Chapter 16 - Molecule Basis for Inheritance(DNA Synthesis)

Question 1

Helic

Answer 1

= a spiral

Question 2

Liga

Answer 2

= bound or tied

Question 3

Semi

Answer 3

= half

Question 4

Telos

Answer 4

= an end

Question 5

DNA Ligase

Answer 5

A linking enzyme essential for DNA replication.

Question 6

DNA Polymerase

Answer 6

An enzyme that catalyzes the elongation of new DNA at a replication fork by the addition of nucleotides to the existing chain.

Question 7

Double Helix

Answer 7

The form of DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.

Question 8

Helicase

Answer 8

An enzyme that untwists the double helix of DNA at the replication forks.

Question 9

Lagging Strand

Answer 9

A discontinuously synthesized DNA strand that elongates in a direction away from the replication fork.

Question 10

Leading Strand

Answer 10

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5’ to 3’ direction.

Question 11

Mismatch Repair

Answer 11

The cellular process that uses special enzymes to fix incorrectly pairs nucleotides.

Question 12

Nuclease

Answer 12

An enzyme that can break DNA and RNA into their component nucleotides.

Question 13

Nucleotide Excision Repair

Answer 13

The process of removing and then correctly replacing a damaged segment of DNA using the undamaged strand as a guide.

Question 14

Okazaki Fragment

Answer 14

A short segment of DNA synthesized on a template strand during DNA replication.

Many Okazaki fragments make up the lagging strand of newly synthesized DNA.

Question 15

Origin of Replication

Answer 15

Site where the replication of a DNA molecule begins.

Question 16

Primase

Answer 16

An enzyme that joins RNA nucleotides to make the primer.

Question 17

Primer

Answer 17

An RNA polynucleotide with a free 3’ end, bound by complementary base pairing to the template strand.

Question 18

Replication Fork

Answer 18

A Y-Shaped region on a replicating DNA molecule where new strands are growing.

Question 19

Semiconservative model

Answer 19

Type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand.

Question 20

Single-strand Binding Protein

Answer 20

Molecules that line up along the unpaired DNA strands, holding them apart while the DNA strands serve as templates for the synthesis of complementary strands of DNA.

Question 21

Telomerase

Answer 21

An enzyme that catalyzes the lengthening of telomeres.

Question 22

Telomere

Answer 22

The protective structure at each end of a eukaryotic chromosome.

Question 23

What is DNA?

Answer 23

Deoxyribonucleic Acid.

• Molecule that encodes our heredity information by providing the instructions for the manufacture of proteins.
• this information is passed from parent to offspring and from cell to cell during cell division.

Question 24

DNA Structure

Answer 24

double stranded helical molecule with each strand a polynucleotide comprised of nucleotides.

o	Each nucleotide is made up of a phosphate group covalently bound to deoxyribose (a pentose sugar) and the sugar is covalently bound to one of 4 nitrogenous bases
	Adenine (A)
	Thymine (T)
	Guanine (G)
	Cytosine (C)

o The order of bases contains the genetic code for making proteins
o The 2 strands of DNA are held together by hydrogen bonds between the base pairs and are antiparallel

Question 25

Chargaffs Rule(DNA structure and templating)

Answer 25

• Adenine amounts match with Thymine amounts
• Cytosine amounts matches with Guanine amounts
• These base pair rules allows one strand of DNA to serve as a template or pattern so that DNA can easily make identical copies of itself

Question 26

DNA Replication

Answer 26

S Phase of cell cycle.

