Week 1 Flashcards
The core structure of a nucleotide is the ___ backbone, the _ ___, and the nitrogen rich ____. The number of ____ varies.
phosphate, pentose sugar, bases, phosphates
Sugar number starts with the carbon attached to the ___. The 2’ carbon can be __ or ___. The 5’ carbon attaches to the ___ group
base, OH, H, phosphate
Purines have ___ rings and include ___ and ___.
2, adenine, guanine
Pyrimidines have ___ ring and include __, ___ and ___
1, uracil, thymine, cytosine
Nitrogenous bases are weakly ___ compounds and ____ molecules. Because most bonds in the ring have partial ____ character, pyrimidines are __ while purines have a slight ___.
basic, aromatic, double-bond, planar, pucker
The linear and ring sugar structures are ___ in equilibrium. The ring structure, _____ is found in the nucleotide and nucleoside forms of the bases.
dynamic, beta-furanose
Ring structured sugars have a ___ and can be found in a ____ or ____ confirmation. This pucker changes the ___ of the base and the ___ carbon, which impacts the orientation of the phosphate
pucker, 2’-exo, 3’-exo, orientation, 5’
The 2’OH of ribose favours the ____ ____ conformation, while the 2’ H of deoxyribose favours the _____ ____ conformation
C-3’ endo, C-2’ endo
The nitrogen rich base attaches to the pentose at the ____ C sugar position, making an ____ _____ bond. In a DNA helix, bases are usually found in the _____ conformation around this bond.
1’, 1 N-glycosidic bond, anti
Anti conformations are when the base faces ____ of the sugar and are only possible with ____ due to the steric hindrance with the pentose oxygen
outwards, pyrimidines
Syn conformation are where the base faces _____ towards the sugar and are feasible with ____.
in, purines
the nucleotide has the ending of ______, while the nucleoside, has the ending of ____
-late, -ine
Most nucleotides will have the phosphate groups linked at the ___ carbon on the pentose, these are central in the formation of ____ of nucleotides. Cyclic structures link ___ or ____ and play important roles in cell linkage
5’, polymers, cAMP, cGMP
In the formation of a phosphodiester bond, the ____ will form an ___ with the next nucleotide at its free phosphate group ___ end. The ultimate nucleotide in chain will have a free ____ group, generating directionality in nucleic acid polymers
3’OH, ester, 5’, 3’OH
In the watson-crick model of DNA, the ____ sugar-phosphate backbone lies on the outside, while the nitrogen rich _____ bases are on the inside. The 5’ end is complementary to the 3’ end of the other strand in an ___ configuration
polar, hydrophobic, antiparallel
Rule that says the amount of purines must equal the number of pyrimidines
chargaff’s rules
The antiparallel pairing generates a ___ groove and ___ groove in the DNA. ___ H bonds form between G and C, while ___ H-bonds form between A and T. There are ____ base pairs per helical turn.
major, minor, 3, 2, 10.5
The biggest impact to polymer stability is the ____ ___ ___ sharing between the planar bases in the ___ dimension, resulting in __ ___. the _____ of the nitrogenous bases drive the formation of ____ structures to occlude water from the ___ of these structures (hydrophobic effect). The ___ between the bases in the helix also stabilize the structure and the ___ ___ shield the negative charges of the backbone phosphates
delocalized electron sharing, z, base stacking, hydrophobicity, interior, h-bonding, metal ions
Rotation around the _____ bond in purines presents a new face to form H-bonds with the partner base. ___ interactions can facilitate H-bonds between nucleotides from both sides of the base, forming ___ ___.
N-glycosidic bond, hoogsteen, branched structures
mRNA is always _____ and forms a ____ helix. It is dominated by ____ and can base pair with complementary regions of DNA or RNA.
