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BIOC 302 > Week 1 > Flashcards

Week 1 Flashcards

1
Q

The core structure of a nucleotide is the ___ backbone, the _ ___, and the nitrogen rich ____. The number of ____ varies.

A

phosphate, pentose sugar, bases, phosphates

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2
Q

Sugar number starts with the carbon attached to the ___. The 2’ carbon can be __ or ___. The 5’ carbon attaches to the ___ group

A

base, OH, H, phosphate

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3
Q

Purines have ___ rings and include ___ and ___.

A

2, adenine, guanine

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4
Q

Pyrimidines have ___ ring and include __, ___ and ___

A

1, uracil, thymine, cytosine

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5
Q

Nitrogenous bases are weakly ___ compounds and ____ molecules. Because most bonds in the ring have partial ____ character, pyrimidines are __ while purines have a slight ___.

A

basic, aromatic, double-bond, planar, pucker

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6
Q

The linear and ring sugar structures are ___ in equilibrium. The ring structure, _____ is found in the nucleotide and nucleoside forms of the bases.

A

dynamic, beta-furanose

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7
Q

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

A

pucker, 2’-exo, 3’-exo, orientation, 5’

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8
Q

The 2’OH of ribose favours the ____ ____ conformation, while the 2’ H of deoxyribose favours the _____ ____ conformation

A

C-3’ endo, C-2’ endo

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9
Q

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.

A

1’, 1 N-glycosidic bond, anti

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10
Q

Anti conformations are when the base faces ____ of the sugar and are only possible with ____ due to the steric hindrance with the pentose oxygen

A

outwards, pyrimidines

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11
Q

Syn conformation are where the base faces _____ towards the sugar and are feasible with ____.

A

in, purines

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12
Q

the nucleotide has the ending of ______, while the nucleoside, has the ending of ____

A

-late, -ine

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13
Q

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

A

5’, polymers, cAMP, cGMP

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14
Q

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

A

3’OH, ester, 5’, 3’OH

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15
Q

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

A

polar, hydrophobic, antiparallel

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16
Q

Rule that says the amount of purines must equal the number of pyrimidines

A

chargaff’s rules

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17
Q

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.

A

major, minor, 3, 2, 10.5

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18
Q

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

A

delocalized electron sharing, z, base stacking, hydrophobicity, interior, h-bonding, metal ions

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19
Q

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 ___ ___.

A

N-glycosidic bond, hoogsteen, branched structures

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20
Q

mRNA is always _____ and forms a ____ helix. It is dominated by ____ and can base pair with complementary regions of DNA or RNA.

A

single-stranded, right-handed, base-stacking

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21
Q

___ ___ 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

A

intramolecular, A-form, bulges, loops, palindromic

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22
Q

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

A

base-paired, loops, bulges, hairpins

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23
Q

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

A

3D, charged, ribosome, clover-leaf

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24
Q

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

A

chemical signatures, H-bonding, rotation, pseudouridine

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25
Q

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

A

hydrogen, 2’OH, hoogsteen, W-C

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26
Q

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 ____

A

hydrophobic, insoluble, stacking, van der waals, dipole-dipole, charged, purify, nucleotides, nucleosides

27
Q

All nucleotide bases absorb ___ light and show strong absorption bands near ___ nm

A

UV, 260

28
Q

the observed decrease in the absorption of UV light when complementary strands are paired

A

hypochromic effect

29
Q

the observed increase in the absorption of UV light when a double-stranded nucleic acid is denatured

A

hyperchromic effect

30
Q

the temperature at which 1/2 of DNA is present as separated single strands

A

denaturation temperature

31
Q

denaturation temperature increases with the content of _____ base pairs

A

G-C

32
Q

____ duplexes are more stable to heat denaturation than ___ duplexes. RNA-DNA hybrid stability is generally ____.

A

RNA, DNA, intermediate

33
Q

the melting of the double helix due to pH extremes or high temperatures that disrupt H bonds and base-stacking interactions

A

denaturation

34
Q

The process by which two strands spontaneously rewind when temperature or pH is returned to its normal range

A

anneal

35
Q

____ __ ___ is a method of amplifying DNA segments of interest and relies on ___ ______ that add nucleotides to the ___ ends of preexisting strands called ____

A

Polymerase chain reaction, DNA polymerases, 3’ primers

36
Q

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

A

site directed mutagenesis, amino acid, large, plasmid

37
Q

___ 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 ____

A

2, 10, histone octamer protein, nucleosome

38
Q

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

A

chromatin, 1.6, H2A, H2B, H3, H4

39
Q

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

A

sequence specific, flexible, post-translationally, basic, negative

40
Q

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.

A

in vitro purification, salt, chromosomes

41
Q

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

A

positive, histone, steric repulsion, flexible

42
Q

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.

A

methylated, transcription factors, expression, A, C, s-adenosylmethionine, 5

43
Q

In naked DNA there is a ___ structure with regularly spaced negative charges, which requires __ __ and small ___ molecules to neutralize it and enable flexibility

A

periodic, metal ion, amino-rich

44
Q

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.

A

histone tail, protein complex

45
Q

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

A

single-particle, in situ, heavy metals, mass, absence

46
Q

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

A

fine structural, filtered, energy loss, compressed

47
Q

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

A

electron tomography, angles, number, tilted

48
Q

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

A

30, empty space, density, activate, silence

49
Q

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 ___.

A

staining density, genomic regions, light, duplications, deletions, inversions, karyotyping

50
Q

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 __ ____.

A

fluorophores, anneal, fluorescence light microscopy, chromosome territories

51
Q

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 __ ___

A

chromosome territories, 10nm, epigenetic, spacing, gene expression

52
Q

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.

A

size, function, sub-nuclear spatial, temporal

53
Q

Some proteins and RNA under certain conditions will _____, forming a ____ compartment. They do this by ____ ___ via multivalent domains, or by ___ via disordered/low ____ regions

A

self-solunilize, phase-separated, interlocking proteins, pi-stacking, complexity

54
Q

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 ___ ___.

A

sub-compartmentalized, concentrated, RNA polymerase

55
Q

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

A

protein, fixed, cellular compartments, secondary antibody, DAPI, hoescht, compaction

56
Q

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 _______.

A

de novo, C, T, 11, cryptic splice site, lamin A, progeria

57
Q

An individual with progeria has both a ___ and ___ version of the lamin A ____.

A

normal, shortened, mRNA

58
Q

In SDS-PAGE gel, ____ proteins run higher up on the gel.

A

larger

59
Q

In healthy cells, the nucleus has a smooth ___ shape and lamin localizes mainly to the ____, with some visualized in the ___.

A

oval, periphery, nucleoplasm

60
Q

In progeria cells, the nucleus has a ___ and irregular structure, and lamin is localized throughout the ____.

A

reticulated, nucleoplasm

61
Q

progeria lamin was also more ____ to recover relative to wild type lamin A during a ____ experiment, indicating it is less ____

A

slower, photobleaching, dynamic

62
Q

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

A

GFP, bleached, dynamic nature

63
Q

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 ___

A

oligo, alternatively spliced 11/12, degradation

BIOC 302 (11 decks)

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