4 - Genes, genomes and DNA

Question 1

plastid

Answer 1

Any organelle that is genetically equicalent to a chloroplast, whether functional in photosynthesis or not

Question 2

urkaryote

Answer 2

hypothetical ancestor that provided the genetic information of the eukaryotic nucleus

Question 3

intergenic DNA

Answer 3

noncoding DNA that lies between genes

in humans, some regions have a lot of intergenic DNA, others have genes closer together

Question 4

intervening sequences

Answer 4

introns

segments of genes that do not code for a protein but is transcribed as they are within the gene

Question 5

LINE

Answer 5

long interspersed element. Long sequences found in multiple copies that makes up most og the moderatively repetetive DNA of mammals
thought to be derived from retro-virus-like ancestors

Question 6

pseudogene

Answer 6

defective copy of a gene

Question 7

moderatively repetetive sequences

Answer 7

DNA sequences that exist in hundreds or thousands of copies (25% of the human genome falls into this category)

Question 8

what happens if large numbers of a repeated sequence family are present?

Answer 8

it is typically true that most individual copies are defective and the majority have substantial deletions relative to the parental sequence. Ribosomal RNA genes are the single major exception to this rule

Question 9

SINEs

Answer 9

short intersperesed elements. almost all are nonfunctional. The best known SINE is the 300 bp Alu element, scattered thoughout the human DNA (300,000 to 500,000 copies per haploid genome). Might bind to RNA polymerase II and supress gene transcription

Question 10

satellite DNA

Answer 10

highly repetitive DNA of euk cells that is found as long clusters of tandem repeats and is permanentlu coiled tightly into heterochromatin

Question 11

unequal crossing over

Answer 11

crossing over in which the two segemnts that cross over are of different lenghts; often due to midalignment during pairing of DNA strands.

Question 12

alpha DN

Answer 12

tandem DNA repeats found around the centromere in human DNA

Question 13

CEN

Answer 13

centromere sequence. A recognition sequence founf at the centromere and needed for attachment of the spindle fibers

Question 14

microsatellite and minisatellite

Answer 14

VNTRs. micro = ca 13 bp, mini = ca 25 bp

Question 15

inverted repeat

Answer 15

palindrome. on double stranded DNA, a sequence that is identical when read forwards on one strand and backwards on the complementary strand. As opposed to mirror-like palindrome, which works the same way as words

Inverted repeats are important as recognition sites on DNA for binding of proteins.

Question 16

hairpin vs stem and loop

Answer 16

hairpin is a U with bases on borth sides. energetically unfavorable. Stem and loop is like a penis, paired along the shaft with unpaired bases at the head in a loop.

Question 17

bent DNA

Answer 17

ddouble helical DNA that is bent due to several runs of A’s; three to fiev A-runs separated by 10 bp forms bends in the helix. Causes increased resistance in agarose gel electrophoresis

Question 18

G-quadruplex

Answer 18

tend to form in one strand when the helix is opened up (transcription or replication). Stable - can block replication or transcription. helicase enzymes can unfold them.

some guanine rich DNA strands can fold into four-stranded helical structures (G-quadruplexes). formation requires four tracts of three or more gunines separated by one to seven other bases in one strand of the DNA.

Question 19

Supercoiling

Answer 19

telefon-ledning. double helix is a right-hand twist, negative supercoiling is left-handed. negative helps promote the unwinfding and strand separation under transcription and replication.

Question 20

cccDNA

Answer 20

covalently closed circular DNA. no nicks in either strand (if so, it can unravel and is known as an open circle) Bacterial chromosomes and plasmids.

Question 21

nucleiod

Answer 21

area within bacterial cell that contains the genome; not surrounded by membranes.

Question 22

partitioning

Answer 22

movement of each replicated copy of the chromosome into each respective daugther cell during cell division.
Mediated by ParA, ParB and specific DNA sequences near the origin of replication (/parS/ sites).
ParB binds to /parS/ on DNA, spreads along the DNA to coved adjecent nucleotides, creating a nucleoprotein filament that acts somewht like the euk centromere. This structure then binds ParA, an ATPase that creates long polymers that help partition the new chromosome into wach half of the cell. ParB also attracts condensin (a protein complex that maintains chromosome structure in both prok and euks.

Question 23

Linking number (L)

Answer 23

Sum of the superhelical turns (the writhe, W) plus the double helical turns (the twist, T). basically double helix + supercoiling. L = W + T

Question 24

topoisomers

Answer 24

The same circular DNA molecule can have different numbers of supercoils
Isomeric forms that differ in topology (i.e., their level of supercoiling and catenation) but not in seq

Question 25

catenates

Answer 25

structure in which two or more circles of DNA are interlocked

Question 26

topoisomerases

Answer 26

the enzymes that insert ot remove supercoils.
Type I break only one strand of DNA (changes L in steps of one).

