Cell Biology

4. DNA, Chromosomes, and Genomes

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Cell Biology
4. DNA, Chromosomes, and Genomes

CONCEPT: DNA DISCOVERY

● It took many years for DNA to be discovered as the source of genetic information
□ Protein, not DNA, was first thought to be the _____________________ molecule for genetic information (1900s)

- Proteins have 20 amino acids = more combinations, DNA only had 4 bases

□ Oswald Avery showed that DNA was the genetic material of bacteria (1940s)

- Injected mice with two bacteria (a noninfectious, and dead infectious type) – but mice became infected

- Showed that nucleic acids were the reason for the conferred infectivity

□ Hershey/Chase showed that DNA was the genetic material of viruses (1950s)

- Used radioactively labeled bacteriophages (viruses that infect bacteria)

- Differentially labeled protein and DNA and followed which was transferred to bacteria - it was the DNA

□ James Watson and Francis Crick discovered the ___________________________________ (1953)

- Provided an explanation for how genetic information is stored, replicated, and inherited

EXAMPLE: Model of the Avery experiment

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PRACTICE:

1. Which of the following was not a crucial experiment that led to the knowledge that DNA was the source of genetic
information?
a. Oswald Avery’s experiments with bacteria and mice
b. Watson and Cricks discovery of the DNA double helix
c. The Hershey/Chase experiments with bacteriophages
d. Barbara McClintock’s experiments with maize (corn)

2. Which of the following scientists discovered that DNA was the genetic material in viruses?
a. Oswald Avery
b. Hershey/Chase
c. James Watson
d. Francis Crick

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3. Which molecule did scientists believe was the source of genetic material first (before DNA)?
a. Protein
b. RNA
c. DNA

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CONCEPT: STRUCTURE AND FUNCTION OF DNA

● Nucleotides are the ______________________________________________________ of DNA

□ There are four nucleotides of DNA: adenine (A), cytosine (C), guanine (G), and thymine (T)

- The pyrimidines (C/T) have one carbon ring

- The purines (A/G) have two carbon rings

□ Chargoff’s rules state that A pairs with T and C pairs with G

- A base pair is the pairing of two nucleotides (A-T or C-G)

- They pair through two (A-T) or three (G-C) hydrogen bonds

- Due to size, a purine can only pair with a pyrimidine

EXAMPLE:

□ The backbone of DNA is created via __________ between sugar and phosphate groups on adjacent nucleotides

- The 5’ phosphate group binds to the 3’ hydroxyl group on the neighboring nucleotide

- This bond gives directionality to the linear DNA strand

□ The string of nucleotides is polar, due to the charged phosphate groups and the hydroxyl groups on the sugar

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EXAMPLE: Linear structure of DNA

● DNA is formed into a double helix

□ A DNA double helix is created via bonds between two linear DNA strands

- Sugar-phosphate backbone forms the outside edges, with the bases facing the ____________________

- There are 10 base pairs per helical turn

- One helical turn adds 3.4nm to length of DNA (0.34nm per nucleotide pair)

□ Two complementary strands run antiparallel to make up the DNA helix

□ The helix forms a major groove and minor groove

EXAMPLE: Structure of the DNA double helix

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□ There are three types of DNA double helices

- B-DNA: is the most common, right handed helix

- A-DNA: is a rare, shorter right handed helix

- Z-DNA: is a left handed helix, with unknown significance

EXAMPLE: Structure of A, B, and Z DNA

PRACTICE:
1. Chargoff’s rules state that…
a. A purine always pairs with a purine
b. A pairs with C and T pairs with G
c. A pairs with T and C pairs with G

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2. True or False: The two complementary DNA strands that make up the double helix run parallel to each other.
a. True
b. False

3. Which of the following is not a purine nucleotide?

a. Adenine
b. Thymine
c. Guanine

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CONCEPT: HELICAL FORMATIONS OF DNA

● Supercoiling is a ________________________________ of helical DNA

□ Supercoiled DNA is DNA that has twisted upon itself

- Can alternate between supercoiled and relaxed states

- Occurs in linear or circular DNA

□ Topoisomerases are enzymes that convert DNA between supercoiled and relaxed states

