Week 3 Textbook Reading

Question 1

homologous genes

Answer 1

When genes from different organisms have similar nucleotide sequences, it is highly likely that they descended from a common ancestral gene
-Such genes and are said to be homologous

Question 2

Mutation within a gene:

Answer 2

An existing gene can be modified by a mutation that changes, deletes or duplicates one or more nucleotides

These mutations can alter the splicing of a gene’s RNA transcript or change the stability, activity, location or interactions of its encoded protein

Question 3

Mutation within regulatory DNA sequences:

Answer 3

When and where a gene is expressed can be affected by a mutation in the stretches of DNA sequence that control transcription of the gene

Question 4

Gene duplication and divergence:

Answer 4

A cell can make an extra copy of an existing gene, or even its whole genome

As this cell and its progeny continue to divide, the original DNA sequence and the duplicate sequence can acquire different mutations and assume new patterns of expressions

Question 5

exon shuffling

Answer 5

Two or more existing genes can be broken and rejoined to make a hybrid gene containing DNA segments that originally belonged to separate genes

-In eukaryotes, such breaking and rejoining often occurs within the long intron sequences, which do not encode protein
-Because these intron sequences are removed by RNA splicing, the breaking and joining do not have to be precise to produce a functional gene

Question 6

transposition of mobile genetic elements

Answer 6

Specialized DNA sequences that can move from one chromosomal location to another can alter the activity or regulation of a gene

They can also promote gene duplication, exon shuffling and other genome rearrangements

Question 7

horizontal gene transfer

Answer 7

A piece of DNA can be passed from the genome of one cell to that of another

Differs from the usual “vertical” transfer of genetic info from parent to progeny

Question 8

sequence conservation

Answer 8

Sequence conservation allows us to trace even the most distant evolutionary relationships
-By comparing sequences of genes in different organisms and seeing how far they have diverged, we can attempt to construct a phylogenetic tree that goes all the way back to the ultimate ancestors

-To construct such a tree, biologists have focused on one particular gene that is conserved in all living species
–The gene that code for the ribosomal RNA of the small ribosomal unit

-The more similar the rRNA sequences, the more recently the 2 species diverged from a common ancestor and the more closely related they must be

Question 9

transposons

Answer 9

More of our genetic real estate is occupied by mobile genetic elements: almost half of our DNA is made up of transposons that have colonized our genome over evolutionary time
Because these elements have accumulated mutations, most can no longer move; rather, they are relics from an early evolutionary era when mobile genetic elements ran rampant through our genome

Question 10

Most of our DNA is in …

Answer 10

non coding introns

Question 11

in situ hybridization

Answer 11

In situ hybridization reveals when and where a gene is expressed

Although RNA sequence can provide a list of gene that are being expressed by a particular tissue at a certain time, it does NOT reveal exactly where in a tissue or organism those RNAs are produced

To do that, investigators use in situ hybridization which allows a specific nucleic acid sequence (RNA or DNA) to be visualized in its normal location

In situ hybridization makes use of single-strand DNA or RNA probes, labelled with either fluorescent dyes or radioactive isotopes, to detect complementary nucleic acid sequences within a cell, tissue or organism

Helped to explore how transcription regulators guide the development of multicellular organisms, providing important clues about when and where these genes carry out their functions
Can detect specific DNA sequences on isolated chromosomes

Question 12

chromosomes

Answer 12

Chromosomes are packages of very long, double-stranded DNA molecules in Eukaryotic cells
After duplication, they can be accurately portioned between the 2 daughter cells at each cell division
The complex task of packaging DNA is accomplished by specialized proteins that bind to and fold the DNA, generating a series of loops and coils that provide increasingly higher levels of organization and prevent the DNA from becoming a tangled, unmanageable mess
Packaged in a way that allows it to remain accessible to all of the enzymes and other proteins that replicate and repair it, and that causes the expression of its genes