single-stranded, right-handed, base-stacking
___ ___ drives the formation of ____ right-handed double helices in RNA. Breaks caused by mismatched or unmatched bases results in ___ or internal ___ which form between ____ sequences
intramolecular, A-form, bulges, loops, palindromic
In RNA the primary structure is the base sequence with extensive ____ helical segments. The secondary structure is the 2D representation of ____ and ____. ____ are the most common type. The tertiary structure is the 3D fold
base-paired, loops, bulges, hairpins
tRNA adopts a canonical ____ fold enabling it to be ___ with an amino acid and so that it fit into the ___ during peptide synthesis. The ______ structure folds into the upside down hockey stick conformation
3D, charged, ribosome, clover-leaf
Post replication or transcription bases can be modified with different __ ___. The impact of the modification is usually on the ____ potential and sometimes impacts ___ around the N-glycosidic bond. For example, ___ is a uracil base with an alternative N-glycosidic linkage critical in RNA folding
chemical signatures, H-bonding, rotation, pseudouridine
the folding of tRNA is established by the atypical ____ bond with the ____ group, ___ interactions and ___ interactions, and ___ bases. This changes the H-bond capacity of these regions and drives specific 3D structure
hydrogen, 2’OH, hoogsteen, W-C
nucleosides are ___ and relatively ___ in pH 7 water. This leads to ___ interactions, like ____ ___ ___ and _____ interactions. At acidic and alkaline pH, they are ___ and more soluble. This can be used to isolate and ____ nucleic acids from a biological solution. ____ are more soluble than ____
hydrophobic, insoluble, stacking, van der waals, dipole-dipole, charged, purify, nucleotides, nucleosides
All nucleotide bases absorb ___ light and show strong absorption bands near ___ nm
UV, 260
the observed decrease in the absorption of UV light when complementary strands are paired
hypochromic effect
the observed increase in the absorption of UV light when a double-stranded nucleic acid is denatured
hyperchromic effect
the temperature at which 1/2 of DNA is present as separated single strands
denaturation temperature
denaturation temperature increases with the content of _____ base pairs
G-C
____ duplexes are more stable to heat denaturation than ___ duplexes. RNA-DNA hybrid stability is generally ____.
RNA, DNA, intermediate
the melting of the double helix due to pH extremes or high temperatures that disrupt H bonds and base-stacking interactions
denaturation
The process by which two strands spontaneously rewind when temperature or pH is returned to its normal range
anneal
____ __ ___ is a method of amplifying DNA segments of interest and relies on ___ ______ that add nucleotides to the ___ ends of preexisting strands called ____
Polymerase chain reaction, DNA polymerases, 3’ primers
In ___ ____ ____, the primers are designed to flank the mutation you are interested in making and encode for the new __ __ or change. ____ primers are required and faithful replication of the entire ____ is required with DNA polymerase
site directed mutagenesis, amino acid, large, plasmid
___ m of DNA is compacted into the nucleus. The first order of organization is the ___ nm chromatin fiber. DNA wraps around a core __ ___ ___ complex to form a ____
2, 10, histone octamer protein, nucleosome
DNA inside the eukaryotic cell is packaged as ___. DNA wraps _____ turns around a complex of histone proteins, forming nucleosomes. Two copies of histone proteins ___, ___ , ____ and ____ form the octamer
chromatin, 1.6, H2A, H2B, H3, H4
Histones makes tight but not __ ___ contacts between the DNA and the positively charged histone proteins. Histones tails are ___ unstructured domains that stick out from the nucleosome and can be ____ _____ to alter gene expression. ____ properties of the core histone proteins help neutralize the ____ charge of the DNA phosphate backbone
sequence specific, flexible, post-translationally, basic, negative
30nm fibers and higher order fibers are an artifact of ____ _____ ____. These can be created by changing the ____ conditions of the solution. 10 nm fibers are packaged into the mitotic ___, and chromatin is regulated without changes between the 10 and 30 nm fibers.
in vitro purification, salt, chromosomes
In chromatin, the negative charge of the phosphate sugar backbone is stabilized by the ___ charges of the ___ proteins, and there is reduced __ ___ , enabling bending and ____ polymer properties
positive, histone, steric repulsion, flexible
Some bases of DNA are ____ which changes the recruitment of ____ ___ and gene ____. __ and __ are methylated more frequently than G and T. All known DNA methylases use ______ as a methyl group donor. In eukaryotes, ___% of cytidine residues are methylated.
methylated, transcription factors, expression, A, C, s-adenosylmethionine, 5
In naked DNA there is a ___ structure with regularly spaced negative charges, which requires __ __ and small ___ molecules to neutralize it and enable flexibility
periodic, metal ion, amino-rich
Modifications to the ___ __ can also change nucleosome packaging. They can also provide platforms for recruiting different ___ ____ that will activate or silence particular regions of the genome.
