IPS1-Introduction to Nucleic Acids p3

Primary structure

The phosphodiester linkage of monomer units into a polymeric molecule is called the _____

sequence

[PRIMARY STRUCTURE]

____-

• Is the order of nucleotides in DNA

• Holds genetic information.

True

[PRIMARY STRUCTURE]

[T/F]

A sequence can be written as ACGTT (from 5’ to 3’) or the opposite strand as TTGCA (from 3’ to 5’)

DNA

The main job of _____ is to pass genetic information from parents to offspring

DNA replication

____- must be done completely and accurately to keep genes stable in the organism and species.

DNA replication

_____- is complex and has many steps to make sure it copies correctly

Conservative

[Conservative / Semiconservative]

Old strand acts as a template

Semiconservative

[Conservative / Semiconservative]

Old strand splits apart and acts as a template

Conservative

[Conservative / Semiconservative]

One daughter strand is the original template while the other strand is composed entirely out of new nucleotides

Semiconservative

[Conservative / Semiconservative]

Both daughter strands are composed of one of the old strands and one comprised out of new nucleotides

semiconservative

DNA replication is _____ [conservative / semiconservative]

semiconservative model

In their brief paper, Molecular Structure of Nucleic Acids, James Watson and Francis Crick (1953) wrote: 

• The way the DNA bases pair up suggests a way for how DNA copies itself.

  • This copying method is called the_____ model

1. Find the starting point, called the origin, for copying the DNA.

2. Unwind the double-stranded DNA to make two single strands.

3. Create replication forks, which are the areas where the copying happens.

4. Start and continue making the new DNA strands.

5. Form replication bubbles and join the new DNA pieces together.

6. Restore the DNA’s normal structure with proteins, which is called chromatin.

Steps involved in DNA Replication in Eukaryotes [6]

origin of replication

Replication begins at a specific site in the DNA called the_____

• prokaryotic cells

• eukaryotic cells

• In _____ [eukaryotic / prokaryotic] cells, the circular DNA has one origin of replication.

• In _____ [eukaryotic / prokaryotic] DNA, there are multiple origins of replication

Replication fork

_____-

• Are the place where DNA is copied

• Special proteins attach to the single DNA strands to keep them from sticking back together during copying.

• Leading Strand

• Lagging Strand

There are two strands being synthesized such as ___ 

Leading Strand

[Type of Strand]

____- is synthesized continuously.

Lagging Strand

[Type of Strand]

____-is synthesized discontinuously, in small pieces.

RNA primer

A short double-stranded piece of RNA with a free 3’ OH end

primase

RNA primer is made by ____ (an RNA-making enzyme)

primase

____- is an RNA-making enzyme

DNA Polymerases

_____-

• Copies the DNA template.

• Can only add new nucleotides to the 3’ end of an existing strand.

DNA Polymerases

Builds the new DNA strand by adding one nucleotide at a time to the 3’ end.

DNA Polymerases III

_____-

• Replaces the primase and is able to add DNA nucleotides to the RNA primer

• Catalyze DNA chain elongation

DNA polymerase I

_____-

• digests away the RNA primer and replaces the RNA nucleotides of the primer with the proper DNA nucleotides to fill the gap

DNA ligase

The DNA fragments on the lagging strand are hooked together by the enzyme______

Okazaki fragments

____-

• Short fragment or sequences of discontinuous DNA

• Eventually joined to become a single continuous strand

DNA polymerases

[Class of Protein (enzymes)  involved in Replication]

Perform deoxynucleotide polymerization.

Helicases

[Class of Protein (enzymes)  involved in Replication]

Perform the processive unwinding of DNA.

Topoisomerases

[Class of Protein (enzymes)  involved in Replication]

Relieve the torsional strain that results from helicase-induced unwinding.

DNA primase

[Class of Protein (enzymes)  involved in Replication]

Initiates the synthesis of RNA primers.

Single-strand binding proteins

[Class of Protein (enzymes)  involved in Replication]

Prevent the premature reannealing of double-stranded DNA.

DNA ligase

[Class of Protein (enzymes)  involved in Replication]

Seals the single strand nick between the nascent chain and Okazaki fragments on the lagging strand.

