nucleotides, genes, and chromosomes Flashcards
list the basic structural components of a nucleotide
phosphate(s), base, sugar
list the basic structural components of a nucleoside
base, sugar
which has a phosphate: nucleotide or nucleoside
nucleotide has a phosphate
list the 2 types of nitrogenous bases
purine or pyrimidine
which type of sugar does a nucleotide/side have
pentose
T or F: a nucleotide can have one or more phosphates
true
how many rings do purines have
2
how many nitrogens do nitrogenous bases have PER RING
2 N per ring
how many rings do pyrimidines have
1
how many N do purines have
4 N
how many N do pyrimidines have
2 N
what type of bond links the nitrogenous base to the pentose sugar
covalently
in the covalent bonds between nitrogenous base and sugar, between which atoms does the covalent bond occur
nitrogen of the base with carbon of the sugar
which nitrogen in purines hold the covalent bond to the base
N 9
which nitrogen in pyrimidines hold the covalent bond to the base
N 1
T or F: thymine can occur in RNA
true, but this is rare
T or F: uracil can occur in DNA
true, but this is rare
by which bond does the phosphate join to the pentose sugar in a nucleotide
ester
by which bond is the base bound to the pentose sugar in a nucleotide/side
N-b-glycosyl bond
what sugars do RNA have
ribose
what sugars do DNA have
2’-deoxy-ribose
which atom in a nucleotide/side is denoted with primes (‘)
carbons
why do we denote sugar carbons in a nucleotide/side with primes (and not just the number on its own?)
bc it helps us distinguish between sugar carbons and base carbons
in a nucleotide/side, which carbon is denoted with primes: sugar carbons or base carbons
sugar carbons get primes
T or F: DNA and RNA also contain some additional nitrogenous bases in minor concentrations
true, but rare
describe 2 minor changes that can occur to RNA/DNA structure
methyl groups added to a ring carbon or an exocyclic group (methyl group modification)
T or F: methyl group modification on nucleotides is very common
false; it’s not super common
are RNA/DNA backbones hydrophilic or hydrophobic
hydrophilic
describe why the RNA/DNA backbone is hydrophilic
OH of sugars usually hydrogen bond with water. The fully ionized phosphate groups usually ionically interact with + charges on proteins or metal ions
linkages of nucleotides are formed by which type of reactions
dehydration
T or F: both purines and pyrimidines are aromatic
true
since purines/pyrimidines are aromatic, describe the types of bonds found within them
most of the bonds have a partial double bond character
since purines/pyrimidines are aromatic, describe what happens to the electrons
they delocalize
what is the UV absorption of purines/pyrimidines
260 nm
since purines/pyrimidines are aromatic, describe the general shape
pyrimidines = planar, purines = puckered (nearly planar)
T or F: purines/pyrimidines can exists as 2+ readily interconvertible isomers (tautomers)
true
list chargaff’s rules (4)
- base composition of DNA varies between species
- DNA from dif tissues of the same species have the same base composition
- base composition of DNA doesn’t change with organism’s age, nutritional state, or environment
- # A = # T, and # G = #C, and AG = purine, CT = pyrimidine
which bases are purines
adenosine and guanosine
which bases are pyrimidines
cytidine and thymidine
what are the two repeating periodicities of DNA
3.4 A and 34 A
why did watson and crick propose antiparallel strands for the DNA model
that’s the only way the hydrogen bonds line up
why do the antiparallel DNA strands become helical
the phosphodiester bonds that make up a stretch of nucleic acids make the molecule inherently diagonal. The only way to get hydrogen bonding is if the two strands twist around one another
what is the distance between each base in DNA
3.4 A
what is the width of the DNA helix
20 A
what is the width of the DNA helix when only the backbone is considered
11 A
how many stacked bases are there per turn
10.5 bases
what is the length of the 10.5 stacked bases in a turn
36 A
which is stronger: AT bonds or GC bonds
GC
why are GC bonds stronger than AT
GC have 3 hydrogen bonds whereas AT have only two
what are the two types of helical grooves
major and minor
what do the major and minor grooves dictate?
how easily proteins can bind to the molecule
T or F: a nucleotide is flexible around its bonds
true
why is a nucleotide flexible
it rotates around 7 different bonds
how many bonds does a nucleotide rotate around
7
which has two forms due to steric hindrance: purines or pyrimidines
purines
which two forms do purines have due to steric hindrance
anti and syn
which form do pyrimidines have: anti or syn
anti
which has less steric hindrance: anti or syn
anti
what is the name of the most stable watson-crick DNA structure
B form
other than B form, what are the two other forms
A and Z
when is A form common
in low-water conditions
when is Z form common
can occur when there’s alternating G/C residues
how does the major groove change in A form vs B
in A, the major groove is more pronounced
how does the major groove change in Z form vs B
in Z, the major groove is less pronounced
which has a wider helix w/ more base pairs per helical turn than B form: A or Z
A
which has a skinnier helix with more bp per helical turn than B: A or Z
Z
rank the DNA forms from widest to skinniest: A B and Z
A, B, Z
what is the handedness of B form
right
what is the handedness of A form
right
what is the handedness of Z form
left!!!!