Question 13

chromatin

Answer 13

Each chromosome consists of a single, long, linear DNA molecule associated with proteins that fold and pack the fine thread of DNA into a more compact structure called chromatin

Question 14

homologous chromosomes

Answer 14

With the exception of gametes, and highly specialized cells that lack DNA entirely, human cells each contain 2 copies of every chromosome

The maternal and paternal versions of each chromosome are called homologous chromosomes

Question 15

karyotype

Answer 15

An ordered display of the full set of an organism’s chromosomes present in humans is called a karyotype
If parts of a chromosome are lost, or moved from one chromosome to another, the changes are easy to see in a karyotype
Used to detect chromosomal abnormalities that are associated with some inherited disorders

Question 16

gene

Answer 16

Chromosomes organize and carry genetic info
A gene can be defined as a segment of DNA that contains the instructions for making a particular protein or RNA molecule
The more complex an organism, the larger its genome

Question 17

To form a functional chromosome, a DNA molecule must do more than carry genes:

Answer 17

it has to be able to be replicated, and the replicated copies must be separated and split equally into 2 daughter cells
These processes occur through an ordered series of events, known as the cell cycle
Interphase is when chromosomes are duplicated and mitosis is when duplicated chromosomes are distributed or segregated to the 2 daughter nuclei

Question 18

replication origin

Answer 18

One type of nucleotide sequence called a replication origin, is the site where DNA replication begins

Question 19

telomere

Answer 19

Another DNA sequence forms the telomeres that mark the ends of each chromosome

Telomeres contain repeated nucleotide sequences that are required for the ends of chromosomes to be fully replicated

Also serve as a protective cap that keeps the chromosome tips from being mistaken by the cell as broken DNA in need of repair

Question 20

centromere

Answer 20

Also contain a 3rd type of specialized DNA sequence, called the centromere, that allows duplicated chromosomes to be separated during M phase

During this stage, DNA coils up, adopting a more compact structure, forming mitotic chromosomes

Question 21

nuclear envelope vs nuclear lamina

Answer 21

Some chromosomal regions are physically attached to particular sites on the nuclear envelope (the pair of concentric membranes that surround the nucleus) or the nuclear lamina (the protein meshwork that supports the envelope

Question 22

nucleolus

Answer 22

The most easy organization in the interphase nucleus is the nucleolus → a large structure within the nucleus where ribosomal RNA is transcribed and ribosomal subunits are assembled

Question 23

The proteins that bind to DNA to form eukaryotic chromosomes are divided into 2 general classes:

Answer 23

histones and non-histone chromosomal proteins

Question 24

chromatin

Answer 24

The complex formed by histone and non-histone chromosomal proteins and nuclear DNA is called chromatin

Question 25

Histones are responsible for the first and most important level of chromatin packing:

Answer 25

the formation of the nucleosome
Nucleosomes convert the DNA molecules in an interphase nucleus into a chromatin fiber

Question 26

nucleases

Answer 26

To determine the structure of the nucleosome core particle, investigators treated chromatin in its unfolded form with enzymes called nucleases, which cut the DNA by breaking the phosphodiester bonds between nucleotides

Question 27

histone octamer

Answer 27

An individual nucleosome core particle consists of a complex of 8 histone proteins along with a segment of double-stranded DNA that winds around a histone octamer

Question 28

structure of the octamer

Answer 28

All 4 of the histones that make up the octamer are small proteins with a high proportion of positively charged AA
-Positive charges help the histones bind tightly to the negatively charged sugar-phosphate backbone of DNA

Each of the histones in the octamer have a long, unstructured N-terminal amino acid “tail” that extends out from the nucleosome core particle
-Histone tails control many parts of chromatin structure

The additional packing of nucleosomes into a chromatin fiber can be aided by a 5th histone called histone H1
-This ‘linker’ histone changes the path the DNA takes as it exits the nucleosome core
–The binding of histone H1 helps to pull adjacent nucleosomes together, producing a more condensed chromatin fiber