- Type 1: introduces single-strand breaks into DNA to release tension

- Type 2: introduces double-strand breaks into DNA to release tension

EXAMPLE: Example of a circular supercoiled DNA molecule

● Denaturing (separating) and renaturing (rejoining) strands of DNA happens in cells, and in laboratories
□ Denaturing of DNA strands occurs by __________________________________ hydrogen bonds

- Can occur through an increase in heat, change in pH, and exposure to UV light

□ The DNA melting temperature (Tm) is a specific temperature that separates DNA strands

- Depends on the number of hydrogen bonds

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- G-C pairs have an extra bond, therefore raising the energy and temperature needed to break them

EXAMPLE: Denaturation of the DNA double helix

PRACTICE

1. Which of the following property is false regarding supercoiled DNA?

a. Supercoiling is a helix that has twisted upon itself
b. Supercoiling can be fixed by topoisomerases
c. Supercoiling only happens in circular DNA
d. Supercoiling can happen in both circular and linear DNA

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2. Which enzyme is responsible for repairing supercoiling through double strand breaks?
a. Topoisomerase Type 1
b. Topoisomerase Type 2
c. Topoisomerase Type 3

3. What is the name of the temperature that causes two complementary DNA strands to separate?
a. Annealing Temperature
b. Melting Temperature
c. Dissolving Temperature
d. Separation Temperature

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CONCEPT: DNA VS. RNA

● RNA _____________________ from DNA in many crucial ways

□ RNA contains the base Uracil (U) in place of Thymine (T)

□ RNAs are more commonly found as single-stranded polymers compared to double stranded polymers

□ RNAs have the ability for form complex 3D structures – whereas DNA forms only a double helix

- Hairpins: small 5-10 pairing of bases with each other

- Stem loops: base pairing of >10 nucleotides that contains an unpaired loop

□ RNAs can have catalytic activities (Ribozymes) and DNAs cannot

EXAMPLE: A 3D RNA structure

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PRACTICE:

1. Which of the following is not a property of RNA?

a. Contains the base Uracil instead of Thymine
b. RNA can form 3D structures with complex functions
c. RNA is commonly found as a double helix
d. RNA can act as enzymes

2. Which of the following differences between RNA and DNA is not true?
a. RNA has Uracil, DNA has Thymine
b. RNA is single stranded, DNA is double stranded
c. RNA can act as an enzyme, DNA cannot act as an enzyme
d. RNA contains the base cytosine, DNA contains the base Uracil

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CONCEPT: DNA PACKAGE

● Packaging of DNA is necessary in order to _____________________ within the confines of a cell

□ Average human cell contains 2 meters of DNA

- Cell nucleus is only 5-8 µm in diameter

□ There are four packaging levels of DNA: nucleosome (2), 30nm-fiber (3), looping (4), chromosomes (5)

EXAMPLE: Four packaging levels of DNA

Nucleosome:

● The nucleosome consists of DNA and histone proteins

□ Discovered by Dean Hewish and Leigh Burgonye

- Used nucleases that chopped DNA bound to protein – Found it cut only in 200 base-pair fragments

□ Histone proteins are a major class of proteins __________________________ to DNA to form the nucleosome

- There are five classes of histone proteins: H1, H2A, H2B, H3, H4

- Classified by the ratio of lysine:arginine amino acids present on the protein

□ Eight histone proteins compose a positively charged core around which the negatively charged DNA winds

- two H2A:H2B pairs (dimers) and two H3:H4 pairs

- The H1 histone acts as a linker histone connecting each core together (chromatosome)

□ Nucleosomes are about 10nm long

- 147 bp DNA wrapped 1.67 times around the histone core

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EXAMPLE: Nucleosome structure of DNA

Chromatin Fiber:

● Nucleosomes are packaged into a 30nm chromatin fiber through the H1 protein
□ The H1 histone protein connects _________________ nucleosomes and is required for the 30nm fiber formation

□ Nucleosomes are packaged in zig-zags and wound into a double helix

DNA Looping:

● The 30nm fiber is then packaged into a looping structure that consists of thicker fibers
□ Each loop contains 50,000-100,000 base pairs

