Lecture 1- Genome Structure

Question 1

What is the order of genome structure?

Answer 1

DNA- chromosome- double helix- gene

Question 2

Where is DNA found in eukaryotic and prokarytoic cells

Answer 2

The nucleus in eukaryotic cells
The nucleoid in prokaryotic cells

Question 3

How many chromosomes do we have

Answer 3

46 (2 sets of 23)

Question 4

How many sex chromosomes

Answer 4

4 (2 sets of 2)

Question 5

How many autosomal chromosomes

Answer 5

44 (22 sets of 2)

Question 6

What is the double helix

Answer 6

Described by Watson and Creek, it is two polymeric strands woven around a common axis in an antiparallel orientation (5’ and 3’)

Question 7

A bound to T has how many hydrogen bonds?

Answer 7

2

Question 8

G to C has how many bonds?

Answer 8

3

Question 9

What is a gene

Answer 9

It is the length of DNA that directs the synthesis of one protein

Question 10

DNA consists of:

Answer 10

1. Sugar (deoxyribose)
2. Phosphate
3. Nitrogen basesous

Question 11

Why are the bases in the middle of the DNA strand?

Answer 11

This is because the bases are hydrophobic and the sugar-phosphate backbone is negatively charged and hydrophilic so it can form bonds with water.

Question 12

Nitrogenous bases in DNA:

Answer 12

Purines: Adenine and Guanine
Pyrimidines: Cytosine, Thymine, Uracil

Question 13

Sugar-Phosphate Backbone:

Answer 13

-It forms the structural framework of nucleic acids
-It is composed of alternating sugar and phosphate groups, and defines directionality of the molecule.
-The sigar is the 3’ end and the phosphate is the 5’ end.

Question 14

How are Phosphodiester bonds formed

Answer 14

-The phosphate group links C3 (3’ carbon) of a sugar to C5 of a neighbouring sugar

Question 15

What are phosphodiester bonds

Answer 15

They are covalent bonds that link nucleotides together.

Question 16

Why are GC rich regions more thermodynamically stable than A-T regions

Answer 16

Because they have 3 hydrogen bonds

Question 17

Types of Covalent Bonds:

Answer 17

Phosphodiester bonds

Question 18

Non-covalent bonds:

Answer 18

-Base stacking (van der waals interactions)
-Hydrogen bonding between nucleotides

Question 19

Which is the strongest non-covalent bond in DNA

Answer 19

Van der Waals interactions between the stacked base pairs

Question 20

What is hybridisation

Answer 20

When two complementary single stranded DNA/RNA molecules bond together to form a double strand

Question 21

What technique utalizes hybridisation

Answer 21

PCR (polymerase chain reaction)

Question 22

What structures is DNA condensed into

Answer 22

Basic helix to nucleosome to chromatin to scaffold to loops to chromosome

Question 23

What is chromatin and what are the two types:

Answer 23

It is DNA & Protein structure allowing controlled genome organisation and folding
1. Euchromatin
2. Heterochromatin

Question 24

Euchromatin:

Answer 24

-Less condensed
-Transcriptionally active
-G-C rich
-Stains poorly with Giemsa stain
-Weak binding to H1

Question 25

Heterochomatin:

Answer 25

-Higly condensed -Transcriptionally inactive -A-T rich -Stains darkly -Tightly bound to H1

Question 26

Nucleosome structure:

Answer 26

-Refered to as 'string of beads' Contains an octamer core particle, 146 bp of DNA wrap around the octomer (linker DNA), the histone 1 (H1) holds it together.

Question 27

What is the octomer core

Answer 27

Contains 8 histone proteins -H2A, H2B, H3 and H4 (X2) -Has a positive charge

Question 28

Chromsome structure:

Answer 28

-Contains two identical chromatids (one half) -P arm: short arm structure -Centromere: constricted point of the chromosme Q arm: Long arm structure

Question 29

Other components of chromosome:

Answer 29

-Centromers -Origin of replication -Telomers

Question 30

Centromeres

Answer 30

Essential for mitotic spindle Characterised by repetitive DNA

Question 31

Origin of replication

Answer 31

Point where DNA synthesis is initited Multiple origins on a chromosome which speeds replication

Question 32

Telomeres

Answer 32

Caps the end of chromosmes which act as a buffer Maintains structure integrity

Question 33

Ways to stain chromsome

Answer 33

-Karyotyping (picture of individual chromosome) -Trypsin or Giesma stain (will show dark or light bands to correlate with the density of chromatin folding)

Question 34

Cell types and chromosomes number:

Answer 34

Somatic cells are diploid (46 chromsomes) Gamete cells are haploid (23 chromsomes)

Question 35

Nuclear Genome

Answer 35

-Linear molecules with 3.3 billion base pairs -93% non coding -Has chromatin -Inheritance is equal between parents

Question 36

Mitochondrial Genome

Answer 36

-Circular molecules with 16,569 thousand base pairs -Involved in oxidative phosphorylation system -3% non coding -No chromatin -Inheritance is only maternal

Question 37

Coding DNA

Answer 37

-5% of our genome codes for genes and is conserved. -95% is non conserved and can evolve quickly

Question 38

Non-coding DNA

Answer 38

Is highly variable and constitutes 30%-99% of the total genome It is made up of: -Transposons: mobile DNA sequences that can migrate to different regions of the genome (approx 40%) -Microsatellites (approx 5%) -Other Repeat DNA (approx 50%)

Question 39

Non-coding elements:

Answer 39

Introns Promoters Ehancers Inhibitors Pseudogene Telomeres (see slide 32 and 33 for explinations)