histone tail, protein complex
Electron microscopy is good for structural studies using ___ imaging techniques ____ ____. high energy electrons pass through the sample which is often stained with __ ___. Regions within the sample that have more ____ stain more densely with the heavy metals and results in an _____ of electrons reaching the detector
single-particle, in situ, heavy metals, mass, absence
Heavy metals obscure ___ ___ details of chromatin fibers. The solution is ___ or ___ ___ images that reveal where specific elements are enriched in the sample without heavy metal staining. The information is still ____ due to the projection limitation of the electron lens
fine structural, filtered, energy loss, compressed
In ___ ___, a series of images are taken at different __ and then computationally recombined to overcome the projection limitation of the microscope. The ___ of images and how far the sample can be ____ determine the features that can be resolves in the reconstruction
electron tomography, angles, number, tilted
When a 10nm fiber is wrapped into a ____nm one, you end up with ___ __ inside the fiber, which wastes spaces in the nucleus. Newer models suggest that proteins could change the ___ of chromatin regions or provide a chemical distinctive platform for recruiting other proteins to these regions to ___ or ___ them
30, empty space, density, activate, silence
the length and even the __ ___ of ___ ___ of chromosomes can be assessed using ___ microscopy. Disease states are often associated with massive changes to the genome such as ___, ___ and ___, and can be visualized with ___.
staining density, genomic regions, light, duplications, deletions, inversions, karyotyping
in sky-FISH experiments, specific sequences of DNA within a chromosome are labeled with a unique combination of ___. The DNA is denatured after fixation so the probe can ___. The fluorophores are visualized using ___ ___ ___. Distinct domains of chromatin fibers from individual chromosomes form individual __ ____.
fluorophores, anneal, fluorescence light microscopy, chromosome territories
chromatin during most of the cell cycle is organized into compact discrete structures known as ____ ____. The fibers within them are composed of _____ chromatin fibers. ____ modifications may change the local chromatin environment, either by changing the ____ between nucleosomes, or by providing a platform for other proteins to bind and regulate __ ___
chromosome territories, 10nm, epigenetic, spacing, gene expression
Nuclear bodies vary in _____ and ____. They are non-membrane bound _____ compartments with a specific function. They are involved in the __ and ____ regulation of nuclear processes.
size, function, sub-nuclear spatial, temporal
Some proteins and RNA under certain conditions will _____, forming a ____ compartment. They do this by ____ ___ via multivalent domains, or by ___ via disordered/low ____ regions
self-solunilize, phase-separated, interlocking proteins, pi-stacking, complexity
many functions are _______ in the nucleus. For example, even though there are many sites in the genome with active genes, there are only a few ____ regions containing transcription factories that contain poised and active ___ ___.
sub-compartmentalized, concentrated, RNA polymerase
In fluorescent microscopy, antibodies are raised to detect a specific ___ of interest. The cells are ___ and permeabilized so the antibodies can fit into the ___ ____. When using antibody detection method, a fluorescently tagged ___ ___ is often used. DNA counterstains such as ____ or ____ will define the nucleus and can give you a sense of regions of more or less DNA and therefore ____/heterochromatin
protein, fixed, cellular compartments, secondary antibody, DAPI, hoescht, compaction
A ___ ___error, or a meiotic polymerase replication error, causes a _____ to ___ mutation in exon ____. This mutation generates a ___ ___ ____. From one allele, some of the alternatively spliced __ ___ protein is expressed, causing _______.
de novo, C, T, 11, cryptic splice site, lamin A, progeria
An individual with progeria has both a ___ and ___ version of the lamin A ____.
normal, shortened, mRNA
In SDS-PAGE gel, ____ proteins run higher up on the gel.
larger
In healthy cells, the nucleus has a smooth ___ shape and lamin localizes mainly to the ____, with some visualized in the ___.
oval, periphery, nucleoplasm
In progeria cells, the nucleus has a ___ and irregular structure, and lamin is localized throughout the ____.
reticulated, nucleoplasm
progeria lamin was also more ____ to recover relative to wild type lamin A during a ____ experiment, indicating it is less ____
slower, photobleaching, dynamic
in photobleaching, the protein is labeled with ___ and the area is ____. The return of the fluorescence is measured. Proteins with high ___ ____ have a fast recovery time
GFP, bleached, dynamic nature
Increasing the amount of ____ added to progeria cells decreases the amount of ___ ___ lamin A mRNA and the amount by targeting the cryptic exon ____ boundary which sends the RNA product for ___
oligo, alternatively spliced 11/12, degradation