DNA Topoisomerase I

[DNA Topoisomerase I vs. DNA Topoisomerase II]

_____-

• Fixes the twisting tension in DNA that is caused by unwinding.

• It cuts one DNA strand to let the helix spin and relax.

• Then, it reconnects the cut strands.

DNA Topoisomerase I

[DNA Topoisomerase I vs. DNA Topoisomerase II]

_____-

• It works on different types of twists in bacteria and in eukaryotes.

• It can both cut and reseal the DNA strands.

DNA Topoisomerase II

[DNA Topoisomerase I vs. DNA Topoisomerase II]

_____- makes transient breaks in both strands

• Chain elongation

• Processivity

• Proofreading 

Important Properties of DNA Polymerases [3]

• DNA polymerase I

• DNA polymerase alpha (α)

[PROKARYOTIC AND EUKARYOTIC DNA POLYMERASES]

• In E. coli, _____ has the function of gap filling and synthesis of the lagging strand. In mammals, ______ does this.

• DNA polymerase II

• DNA polymerase epsilon (ε)

[PROKARYOTIC AND EUKARYOTIC DNA POLYMERASES]

• In E. coli, ______is involved in DNA proofreading and repair. In mammals, _____ does this.

DNA polymerase beta (β)

[PROKARYOTIC AND EUKARYOTIC DNA POLYMERASES]

Mammals also have______ for DNA repair

DNA polymerase gamma (γ)

[PROKARYOTIC AND EUKARYOTIC DNA POLYMERASES]

• Mammals have _____ for mitochondrial DNA synthesis.

DNA polymerase III

DNA polymerase delta (δ)

[PROKARYOTIC AND EUKARYOTIC DNA POLYMERASES]

• In E. coli, ______is the processive enzyme for leading strand synthesis. In mammals, ______does this.

Endonuclease

[Endonuclease vs. Exonuclease]

Cleave within the chain to produce singlestranded nicks

Exonuclease

[Endonuclease vs. Exonuclease]

Cleave from the end of the chain, releasing single nucleotide

Histones

_____- are basic proteins tightly attached to DNA in eukaryotic cells

• H1

• H2A

• H2B

• H3

• H4

5 types of histones such as ___

H1

[5 Types of Histones]

____- binds between the nucleosome beads and helps pack the DNA into tighter structures.

nucleosome

____- is like a "bead" made of two copies each of the histones H2A, H2B, H3, and H4, with DNA wrapped around them almost two times.

Linker DNA

Nucleosomes are connected by short pieces of DNA called ____

50

Linker" DNA is about _____ nucleotides long

polynucleosome or nucleofilament

Nucleosomes are connected by short pieces of DNA called "linker" DNA, which is about 50 nucleotides long. This forms a chain called a______ 

nucleofilament

polynucleosome is aka ___

G1 Stage

[Stage of Cell Cycle]

____-

• Growth and increase in cell size

• This lasts for 10 hours.

S Stage

[Stage of Cell Cycle]

____-

• This is the period of DNA synthesis

• This lasts for 8 hours.

G2 Stage

[Stage of Cell Cycle]

____-

• This is the post-DNA synthesis phase where the cell prepares for division.

• This lasts for 5 hours.

M Stage

[Stage of Cell Cycle]

____-

• This is mitosis

• This is the shortest stage, lasting only 1 hour.

1. UV Light - Radiation

2. Chemicals

3. Other Agents

Causes of DNA Damage [3]

• Base Alteration

• Removal or Loss of Nucleotide Base

DNA damage can be ___ [2]

Benzo[a]pyrene

[Different substances that can cause DNA damage]

_____- 

• This comes from smoke. It intercalates, or sticks, into DNA, which causes frameshifts.

• It is also metabolized to a product that binds to residues, causing base substitutions.

Nitrous Acid (HO-N=O)

[Different substances that can cause DNA damage]

_____- 

• This is found in some prepared foods.

• It deaminates the base C (cytosine) into U (uracil), which leads to missense mutations.

Dimethyl Nitrosamine

[Different substances that can cause DNA damage]

_____- 

• This is also found in some prepared foods

• It is a methylating agent that modifies bases, which yields missense mutations.