• semi-conservative manner
  o Of the 2 resulting daughter DNA molecules, each is a mixture of one parental strand and one daughter strand

Question 27

Eukaryotic chromosome shape and replication

Answer 27

• Linear with replication beginning at multiple origins and going in both directions away from the origins.

o When the parental DNA strands are separated, a replication bubble forms to allow the new daughter nucleotides access to the template strands of DNA

Question 28

Synthesizing a new DNA strand or repair of an existing strand requires several enzymes

Answer 28

o DNA polymerases is a family of enzymes responsible for adding new nucleotides to the growing strand, replacing damaged nucleotides or replacing RNA primers

o Helicase untwists the double helix and separates the parental DNA strands

o Single strand binding proteins keeps the 2 parental strands from reforming their original base pairs during replication

o Topoisomerase prevents overwinding of the DNA strands
o Primase assembles RNA nucleotides into primers

o DNA ligase seals fragments of DNA together

o Nuclease can cut out damaged parts of DNA

Question 29

DNA Polymerases(DNA Synthesis)

Answer 29

A family of enzymes responsible for adding new nucleotides to the growing strand, replacing damaged nucleotides or replacing RNA primers.

Question 30

Helicase(DNA Synthesis)

Answer 30

untwists the double helix and separates the parental DNA strands.

Question 31

Single Strand binding Proteins(DNA Synthesis)

Answer 31

keeps the 2 parental strands from reforming their original base pairs during replication.

Question 32

Topoisomerase(DNA Synthesis)

Answer 32

prevents overwinding of the DNA strands.

Question 33

Primase(DNA Synthesis)

Answer 33

assembles RNA nucleotides into primers.

Question 34

DNA Ligase(DNA Synthesis)

Answer 34

seals fragments of DNA together.

Question 35

Nuclease(DNA Synthesis)

Answer 35

Can cut out damaged parts of DNA.

Question 36

DNA polymerase requires the binding of an RNA primer to initiate replication

Answer 36

o Once the RNA primer is in place (base pairing with the DNA parental strands), DNA polymerase can add DNA nucleotides to the 3’ end of the primer so DNA replication proceeds in a 5’ to 3’ direction on the new daughter strand

o From each origin of replication, replication can proceed in both directions
 The new daughter strand that has a free 3’ end is called the leading strand and only requires one primer
 The new daughter strand that does not have a free 3’ end is called the lagging strand and must be made in a series of small pieces called Okasaki fragments, each fragment requiring its own primer

Question 37

What happens after DNA replication?

Answer 37

After both strands are replicated, the RNA primers are removed and DNA polymerase replaces the RNA nucleotides with DNA nucleotides and DNA ligase seals the fragments.

Question 38

If an incorrect base pairing occurs (mismatch),

Answer 38

DNA polymerase can often immediately correct the mistake.

Question 39

Later damage to the DNA molecule can sometimes be fixed by a nucleotide excision repair in which the damaged section is removed by nuclease,

Answer 39

DNA polymerase adds back correct nucleotides and DNA ligase seals the fragment.

Question 40

What are mutations?

Answer 40

changes in the DNA sequence and may or may not pass on to future generations.

Question 41

The end replication problem is caused because at the end of linear chromosomes, the last Okasaki fragment’s primer is removed but can not be replaced by DNA polymerase because there is no free 3’ end for the enzyme to work with

Answer 41

o This causes chromosomes to become shorter with each round of replication

o Telomere regions at the ends of eukaryotic chromosomes do not contain coding regions and therefore are protective “caps” that prevent coding genes from being degraded for a time
 When real coding regions are affected, the cell typically ceases to function

o Telomerase is an enzyme present in germ line cells which allows chromosomes to be lengthened for gamete formation
 Some cancer cells also have active telomerase which may explain some of their “immortal” characteristics

Question 42

DNA is packaged in the nucleus along with proteins called histones that wind the DNA into bead like structures called nucleosomes

Answer 42

o Euchromatin is more loosely packaged and will allow gene transcription for protein synthesis during interphase

o Heterochomatin, which is present at the telomere and centromere regions, is more tightly packed and prevents access to the DNA located there so these regions do not code for any proteins

o DNA is relatively diffuse during most of the cell cycle but condenses and loops around the histones during cell divisions to allow easier separation of the chromosomes

Question 43

Structure of DNA and Base Pairing Rules

Answer 43

DNA’s double helix structure allows it to be easily replicated which is necessary to pass the genetic material from parent to daughter cells.

The base pairing rules involve only matching certain nitrogenous bases with other ones. The rules are that adenine pairs with thymine and cytosine pairs with guanine.

