Module 3.1 Flashcards
DNA or deoxyribonucleic acid is a macromolecule composed of a chain of __________.
nucleotides
Each nucleotide is composed of a pentose sugar called _________, which has a ________ group attached to its 4th carbon, and a ________attached to its 1st carbon.
deoxyribose,
phosphate group,
nitrogenous base
Adjacent nucleotides are joined by _________, which forms through condensation accompanied by the release of water.
phosphodiester bond
The two DNA strands are
antiparallel
the upper end of the _______ strand is labelled 5’ end while the _____ strand is labelled 3’ end.
left,
right
backbone of the DNA molecule
sugar and phosphate
2 types of nitrogenous bases
purines and pyrimidines
purines (2)
Adenine and Guanine
(All Gods are Pure)
pyrimidines (2)
cytosine and thymine
have double ring structures
purines
have single ring structures
pyrimidines
base pairing of the nitrogenous bases and why
A-T and G-C (purines-pyrimidines) since if
purine-purine: not enough space
pyrimidine-pyrimidine: too much space
A-C and G-T: do not fit well together, they do not easily form H bonds.
what bonds form between G-C and A-T pairs
hydrogen bonds
T or F.
H bonds are weak bonds, so DNA molecule don’t have a stable structure.
Although H bonds are weak bonds, so many of them in the entire DNA molecule can give the DNA molecule a stable structure.
3 H bonds - G-C
2 H bonds - A-T
discovered Chargaff’s rule of base-pairing
Erwin Chargaff
states that in a given DNA molecule, there should be the same number of adenine and thymine and the same guanine and cytosine.
was a big help to Watson and Crick when they were developing their base pair model for the double helix structure of DNA.
Chargaff’s rule
Prokaryotic cells usually have a single chromosome and one or a few _______, which are extrachromosomal DNA molecules with their own replicons that carry non-essential genes
plasmids
plasmid function (3)
- increase adaptation of their host cells to specific environments
- aid growth in specific conditions
- encode antibiotic resistance
T or F
Prokaryotic chromosomes are almost always circular. They are either completely devoid of centromeres or carry the so-called “plasmid centromeres” which are not essential.
True
In terms of condensation and packing, _______ appears naked in that the isolated nucleoids look like a collection of wire loops, loosely held together by a proteinaceous core. _______ are always known to segregate continuously, as they replicate, and without additional condensation.
prokaryotic DNA, Prokaryotic nucleoids
Supercoiling, which is one way that prokaryotes compress their DNA into smaller spaces, is made possible with the help of unique _________.
topoisomerases
Supercoils are either negative or right-handed or positive or left-handed supercoil. Mesophilic prokaryotes use DNA gyrase to create _______ while thermophilic prokaryotes use reverse gyrase to create __________.
negative supercoils; positive supercoils
Genomes can be ___________, meaning that the DNA is twisted in the opposite direction of the double helix, or ________, meaning that the DNA is twisted in the same direction as the double helix.
negatively supercoiled;
positively supercoiled (higher temp=maintains double strand)
Most bacterial genomes are (positively/negatively) supercoiled during normal growth
negatively
Once the genome has been condensed, _________(3)
help maintain the supercoils.
DNA topoisomerase I, DNA gyrase, and other proteins
is wrapped around protein nucleosomes and is further organized by histones and other proteins into a coil of 30-nm solenoid fiber.
- multiple chromosome, linear chromosome, is protein-mediated
Eukaryotic DNA
- offers an additional mechanism for controlling gene expression
- cells can control access to their DNA by
modifying the structure of their ______
chromatin
Highly compacted chromatin simply isn’t accessible to the enzymes involved in DNA transcription,
replication, or repair.
- regions of chromatin where active transcription is taking place (transcriptionally active)
- are less condensed than regions where transcription is inactive
Euchromatin
- tightly compacted regions of chromosomes
- transcriptionally inactive
heterochromatin
2 types of heterochromatin
- Constitutive heterochromatin - permanently inactive
- Facultative heterochromatin - interconvert between euchromatin and heterochromatin
- single circular chromosome in many
- condensed in the nucleoid via DNA supercoiling and the binding of various architectural proteins.
- Most prokaryotes contain only one copy of each gene (i.e., they are haploid).
- Nonessential prokaryotic genes are commonly encoded on extrachromosomal plasmids.
- Prokaryotic genomes are efficient and compact, containing little repetitive DNA
Prokaryotic chromosome
- multiple linear chromosomes
- condensed in a membrane-bound nucleus via histones.
- Most eukaryotes contain two copies of each gene (i.e., they are diploid).
- Some eukaryotic genomes are organized into operons, but most are not.
- Extrachromosomal plasmids are not commonly present in eukaryotes.
- Eukaryotes contain large amounts of noncoding and repetitive DNA.
Eukaryotic chromosome
Three Modes of Replication
- Semiconservative model
- Conservative model
- Dispersive model
mode of replication
- fits our DNA’s mode of replication
- 1: one strand of old, one strand of new DNA
- 2: old & new, old & old
semiconservative model
mode of replication
- 1: one strand of old, one strand of new DNA
- 2: old & new, old & old
conservative model
mode of replication
- 1: partly pink and partly blue
- each subsequent round of replication would then produce double helices with greater amounts of new DNA
dispersive model
Prokaryotic chromosomes, with their unique replication origin (R.O.) which is a hundred nucleotides in length, have a defined zone, called the ________, where converging replication forks fuse.
terminus
Prokaryotic chromosomes can have several replication rounds in the same chromosome, reaching a maximum of : origin/terminus ratio (replicated DNA to unreplicated DNA)
8:1
eukaryotic- 2:1
the melting of double-stranded DNA to generate two single strands. This involves breakage of H bonds
DNA denaturation
the region formed after the separation of the 2 DNA strands. It is the opened-up area in the circular chromosome on the left.
