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Integrated Science: Exam 2 study
Terms in this set (57)
The components of nucleic acids for DNA & RNA are:
1) 5-carbon sugar: Ribose for RNA, deoxyribose for DNA
2) Phosphate, links the sugars together, and at the beginning of the molecule.
3) nitrogenous base
How are the the sugars of DNA and RNA numbered?
Where the sugar is attached to a base, the carbon atoms are numbered from 1′ to 5′ to distinguish it from the base. (1' carbon is attached to base)
How are bases linked together in a polynucleotide?
• The phosphate links the 3' end of the previous sugar to the 5' end of the next sugar, generating the phosphate backbone.
• The base is linked to the 1' carbon of the sugar by a N-glycosidic bond.
What are the nucleoside composition?
a five-carbon sugar & nitrogenous base
What are the nucleotides composition?
A nucleotide is a nucleoside with an inorganic phosphate attached to a 5′-hydroxyl group of the sugar in ester linkage
What is the concept of Base Pairing?
two polynucleotide chains joined by hydrogen bonds between the bases.
In each base pair, a purine on one strand forms hydrogen bonds with a pyrimidine on the other strand. DNA: A-T, C-G
also allows a strand of DNA to serve as a template for the synthesis of a complementary strand of RNA.
General structure of DNA?
DNA has a double helix structure formed by two antiparallel strands.
Polarity is 5' to 3'
phosphate groups contain one -O atom that provides the phosphodiester backbone with a negative charge.
What are the effects of alkali on DNA and RNA?
DNA strands stay intact but they separate.
RNA strands are degraded to nucleotides.
(hydroxyl group on 2′-carbon losing its proton)
Use: allows purification of DNA away from RNA
The process by which a single-stranded DNA anneals with complementary strands of RNA?
Hybridization is used extensively in research and clinical testing
DNA-RNA hybrid pairing?
A-U & C-G
DNA serves as the template for RNA synthesis
Difference between DNA & RNA?
DNA is a long polymer with deoxyriboses and phosphate backbone. Four different nitrogenous bases: adenine, guanine, cytosine and thymine.
RNA is a polymer with a ribose and phosphate backbone. Four different nitrogenous bases: adenine, guanine, cytosine, and uracil.
Eukaryotic cell cycle
G1 - growth & metabolism
S - DNA replication
G2 - preparation for cell divisions
M - mitosis
DNA content 2n (diploid)
after DNA replication 4n (tetraploid).
General Features of DNA Replication?
• DNA replication is semiconservative.
(meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand.)
• Parental strands are used as template.
• DNA replication occurs within a replication fork, which forms by unwinding
How is DNA replication initiated?
DNA polymerase cannot initiate alone.
a short primer is produced which contains ribonucleotides (RNA).
DNA polymerase can add deoxyribonucleotides to the 3′-end of this primer.
This RNA primer is subsequently removed and replaced by deoxyribonucleotides.
Effects and solutions of topological stress on DNA?
DNA is unwound, the turns in the DNA double helix are compressed leading to generation of topological constraint.
supercoiling - where the end of the DNA cannot rotate from unwinding.
Topoisomerase relieve this constraint by cleaving one strand (topo I) and allowing it to rotate.
(Break, unwind, and then rejoin)
Features of DNA polymerases?
Enzymes that catalyze the synthesis of DNA
DNA Polymerase Proofreads during DNA Synthesis
Function of Bacterial DNA Polymerases - Pol I
Filling of gap after removal of RNA primer
Removal of RNA primer in conjunction with RNase H
5′-to-3′ and 3′-to-5′
Function of Bacterial DNA Polymerases - Pol II
Function of Bacterial DNA Polymerases - Pol III
Replication; synthesis of DNA
How are DNA strands synthesized?
The newly synthesized strands grow by consecutive incorporation of nucleotides by a DNA polymerase
Deoxyribonucleoside triphosphates serve as precursors (substrates) used by DNA polymerase to lengthen the DNA chain.
DNA polymerase copies the DNA template strand in the 3′-to-5′ direction. The new strand grows in the 5′-to-3′ direction.
Synthesis of new DNA strands always occurs in a 5′-to-3′ direction!!
What is the Replication Fork of DNA synthesis?
area where the replication of DNA will actually take place.
two strands of DNA that are exposed once the double helix is opened
One strand is referred to as the leading strand, and the other strand is referred to as the lagging strand.
The leading strand?
This strand is made continuously
in the 5′-to-3′ direction toward the fork.
The lagging strand?
produced in a 5′-to-3′ direction
(away from the fork)
synthesized discontinuously in short fragments, forms gaps in chain.
(because DNA polymerase must come off and reattach on the newly exposed DNA)
Called Okazaki fragments
gaps are joined together so that, overall, synthesis proceeds toward the replication fork.