Question 29

smc and interphase chromosomes

Answer 29

The extrusion of these loops is made possible by a family of protein that form large rings through which a chromatin fiber can pass

At the heart of this complex is a pair of proteins- the SMC (Structural Maintenance of Chromosome) proteins- that forms the actual ring

These associate with additional proteins to form an SMC ring complex that uses the energy of ATP hydrolysis to motor along the DNA, pushing out a loop of DNA

Question 30

cohesin

Answer 30

The SMC ring complex that organizes the structure of interphase chromosomes is called cohesin

Multiple cohesins load onto each interphase chromosome, where they produce an extended series of loops

Cohesin rings will travel along the DNA, extruding loops until they run up against a special sequence-specific clamp protein

It’s the spacing and location of the clamp proteins that dictates the size and contents of each chromosomal loop

The resulting structures help to regulate the expression of genes

Question 31

condesin

Answer 31

Condesin is a ring-shaped SMC protein complex that compacts duplicated chromosomes for segregation by forming both loops and loops within loops
As cells prepare to divide, condensins replace most of the cohesins that formed the loops in the interphase chromosome
These condensins then use the energy of ATP hydrolysis to form loops of their own which wind the chromatin into a tighter mass of coils
It is this final level of condensation that’s thought to produce the familiar structure of the mitotic chromosome

Question 32

chromatin-remodeling complexes

Answer 32

Changes in nucleosomes allow access to DNA
Eukaryotic cells have many ways to adjust the local structure of their chromatin quickly and selectively
One mechanism takes advantage of a set of ATP-dependent chromatin-remodeling complexes
Use the energy of ATP hydrolysis to change the positions of nucleosomes in eukaryotic chromosomes, changing the accessibility of the DNA to other proteins

Question 33

during mitosis, why are chromatin-remodeling complexes inactivated?

Answer 33

During mitosis, many of these complexes are inactivated, which may help mitotic chromosomes maintain their tightly packed structure

Question 34

histone-modifying enzymes

Answer 34

Another way of altering chromatin structure relies on the reversible chemical modification of histones catalyzed by a histone-modifying enzymes

-The tails of all 4 of the core histones are subject to these covalent modifications, which include the addition (and removal) of acetyl, phosphate or methyl groups

-Both enzymes are tightly regulated

Question 35

regions of chromosomes with actively expressed genes vs silent genes

Answer 35

Interphase chromosomes contain both highly condensed and more extended forms of chromatin

Regions of the chromosome containing genes that are being actively expressed are generally more extended, whereas those that contain silent genes are more condensed

Question 36

heterochromatin

Answer 36

The most highly condensed form of interphase chromatin is called heterochromatin

About half of it remains permanently condensed in the regions around the centromere and the telomeres that cap chromosome ends

Question 37

euchromatin

Answer 37

Euchromatin is the other main state in which chromatin exists within an interphase cell

Its less compact structure allows access for proteins involved in transcription

Question 38

DNA replication

Answer 38

DNA replication and repair
-DNA replication must occur before a cell can divide to produce 2 genetically identical daughter cells

-Despite the molecular safeguards that have evolved to protect a cell’s DNA from copying errors and accidental damage, permanent changes or mutations-sometimes do occur
–Sometimes beneficial, mutations can make bacteria resistant to antibiotics that are used to kill them
–Changes in DNA sequence can produce small variations that underlie the differences between individuals of the same species

DNA replication
At each cell division, a cell must copy its genome with a high degree of accuracy

Question 39

how does base-pairing enable DNA replication?