rank the DNA forms from least to most bp per helical turn: A, B, Z
B, A, Z
what is the primary structure of nucleic acids
nucleotide sequence
what is the secondary structure of nucleic acids
regular, stable structures of some/all nucleotides
what is the tertiary structure of nucleic acids
complex folding of chromosomes, tRNA, and rRNA molecules
what is a palindrome
repeated section on a dif strand (complementary across a vertical axis on the other strand)
what is a mirror repeat
repeated section on the same strand (identical across a vertical axis)
which two structures can palindromes form
single-strand hairpins, double-strand cruciform
what causes RNA to fold weird
G-U pairings (unusual)
in the unusual G-U pairings that can occur in RNA, when does it occur: during folding or synthesis
folding
T or F: DNA molecules are much larger than the structures that house them
true
only about __% of human DNA codes for exons
1.5%
how much of our DNA is made up of introns
almost a quarter
considering both exons and introns, how much of the human genome consists of protein-coding genes
30%
what does SSR stand for
simple sequence repeat
what are SSRs (structure) + give 2 examples of DNA regions that contain lots of SSRs
short sequences less than 10 bp long, examples = telomeres and centromere
what is the centromere
DNA that serves as an attachment point for proteins during cell division
T or F: the telomere DNA sequence is different in everyone
false! it’s the same in everyone
T or F: the number of SSR repeats in telomeres is the same in everyone
false; it’s different in everyone
describe how telomeres are unique and similar amongst humans
everyone has the same SSR sequence in telomeres, but the number of SSRs is what differs
what does CODIS stand for
combined DNA index system
what does CODIS do
analyzes SSRs in two samples and shows you if there’s a match (ie in paternity tests, crime, etc)
using SSRs, how do you determine a parental match (ie is he the father?)
you get one SSR allele from each parent, so if one SSR is different then the suspected person is not the father
contrast a coil with a supercoil
coil = DNA double helix
supercoil = double helix coiling around itself
what do we call DNA that is not supercoiled
relaxed
T or F: relaxed DNA has no coils
false; it is coiled (double helix), but the coil does not coil around itself
T or F: supercoiling is an intrinsic property of DNA
true
in which DNA form are closed circular plasmids
B form
in closed circular plasmids (B form), how many bp are there per helical turn
10.5 bp
supercoiling often results from DNA that is (overwound/underwound) relative to B form
underwound
since supercoiling results from underwound DNA relative to the B form, describe how the bp per helical turn + number of helical turns change
bp per helical turn increases, number of helical turns overall decreases
T or F: so little as 1 extra/less helical turn from the relaxed # of helical turns can cause DNA to supercoil
true
what are two possible ways a DNA molecule will accommodate strain
supercoiling, strand separation
which is more likely: supercoiling or strand separation? why
supercoiling = more common. Strand separation requires the breaking of hydrogen bonds
describe supercoiling during DNA transcription
DNA transcription requires strand separation = strain. DNA is overwound ahead of DNA pol, and underwound behind it
is DNA typically overwound or underwound
underwound
what happens if there is a nick in a supercoiled DNA
converts it to the relaxed state (circular)
what is the linking number a measure of
the number of times a strand pierces the surface of a second strand
T or F: as long as the strands are intact, the linking number is the same regardless of DNA bending or deformation
true
T or F: linking number is always an integer
true
T or F: linking number is almost always positive
true
what letters represent linking number in an equation
Lk
formula for determining linking number?
Lk = total # bp/number of bp per turn
for relaxed DNA, how is Lk referred to as
Lk0
formula for Lk0?
Lk0 = total # bp/10.5 bp per turn
formula for delta Lk?
delta Lk = Lk - Lk0
what does it mean to have a negative delta Lk
underwinding by n turns = n negative supercoils have been introduced
what does it mean to have a positive delta Lk
overwinding by n turns = n positive supercoils have been introduced
what is the handedness of a positive supercoil
left
what is the handedness of a negative supercoil
right
what is the Lk when the closed circular DNA has a nick? why?
no defined Lk because it could theoretically completely separate
define superhelical density
a percentage of unwound or overwound turns
formula for superhelical density?