□ Maintained by non-histone proteins that form and attach DNA to a scaffold

EXAMPLE: Structure of the 30nm fiber and higher-order looping

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Chromosomes:
● Finally, the chromatin is packed into chromosomes, which contain long strings of genes
□ Chromosomes exist in ____________________ distinct states

- Interphase chromosomes: Less condensed long threads of DNA; Occupy particular nuclear regions

- Metaphase chromosomes: More condensed; Can be seen during cell division

□ Chromosomes contain structural characteristics

- Centromere: specialized DNA sequence that holds sister chromatids of a chromosome together

- consists of large sequences of repetitive DNA

- Kinetochore: protein structure assembled on the centromere where the spindle fibers attach during cell division

- Telomere: sequence of repetitive DNA at the end of a chromosome that protects the chromosome from
degradation

EXAMPLE: Structure of a metaphase chromosome

□ A karyotype is an ordered ___________________________ of the full set of an organism’s chromosomes

- In humans, chromosomes exist in homologous pairs (exception = the “Y” sex chromosomes)

EXAMPLE: A karyotype of the 23 human chromosomes

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Conservation of DNA Packaging

● Packaging of DNA is highly ____________________________

□ Histone proteins are extremely well conserved

- H3 sequence of sea urchin and calf thymus differs by 1 amino acid

□ Histone variants do exist, but usually have a distinct function

- Centromeric H3 (CenH3) exists only at centromeres for the assembly of kinetochore proteins

EXAMPLE: Histone H1 conservation

Unusual Chromosomal Structures

● Certain organisms contain ___________________________ chromosomal structures

□ Polytene chromosomes are found in Drosophilia (fruit flies)

- Form by linking chromosomes together, instead of separating them during division

- Has characteristic banding, which is created through differential condensation of DNA

□ Lampbrush chromosomes are found in many animal’s oocytes (ovarian cells), but not mammals

- Are the largest chromosomes known – visible in light microscope

EXAMPLE: Polytene chromosomes

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PRACTICE:

1. Which of the following histone proteins do not form dimers that make up the nucleosome core?
a. H2A
b. H2B
c. H3
d. H4
e. H1

2. How many histone proteins are found within the nucleosome core?
a. 2
b. 4
c. 8
d. 9

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3. True or False: Interphase chromosomes are more condensed than other forms of chromosomes?
a. True
b. False

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CONCEPT: THE EPIGENETIC CODE

Chromatin Structure

● Chromatin exists in two states: Euchromatin and Heterochromatin

□ Euchromatin is a less ______________________ DNA structure

- Allows for the packaged DNA to be accessible to other proteins

□ Heterochromatin is a more condensed DNA structure

- Genes present in heterochromatin areas are not expressed, therefore it contains few genes

- Found mainly in centromeres and telomeres

□ The zone of inactivation describes restriction of gene expression of genes placed near heterochromatin

- Due to position effects, the activity of a gene depends on relative location to heterochromatin

EXAMPLE: Structure of euchromatin and heterochromatin

Histone Protein Modifications

● Histone proteins control the packaging and condensation of the DNA

□ Each histone protein contains an N-terminal ______________________

- Amino acids on this tail can be covalently modified to effect condensation of the DNA

□ Acetylation (C2H3O) and Methylation (CH3) are the two most common modifications

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- Acetylation removes the ___________________ charge from the histone and loosens chromatin structure

- Methylation tightens chromatin structure and prevents acetylation

□ Occasionally a chain reaction can initiation a long linear chain of similar histone modifications

- Eventually stopped by barrier sequences which separate condensed and noncondensed chromatin

EXAMPLE: Histone modifications in a nucleosome core

Reading the Epigenetic Code

● Reading the epigenetic code (histone modification code) is an extremely difficult process
□ Each nucleosome has a different ___________________________ of modification, which is carefully controlled
- Once modified, they can attract other proteins

- These modifications are constantly changing to adapt to the cells needs

□ Chromatin remodeling complexes use ATP energy to change the position of DNA on a nucleosome

- Allow for specific sequences to become more or less condensed

EXAMPLE: Histone remolding allows for gene access

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● Epigenetic inheritance is the process of inheriting chromatin structure

□ Histone modifications are passed to daughter cells

- Amino acids on this tail can be covalently modified to effect condensation of the DNA

