DNA and the Organization of the Genome

Question 1

DNA Structure

Answer 1

• Double Helix
• Made of nucleotides with sugar-phosphate backbone
• Two strands held together via hydrogen bonds
• Each strand has a 5’ and 3’ end
• Each strand runs in opposite direction (Anti-Parallel)

Question 2

DNA Replication

Answer 2

1. ) Enzyme Helicase unzips the DNA strands forming a replication fork
2. ) Enzyme Primase makes piece of RNA called a Primer on the template which marks the starting point of the new strand of DNA
3. ) Enzyme DNA Polymerase binds to the primer and makes the NEW strand of DNA from 5’ to 3’
4. ) Enzyme Exonuclease removes the primers and DNA Polymerase fills the gaps with DNA
5. ) Enzyme DNA Ligase seals up the fragments of DNA in both strands to form continuous double strand

Question 3

Leading strand

Answer 3

• New strand of DNA during DNA replication

- Made continuously from 5’ to 3’

Question 4

Lagging strand

Answer 4

• New strand of DNA during DNA replication
• NOT made continuously as it runs in the opposite direction of the leading strand
• Still made in the 5’ to 3’ direction
• Made in small chunks called Okazaki Fragments, each of which is started with an RNA primer

Question 5

Exonuclease

Answer 5

• Enzyme that removes the RNA primers from both the leading and lagging strand after the new strand of DNA is completed
• Another DNA Polymerase then fills in the gaps with DNA

Question 6

DNA Ligase

Answer 6

Enzyme that seals up the fragments of DNA in both strands to form continuous double strand

Question 7

Semi-Conservative DNA Replication

Answer 7

Each new DNA molecule has one old (conserved) strand and one new strand

Question 8

Number of chromosomes in human somatic (non-germline) cells

Answer 8

• 46 Chromosomes

- Arranged in 23 pairs: 22 pairs of autosomes (non-sex chromosomes) and 1 pair of sex cells

Question 9

Autosome

Answer 9

Any chromosome that is not a sex chromosome

Question 10

Sex cells

Male and Female

Answer 10

Male: XY
Female: XX

Question 11

Chromatin

Answer 11

The complex of DNA and proteins of which chromosomes are composed

Question 12

Nucleosome

Answer 12

• Primary structural unit of chromatin, consisting of DNA wrapped twice around a core of 8 histone molecules
• Histones have (+) charge
• Phosphate groups on DNA have (-) charge

Question 13

Histones

Answer 13

Proteins associated with DNA in chromatin. Two copies each of histones H2A, H2B, H3, and H4 make an octamer that is the core of a nucleosome

Question 14

When is chromatin condensed into compact chromosomes?

Answer 14

• During cell division the chromatin is condensed into compact chromosomes that can easily be separated into two daughter cells
• When not in cell division the chromatin is in its decondensed state in the nucleus to allow access to the DNA for gene expression

Question 15

Gene

Answer 15

• Functional hereditary unit of the genome

- Sequence of chromosomal DNA that is required for the production of a functional product

Question 16

Protein-coding gene

Answer 16

Segment of DNA containing the code for the amino acid sequence of a polypeptide chain and the regulatory sequences necessary for its expression

Question 17

What is the product of noncoding genes?

Answer 17

RNA products

Question 18

What direction does transcription occur along DNA?

Answer 18

5’ to 3’

Question 19

• What direction of DNA is considered upstream?

- What direction is downstream?

Answer 19

• The 5’ end is upstream
• The 3’ end is downstream
• This is because transcription is read from 5’ to 3’ along the DNA

Question 20

Promotor sequences

Answer 20

• At the 5’ end of each gene
• Includes sequences responsible for the proper initiation of transcription
• Common sequence that determines the start site in many genes is the TATA box
• Promoter sequences are binding sites for the proteins called transcription factors

Question 21

Exons

Answer 21

• Segments of genes that ultimately determine the amino acid sequence of the protein
• Kept in the mature mRNA during splicing

Question 22

Introns

Answer 22

• Intervening sequences present in the genomic DNA but removed from the mRNA during splicing
• Not represented in the final protein product

Question 23

Cis Regulatory Elements

Answer 23

Sequences on the same molecule of DNA as the gene they regulate

Question 24

Trans Regulatory Elements

Answer 24

Sequences that regulate genes distant from the gene from which they were transcribed

Question 25

Enhancer

Answer 25

- Regulatory element | - DNA sequence that acts in cis to increase transcription of a gene

Question 26

Locus Control Region (LCR)

Answer 26

A DNA domain, situation outside a cluster of structural genes, responsible for appropriate expression of the genes within the cluster

Question 27

Silencer

Answer 27

A DNA sequence that acts in cis to decrease transcription of a nearby gene

Question 28

Transcription Factor

Answer 28

- Large class of proteins - Regulates transcription by forming complexes that bind to regulatory regions of genes to either promote or inhibit transcription

Question 29

Nucleotide general structure

Answer 29

- Phosphate Group - 5-Carbon Sugar - Nitrogenous Base

Question 30

4 Nucleotide Bases in DNA

Answer 30

- Adenine (A) - Thymine (T) - Cytosine (C) - Guanine (G)

Question 31

Purines

Answer 31

- Adenine (A) - Guanine (G) - Made of 2 rings

Question 32

Pyrimidines

Answer 32

- Cytosine (C) - Uracil (U) - (RNA only) - Thymine (T) - Made of 1 ring

Question 33

Nucleotide Complementary Base Pairing

Answer 33

(A) binds to (T) via 2 Hydrogen Bonds (C) Binds with (G) via 3 Hydrogen Bonds

Question 34

Interphase Subphases

Answer 34

- G1 Phase: - S Phase: DNA Replication - G2 Phase:

Question 35

DNA Replication 3 Main Steps

Answer 35

1. ) Initiation 2. ) Elongation 3. ) Termination

Question 36

Initiation Main Steps

Answer 36

1. ) Group of protein form the pre-replication complex 2. ) Looks for specific nucleotide sequences (Origins of Replication) along the DNA strand (lots of A and T bases) 3. ) DNA Helicase can easily separate strands here (A = T only has 2 hydrogen bonds) 4. ) Creates replication fork

Question 37

Single Stranded DNA Binding Proteins

Answer 37

Stabilize the unstable single DNA stands during DNA replication

Question 38

DNA Topoisomerase

Answer 38

- DNA that is double stranded becomes more tight when nearby DNA is unzipped into single strands - DNA Topoisomerase loosens up this tight DNA coil

Question 39

Elongation Main Steps

Answer 39

1. ) RNA Primase randomly synthesizes small lengths of RNA called RNA Primers 2. ) RNA Primers bind to complementary strands of DNA 3. ) DNA Polymerase attaches to this segment of DNA + RNA Primer 4. ) DNA Polymerase adds complementary nucleotides to the signle stranded DNA (Moves 3' to 5' and synthesizes 5' to 3')

Question 40

What is the structural difference between DNA and RNA?

Answer 40

- DNA uses Thymine (T) and RNA uses Uracil (U) | - DNA uses Deoxyribose sugars and RNA uses Ribose sugars

Question 41

Termination mains steps

Answer 41

1. ) Telomere (repeating sequences of TTAGGG) at the end of the chromosome signals DNA Polymerase to hop off the strand 2. ) The two new (semi-conserved) DNA strands separate, finalizing DNA replication