Molecular Genetics - Bio 12

What is the structure of DNA?

A nitrogenous base, a phosphate group, and a deoxyribose sugar

What is the difference between a ribose sugar and a deoxyribose sugar?

A deoxyribose sugar doesn’t have an oxygen at carbon 2’

What are the 4 different nitrogenous bases in dna?

Adenine, Thymine, Guanine, Cytosine

What are the 4 different nitrogenous bases in RNA?

Adenine, Uracil, Guanine, Cytosine

What are the complementary base pairs?

A-T(U)
G - C

How many H bonds does Adenine and Thymine form?

Two Hydrogen Bonds

How Many H bonds does Guanine and Cytosine form?

Three Hydrogen Bonds

Which way does the DNA strand run?

Antiparallel

What are the two ends of the DNA strand?

3’ and 5’

What is attached to the 3’ end of the strand?

A hydroxyl group

What is attached to the 5’ end of the strand?

A phosphate group

What enzyme writes new DNA code?

DNA Polymerase

Which way does DNA Polymerase write new code?

5’ to 3’

Which way does DNA Polymerase read code?

3’ to 5’

What is DNA replication?

The copying of one DNA molecule into two

What is the semi conservative method of DNA replication?

The original DNA Double strand is split into two daughter strands, and the two daughter strands turn into double strands via complementary base pairing.

What are the three steps in Semi-Conservative replication?

Initiation, Elongation, Termination

What happens in the initiation phase of DNA Replication?

Several initiator proteins bind to the DNA, and begin to unwind it. The enzyme helicase cleaves the hydrogen bonds off of the nitrogenous bases, forming 2 single strands.

What protein stabilizes the new single strands, and prevents them from turning back into a helix?

Single-strand-binding proteins

Which enzyme helps to relieve the strain on the double helix sections ahead of the replication fork?

Topoisomerase II

What are the steps to Intiation in DNA Replication?

Initiation proteins bind to the helix, begin to unwind it. Helicase cleaves off the hydrogen bonds. Topoisomerase 2 and single-strand-binding proteins stabilize the single strand and double helix. Replication forks move in opposite directions.

What happens in the Elongation phase of Semi-conservative replication?

New DNA strands are synthesized, by joining free nucleotides togetherW

Which enzyme adds new nucleotides to the complementary strand in Elongation?

DNA Polymerase III

Which end of the original DNA strand does DNA Polym. 3 act on?

It only attaches free nucleotides to the free 3’ hydroxyl end

What is the strand called that is made by DNA Polym. 3?

The leading strandW

Which direction is the leading strand synthesized?

5’ to 3’, towards the replication fork

What is the strand called that is synthesized complementary to the 5’ strand of the original DNA Strand

Lagging strandWh

Which direction is the lagging strand synthesized in?

5’ to 3’, away from the replication fork. Synthesized in short segments

What are the RNA strands which start the synthesis of RNA called?

RNA Primer

Which enzyme produces RNA Primer?

Primase

How does RNA Primer work?

It’s complementary to a section of the parent DNA. It forms a small strand, and DNA Polym. 3 extends the strand away from the replication fork.

What are the DNA fragments called which are synthesized off of RNA Primer?

Okazaki fragments

What is the function of DNA polymerase 1?

Remove RNA Primer, and fill in the space by extending the DNA FragmentW

What enzyme joins the Okazaki fragments together?

DNA Ligase

What happens in the termination phase of DNA replication?

The two new DNA molecules separate from each other, replication machine is dismantled

What is the function of Helicase?

Unwinds the parent DNA (breaks the hydrogen bonds)W

What is the function of primase?

Makes RNA primer

What is the function of single stranded binding proteins?

Stabilize the single strands of DNA, preventing them from winding up again

What is the function of Topoisomerase 2

Relieves the strain on the still winded double helix, during replication

What is the function of DNA Polymerase 1?

Removes RNA Primer and fills in the gap by extending the neighbouring DNA Strand

What is the function of DNA Polymerase 2 (PM 1 does it as well)

Proofreads the new DNA strands

What is the function of DNA Polymerase 3?

Adds free nucleotides to the 3’ strands, and extends Okazaki fragments

What is the function of DNA ligase?

Joins together Okazaki fragments

Which enzymes proofread DNA in humans?

DNA polymerase I and II

What happens when DNA Polymerase I or II detect an incorrectly placed nucleotide?

They remove it, and replace it with the correct one.

What is the genetic code?

A set of rules which determine how genetic information from a nucleotide is converted to amino acid

What are the 4 RNA nucleotides?

A, C, G, U

How many nucleotide bases are read at a time?

Three

What is an mRNA codon?