Replication bubble
the Y-shaped region on each side of the replication bubble
Replication fork
(Prokaryotic/Eukaryotic) __________ chromosomes have multiple and alternative replication origins, generating up to hundreds of replication bubbles per chromosome
Eukaryotic
DNA is polymorphic and dynamic.
DNA can assume many conformations depending on the:
- condition of the environment,
- activity of the part involved and
- need of the organism.
These are the 3 forms of DNA
A form
B form
Z form
form of DNA
* the canonical right-handed DNA helix that is the most common form of DNA.
* has a smooth backbone
* conformation is actually highly variable and malleable. It can adopt
multiple conformations in response to the environment which can
affect protein recognition.
B-DNA
form of DNA
* right-handed antiparallel helical duplex
* underwound structure that is more compact along the helix axis and broader overall across the helix relative to B-DNA.
* may either form upon binding of certain
proteins to DNA, or be an important intermediate step in forming the strongly distorted DNA conformation observed within at least some complexes with proteins.
A-DNA
biological relevance of A-DNA: underwinding for replication fidelity
▪ by inducing the A-form, the polymerase exploits the structural
features of the highly accessible minor-groove to ensure that
the correct base has been added relative to the template
sequence.
form of DNA
* left-handed, the most underwound form of the double-helix, has been mostly found in alternating purine-pyrimidine sequences (CG)n and (TG)n.
* usually in locations near the site of transcription initiation.
Z-DNA
The biological function of Z-DNA:
* Being the most underwound form of the double-helix, it consequently serves as a sink for the torsional tension (superhelical tension) in negatively supercoiled DNA. This expands the range of cellular situations that could support the formation, at least transiently, of ZDNA.
- Z-DNA helps to maintain the gene (close to it) in its activated, nucleosome-free state (nucleosomes do not bind to the very rigid ZDNA form) - regulation of gene expression
- Z-forming sequences accumulate near the transcription start site of genes in humans and other eukaryotes (~80% of the genes in human chromosome 22 have at least one Z-DNA sequence in the vicinity of their transcription start sites)
- suggested additional functions: RNA editing and gene transactivation.
- has several potential functions may be either beneficial or deleterious to the cell.
Why do different forms of DNA exist?
There is simply not enough room for the DNA to be stretched out in a perfect, linear B-DNA conformation.
The 3-stranded and 4-stranded DNA structures
H-DNA: 3 strands
Holliday Junction: 4
G-Quadruplex: 4
i-Motif: 4
- formed when a single DNA strand invades the major groove of a DNA duplex (but in order for the duplex to accommodate this third strand, it must unwind to broaden the major groove)
- triple-stranded helices are favored in negatively supercoiled DNA (The invading third strand can be intermolecular or intramolecular.)
- the interaction between strands involves the H* edge of the Watson Crick base pairs of the duplex to form base triplets which explains its name.
- Its presence in large numbers suggests that
naturally occurring DNA sequences can
cause increased mutagenesis when they
assume the non-standard DNA structure
formation
H-DNA: 3 strands
the meaning of H in H-DNA
Hoogsten
is formed primarily in mirror repeat sequences (sequences that have dyad symmetry within a strand, as in …AGAGGGnnnGGGAGA. (If you read it backward, the sequence of bases is the same as when you read it forward.) Mirror-repeats occur more frequently in eukaryotic genomes and have been documented to have effects on gene expression of several disease related genes.
H-DNA
- essential to several cellular processes including:
➢ recombination-dependent DNA lesion
repair
➢ viral integration
➢ restarting of stalled replication forks, and
➢ proper segregation of homologous chromosomes during meiosis - essential intermediates in double-strand break repair
HJ (Holliday Junction)
- The four-stranded structures assembled from guanine-rich sequences found primarily in
➢ telomeric DNA repeats (3’-overhangs at chromosome ends)
➢ also, in central regions of the genome: like in centromeric sequences and in the immunoglobulin switch region.
G-quadruplexes (G refers to guanine)
Are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3’ or the 5’ end occurs
Exonucleases
cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain.
Endonucleases
Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover of mRNA:
- 5’ to 3’ exonuclease - dependent decapping protein
- 3’ to 5’ exonuclease - an independent
protein - poly(A)-specific 3’ to 5’ exonuclease.
those with ________ activity
are the ones which are involved in proofreading.
exonuclease activity
provides a 3’ free -OH end to which DNA polymerase can attach the appropriate nucleotide. That means that without this, there will be no DNA synthesis
primer
Primase, together with DNA helicase, comprise what is called a
primosome
in ________cells, DNA primase is its own entity and works in a complex with the DNA helicase
prokaryotic cells
In __________ cells, DNA primase is associated with another polymerase, DNA polymerase α, which initiates the leading strand and all Okazaki fragments.
eukaryotic cells
