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