the previous nucleotide?
• Steps in DNA replication
• Since DNA Pol only goes in 5'–3' direction,
replication along leading strand is continuous and
is discontinuous along lagging strand
• Why is it discontinuous on lagging strand?
• Short Okazaki fragments are synthesized as DNA
Pol works on lagging strand
• RNA primers are replaced with DNA nucleotides
using DNA Pol
• Covalent bonds are formed between Okazaki
fragments with DNA ligase

Figure 9 Semiconservative Replication of DNA

• Genome – all of DNA in organism's cell
• DNA contains instructions for life in form of
genes
• Human genome has 20,000 genes
scattered among 3 billion base pairs of
DNA!
• What is the study of genomics?
• What was the purpose of the human
genome project that was completed in
2003?
2.4 RNA and Protein Synthesis
• Transcription – genes are copied

(transcribed) from DNA code into
RNA code
• Translation – RNA code (exact
copies of genes) is read into a
protein
Figure 10 The Flow of Genetic
Information in Cells DNA in copied into
RNA during the process of transcription.
RNA directs the synthesis of proteins
during translation. Through proteins, gene
control the metabolic and physical
properties or traits of an organism
• Through production of RNA and protein synthesis DNA controls

properties of the cell and its traits
• Give an example of a trait using the words in the above figure.


• Transcription
– Occurs only in segments of chromosomes that contain
genes
– RNA polymerase unwinds DNA helix and copies one
strand of DNA into RNA
• Binds to a promoter region – consensus nucleotide sequence
• Transcription factor (TF) proteins are DNA binding proteins
that bind to specific regions on DNA – purpose of transcription
factors is to help RNA Pol find the promoter
– TF can act to speed up transcription or stop transcription
• Enhancers are DNA nucleotides that also play role in
transcription

• Transcription
• After RNA Pol binds to promoter, it unwinds a region of DNA to
separate the 2 strands
• The template strand is copied by RNA Pol
• Copies template DNA in a 5' to 3' direction into RNA
• Uses nucleotides
– Adenine, uracil, guanine, and cytosine
– A-U, C-G
– What kind of covalent bond is formed between
ribonucleotides?
– At end of gene, RNA polymerase encounters the termination
sequence to create loops at the end of RNA so RNA
polymerase and newly formed strand of RNA are released from
DNA molecule
– RNA strand is called a messenger RNA (mRNA)
– Multiple copies of mRNA are transcribed from each gene during
transcription
Figure 11 Transcription. During transcription, RNA

polymerase binds to DNA at a promoter region adjacent
to a gene sequence and unwinds the DNA. RNA
polymerase moves along the DNA template, copying
one strand olinto a molecule of RNA. When RNA
pymerase reaches a termination sequence, it releases
© 2013 Pearson Education, Inc. from the DNA and transcription ends.
• mRNA is not the only type of RNA that gets

transcribed.
• Name 2 other types of RNA that are produced

by transcription.
• Do these 2 types of RNA carry information that

directly codes for synthesis of protein? Work
in groups and explain.
• New class of non-protein coding RNA: microRNA

• mRNA Processing
– Initial mRNA produced is the primary transcript
• Immature and not fully functional
– Three modifications before primary transcripts are
ready for protein synthesis (takes place in nucleus)
• RNA splicing – splice out the DNA not coding for proteins
(introns) and retain the protein coding sequence of the gene
(exons)
– Alternative splicing – multiple proteins produced from single
gene
• 3' PolyA tail – 100–300 adenine nucleotides added to protect
mRNA from RNA degrading enzymes; increase its stability and
availability for translation
• Addition of a 5' cap – guanine base containing methyl group
allows ribosome recognition


Figure 12 Eukaryotic Gene and mRNA
processing. (a) Transcription of a eukaryotic gene
produces a primary transcript or pre-mRNA, which
undergoes processing through RNA slicing, the
addition of a 5 cap, and polyadenylation. After
processing, the final, mature mRNA is ready for
export to the cytoplasm, where it will be translated
into a protein. (b) Alternative splicing can produce
different mRNAs and protein products from the
same gene. Notice that the larger mRNA on the left
contains three exons spliced together but that the
shorter mRNA on the right contains only two exons
spliced together.
• Components of translation – in cytoplasm

• mRNA – copy of gene (acts as messenger
by carrying genetic code from nucleus to
cytoplasm where info is read into protein)
• tRNA – molecules that transport amino
acids to ribosomes during protein synthesis
• rRNA – short single stranded RNA
molecules and are components of
ribosomes
• Ribosomes – what is their function?

• How is mRNA read?

