Biochem Exam #4
A methylated nitrogen base is founnd in eukaryotes when genes are imprinted to distinguish if the chromosomal DNA is inherited from the mother or father or when one strand of DNA needs to be differentiated from the other for DNA repair. The name of this methylated base is _____.
5-hydroxymethylcysteine
The sigma subunit of prokaryotic RNA polymerase first binds to the ___.
-35 region
Double Helix
2 anti-parallel DNA strands coiled around the same axis
A double stranded DNA molecule is found to contain 30% thymidine. The percentage of cytidine is ____.
20%
About how many genes do humans have?
20-30,000
The double stranded DNA molecule is found to contain 22% adenine, what is the percentage of cytosine?
28%
A Wobble base binds to ___.
3'-end of the codon
2° structure of nucleic acid polymer
3-D conformation of the polynucleotide backbone
DNA polymerase always synthesizes a new strand in which direction?
5' to 3'
The fact that more than one codon can code for the same amino acid makes the genetic code ____.
Degenerate
Semi-conservative replication
Each daughter double helix contains one template strand and one newly synthesized strand
Mismatch repair
Enzymes recognize that two bases are incorrectly paired, the area of mismatch is removed, and the area is replicated again.
Topoisomerases
Enzymes that control the supercoiled state of DNA
Okazaki fragments
Formed on the lagging strand due to the requirement for DNA synthesis in the 5'->3' direction
Ribosomal RNA (rRNA)
Found in ribosomes, the site of protein synthesis. Only a few types exist in cells. Ribosomes are mostly rRNA by mass.
Since DNA synthesis is bidirectional from the origin of replication, the number of DNA templates being read simultaneously in E. coli is ___.
Four
Since DNA synthesis is bidirectional from the origin of replication, the number of DNA templates being read simultaneously in E. coli is:
Four
How many replication origins does each chromosome have?
Hundreds.
The two strands of DNA are held together by
Hydrogen bonds
What type of bonds holds the two strands of DNA together?
Hydrogen bonds
Two strands of DNA are held together in a double helix by which type of bonds?
Hydrogen bonds!
Three main Polymerases
I- Repair II- Specialized repair III- Main Polymerizing enzyme
To utilize an expression vector to produce a human protein in bacteria, the gene for the human protein cannot contain ____.
Introns
A helix-turn-helix motif ____.
Binds to a major groove within upstream elements of B-DNA.
Which feature of DNA replication in eukaryotes is different from that in prokaryotes?
Multiple origins of replication are used.
B-DNA
Natural form, right-handed (DNA winds upwards in direction fingers are pointing)
Is DNA negatively or positively charged?
Negatively
The parts of nucleotides involved in RNA:DNA complementation are the ____.
Nitrogen bases
DNA and RNA are polymers of what?
Nucleotides
Where is DNA located in eukaryotic cells?
Nucleus- linear
DNA replication in eukaryotes ____.
Occurs simultaneously at multiple origins of replication
A nucleoside consists of what subunits?
One sugar and one base
A nucleotide consists of what subunits?
One sugar, one base, and one phosphate
What bonds are nucleotides linked by?
Phosphodiester
The role of chaperones is most important during ____.
Post-translational processing
DNA replication in E. coli is initiated by the generation of short RNA sequences by ___
Primase
Transcription
The synthesis of RNA from a DNA template. Catalyzed by RNA Polymerase
How many H-bonds does G-C have?
Three
For each origin of DNA replication in prokaryotes and eukaryotes ___ leading strands are made.
Two
How many H-bonds does A-T have?
Two
How many replication forks are there at each origin of replication?
Two
The Tm (melting temp) of DNA that has a cytosine-guanine content of 60% will be ___ DNA with a cytosine-guanine content of 30%?
higher than
DNA polymerase always synthesizes a new DNA strand ___.
in the 5' to 3' direction
Oxygen binding affinity to hemoglobin decreases with
increasing CO2 concentration in the blood
For each step of chain elongation in protein synthesis, new aminoacyl tRNAs are first bound to the ____ site of the 70S ribosome.
A
Chromatin
A complex of DNA wound around histones in a bead-like structure. Each 'bead' is a nucleosome.
3'-5' -exonuclease activity of DNA Pol I
A proofreading function which corrects incorrect nucleotides during DNA synthesis
The following type of base pairs often found in RNA is ____.
AU
4° structure of nucleic acid polymer
DNA/protein interactions
Amino acids are attached to the 3'-end of tRNA by their
Carboxyl group
In protein synthesis, N-formyl methionine is used in ___.