A set of three nucleic acids in mRNA

What are the three important characteristics of Genetic Code?

1. genetic code is redundant. more then one codon can code for the same amino acid

2. Genetic code is continuous. It’s read in a series of three letters, with no punctuation or spaces. Therefore a shift in one or two nucleotides can mess up an amino acid sequence

3. Genetic code is universal, the same codons in a fruit fly code for the same amino acids in a human.

What is gene expression?

The synthesis of a protein based on the DNA sequence of a gene

What are the two steps in the expression of a gene?

Transcription and translation

What is transcription?

The conversion of DNA to mRNA (messenger RNA)W

What is translation?

The conversion of mRNA into amino acids (proteins)

When does transcription begin in gene expression?

When the cell receives a chemical signal indicating the need for a specific protein

What is the key enzyme involved in gene expression transcription?

RNA PolymeraseW

Where does RNA Polymerase bind to on the DNA strand?

On a specific promoter region, upstream of the gene to be copied

What does RNA Polymerase do?

Uncoils and unzips the DNA in the region of the gene. Then it makes a copy of the template strand, which is identical to the coding strand (U replaces T). It continues copying until it hits a terminator sequence.

What is the template strand?

The DNA strand actively being copied

What is the coding strand?

The DNA strand complementary to the template strand

What are the three steps of transcription?

Initiation, Elongation, Termination (trans)

What happens in initiation in gene expression?

RNA Polymerase arranges on template strand and binds @ promoter region

What does the promoter on a DNA sequence do?

Tells the RNA polymerase where to start transcription, which strand of DNA to transcribe, and which direction to move inW

What code is the promoter?

TATA (TATA Box)

What happens in elongation in gene expression?

RNA Polymerase unwinds and opens the section of the double helix, starts transcribing at the initiation site.

Which direction does RNA Polymerase read the DNA strand in?

3’ to 5’

Which direction does RNA Polymerase write mRNA in?

5’ —> 3’ (RPOLYM)

How is Precursor mRNA converted to mRNA?

5’ Guanine cap is added, Introns are spliced out, 3’ poly-A tail is added

What are exons?

The actual code in mRNA

What enzymes splice pre-mRNA?

Spliceosomes

What function does the guanine cap serve?

Allows ribosomes to recognize the mRNA

What function does the polyA tail serve?

Protects the mRNA from degrading by exonucleases

What are introns?

Non-coding regions of mRNA

What is the function of mRNA?

Contains genetic info which can be converted into amino acids

What is the function of tRNA?

Contains the anticodon for an mRNA codon, has the respective amino acid attached to it

What is the function of ribosomes?

To synthesize protein using mRNA and tRNA

What are translation factors?

essential proteins that guide and regulate the stages of protein synthesis (translation) in cells

What 2d shape does tRNA form?

A 3 leaf clover

What 3d shape does tRNA form?

Boot shaped structure

What are the stem loops in tRNA?

Double stranded RNA formed through intramolecular base pairing

What is the anticodon loop?

The loop which contains three nucleotides which are complementary to a specific mRNA codon (anticodon)

What is opposite of the anticodon on the tRNA?

Acceptor stemW

Which side is the acceptor stem on?

The 3’ side

What is contained on the acceptor stem?

The respective amino acid

Which enzyme is responsible for attaching the appropriate amino acid to tRNA?

Aminoacyl-tRNA synthetase

Which direction are Anticodons written in?

3’ to 5’ (antic)

What direction are nucleotide sequences written in?

5’ to 3’

What are ribosomes made of?

Proteins and ribosomal RNA

How do ribosomes synthesize protein?

It has 1 binding site for mRNA, and three binding sites for tRNA. The binding sites allow for complementary base pairing between the codons and anticodons.

What is a polyribosome?

After the initial portion of mRNA is translated by the ribosome, it moves down and another ribosome attaches. Several ribosomes attach forming several proteins at once, called a polyribosome.

What genes are always active?

Constitutive genes

What is gene regulation?

The control of the level of gene expression (gene is active or inactive)

What are genes regulated by?

Transcription factors

What are transcription factors?

Proteins which bind to DNA, and control whether RNA polymerase can transcribe genes

What can transcription factors do?

Activate transcription, or repress transcription

When can gene expression be regulated in prokaryotes?

During transcription, during translation, or after the protein is synthesized

What is an operon?

A region in a prokaryote cell where many genes are clustered under one single promoter, and operator

What is an operator?

A DNA sequence in prokaryotes where a repressor is able to bind to

What is a repressor?

A protein that binds to an operator, and inhibits transcription

What is the lac operon?

A region on the E. Coli chromosomes which codes for enzymes that break down lactose