Lecture 1: DNA, Chromosomes, and Genomes Flashcards Preview

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Flashcards in Lecture 1: DNA, Chromosomes, and Genomes Deck (31)
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1
Q

A DNA molecule consists of…

A

Two complementary chains of nucleotides.

2
Q

What makes up a nucleotide?

A

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

3
Q

Describe how nucleotides are linked together to form DNA.

A

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.

4
Q

Which base is this?

A

adenine

5
Q

Which base is this?

A

cytosine

6
Q

Name some physical properties of Nucleosides and Nucleotides.

A
  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
7
Q

Explain the structural properties of Nucleosides and Nucleotides

A
  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
8
Q

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

A
9
Q

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

A
10
Q

Define the term genome

A

The complete set of information in an organism’s DNA

11
Q

Is anti or syn conformations preferred in purines and pyramidines?

A

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.

12
Q

What does semi-conservative replication mean?

A

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

13
Q

What does “c value” mean?

A

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

14
Q

Define the term “karyotype”.

A

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.

15
Q

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

A

Humans: 3.2 x 10^9 nucleotides

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

16
Q

Define a gene

Exons vs introns

A

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

17
Q

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

A

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

18
Q

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?

A

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

19
Q

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

A

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.

20
Q

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)

A
21
Q

How do histones fold together to make the histone octomer?

A

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.
22
Q

Explain how nucleosomes can be very dynamic.

A

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.

23
Q

Nucleosomes are packed together to form a (what)?

Explain the importance of H4 and H1.

A

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.

24
Q

Heterochromatin vs euchromatin

A

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

25
Q

Can chromain structure be inherited?

A

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.

26
Q

Explain how the following picture relates to position effect.

A

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.

27
Q

We can regulate chromatin structure and gene expression by modifying which parts of histones?

What are the four covalent modification examples?

A

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

28
Q

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

A

Reader-Writer Complexes and ATP-dependent chromatin remodeling proteins

29
Q

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

A

Barrier DNA sequences block the spread of reader-writer complexes.

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

30
Q

Which base is this?

A

thymine

31
Q

Which base is this?

A

Guanine