σ = delta Lk/Lk0
underwinding DNA leads to a (+/-) σ
negative
overwinding DNA leads to a (+/-) σ
positive
what is the name for enzymes that increase or decrease the extent of DNA underwinding
topoisomerases
what do topoisomerases do to DNA
they change the Lk
when do topoisomerases manage strain in the DNA
during replication
how many types of topoisomerases are there
2
describe the role of type I topoisomerase
transiently breaks one of the two DNA strands, then passes the unbroken strand through the break and then rejoins the break
by how much do type I topoisomerases change the Lk (and is it adding or reducing)
reduces it by 1
describe the role of type II topoisomerase
transiently breaks both strands and passes another part of the helix through the gap
by how much do type II topoisomerases change the Lk (and is it adding or reducing)
reduces it by 2
describe the full mechanism of topoisomerases (type 1)
open conformation: active site Tyr attacks a phosphodiester bond in one strand = cleaving it. Unbroken DNA passes through the break.
closed conformation: cleaved DNA is re-ligated
in solution, what is the structure of supercoiled DNA
plectonemic
describe plectonemic structure
simple, intertwined structure
does plectonemic structure provide sufficient compaction?
no
when stabilized by proteins, what structure does DNA take the form of
solenoid
describe solenoidal structure
like a garden hose
which is more compact: solenoidal or plectonemic
solenoidal is more compact
T or F: DNA can easily interchange between plectonemic and solenoidal supercoiling
true
in what form is DNA in non-dividing cells, G1, G2, and S
an anamorphous + randomly dispersed blob
in which phase of the cell cycle do chromosomes condense and take the form of well-defined pairs of sister chromatids
prophase
what is chromatin
the material within a chromosome
chromatin is __% protein and __% DNA
50/50
which proteins are the main component of chromatin
histone proteins
how many monomers makes up a histone
8
how many bp of DNA wrap around the histone octamer
200 bp
list the classes of histones
H1, H2A, H2B, H3, H4
how many times does the histone octamer wrap around the DNA
1.67 x
how many bp serve as linker DNA between histones
50 bp
which histones/how many histones do nucleosomes have
contains two copies of H2A, H2B, H3, and H4
in which type of supercoil does DNA wrap around a histone
solendoial supercoil
how is contact formed between nucleosomes
histones have disordered N-terminal tails that extend outwords
T or F: histone tails can be modified
true
give 2 examples of histone tail modification
methylation, ubiquitinylation
how many nm are the beads on a string structure
10 nm
in the compaction hierarchy, what comes after the 10 nm beads on a string
30 nm fiber
how is formation of the 30 nm fiber initiated
initiated by histone H1 binding to the linker DNA between histone octamers
in the compaction hierarchy, which two forms come after the 30 nm fiber
use of scaffolding proteins and rosette coiling
what does SMC stand for
structural maintenance of chromosomes
how many domains do SMC proteins have
5
list the 5 domains of SMC proteins
N term globular head, N term a-helical connector, hinge domain, C term a-helical connector, C term globular head
in regards to SMC protein structure, when can ATP hydrolysis occur? explain
N and C globular heads each contain part of an ATP hydrolysis site, so when they’re folded then these sites can interact and ATP hydrolysis can occur
describe the structure when SMC proteins fold
V-shaped dimer where monomers are connected at the hinge site
T or F: SMC proteins are found in all organisms
true
list the two major eukaryotic SMC families
cohesin and condensin
role of cohesins?
help link together sister chromatids immediately after replication and keep them together until metaphase
how do cohesins keep sister chromatids together
they form a ring around them that ties DNA together
role of condensins?
help chromosomes condense for the entirety of mitosis
how do condensins keep chromosomes condensed
they induce overwinding/positive supercoiling
briefly describe the condensin mechanism
initially DNA is bound at the hinge region inside a ring formed by the condensin dimer. ATP binding and hydrolysis changes the condensin conformation and the protein then induces positive supercoiling (supercoiling can happen two ways)
describe the two ways of supercoiling that can occur via condensin
DNA can coil between hinge regions (=fibers), or around the hinge regions (=rings)
SMC mechanism: describe the steps
cohesins are loaded onto the chromosomes during S phase and tie the sister chromatids together during replication. At the onset of mitosis, condensins bind and maintain the chromosomes in the condensed state. Right before anaphase, the enzyme separase degrades the cogesisn and the chromatids can separate. At the end of mitosis, condensins begin to unload and the daughter chromosomes return to the uncondensed state
T or F: The entire eukaryotic chromosome, once condensed, is limited to a particular subnuclear domain or chromosome territory
true
T or F: there is little interaction between DNA in different territories
true
where is euchromatin located in a cell? why
near the center of the nucleus because they have many actively expressed genes
where is heterochromatin located in a cell
in the peripheral territories
bacterial DNA is compacted in a structure called the _________
nucleoid
describe the organization of bacterial DNA in the cell
circular DNA is looped into domains of 10,000 bp by scaffolds. There’s 500 of these looped domains
why doesn’t bacterial DNA condense or form DNA-protein interactions
because it needs to be accessible for replication more often
