Lecture 1: DNA, Chromosomes, and Genomes

Question 1

A DNA molecule consists of…

Answer 1

Two complementary chains of nucleotides.

Question 2

What makes up a nucleotide?

Answer 2

Each nucleotide contains a 5 carbon sugar (deoxyribose), a phosphate, and a base.

Question 3

Describe how nucleotides are linked together to form DNA.

Answer 3

The nucleotides are covalently linked into a polynucleotide chain (a DNA strand) through the sugars and phosphates, forming a “backbone.” A DNA strand has its chemical polarity (5’ and 3’). A DNA molecule is composed to two DNA strands held together antiparallel by hydrogen bonds between the paired bases. This results in the double helix structure of DNA.

Question 4

Which base is this?

Answer 4

adenine

Question 5

Which base is this?

Answer 5

cytosine

Question 6

Name some physical properties of Nucleosides and Nucleotides.

Answer 6

1. Very soluble in water
2. Nucleobases and nucleosides are uncharged at biologically relevent pH’s
3. Nucleotides carry negative charge at physiological pH
4. Nucleosides and nucleotides are relatively stable over a wide range of pH’s
5. Purine and pyrimidine bases absorb uv strongly at 260 nm

Question 7

Explain the structural properties of Nucleosides and Nucleotides

Answer 7

1. The five membered ring in pentose sugards is very flexible
2. The rings are not co planar and two of the atoms twist outside of the plane
3. Due to the substitution patterns in nucleosides, two conformations are preffered
4. This “sugar puckering” is defined by the 2’ and 3’ carbons above the plane and are known as C2’-endo and C3’-endo conformations
5. These two conformations are in rapid flux in solution

Question 8

Draw the C-2 Endo Formation. What kind of molecule is it preffered in?

Answer 8

Question 9

Draw the C-3 endo formation. Where is this preferred?

Answer 9

Question 10

Define the term genome

Answer 10

The complete set of information in an organism’s DNA

Question 11

Is anti or syn conformations preferred in purines and pyramidines?

Answer 11

Anti is preferred in both. SYN doesn’t even exist for pyramidines. It does exist in purines, but syn is preferred. It is due to steric hindrance in both cases.

Question 12

What does semi-conservative replication mean?

Answer 12

It means that one template strand from the parent will be encorporated into each daughter cell

Question 13

What does “c value” mean?

Answer 13

C value is the genomic content. Plants have very large c values

Question 14

Define the term “karyotype”.

Answer 14

Karyotypes describe the number of chromosomes and how they look under a microscope. Attention is paued to their length, position of centromeres, banding pattern, difference between sex chromosomes and physical characteristics.

Question 15

For humans, roughly how many nucleotides do we have? And how many chromosomes?

Answer 15

Humans: 3.2 x 10^9 nucleotides

46 chromosomes total (22 pairs and then X + Y in males or two X’s in Females)

Question 16

Define a gene

Exons vs introns

Answer 16

A gene is usually defined as a segment of DNA that contains instructions for making a certain protein…but some genes produce RNA as their final product

Note: Genes contain both exons and introns

exon: coding region

Intron: non-coding region

Question 17

During which phase of a cell during a eukaryotic cell cycle is there a lot of gene expression? When does DNA replicate itself?

Answer 17

Interphase is where there is a lot of gene expression. Interphase is also where DNA gets replicated.

Question 18

Each DNA molecule that forms a linear chromosome must contain which elements? In other words, what are the DNA sequences reaquired to produce a chromosome that can be replicated and then segregated?

Answer 18

Two telomeres, a centromere, and a few origins of replication

Question 19

Define the following terms: replication origin, telomere, and centromere

Answer 19

Replication Origin: the location at which duplication of DNA beings (Eukaryotic chromosomes have SEVERAL)

Telomere: ends of a chromosome, contain several repeating sequences to protect the ends

Centromere: specialized DNA sequence that allows one copy of each duplicated and condensed chromosome to be pulled into each daughter cell after division…protein complex called kinetochore attaches the duplicated chromosome to mitotic spindle, allowing them to be pulled apart.

Question 20

Explains nucleosomes as the classic “beads on a string”. What does a nucleosome include? How do you break down the linker DNA? If you break down it even further what are the components? (HINT: think of the flowchard from lecture)

Answer 20

Question 21

How do histones fold together to make the histone octomer?

Answer 21

Histone fold “handshake dimer”:

1. The H3-H4 dimers combine to form a tetramer and then bind to DNA.
2. Then, two H2A-H2B dimers are added to complete the nucleosome.

Question 22

Explain how nucleosomes can be very dynamic.

Answer 22

Nucleosome is dynamic when it opens, allowing for DNA binding proteins.

Through ATP hydrolysis, nucleosomes can be slid downstream by ATP-dependent chromatin remodeling complexes.

Question 23

Nucleosomes are packed together to form a (what)?

Explain the importance of H4 and H1.

Answer 23

Nucleosomes are packed together into a compact chromatin fiber.

H4 (histone tail) is important for nucleosome to nucleosome linkages.

H1/”linker histone” (one per nucleosome) is outside the nucleosome. It occupies 20 nucleotides worth of DNA when it binds and bends DNA into a different conformation to make it more compacted.

Question 24

Heterochromatin vs euchromatin

Answer 24

Heterochromatin: highly condensed form (10ish percent is packaged this way)

Euchromatin: lightly packed form of chromatin, rich in gene concentration, and often (but not always) under active transcription…MOST ACTIVE PART OF GENOME… comprises about 90% of genome

Question 25

Can chromain structure be inherited?

Answer 25

YES, certain types of chromatin structure can be directly passed down from a cell to its decendants. Because the cell memory that results is based on an inherited chromatin structure rather than on a change in DNA sequence, this is a form of **epigenetic inheritance.**

Question 26

Explain how the following picture relates to position effect.

Answer 26

In chromosome breakage and rejoining events, the zone of silencing (where euchromatin is converted to heterochromatin) spreads for dirrerent distances in early embryos. These distances are then passed down (once heterochromatic condition is established on chromatin it is inhereited by all progeny. The white gene in flies creates red pigment. White+ aka normal flies have all red eyes. In flies where a normal white gene has been moved near a region of heterochromatin, the eyes are mottled. The presence of red/white patches reveals that the state of transcriptional activity, as determined by the packaging of the gene into chromatin can be passed down/inherited.

Question 27

We can regulate chromatin structure and gene expression by modifying which parts of histones? What are the four covalent modification examples?

Answer 27

**Modification of the core histone tails** regulates chromatin structure and gene expression. Four examples of covalent modification: Acetylation, Methylation, Phosphorylation, Ubiquination Remember: Acetylation generally means activation/opening up for transcription Methylation generally causes in activation

Question 28

What two kinds of complexes can spread chromatin changes along a chromosome?

Answer 28

Reader-Writer Complexes and ATP-dependent chromatin remodeling proteins

Question 29

What do barrier DNA sequences do? Also, what are their three main courses of action?

Answer 29

Barrier DNA sequences **block the spread of reader-writer complexes.** ## Footnote Mechanism of Barrier Action: A. Tethering a region of chromatin to nuclear pore complex B. Tight binding of barrier proteins to nucleotides C. Recruiting group of highly active histone modifying enzymes to erase histone markers

Question 30

Which base is this?

Answer 30

thymine

Question 31

Which base is this?

Answer 31

Guanine