DNA Lecture 6 Flashcards

1
Q

All the DNA that encodes the primary sequence of some final gene product (polypeptide or RNA with a structural or catalytic function)

A

Gene

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2
Q

A single large DNA molecule and its associated proteins, containing many genes. It stores and transmits genetic information

A

Chromosome

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3
Q

Although viral DNA molecules are small, the DNA molecules are much longer than the cells or viral packages in which they are found and vary greatly in size

A

Viruses

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4
Q

These contain much more DNA than viruses, they can have single double-stranded circular DNA molecules, and small circular molecules of DNA free in the cytosol called plasmids

A

Bacteria

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5
Q

These cells have even more DNA than prokaryotic cells, with DNA arranged into chromosomes. The amount of DNA per chromosome and the number of chromosomes is species dependent

A

Eukaryotic cells

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6
Q

Human cells have ____ times more DNA than an E. coli cell

The human body has a total DNA length of

A

700

2x10^11 km
more than 2x the circumference of the Earth

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7
Q

These cell types also have organelles, mitochondria, and chloroplasts than contain DNA.

In animal cells, mitochondrial DNA (mtDNA) is a

A

Eukaryotic cells

Circular Duplex

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8
Q

Genes and regulatory sequences make up almost all of the DNA in

A

Prokaryotes

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9
Q

Many ______ genes have a notable structural feature:

Their nucleotide sequences contain one or more intervening sequences of DNA that don’t code for the amino acid sequence of the polypeptide product

A

Eukaryotic

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10
Q

Non-translated DNA segments in eukaryotic genes are called intervening sequences, aka ____, and the coding segments are called ___

A

Introns

Exons

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11
Q

Cellular DNA is compact and highly organized, the folding into cells of DNA needs to pack it and permit access to the info in DNA.

This important property of DNA means the coiling of a coil, like a telephone cord coiling on itself

A

Supercoilng

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12
Q

DNA is coiled in the form of a

Addition coiling about the axis produces ____, it relieves that structural strain

A

Double helix

Supercoiling

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13
Q

When the is no net bending of the DNA axis onto itself, DNA is in

A

Relaxed State

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14
Q

Replication and transcription of DNA affect and are affected by ____

Both processes require, and helical intertwining complicates this.

A

supercoiling

Strand Separation

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15
Q

Does supercoiling occur in all cellular DNA?

A

Yes

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16
Q

The study of the properties of an object which don’t change under continuous deformations

A

Topology

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17
Q

In DNA, this term means conformational changes due to thermal motion or interaction with proteins or other molecules

A

Continuous Deformation

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18
Q

This means a DNA strand breakage

A

Discontinuous Deformations

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19
Q

Many naturally occurring DNA molecules, particularly bacteria but also DNA found in chloroplasts and mitochondria, are

A

Circular (no 5’ or 3’ end)

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20
Q

A circular DNA structure can be created by forming ____ bonds between the 5’ phosphate of one end and the 3’ OH of the other end of each strand of a linear DNA molecule

A

Phosphodiester

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21
Q

Plasmids and small viral DNAs are small circular DNAs. When they have no strand breaks, they are referred to as

A

Closed-Circular DNAs

22
Q

Closed circular DNA that closely conforms to the B-DNA structure, 10.5 bp/turn, are said to be

Or, in their natural form, they are

A

relaxed

Supercoiled

23
Q

DNA structure is strained, in a manner regulated by the cell, to induce

The strain is usually the result of _____ the DNA double helix in a closed circle.