Chain initiation
DNA gyrase
Class II topoisomerase. A bacterial enzyme that induces negative supercoils into DNA.
Histones
Complex with proteins where supercoiling of eukaryotic DNA occurs. Positively charged protein, rich in Lys and Arg
Messenger RNA (mRNA)
Contains the genetic information from DNA (genes). Translated by ribosomes into a polypeptide sequence. Small amounts, short-lived, varies in length and sequence.
Class I topoisomerases
Cut the phosphodiester backbone of ONE strand, pass the end through and reseal
Class II topoisomerases
Cuts BOTH strands, pass some of the remaining DNA helix between the cut strands and reseal.
Where is DNA located in Bacteria?
Cytoplasm- circular
Origin of replication
DNA double helix unwinds at a specific point
The following are necessary for the creation of recombinant DNA except:
DNA fragements from the same source.
An enyzme that regulates supercoiling and relieves torsional stress in DNA is ___.
DNA gyrase (type II topoisomerase)
The enzyme responsible for the bulk of DNA synthesis during replication in E. coli is ___.
DNA polymerase III
What enzyme is responsible for the bulk of DNA synthesis during replication of E. coli?
DNA polymerase III
The following requires a DNA template: ____
DNA replication and transcription
An enzyme that regulates supercoiling and relieves torsional stress during replication is ___.
DNA topoisomerase
What is RNA used for?
Protein synthesis
What are the 7 main Nitrogen bases?
Pyimidine, cytosine, thymine, uracil, purine, adenine, guanine.
DNA and RNA differ in that:
RNA contains uracil and usually not thymine. RNA usually is single-stranded, DNA is usually double stranded. Native RNA is generally of lower molecular weight than native DNA. RNA contains ribose, DNA contains deoxyribose.
DNA Pol I
Removes the RNA primer
The flow of genetic info in the central dogma of molecular biology is:
Replication -> transcription -> translation
DNA Pol II
Responsible for new strand synthesis
Palindromic sequences in DNA can be cleaved by ___.
Restriction enzymes.
The process for making cDNA from mRNA is called ____.
Reverse transcription
DNA ligase
Seals nicks in DNA
SSB
Single-stranded binding protein. Stabilizes single stranded regions and prevents re-annealing of DNA
Epinephrine plays an important role in glucose metabolism by
Stimulating via kinases the phosphorylation of both glycogen synthase and glycogen phosphorylase, which activates the phosphorylase and inactivates the synthase.
3° structure of nucleic acid polymer
Supercoiling
DNA Polymerase III
Synthesizes new DNA strands
Primase
Synthesizes the RNA primer
RNA polymerase copies the ____ strands of DNA.
Template
Supercoiling
The 3-D arrangement of all atoms of the DNA
1° structure of nucleic acid polymer
The order of bases
Secondary structure of DNA
The ordered arrangement of nucleic acid strands.
Helicase
Unwinds DNA helix and causes strand separation
Severe Combined Immune Deficiency Syndrome is caused by a mutation in the gene for ____.
adenosine deaminase
In eukaryotic mRNA, a Poly-A sequence is found ___.
after the 3' end of the coding region.
The process of transformation involves the uptake of plasmids by ____.
bacteria
UV light can cause dimerization of adjacent thymine bases in DNA that can be repaired by ___.
excinuclease
A method of choice for separating DNA fragments by length is _____.
gel electrophoresis.
Somatic changes in the genetic makeup of a tissue by genetic engineering are ____.
not inherited.
DNA replication in E. coli is initiated by the generation of short RNA primers using
primase
The 3' to 5' exonuclease activity of prokaryotic DNA polymerases is required for ___ during DNA replication
proofreading
A major purpose of methylation of nucleotides in bacterial DNA is to ____.
protect the DNA from digestion.
The region of a plasmid that makkes bacteria with the plasmid resistant to antibiotics is called the ____.
selection gene
Transfer RNA
single-stranded polynucleotide. Carries an aa at its 3' end. Intramolecular H-bonding occurs. Cloverleaf structure.
A molecule that contains anticodons is ____.
tRNA
Protein degredation occurs primarily in ___.
the lysosome.
A Shine-Dalgarno sequence in prokaryotes such as E. coli is ____.
the ribosome binding site.
The process by which DNA is copied into RNA is called ____.
transcription
A protein that controls transcription by binding to a response element upstream of the promoter sequence in DNA is called a
transcription factor
Ribosomal RNA is used in the process of ___
translation