– Genetic code – universal language of genetics used by
virtually all living organisms
• Works in three nucleotide units of mRNA called codons
• Each codon codes for a single amino acid
• One amino acid may be coded for by more than one codon
– There are 64 codons and only 20 amino acids –
degeneracy of the genetic code
• Start codon (AUG) codes for Met and signals starting point for
translation
• Stop codons – UGA, UAA, UAG – do not code for amino acid
but signal end of translation

• Read the genetic code and state which amino acid has the most
codons. Explain.
• Read the genetic code and state which amino acid has the least
amount of redundancy within the genetic code.
• Ribosomes and tRNA molecules

• Ribosomes – aggregates containing rRNA and protein that
make up subunits
– Each ribosome contains 2 subunits: large and small and associate
to form 2 grooves A (aminoacy) site and P (peptidyl) site into
which tRNA molecules bind and also E site which tRNA molecules
leave the ribosome (Figure 13).
– tRNA – small molecules that fold into cloverleaf structure- has site
for amino acid attachment by aminoacyl tRNA synthetase enzyme
• Aminoacyl tRNA bind to A site of ribosome
• Opposite end of tRNA is 3 nucleotide sequence = anticodon
• Each amino acid binds to a different anticodon
• Anticodons form complimentary base pairs with what part
of the mRNA sequence?
• What are the 3 players of translation?
Stages of translation
1. Initiation – small ribosome subunit binds to 5' end of mRNA
• What part of mRNA processing allows this 5' end to be recognized by
ribosome?
– Initiation protein factors help guide small ribosome subunit to mRNA
– Small ribosome subunit moves along the mRNA until the start codon is
found
– Small subunit waits for correct tRNA (initator tRNA)
• Met amino acid is attached to what anticodon?
– Now large subunit binds to complex containing small subunit; initiation
factors; mRNA; initiator tRNA
2. Elongation – tRNAs, carrying the correct amino acid, enter the ribosome, one
at a time, as the mRNA code is read after 2 tRNAs are attached to ribosome
peptidyl transferase catalyzes formation of peptide bond between 2 amino
acids translocation phase: ribosome shifts so tRNA and protein move into P
site
3. Termination – ribosome encounters the stop codon
– Releasing factor proteins interact stop codon to terminate translation
and ribosomal subunits come apart and release the mRNA with newly
formed protein released into the cell

Met Phe
Figure 13. Stage of Protein

Synthesis (a) Each ribosome
contains a large and a small subunit.
Shown here is a ribosome attached
to mRNA; abbreviated steps of
translation are shorn in steps 1 to 4.
(b) Diagrammatic example of the
tRNA symbol used in this text. At
one end of each tRNA is an amino
acid binding site and at the opposite
end is a three-nucleotide anticodon
sequence.
• Basics of Gene Expression Control

– Gene expression refers to the production of mRNA by a cell
• All cells of an organism contain the same genome.
• If they have the same genome, then why are pancreas
cells different from lung cells?
• Not all genes will be turned on at the same time – some
will be upregulated while others will be silenced
• Will a gene coding for a protein that is involved in
concentrating be turned on while you are in this
lecture and while you are relaxing at the beach? Work
in groups to discuss the answer.


– Gene regulation is how genes can be turned
on and off in response to different signals
– There are several levels of gene regulation
– The fastest gene regulation is energetically

the most costly. Work in groups to explain
this idea.

Figure 14 Levels of gene
expression regulation. Prokaryotic
and eukaryotic cells can regulate
gene expression in a variety of
complex ways. This figure
summarizes the primary ways in
which gene expression can be
regulated in eukaryotic cells. Notice
that gene expression regulation can
occur at many different “levels,”
(highlighted in blue boxes) beginning
with how chromatin is folded or
chemically modified to controlling
degradation or turnover of protein
once it is made. Transcriptional
regulation is a commonly used control
mechanism in both prokaryotic and
eukaryotic cells.

– Transcriptional regulation – controlling the amount of
mRNA transcribed from a particular gene as a way to
turn genes on or off
– Promoter is DNA sequence located upstream from the
gene
• Certain sequences found in the promoter region
– TATA box (TATAAAA) (-30) and CAAT box (GGCCAATCT)
(-80)
• RNA polymerase cannot bind to promoter region without
presence of transcription factors – DNA binding proteins
• Enhancer DNA sequences which are located very far upstream
or downstream of a gene can bind to regulatory proteins called
activators
• How can transcription be inhibited? Work in groups to answer

this question.

– Bacteria use operons to regulate gene
expression
• Organization of bacterial genes
• Clusters of several related genes located together
and controlled by a single promoter
• Operator – region within promoter
– Can use operons to regulate gene expression
in response to their nutrient requirements
• lac operon


• Lac operon and its players:

• Laci codes for repressor protein
• 3 genes coded by lac operon: lac z codes for B Gal that breaks down
lactose into glucose and galactose; lacy codes for galacto permease
which is a membrane protein that transports lactose into the cell; lacA
codes for acteyltransferase which has a protective function
• When there is lactose, it acts as an inducer by binding to the repressor
and changing its shape so it falls off the operator and allows RNA Pol
to transcribe the 3 genes
• When there is glucose the repressor stays bound and prevents
transcription
• Why is it energetically favorable to not transcribe the 3 genes
coded by the lac operon when the bacteria is exposed to glucose
and no lactose?
• Why is it necessary to turn transcribe the 3 genes coded by the
lac operon in the presence of lactose and no glucose?
lac operon
Figure 16 The lac Operon. By controlling the lac operon, bacterial cells can regulate gene
expression in response to availability of the sugar lactose. In the absence of lactose, the lac
repressor binds to the operator, blocking its transcription. In the presence of lactose, lactose
© binds and
2013 Pearson inactivates
Education, Inc. the repressor, allowing transcription of the operon to occur.