□ This inheritance allows for cell memory which is ___________________________________ inheritance

PRACTICE:
1. Which of the following terms is associated with condensed chromatin?
a. Acetylation
b. Euchromatin
c. Heterochromatin
d. Cell memory

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2. Which of the following histone tail modifications is most likely to cause closed chromatin?
a. Acetylation
b. Methylation
c. Phosphorylation
d. Ubiquitination

3. True or False: The position of nucleosomes on a region of DNA can never change.
a. True
b. False

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4. True or False: Histone protein modifications can be inherited.

a. True
b. False

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CONCEPT: GENOME EVOLUTION

Mutations in Evolution

● Accumulations in mutations (DNA changes) promote genome ______________________________________

□ Point mutations are changes in a single nucleotide pair

- Can be beneficial or detrimental to the organisms

- Arise from errors in DNA replication

□ Mutations can occur in the gene, or in regulatory DNA

- Gene: effects activity, interaction, stability and is easy to spot

- Regulatory DNA: effects how genes are expressed and are not so easy to find

EXAMPLE: Point mutations can affect amino acid sequence

Gene Duplication in Evolution

● Gene duplication is a main driver of genomic evolution

□ Gene families are groups of genes with similar sequences but ________________________________ functions

- Once a gene is duplicated, each copy is free to accumulate mutations that result in different functions

- Gene families are the result of gene duplication

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EXAMPLE: Structure of hemoglobin demonstrates gene families

□ Gene duplication arises from ________________________ crossing over during mitosis

- Misalignment of chromosomes during homologous recombination can lead to lopsided genetic exchange

- Result: one chromosome with extra gene copy and one with no copy

□ Pseudogenes are duplicated genes that have lost their functional ability but remain in the genome

- Processed pseudogenes occur by changing a mRNA to a DNA and integrating it into a chromosome

□ Whole genome duplication is when the entire genome of an organisms is copied and retained in a single cell

- Polyploidization (whole genome duplications) are common in fungi and plants

EXAMPLE: Unequal crossing over results in duplicated genes

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Introns and Splicing in Evolution

● The presence of introns allows for gene shuffling and gene evolution
□ Genes of most organisms contain Introns and Exons (not completely universal ex: Histone proteins)

- Introns are noncoding regions of a gene that are cut out during gene processing

- Exons are the coding regions of a gene

□ Alternative splicing is the combining of exons from one gene in new orders (occurs in 50-90% of human genes)

- Produce isoforms which are different forms of the same protein produced through alternative splicing

□ Exon shuffling is the combining of exons from two ________________________________ genes

- Can also occur if exons are duplicated or moved to different genomic location

EXAMPLE: Model of alternative splicing

Alternative
Splicing

Repetitive DNA sequences in Evolution

● Repetitive DNA sequences are have evolved in the genomes and are extremely common
□ Simple-sequence repeats are arrays of thousands of copies of a short sequence (1-500 nucleotide)

- Drosophila: ACAAACT

- Not transcribed, and contain no genetic information

□ Mobile genetic elements are DNA sequences that can ___________________________ through the genome

- Contain repetitive DNA flanking protein coding regions

- Transposons are mobile genetic elements and can move through RNA or DNA intermediates

- Insert anywhere in a gene, and can effect gene structure or regulation

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EXAMPLE: Example of sequence repeats in the genetic code

PRACTICE:

1. Which of the following is not a driver of genome evolution?

a. Mutations
b. Gene duplication
c. Alternative Splicing
d. Histone modifications

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2. Which of the following genomic changes are most likely to cause pseudogenes?
a. Point Mutations
b. Gene Duplications
c. Exon Shuffling
d. Transposons

3. Protein isoforms are created through which process?

a. Point Mutations
b. Alternative Splicing
c. Exon Shuffling
d. Simple Sequence Repeats

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CONCEPT: GENOMIC COMPARISON

● Comparing genomic sequences provide insight into evolutionary changes

□ Genome sequences of two species differ by the ____________________________ they have separately evolved

- Purifying selection eliminates individuals carrying mutations effecting genes with important functions

- Conserved sequences are common between organisms, and therefore are critical for a function (5%)