Aflatoxin

[Different substances that can cause DNA damage]

_____- 

• This comes from moldy nuts or grains

• It is an alkylating agent that modifies guanine, which causes missense mutations.

Ultraviolet Light

[Different substances that can cause DNA damage]

_____- 

• This comes from sunlight.

• It causes the formation of pyrimidine dimers in the DNA.

Mismatch Repair

[FOUR MECHANISMS OF DNA REPAIR] 

Copying errors made during DNA replication.

• Methyl-directed strand cutting

• Exonuclease digestion

• Replacement of the wrong section.

[FOUR MECHANISMS OF DNA REPAIR] 

Solutions for Mismatch Repair [3]

Base Excision Repair

[FOUR MECHANISMS OF DNA REPAIR] 

Spontaneous, chemical, or radiation damage to a single base.

• The damaged base is removed by an N-glycosylase enzyme

• Then the abasic sugar is removed, and the section is replaced.

[FOUR MECHANISMS OF DNA REPAIR]  

Solution for BASE EXCISION REPAIR [2]

N-glycosylase enzyme

[FOUR MECHANISMS OF DNA REPAIR] 

In BASE EXCISION REPAIR the damaged is removed by _____ enzyme

Nucleotide Excision Repair

[FOUR MECHANISMS OF DNA REPAIR] 

Spontaneous, chemical, or radiation damage to a segment of DNA.

• Removal of an approximately 30-nucleotide oligomer that contains the damage and 

• Replacement with new DNA.

[FOUR MECHANISMS OF DNA REPAIR] 

Solution for NUCLEOTIDE EXCISION REPAIR [2]

[FOUR MECHANISMS OF DNA REPAIR] 

Damage from ionizing radiation, chemotherapy, or oxidative free radicals that breaks both DNA strands

• Synapsis

• Unwinding

• Alignment

• Ligation of the broken strands.

Solution for DOUBLE-STRAND BREAK REPAIR [4]

permanent mutation

If the DNA damage is not repaired, it becomes a ____ mutation

1. The cells can undergo apoptosis, which is programmed cell death.

2. There can be a loss of control over the proliferation of the mutated cell. This means the damaged cell starts dividing uncontrollably, which can lead to cancer.

If the DNA damage is not repaired

• This can lead to two main outcomes such as ___

apoptosis

____- is programmed cell death.

Xeroderma Pigmentosum (XP)

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

_____- is a rare inherited disease that causes dark spots on sun-exposed skin and a higher risk of skin cancer.

Xeroderma Pigmentosum (XP)

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

It happens because of mutations in genes that help fix damaged DNA through a process called Nucleotide Excision Repair (NER)

Nucleotide Excision Repair (NER)

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

Xeroderma Pigmentosum (XP) happens because of mutations in genes that help fix damaged DNA through a process called_________

Fanconi’s Anemia

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

_____- is a genetic disease that mainly affects the bone marrow.

Fanconi’s Anemia

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

It stops cells from fixing damaged DNA and from getting rid of harmful substances called oxygen-free radicals.

oxygen-free radicals

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

Fanconi’s Anemia stops cells from fixing damaged DNA and from getting rid of harmful substances called ____.

Fanconi’s Anemia

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

People with some birth defects or low blood counts might have this disease.

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

_____- is a rare inherited disease that starts in childhood and affects the brain and other body parts

Ataxia

____- means uncoordinated movements, like trouble walking

Telangiectasia

_____- means small, red, spider-like blood vessels appear just under the skin.

Ataxia-Telangiectasia

[DISEASES RESULTING FROM DISORDERED DNA REPAIR CAPABILITIES]

The disease is caused by problems in the ATM gene, which can cause cells to die abnormally, especially in the part of the brain that controls movement

• has one strand instead of two strands.

• has uracil instead of thymine

• has ribose instead of deoxyribose

RNA is similar to DNA except [3]

nucleus

DNA remains in the ______ , but in order for it to get its instructions translated into proteins, it must send its message to the ribosomes, where proteins are made

mRNA 

DNA remains in the nucleus, but in order for it to get its instructions translated into proteins, it must send its message to the ribosomes, where proteins are made . The chemical used to carry this message is _____