– RNA interference – RNA mechanism of gene silencing
– Short interfering RNA (siRNA) – 22 nucleotide double
stranded non-coding RNA bind to mRNA and regulate
gene expression by "silencing" gene expression
through blocking or interfering with translation of bound
mRNA
– Micro RNA – another category of small RNA molecules
that do not code for proteins
• miRNA silence gene expression by blocking translation of
mRNA or causing degradation of mRNA
• Work in groups and describe an example of how RNA
interference can be used as a gene therapy for a particular
disease.
RNA interference Figure 17 MicroRNAs Silence Gene
Expression. Gene silencing by miRNA is a
multistep process. (1) MicroRNA genes
transcribe a primary transcript called pri-RNA
that (2) folds into a hairpin loop similar to the
folding patterns of tRNA molecules by
Drosha. (3) the enzyme Dicer cleaves pri-
mRNAs into single-stranded miRNAs that are
21 to 22 nucleotides long. (4) MicroRNAs
binds to a cluster of proteins to form a
ribonucleoprotein complex. (5) this miRNA
complex can the bind to mRNA molecules by
complementary base pairing with sequences
that are an exact match or a close match to
complementary sequences in the mRNA and
miRNA. (5a) miRNA binding then silences
gene expression by blocking translation or by
targeting the bound mRNA for degration by
enzymes in the cells.
Drosha - a Class 2 ribonuclease III enzyme that in humans is
encoded by the DROSHA (formerly RNASEN) gene.
Dicer - an enzyme that in humans is encoded by the DICER1 gene.
2.5 Mutations: Causes and Consequences
• Mutation – change in the nucleotide sequence of DNA

– Major cause of genetic diversity
– Can also be detrimental
– Can be spontaneous (due to error during DNA replication) or
induced due to environmental factors including X rays and UV
– They exert their effects on a cell by changing properties of the
protein which affects the trait
• Types of Mutations
• Work in groups to discuss examples of each type of
point mutation and how it can affect the protein
structure and function
– Point mutations
• Silent mutations
• Missense mutations
• Nonsense mutations
• Frameshift mutations
Figure 18 Types of Mutations. Mutations
can influence the genetic code of mRNA
and resulting proteins translated from a
gene. Shown here is a portion of mRNA
copied from a gene, but mutations generally
occur within DNA. Mutation in a gene can
have different effects on the protein that is
translated.

• Gene mutations can be inherited or

acquired
– Inherited mutations are those passed on to
offspring through gametes
• Can cause birth defects or inherited diseases
because the mutation is present in the genome of all
of the offspring's cells
– Acquired mutations occur in the genome of
somatic cells
• Are not passed along to offspring
• These mutations can lead abnormalities in cell
growth and ultimately become cancerous
• Mutations are a major cause of genetic

diversity
– Human genomes are approximately 99.9%
identical
• 0.1% differences in DNA between individuals, or one
base out of every thousand
– Roughly 3 million differences between different individuals
• Most have no obvious effects; other mutations
strongly influence cell functions, behavior, and
susceptibility to genetic diseases
• Most genetic variations are created by SNPs (single
nucleotide polymorphism) – are bad when they
occur in exons and change protein structure so
ultimately can change protein function
End
of
Chapter
2

Genes and Genomes

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CHAPTER 2

PowerPoint® Lecture by:

• 2.1 A Review of Cell Structure

© 2013 Pearson Education, Inc.

• All cells have these structures:

© 2013 Pearson Education, Inc.

• Comparison of Prokaryotic and

Insert table 2.1

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

• Eukaryotic cells (include plant and animal

Insert figure 2.2

© 2013 Pearson Education, Inc.

• Plasma membrane: fluid, dynamic, complex

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

• Building block of DNA = nucleotide

• What is the difference between deoxyribose and

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

• What are the rungs of the ladder?

© 2013 Pearson Education, Inc.

• What is a potential consequence of shortening of telomeres

• Based on the karyotype, which chromosome is the largest?

• A single skin cell would produce how many cells

• In order to accomplish this, the DNA of the parent cell

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

Figure 9 Semiconservative Replication of DNA

© 2013 Pearson Education, Inc.

• Transcription – genes are copied

• Through production of RNA and protein synthesis DNA controls

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

Figure 11 Transcription. During transcription, RNA

• mRNA is not the only type of RNA that gets

• Name 2 other types of RNA that are produced

• Do these 2 types of RNA carry information that

• New class of non-protein coding RNA: microRNA

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc.

• Components of translation – in cytoplasm

© 2013 Pearson Education, Inc.

• How is mRNA read?

© 2013 Pearson Education, Inc.

• Ribosomes and tRNA molecules

© 2013 Pearson Education, Inc.

Figure 13. Stage of Protein

• Basics of Gene Expression Control

© 2013 Pearson Education, Inc.

• Basics of Gene Expression Control

– The fastest gene regulation is energetically

© 2013 Pearson Education, Inc.

• Basics of Gene Expression Control