- Synteny describes stretches of genes whose chromosomal order is conserved

□ Genomic size reflects ______________________________ of DNA addition or loss

- Doesn’t provide information on the number of genes, or organism complexity

- Genomic size depends on balancing the rates of DNA addition and loss

□ Phylogenetic trees are constructed using DNA sequences to trace relationships between organisms

- Rapid changes occur in introns, slower changes occur in conserved genes with critical functions

EXAMPLE: Comparing the genome size of various organisms

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PRACTICE:

1. True or False: The larger the genomic DNA sequence is, the more complex the organism is.
a. True
b. False

2. Stretches of chromosomes where the gene order is conserved among different species is called what?
a. Conserved Sequences
b. Synteny
c. Purifying Selection
d. Conserved Selection

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CONCEPT: HUMAN GENETIC VARIATION

● Sequencing of the human genome revealed knowledge about its structure, size, and composition
□ The human genome contains 3.2 x 109 nucleotide pairs organized in 23 sets of chromosomes

- Less than 2% encode for proteins

□ __________________________________________ of the human genome is:

- 20,000-25,000 protein coding genes (1.2% of genome)

- 50% of mobile genetic elements or “jumping genes”

- 9,000 functional RNAs

□ 5% of the human genome is highly conserved in other organisms

EXAMPLE: Human genome composition

Human Genome Composition

SINE

LINE
8% 13%
3%
3% Protein-coding genes
5% Introns

8% 20% Unique Sequences

Heterochromatin

12% 2%
Duplications

Simple Sequence Repeats

26% DNA transposons

LTR Retrotransposons

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● Comparison of the genomic sequence between humans and other organisms demonstrates similarities and differences
□ Prokaryotes were first sequenced in 1995

- 90% of genome is protein coding

□ Yeast were first sequenced in 1996

- 70% of genome is protein coding

□ C. elegans (worms) were first sequenced in 1998

- 25% of genome is protein coding

□ Drosophila melanogaster (fruit flies) was first sequenced in 2000

- 13% of genome is protein coding

□ Arabidopsis (flowering plant) were first sequenced in 2000

- 25% of genome is protein coding

□ Size of genome does not dictate complexity

EXAMPLE: Genomic comparisons of organisms

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Human Evolution
● Chimpanzees and humans ________________________ from a common ancestor
□ 98% similarity between the human and chimpanzee genomes

□ Human accelerated regions are conserved areas of genome where rapid evolution occurred in humans

- There are around 50 sites within the human genome

- 25% support changes near genes that control brain development

EXAMPLE: Comparison between human and chimpanzee chromosomes

● Human _________________________________ exists between individuals

□ 1 in 1,000 nucleotides differs between one individual person and another

- 3 million genetic differences

□ Single nucleotide polymorphisms (SNPs) are differences in the genome of one population and another

- Two randomly chosen people differ by 2.5 x 106 SNPs

□ Copy-number variation describes differing number of gene copies in one individual and another

□ CA repeats are strings of repeating C,A nucleotides and are very prone to mutations

- DNA fingerprinting uses these to identify specific individuals

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EXAMPLE: Model of genetic variation in different human populations

PRACTICE

1. Which of the following is true regarding genomic genetic variations?

a. Genomic size is proportional to genomic complexity
b. Mobile genetic elements make up a very small proportion of the human genome
c. Sequence variations between one individual and another occurs once every 1000 nucleotides
d. CA repeats are extremely stable genetic elements found in the human genome

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2. True or False: The majority of the human genome encodes for proteins.
a. True
b. False

3. Which of the following genomic variation refers to different number of gene copies between individuals and
populations?
a. Single nucleotide polymorphisms
b. Copy number variants
c. CA Repeats
d. Transposons

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CONCEPT: TRANSPOSONS AND VIRUSES

● Mobile genetic elements (jumping genes) are small DNA segments that are found in nearly every cells
□ ________________________ themselves into any DNA sequence, but are unable to leave the cell

- Make up about 50% of the human genome

- No function other than the exist (called the “selfish genes”)

- Insert themselves anywhere in the genome

□ Barbara McClintock discovered them in the 1940s while studying corn

□ DNA transposons and Retrotransposons (RNA based) are the two major families of mobile genetic elements