Synthesizes RNA primers
Add nucleotides to a strand growing in a 5′-to-3′ direction, copying a DNA template in a 3′-to-5′ direction
Separate parental DNA strands
(unwind the double helix)
Single-strand binding proteins
Prevent single strands of DNA from reassociating
Relieve torsional strain on parental duplex caused by unwinding
Enzymes that remove primers
RNase H hydrolyzes RNA of DNA-RNA hybrids
Flap endonuclease 1 (FEN1) recognizes "flap"
(Unannealed portion of RNA) near 5′-end of primer and cleaves downstream in DNA region of primer; the flap is created by polymerase δ displacing the primer as the Okazaki fragment is synthesized
Joins, by forming a phosphodiester bond, two adjacent DNA strands that are bound to the same template
PCNA (proliferating cell nuclear antigen)
Enhances processivity of the DNA polymerases
binds to many proteins present at the replication fork
How are ends of chromosomes are synthesized?
RNA present in telomerase base-pairs with the overhanging 3′-end of telomeres and extends it by acting as both a template and a reverse transcriptase.
After copying a small number of repeats, the complex moves down to the 3′- end of the overhang and repeats the process. There are multiple copies of telomere sequence at the end of the chromosomes.
What are carcinogens?
Mutagens that cause normal cells to become cancer cells.
act by Damaging DNA.
What are mutagens?
chemicals produced in cells, inhaled, or absorbed from the environment which cause mutations.
Types of mutagens and carcinogens?
Cigarette smoke, X-ray, UV light
Cigarette smoke damage on DNA
contains carcinogens such as the aromatic polycyclic hydrocarbon
Benzo[a]pyrene is not carcinogenic until it is oxidized within cells.
Then, it can bind covalently to guanine residues in DNA, interrupting hydrogen bonding in G-C base pairs and producing distortions of the helix, interfering with replication of the DNA at this site.
result in a mutation on DNA. This is irreversible.
Ultraviolet light damage on DNA
• is absorbed by bases in DNA.
• provides the energy to form intra-strand (same strands) crosslinks between adjacent pyrimidines.
• The most common dimers are thymine dimers (T-T).
• crosslink affects DNA replication and transcription, blocking the polymerases.
The Common steps in DNA Repair?
1.- Recognition of damage
2.- Excision (removal) of damage
3.- Resynthesis of removed DNA.
What are the 3 types of excision repair pathways?
1. Base excision repair: damaged bases (oxidative)
2. Nucleotide Excision repair:
(DNA adducts, UV x-links)
3. DNA Mismatch repair: polymerase errors
Steps in base excision repair?
the glycosylase recognizes the damaged base.
then cleaves the glycosidic bond between the altered base and ribose
results in the removal of the damaged base.
gap is created then filled in by a DNA polymerase.
Steps in nucleotide excision repair?
the entire nucleotide (~22 nt gap!!) is removed at once.
gap formed by the incision (cut) and excision (removal) endonucleases results in a gap.
gap is created then filled in by a DNA polymerase.
Mismatched bases are recognized by enzymes of the mismatch repair system.
mismatch bases are undamaged
repair enzymes must determine which base of the mismatched pair to correct. (In e.coli, the original strand, or old strand, is the strand that is methylated!!)
The mismatch-repair enzyme complex acts during replication when an incorrect but normal base is incorporated into the growing chain
Key steps in homologous recombination?
(another form of DNA repair)
occurs between chromosomal segments with the same sequences
or if chromosomes have regions with the same sequence as other non-homologous chromosomes.
Damaged strand invades homologous neighbor forms a D-LOOP
strands exchange ends
ligation (fuses gaps)
Holiday Structure (Chi) & covalently bonded
Twist & Isomerize
Resolution by Nucleases cut (cut locations vary)
Different variations occur in end
When is Chromosomal Translocation produced?
homologous recombination gone wrong!
when free ends of the DNA at the break point reseal with the free ends of a different broken chromosome.
Breaks in chromosome are caused by agents such as X-rays or chemical carcinogens
Synthesis of RNA from a DNA template.
What enzymes transcribe genes to generate a single-stranded RNA identical in sequence (with the exception of U in place of T) to one of the strands of the double-stranded DNA?
What is a gene?
a segment of DNA that functions as a unit to generate an RNA product through the
processes of transcription.
then a polypeptide chain is generated by translation.
A gene also includes regions of DNA that regulate production of the encoded product called?
a promoter region.
What does the transcribed region contain?
the coding sequences that dictate the amino acid sequence of a polypeptide chain.
Where is "upstream" ?
is toward the 5' end of the coding strand for gene.
promoter & other regulatory sequences.
Where is "downstream" ?
is toward the 3' end.
Coding region of the gene.
How is RNA synthesized?
during Transcription occurs 5' to 3' direction (polarity)
Requires DNA as the Template
Unlike DNA synthesis, the transcription RNA polymerase does not require a primer. Can be initiated by itself.
RNA polymerase I
Product: Ribosomal RNA (rRNA)
RNA polymerase II
Product: Messenger RNA (mRNA) + microRNA (miRNA)(regulate gene expression)
RNA polymerase III
Product: Transfer RNA (tRNA) + other small RNAs
What is the coding strand (top strand) of DNA?
the sense strand, or the nontemplate strand.
Describe the DNA template strand?
or antisense strand
is the strand that is used by RNA polymerase during the process of transcription.
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