A

supercoiling

Underwinding

24
Q

In isolated closed, circular DNA, the strain is accommodated by supercoiling rather than strand separation because less energy is required to supercoil than to break

A

Hydrogen bonds

25
In vivo, underwinding DNA makes it easier to separate strands, and gives access to the information they contain Every cell actively underwinds DNA with ____ processes. The resulting strain represents
Enzymatic Stored Energy
26
A topological property of double DNA, that doesn't vary with deformations as long as the two strands remain intacts It is defined as the number of times one closed, circular DNA strand is wound about another
Linking Number
27
DNA underwinding is defined by
Topological linking number
28
These type of properties are changed only by breaking and rejoining of backbone of one or both DNA strands The linking number for a closed, circular DNA is always
Topological An integer
29
If two DNA strands are interwound in a right handed helix, the linking number is Conversely, if the strands are interwound in a left handed helix, the linking number is In DNA, linking numbers are typically
Positive Negative Positive
30
Consider a closed circular DNA with 2100 bp In the relaxed state, there are 10.5 bp/turn LK is _____ If two turns are removed by underwinding the molecule, the linking number becomes _____ and the (delta)lk =
200 198 -2
31
If there is a nick (break) in a DNA strand, Lk is
Undefined
32
Specific linking difference can also be called
Superhelical Density
33
Superhelical density ( σ)can by calculated as the number of turns removed to the number of turns present in relaxed DNA
σ = ∆Lk/Lko
34
In the previous example ∆Lk=-2 and Lko = 200, what is the superhelical density
σ = -2/200 = 0.01 = 1% 1 percent of helical turns present have been removed
35
The degree of unwinding in cellular DNA is..
5 to 7% or σ =0.05 to 0.07
36
The negative sign in supercoiling means the DNA is The positive sign means that it is
Underwound Overwound
37
The linking number can be changed + or - _____ by breaking one DNA strand, rotating the ends 360 degrees about the unbroken strand and rejoining the broken ends
+ or - one
38
Two forms of circular DNA that differ only in a topological property such as a linking number
Topoisomers
39
Linking number (the number of times the two strands are linked together) can be broken down into two structural components, what are they?
Write (Wr) and Twise (Tw)
40
A measure of the of the coiling of the helix axis (supercoiling) Determines the local twisting or spatial relationship of neighboring base pairs
Writhe Twise
41
In terms of writhe and twist, linking number is equal to
Lk= Tw + Wr
42
Do Tw and Wr have to be integers?
No
43
In the example in the figure, the B form of DNA is bent into a circle. Since there are 105 bp and 10.5 bp/turn, what is the twist? The ends are sealed together without twisting to give a relaxed circle, so T= W= L= This is a ___ circle
10 T=10 W=0 L=10 Relaxed
44
In another example, the DNA is underwound by one turn and then the ends are joined together to form a circle (L used to be 10) What is T? What is W? What is L? How many bp/turn? This is a ___ circle
T=9 W=0 L=9 105/9 = 11.67 Strained
45
In another example, the DNA molecule (L=10) supercoils rather than absorbing the strain with a change in twist. The one twist of the coil is right-handed, so it is defined as W= T= L= What type of structure is this?
Negative Supercoil W=-1 T= 1- L=9 Tertiary Structure
46
Most naturally occurring supercoiled DNA molecules are left or right handed? W will be ____ if the DNA is overwound such that the supercoil will be lefthanded
Right handed (-W) Positive
47
In addition to supercoiling and strand separation, the underwinding of DNA also helps promote a number of structural changes in the molecule For example, underwinding a DNA helix keeps the required strand separation need to form the ___ structure described in the last lecture Also, underwinding a right -handed DNA helix facilitates formation of short stretches of left handed DNA in regions where base sequence favors ____
Cruciform Z form
48
Enzymes that increase or decrease the extent of DNA underwinding. They change the linking number. They play an important role in replication and DNA packing
Topisomerases
49
This topoisomerase breaks on of the two DNA strands, the change in Lk is ±1
Type I topisomerase
50
This topoisomerase breaks both DNA strands, and the change in LK is ±2
Type II topoisomerase
51
The effects of the topoisomerase enzymes can be demonstrated by More supercoiled structure are compact, so they move farther down the gel
Agarose Gel electrophresis