□ Viral genomes, especially retroviral genomes, also insert into genome in similar ways as mobile genetic elements

EXAMPLE: Movement of mobile genetic elements

Transposon Gene

Gene Transposon Gene

DNA transposons

● DNA transposons are mobile genetic elements that move through a ________________________ intermediate
□ Most commonly found in bacteria

- Eukaryotic DNA transposons have lost their ability to move (3% of human genome)

□ Move in the genome by the “cut and paste” method; They are “cut” from one region and “pasted” into another

- If cut during DNA replication then the transposon can duplicate

□ Structure contains inverted repeats of ~50 base pairs flanking a DNA sequence that codes for a transpose

- Transposase is the enzyme responsible for _______________ the transposon out of the DNA sequence

- Doesn’t lose length when inserting

- Double strand break repair “pastes” the transposons into a different genomic location

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EXAMPLE: Structure of a DNA transposon

DNA Transposon

Repeats Repeats

Protein Coding Regions

Retrotransposons

● Retrotransposons are mobile genetic elements that move through an ________________________ intermediate
□ They are transcribed into RNA before being processed changed back into DNA for insertion

- Reverse transcriptase is the process of changing (reverse transcribing) RNA back into DNA

EXAMPLE: Integration of a retrotransposon into the genome

□ The Long Terminal Repeat (LTR) retrotransposons are one class of retrotransposons (8% of human genome)

- Structure consists of direct repeats (250-600 base pairs) that flank a protein coding region

□ Non-LTR retrotransposons are a second class of retrotransposons

- LINES (Long Interspersed Elements) are _______________ commonly found in mammals (6kbp long)

- L1, L2, and L3 are the three classes – Only L1 still transposes

- 21% of human genome

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- Structure consists of short direct repeats flanked by two long protein coding regions

- SINES (Short Interspersed Elements) are commonly found in mammals (300 bp long)

- Most common is Alu element, which still transposes in human genome

- 13% of human genome (10% of SINES are Alu sites in humans)

- Most lack protein coding region, and depend on other mobile elements to provide proteins

EXAMPLE: Structure of LINEs

Viruses as Mobile Genetic Elements

● Viruses are mobile entities that can ________________________ their genome into a host cells genome
□ Contain a protein coat surrounding a small amount of genetic information (few – 100s of genes)

- Can be DNA or RNA based

- Disease causing agents

□ Bacteriophages are viruses that infect bacteria and insert their genome into the host bacterium

□ Retroviruses store their genetic information as RNA and use it as a ___________________ to produce DNA

- Reverse transcriptase is typically encoded in the viral genome

EXAMPLE: Structure of a retrovirus

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□ Viral genome is generally _____________________________ into the host genome

- Integrase is the enzyme responsible for integrating the viral DNA into the host genome

- Does lose length when inserting

- Double strand break repair “pastes” the transposons into a different genomic location

EXAMPLE: Genomic integration of the HIV genome into a host cell DNA

Mobile Genetic Elements in Evolution

● Mobile genetic elements play a major role in _____________________________

□ Mobile genetic elements cause mutations with their jumps

- Bacteria: every 105 cell division

- Can confer antibiotic resistance

- Drosophila: 50% of spontaneous mutations

- Mice: has caused about 10% of total mouse mutations

- Humans: 1 in 1000 mutations (0.1%-0.2% of all mutations)

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- Can cause disease- Hemophilia

□ Occasionally they can carry additional portions of the genome with them when they move

□ Some important proteins were thought to have evolved from transposable element sequences

- Transcription factors bind to DNA and control gene expression

- Telomerase is thought to have evolved from a reverse transcriptase encoded by an ancient transposon

□ They can effect expression of genes and proteins

□ They can be inherited

PRACTICE:
1. Which of the following is not considered a mobile genetic element?
a. DNA transposons
b. SINEs
c. Transposase
d. Retrotransposons

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2. Which of the following transposons still jumps in the human genome?

a. L1 LINE
b. L2 LINE
c. L3 LINE

3. What is the name of the enzyme responsible for allowing the transposon to jump within the genome?
a. Reverse Transcriptase
b. Transposase
c. Transposonase
d. Integrase

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4. True or False: Some transposons encode for a protein.

a. True
b. False

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