topic 3: molecular basis of inheritance Flashcards
who were the two scientists that produced the double-helical model for DNA structure?
James Watson and Francis Crick
what year was the double-helical structure of DNA discovered?
1953
describe the structure of DNA
- 2 antiparallel sugar-phosphate backbones
- the nitrogenous base pairs are in the molecule’s interior
what is Chargaff’s rule?
in any species, there is an equal number of A and T bases, and an equal number of G and C bases
which of the nitrogenous bases are purines, and which are pyrimidines?
purines: adenine, guanine (two-carbon nitrogen ring bases)
pyrimidines: thymine, cytosine (one-carbon nitrogen ring bases)
there are ___ hydrogen bonds between A and T, and ___ hydrogen bonds between C and G
2, 3
in what direction do the two helices of DNA run?
in an anti-parallel manner
monomers of DNA are known as
nucleotides
what does each DNA nucleotide consist of?
- a nitrogenous base
- a pentose sugar (deoxyribose)
- a phosphate group
what is a nucleoside?
nitrogenous base + pentose sugar
(excluding the phosphate group)
describe eukaryotic DNA molecules
- consist of 2 polynucleotide strands that spiral around an imaginary axis forming a double helix
- anti-parallel strands: each strand runs in an opposite direction to the other (3’ –> 5’ and 5’ –> 3’)
- sugar-phosphate backbone is on the outside
- the nitrogenous bases form hydrogen bonds in a complementary fashion:
- A - T, C - G
- the 2 strands are complementary: knowing one sequence, we can derive the other
how are nucleotides connected to create a polymer?
in a 3’ to 5’ phosphodiester bond
- between the 3’ -OH group of the sugar molecule of one nucleotide and the 5’ -phosphate group of the second nucleotide
explain the difference between bacterial chromosomes and eukaryotic chromosomes
bacterial chromosomes:
- double-stranded circular DNA molecule associated with a small amount of protein
- DNA is supercoiled in the nucleoid
eukaryotic chromosomes:
- double-strand linear DNA molecules associated with a large amount of proteins (histones)
- located in the nucleus
- consist of chromatin
- chromosomes are packed and supercoiled in different levels in order to fit into the nucleus
what is chromatin?
DNA + histones (proteins)
what is the diameter of the DNA double helix?
SOS
2 nm
what is the diameter of a nucleosome?
SOS
10 nm
what are the levels of chromatin packing in a eukaryotic chromosome?
SOS
- DNA, double helix (2 nm)
- DNA comes together with the histones to create nucleosomes (10 nm)
- nucleosomes are wrapped around themselves (to form 30 nm fibers)
- looped domains – the fibers form loops to fit in the nucleus (300 nm)
- the condensed metaphase chromosome (2 chromatids, each 700 nm)
how are nucleosomes made?
DNA is wrapped twice around a set of eight proteins – histone octamer
what are the diameters of each step of chromatin packing?
SOS
- DNA double helix: 2 nm
- DNA + histones: 10 or 11 nm (depending on histone 1)
- nucleosomes wrapped around themselves: 30 nm fibers
- looped domaines: 300 nm
- metaphase chromatids: 700 nm each
- metaphase chromosome: 1400 nm or 1.4 μm
what is the structure of a nucleosome?
- each nucleosome consists of 8 histone molecules
- (H2A, H2B, H3, H4) x 2
- +ds DNA (168 base pairs)
- with histone one
what is histone 1 (H1)?
- located between the nucleosome (NOT part of the octamer core)
- role: stabilizes the interaction between DNA and nucleosomal histones
(1) what is the diameter and (2) how many base pairs is DNA with and without histone 1?
- without H1: 146 base pairs, 10 nm
- with H1: 168 base pairs, 11 nm
what is euchromatin?
- ACTIVE FORM
- loosely packed chromatin
- enables replication and transcription
- enables gene expression
what is heterochromatin?
- INACTIVE FORM
- highly condensed chromatin
- inhibits replication and transcription
- inhibits gene expression
at what stage of the cell cycle is chromatin (1) in the form of euchromatin and (2) in the form of heterochromatin?
- euchromatin: during interphase
- heterochromatin: during mitosis
explain why the forms of chromatin occur at their respective phases of the cell cycle
- gene expression occurs during interphase, therefore chromatin has to be in its active form (euchromatin)
- during mitosis, the cell is actively undergoing cell division (no gene expression) so the inactive form of chromatin is present
what are the two exceptions (structures) of chromosomes that are ALWAYS in heterochromatin form?
- centromeres and telomeres
- these two structures are always in heterochromatin form because they have structural roles (are not transcribed/translated)
what are the chemical modifications histones can undergo that results in changes in gene expression?