Type II (including DNA gyrases) break borh strands of the DNA and pass another part of the double helic through the gap. Changes L in steps of 2

Question 27

gyrase

Answer 27

type of Type II topoisomerase. Introduces negative supercoils into closed circular molecules of DNA. cut strands, twist, rejoin strands.

changes conformation to inactive form after introducing a coil. Reactivation demands energy.

Can also remove negative (not positive) supercoils without using ATP (slower).

to subuntis; GyrA cuts and rejoins, GyrB provides energy by ATP hydrolysis

Question 28

Quinolone antiboitics

Answer 28

inhibit DNA gyrase by binding to the GyrA protein

Question 29

What must happen in order for replication or transcription to proceed more than a short distance?

Answer 29

When the double helix is unwound, it creates positive supercoiling ahead (even though the negative supercoiling aids the unwinding, it is not enough). Therefore, Gyrase must insert negative supercoils to cancel out the new positive ones. Behind the replication/transcription apparatus, negative supercoiling is generated. Topoisomerase I removes any excess neg supercoils.

Question 30

How does supercoiling affect DNA structure?

Answer 30

supercoiling places DNA under strain. May lead to alterations in DNA structure to relieve the strain. Three examples: crucifom structures, Z-DNA, H-DNA. Depend on cerain special characteristics within the DNA sequence, as well as supercoiling stress

Question 31

crucifom structures

Answer 31

Cross-like. Formend when strands in a palindrome are separated and formed into two stem-and-loops opposite each other. chance of forming increases with the level of negative supercoiling and the lenght of the inverted repeat. in practice, 4-8 base sequences recognized by most regulatory proteins and REs are too short to yield stable cruciformstructures, palindromed of 15-20 will produce crucifom structures.

Question 32

Z-DNA (OBS! Mer 121-122)

Answer 32

alternative form for the DNA; left-handed turns and 12 bp per turn
longer and thinner than B-dna.
high sat favors Z-DNA as it decreases repulsion between the negatively charged phosphates of the DNA backbone.
formed in regions of DNA with many alternating GT or GC paris (abbreviated (GC)n(GC)n and (GT)n(AC)n

helps remove supercoiling stress.

Question 33

H-DNA

Answer 33

triple helix, formation is promoted by acid conditions and by runs of purine bases

Question 34

why cant electrophoresis happen in free solution?

Answer 34

larger fragments have more negative charge - in free solution this will make up for the added restistance = no separation

Question 35

Agarose

Answer 35

most common gel electophoresis
polysaccharide from seaweed
water + agarose + boiing = homogenous solution. Cooling = meshwork with pores/openings filled with water. Pore size suitable for separation of fragments with several hundre nt or longer. If shorter, polyacrylamide is used

Question 36

polyacrylamide

Answer 36

finer pores than agarose, can separate smaller fragments better

Question 37

How to visualize a gel

Answer 37

staining with ethidium bromide. Examine under UV light.
ethidium bromid is a DNA mutagen - less toxic dyes are sometimes used, like methylene blue and SYBR green. Less sensitive, but do their job.

Question 38

How will cccDNA etc act in gel electrophoresis?

Answer 38

cccDNA: faster than linear DNA
open circular DNA: slower than linear DNA
the more superhelical twists, the more compact the molecule and the further it will go.

Question 39

B-form DNA/B-DNA

Answer 39

Watson and Crick form

Question 40

A-DNA

Answer 40

shorter and fatter double helix than the B-form. 11 bp per turn. More common in dsRNA, rare for DNA bases tilt away from the axes, minor groove = broader and shallower, major groove = narrower and deeper. dsRNA, or a ds RNA/DNA hybrid usually form an A-helix, as the extra OH in RNA prevents the formation of a B-helix. dsDNA usually only forms A-helix if dehydrated or high [salt].

Question 41

Hoogsteen base pair

Answer 41

type of non-standard base pair found in triplex DNA, in which a pyrimidine is bound sideways on a purine.
in H-DNA, A pairs with two Ts, G with two Cs. An extra proton is needed for the H-bonds.

Question 42

DNA packaging

Answer 42

DNA is wound around special proteins called HISTONES. 8 histone = core unit, two of H2A, teo H2B, 2H2C and 2H2D. DNA wraps around the ball of histones twice. Thus structure is calles a NUCLEOSOME. CHROMATIN = DNA + proteins required for control of conformation. Chromatin varies in structure based on condensation. Between each core unit, there is a string of “free” DNA protected by one single histone, H1.

Question 43

30 nm fiber

Answer 43

The chain of nucleosomes is wound into a giant helical structure with six nucleosomes per turn

Question 44

heterochromatin

Answer 44

highly condensed form of chromatin that cannot be transcribed as it is unaccessible for RNA pol.

Question 45

euchromatin

Answer 45

normal chromatin, as opposed to heterochromatin

Question 46

chromatid

Answer 46

Single double-helical DNA molecule making up whole or half of a chromosome; a chromatid also contains histones and other DNA-associated proteins.