Bio Lecture 13

Question 1

What states does DNA go through to become mRNA that is ready for translation?

Answer 1

DNA is transcribed to pre-RNA which includes introns and exons and a cap and a poly A tail. Through RNA processing the introns are removed and mRNA is produced.

Question 2

What are the sequences in the DNA before and after a gene?

Answer 2

Promoters: at the beginning of the gene
Terminators: at the end of the gene

Question 3

What is a nucleotide?

Answer 3

Nitrogenous base plus ribose sugar plus 1-3 phosphates.

Question 4

What is a nucleoside?

Answer 4

Nitrogenous base plus ribose sugar but excludes any phosphate groups.

Question 5

What is the difference between a nucleoside and a deoxynucleoside?

Answer 5

Nucleosides are used to make RNA whereas deoxynucleosides are used for DNA. The only difference is the presence or absence of the OH group on the 2’ carbon of the sugar.

Question 6

Why are the carbons on the sugar called C’ (prime)?

Answer 6

The prime is just to distinguish it from the carbons in the base.

Question 7

What makes up the backbone of DNA?

Answer 7

The phosphate groups on the sugars covalently bond to form a negatively charged phosphodiester backbone.

Question 8

How are the nucleotide bases attached to the backbone on DNA?

Answer 8

Through covalent bonds to the deoxyribose sugars.

Question 9

How do the bases interact in the formation of the double helix?

Answer 9

They form hydrogen bonds between them.

Question 10

Describe the features of a phosphodiester bond.

Answer 10

The 3’ OH group binds covalently to the phosphate group that is bound to the 5’ carbon of the adjacent sugar.

Question 11

In which direction are DNA chains assembled?

Answer 11

DNA is assembled from the 5’ end to the 3’ end. New nucleotides are added to the 3’ end only. This is because the phosphate group on the 5’ end of new nucleotides often goes from having 3 to having just one when it forms the phosphodiester bond. Additions cannot be made to the 5’ end of the DNA.

Question 12

What are the two types of nucleotide bases?

Answer 12

Purines: two-ring structure, Adenine and Guanine
Pyrimidines: one-ring, Cytosine, Thymine, Uracil

Question 13

What allows the bases to form hydrogen bonds with each other?

Answer 13

The presence of electronegative atoms such as Oxygen, and Nitrogen.

Question 14

Which bases bind together?

Answer 14

G-C
A-T (DNA)
A-U (RNA)

Question 15

How many hydrogen bonds does each base pair have?

Answer 15

G-C has 3 hydrogen bonds

A-T has 2 hydrogen bonds

Question 16

Why is hydrogen bonding between bases important for DNA?

Answer 16

1. Stabilizes the double helix
2. Allows correct matching of bases for transcription
3. Correct matching of nucleotides for DNA replication

Question 17

What direction does a DNA helix coil?

Answer 17

It is a right-handed helix.

Question 18

What is the orientation of the bases in relation to the axis of the helix?

Answer 18

They stack in dinner plate fashion perpendicular to the axis of the helix.

Question 19

Is the outer edge of the DNA charged?

Answer 19

Yes. The phosphodiester backbone is negatively charged.

Question 20

What stabilizes DNA?

Answer 20

1. Hydrogen bonding between bases and between H2O and and the electronegative atoms in DNA
2. Base-Stacking Van Der Waals forces between the aromatic rings of each base
3. Ionic bonding between the negatively charge backbone and positively charged divalent cations. This shields the negative charge repulsion between phosphate groups.

Question 21

What are the surface grooves on DNA?

Answer 21

There are major and minor grooves that naturally form in the DNA helix.

Question 22

What is the melting temperature of DNA and how is it related to G-C bonds?

Answer 22

Temperature where DNA strands split apart. G-C bonds are stronger than A-T so the more you have the higher the melting temp.

Question 23

What is chromatin?

Answer 23

A complex made up of DNA and proteins that are used to help organize the DNA.

Question 24

What is a nucleosome?

Answer 24

DNA wrapped around histones which makes up beads on a string.

Question 25

What are the four histone proteins and where are they found?

Answer 25

H1 is a linker histone and is outside the nucleosome core | H2A, H2B, H3, H4 are all present on the core particle and there are two of each in the core.

Question 26

What is a chromatosome?

Answer 26

A nucleosome (DNA+hitone core) and the linker histone H1 included.

Question 27

What is the role of the H1 histone?

Answer 27

It helps to stabilize higher order chromatin structures.

Question 28

What are the first two diameters of the fibers made by necleosomes compacting DNA?

Answer 28

Beads on a string are 10nm | These compact into 30nm fibers

Question 29

How are the 30nm fibers stabilized?

Answer 29

Linker histone (H1) Histone N-Terminal tails Linker DNA

Question 30

What is linker DNA?

Answer 30

The part of the strand that is not wrapped around histones.

Question 31

How is the structural organization of DNA related to transcription for proteins?

Answer 31

Structural organization of DNA is a regulatory means of gene expression. Transcription proteins need access to the DNA before transcription can happen. Fully condensed DNA is inert.

Question 32

Summarize the 6 sizes of packing that DNA can go through.

Answer 32

2nm (just DNA helix) 10nm (DNA + histones) 30nm (packed nucleosomes) 300nm (loop domains of chromosome) 700nm (condensed section of a chromosome) 1400nm ( entire chromosome with both arms)

Question 33

What are euchromatin and heterochromatin?

Answer 33

Euchromatin: transcriptionally active form of DNA in 10nm and 30nm fibers Heterochromatin: highly condensed DNA that is transcriptionally inert

Question 34

What are the two types of heterochromatin.

Answer 34

Constitutive: DNA sequences that are generally not transcribed such as centromeres and telomeres Facultative: Genes that may not be transcribed in this cell, but could be used in another type of cell

Question 35

What are regulatory regions on DNA?

Answer 35

Nucleosome-free zones (linker DNA) interspersed with nucleosome-bound regions where transcription factors can gain access to the DNA.

Question 36

How does histone wrapping influence transcription?

Answer 36

The tighter DNA is wrapped the harder to transcribe. And the opposite for when it is wrapped more loosely.

Question 37

What are histone tails and how do they affect transcription?

Answer 37

Histone tails come off the N-terminus of the proteins that make up histones. The tails can be acetylated, methylated, and phosphorylated to affect how DNA is wrapped around it.

Question 38

What part of histones interacts with the DNA?

Answer 38

There is a lot of positively charged Lysine in the tails of histone that interacts with the negative backbone of DNA to hold it in place.

Question 39

How does acetylation affect the histones?

Answer 39

Acetylation happens to the Lysines in the tails of the histones and this removes the positive charge that was used to bind to the phosphates in the DNA. This loosens the wrap of DNA.

Question 40

What are the two types of enzymes involved with acetylation of histones?

Answer 40

``` Histone acetyltransferases (HATs) loosen by adding an acetyl group and this increases transcription Histone deacetylases (HDACs) tightens by removing acetyl groups and decreases transcription ```

Question 41

Describe the characteristics of histone methylation.

Answer 41

The lysines in the tails can have methyl groups added to them. This does not remove the positive charge that they have. They can have 1, 2, or 3 methyl groups added.

Question 42

Explain the phosphorylation of histones.

Answer 42

Serine and threonine residues in histones can be phosphorylated. The overall pattern of phosphorylation, methylation, and acetylation alters the binding of transcription complexes and regulatory proteins.