- methylation
- acetylation
what could be a consequence of histone modification?
- gene silencing (inhibition of gene expression)
- could result in diseases (ex: cancer)
- hypo-acetylation of histones causes a condensed or closed chromatin structure, disabling gene expression
what is histone acetylation?
- converts heterochromatin into euchromatin
- ACTIVATES chromatin, ACTIVATES gene expression
- loss of histone (+) charge due to acetylation weakens their interactions with DNA (-) charge
what is histone deacetylation?
- INACTIVATES chromatin
- converts it into heterochromatin
- restores (+) charge of histone –> strengthens their interaction with DNA
what are the enzymes responsible for (1) histone acetylation and (2) histone de-acetylation?
- histone acetyl-transferases (HAT): is responsible for histone acetylation
- histone deacetylases (HDAC): is responsible for histone deacetylation
what is the semiconservative model of replication?
when a double helix replicates, each daughter molecule will have 1 old strand (derived or conserved from the parent) and 1 newly synthesized strand
replication begins at special sites called _____, and are separated opening up a _____
- origins of replication
- replication “bubble”
what type of replication does the DNA double helix undergo?
- bidirectional replication: replication proceeds in both directions from each origin until the entire molecule is copied
compare prokaryotic and eukaryotic origins of replication
prokaryotic:
- circular DNA, only 1 origin of replication
- replication is bidirectional
eukaryotic:
- linear DNA, several replication origins
- replication is also bidirectional
what is the replication fork?
a Y shaped region at the end of each replication bubble where new DNA strands are elongating
what are helicases?
enzymes that untwist the double helix at the replication forks
what is topoisomerase?
enzyme that corrects “overwinding” of replication forks by breaking, shriveling, and rejoining DNA strands
what are single-strand binding proteins used for?
protein that binds and stabilizes single-stranded DNA until it can be used as a template
what enzyme fixes the action of helicases?
topoisomerase
what is DNA polymerase used for?
enzymes that catalyze the elongation of new DNA at a replication fork
what are the two limitations of DNA polymerases?
- they can only add nucleotides to a pre-existing nucleotide chain (cannot add from scratch)
- they can only add nucleotides in the 5’ –> 3’ direction (not the other way around)
what 2 things does DNA polymerase require?
- a primer
- a DNA template strand
what is used to fix the DNA polymerase limitation of only adding nucleotides to a pre-existing chain?
a short RNA primer has a free 3’ end that serves as the starting point for synthesis of the new DNA strand by DNA polymerase
what is primase?
the enzyme that synthesizes a short RNA primer from scratch using parental DNA as a template
where does each nucleotide being added to a growing DNA strand come from?
a nucleoside triphosphate (NTP)
what will the 2 phosphate groups (from NTP) leave the reaction as?
pyrophosphate
what are nucleoside analogues?
- drugs that have a modified 3’ -OH group, as a N3 group
- block replication, as cells think it is a nucleoside triphosphate, but the next nucleotide cannot bind to the N3 group
give an example of a nucleoside analogues
- an example is AZT (azido-deoxy-thymidine)
- blocks replication due to modified 3’ -OH group
- an anti-retroviral drug (given to HIV patients)
- also given to cancer patients
which DNA polymerase is responsible for synthesis of the leading strand?
DNA polymerase III
how is the leading strand synthesized?
- DNA polymerase III copies the 3’ - 5’ strand
- synthesizes a leading strand continuously in the 5’ –> 3’ direction
- 2 leading strands per bubble are made
since DNA polymerase cannot add nucleotides in the 3’ to 5’ direction, what does this cause?
the lagging strand
how is the lagging strand synthesized?
- to copy the 5’ - 3’ strand, DNA polymerase III must work in the direction AWAY from the replication fork (5’ to 3’)
1. primase: synthesizes short RNA primers
2. DNA polymerase III: synthesizes discontinuously what are known as Okazaki fragments by adding DNA nucleotides to each primer
3. DNA polymerase I: degrades RNA primers, replaces with DNA nucleotides
4. DNA ligase: joins DNA fragments to the subsequent Okazaki fragments
what problem does DNA polymerase create after many rounds of replication?
- the replication machinery does not provide a way to complete the 5’ ends
- repeated rounds of replication produce shorter DNA molecules
why are only eukaryotic chromosomes affected by this DNA polymerase limitation?
because prokaryotes have circular DNA
what are telomeres?
- the ends of eukaryotic chromosomes
- they protect chromosomal ends from erosion, degradation, and recombination with other chromosomes
- since they have a structural role, they do not get transcribed/translated
is DNA shortening preventable?
no, telomeres only postpone the shortening of DNA but do not prevent it
what is shortening of telomeres (or DNA) connected to?
aging