Answer 39

Each strand can serve as a template, or mold for the synthesis of a new complementary strand

Each separated strand serves as a template for the production of a new complementary partner strand that’s identical to its former partner

This ability enables a cell to copy or replicate its genes before passing them on to its descendants

DNA replication produces 2 complete double helices from the original DNA molecule, with each new DNA helix being identical in nucleotide sequence (except for errors) to the original DNA double helix

Question 40

semiconservative replication

Answer 40

Because each parent strand serves as the template for one new strand, each of the daughter DNA double helices ends up with one of the original (old) strands plus one strand that’s completely new; this style of replication called semiconservative

Question 41

DNA synthesis begins at replication origins

Answer 41

To be used as a template, the double helix must first be opened up and the 2 strands separated to expose the nucleotide bases
The process of DNA synthesis is begun by initiator proteins that bind to specific DNA sequences called replication origins
Here, the initiator proteins pry the 2 DNA strands apart, breaking the hydrogen bonds between the bases
Although the hydrogen bonds together make the DNA helix very stable, individually each hydrogen bond is weak
Can be easily unzipped at low temps

Question 42

what happens after an initiator protein bind to DNA at a replication origin…

Answer 42

it locally opens up the double helix, it attracts a group of proteins that carry out DNA replication

These proteins form a replication machine, in which each protein carries out a specific function

Each time a cell copies its genome, it is critical that DNA synthesis be initiated once at every replication origin

Failure to properly regulate this process could cause genes to be copied too many times or even lost

Question 43

replication forks

Answer 43

2 replication forks form at each replication origin
DNA molecules in the process of being replicated contain Y-shaped junctions called replication forks
2 replication forks are formed at each replication origin
At each fork, a replication machine moves along the DNA, opening up the double helix in front of it and using each strand as a template to make a new daughter strand

Question 44

how do we know DNA is bidirectional

Answer 44

The 2 forks move away from the origin in OPPOSITE directions, unzipping the DNA double helix and copying the DNA

Question 45

DNA polymerase

Answer 45

DNA polymerase synthesizes DNA using a parent strand as a template
The movement of a replication fork is driven by the action of the replication machine, at the heart of which is an enzyme called DNA polymerase
Catalyzes the synthesis of a DNA molecule from a DNA template using deoxyribonucleoside triphosphate precursors
Final product is a new strand of DNA that’s complementary in nucleotide sequence to the template

Question 46

deoxyribonucleoside triphosphate

Answer 46

The polymerization rxn involves the formation of a phosphodiester bond between the 3’ end of the chain and the 5’ -phosphate group of the incoming nucleotide, which enters the rxn as deoxyribonucleoside triphosphate

Question 47

pyrophosphate

Answer 47

Hydrolysis of one of the high-energy phosphate bonds drives the rxn that links it to the chain, releasing pyrophosphate

Pyrophosphate is further hydrolyzed to 2 molecules of phosphate, which makes the polymerization rxn effectively irreversible

Question 48

true or false:
DNA polymerase does not dissociate from the DNA each time it adds a new nucleotide to the growing strand

Answer 48

TRUE
DNA polymerase does not dissociate from the DNA each time it adds a new nucleotide to the growing strand; rather, it stays associated with the DNA and moves along the template strand for many cycles of the polymerization rxn

Question 49

how is the replication fork asymmetrical?

Answer 49

The 5’ to 3’ direction of the DNA polymerization rxn makes a problem at the replication fork
At each replication fork, one new DNA strand is being made on a template that runs in one direction (3’ to 5’), whereas the other new strand is being made on a template that runs in the opposite way

Question 50

Does the cell have 2 types of DNA polymerase, one for each direction?

Answer 50

No, all DNA polymerases add new subunits only to the 3’ end of a DNA strand

Question 51

New DNA chain can be synthesized only in a ______ direction

Answer 51

5’ to 3’

Question 52

okazaki fragments

Answer 52

Resulting small DNA pieces called Okazaki fragments are later joined together to form a continuous new strand

Question 53

lagging strand

Answer 53

The DNA strand is made discontinuously in this way is called the lagging strand, because the mechanism imparts a delay to its synthesis

Question 54

leading strand

Answer 54

The other strand which is synthesized continuously, is called the leading strand