These rules allows one strand of DNA to act as a template so that new nucleotides come in after the original strands separate and base pair appropriately, creating a new daughter strand.

Question 44

Describe the components of DNA including what comprises a nucleotide.

Answer 44

DNA is a nucleic acid and the monomer of nucleic acids is the nucleotide.

All nucleotides are made of a 5 carbon sugar, phosphate group and a nitrogenous base. In DNA, the sugar is called deoxyribose.

Nitrogenous bases can be classified as purines (double ring of nitrogens) or pyrimidines (single ring). Adenines and guanines are purines and cytosines and thymines are pyrimidines.

Question 45

Describe the overall process of DNA replication.

Answer 45

At certain points (origins of replication) along the double strand of DNA, the 2 strands separate creating a replication bubble. Bubbles form at multiple points along the long strand of DNA.

Replication can then progress going in either direction of the strand to make the process happen quickly.

Once the strands are separated, new nucleotides come in and base pair appropriately with the nucleotides on the template strand.

After all nucleotides are matched up, there will be 2 double stranded DNA molecules, each possessing one parental (old) set of nucleotides and one daughter (new) set of nucleotides.

This method is called
the semi-conservative process of DNA replication.

Question 46

Explain the role of DNA polymerases in replication. What are DNA polymerase’s limitations?

Answer 46

DNA polymerases are enzymes that help add new nucleotides to the growing daughter strands of DNA. They also help in repairing nucleotide mistakes when mutations occur and replacing the RNA primers with DNA nucleotides.

DNA polymerases can only add nucleotides to the 3’ end of the daughter strand. It can also only add nucleotides to a strand that is primed with a RNA primer.

Question 47

Distinguish between the leading strand and the lagging strand. Define Okazaki fragments.

Answer 47

The leading strand is the daughter strand that is made continuously in the 5’ to 3’ direction as DNA polymerase adds new nucleotides to the 3’ end.

The lagging strand can not be made continuously but instead short segments are primed with RNA primers and nucleotides added to the 3’ ends at various places along the template strand, forming Okazaki fragments.

These fragments are later fused together with DNA ligase after the RNA primers are replaced with DNA nucleotides.

Question 48

Explain the roles of DNA ligase, primer, primase, helicase, and single-strand binding
proteins in DNA synthesis.

Answer 48

DNA ligase: Enzyme that seals Okazaki fragments together. Also seals nicks when nucleotide mistakes are removed and replacement nucleotides are brought
it.

Primer: Short stretch of RNA nucleotides that base pair with the template strand
of DNA to get the replication process started.

Primase: Enzyme that makes the RNA primer.

Helicase: Enzyme that helps unwind the double helix of the parental DNA to allow for replication.

Single stranded binding proteins: Help the parental strands of DNA to stay unwound and allow for replication.

Question 49

Explain the mechanisms in place to repair DNA mistakes and damage.

Answer 49

A mismatch repair happens during initial pairing when the wrong base pairs with a non-complementary partner.

These mistakes can be fixed immediately by DNA polymerase much like deleting a wrong letter on a keyboard and typing the correct one.

An excision repair occurs when DNA is damaged later by environmental conditions such as chemicals, radiation, UV light, etc. Nuclease is an enzyme that cuts out the damage and DNA polymerase replaces the area with correct nucleotides and ligase seals the nicks between the new section of nucleotides and the rest of the strand.

Question 50

Describe the significance of telomeres.

Answer 50

Because DNA polymerase needs a RNA primer to initiate DNA replication and it can only add to the 3’ end of a growing strand, when the primer is removed at the
ends of the linear DNA molecule, there will remain a gap that can not be replaced with DNA nucleotides. This results in a shortening of the chromosomes with
each round of replication.

To avoid the shortening of real genes, the ends of linear DNA have non-coding stretches of DNA called telomeres in order to protect the real genes. This means that older somatic cells all have shorter chromosomes than young ones.

It is believed that eventually the shortening will begin to impact important genes and this will trigger cell death. Only cells such as gametes or some cancer cells have an enzyme called telomerase that can lengthen shortened
telomeres.