Chapter 3: Nucleic Acids and Transcription



A linear polymer of four subunits; the information archive in all organisms.


The unit of heredity; the stretch of DNA that affects one or more traits in an organism, usually through an encoded protein or noncoding RNA.

Can genetic information be transmitted between two strains of bacteria?

In the 1920s, it was not clear which biological molecule carries genetic information. Conclusion: Griffith concluded that the virulent bacteria, although dead, had somehow caused the nonvirulent bacteria to become virulent. He asserted that a molecule tha

Which molecule carries genetic information?

DNA is the molecule responsible for transforming nonvirulent bacteria into virulent bacteria. This experiment provided a key piece of evidence for the idea that DNA is the genetic material.


consist of a 5-carbon sugar (deoxyribose), a base, and one or more phosphate groups

What are the four bases attached to the 1' carbon of the sugar

What are nucleosides and nucleotides

A nucleoside is a sugar attached to a base, and nucleotides are nucleosides with one, two, or three phosphate groups attached. Thus, a nucleotide is a nucleoside phosphate.

Why are nucleoside triphosphates important?

they are the molecules that are used to form DNA and RNA. In addition, nucleoside triphosphates have other functions in the cell, notably as carriers of chemical energy in the form of ATP and GTP.

What is a phosphodiester bond?

A covalent bond that forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another nucleotide. Phosphodiester bonds are relatively stable and form the backbone of a DNA strand.

strand polarity

the orientation of a nucleic acid strand indicating its 5' phosphate and 3' hydroxyl ends

How is base pairing maintained?

through weak hydrogen bonds between them, three in the case of G paired with C, and two in the cae of A paired with T. also base stacking

What is base stacking?

When non polar flat surfaces of bases in DNA strand group together away from water and stack on top of each other. van der waals forces

We identify nucleic acid strand orientation on the basis of important chemical functional groups. These are the _________ group attached to the 5' carbon atom of the sugar portion of a nucleotide and the __________ group attached to the ___ carbon atom.

phosphate; hydroxyl; 3'

When we consider the orientations of the two strands of DNA that make up a double helix, we see that they are:


The information carried by DNA is in the _______ and their ___________.

bases; sequence

In which aspect of DNA structure are hydrogen bonds important?

base-to-base pairing

Which of the following do you think best describes the way that base pairing stabilizes the double helix of DNA?

The arrangement of atoms allows precise hydrogen bonding.

The regions on a DNA helix where the strands must be separated so processes like transcription can start often have an A-T pair bias, that is, there are more A-T pairs than G-C pairs. What might you suggest as the basis for this bias?

A-T pairs have fewer H-bonds to break, so it requires less energy.

What are the three structural features of DNA?

1. DNA is made up of subunits called bases.
2. DNA is a linear polymer of nucleotides linked by phsphodiester bonds.
3. Cellular DNA is a double helix with two strands that are antiparallel to each other.

The letter R is conventionally used to represent any purine base (A or G) and Y to represent any pyrimidine base (T or C). In double-stranded DNA, what is the relation between the number of molecules of R and the number of molecules of Y?

It follows that number of R = number of Y.


The process of copying DNA so genetic information can be passed from cell to cell or from an organism to its progeny.

What is a mutation?

a change int he genetic information in DNA. A mutation in DNA causes the genetic difference between virulent and novirulent bacteria in the experiments. most are harmful, but rare favorable mutations are essential in the process of evolution bc they allow

What is ribonucleic acid?

To specify the amino acid sequence of proteins, DNA acts through an intermediary molecule known as RNA, another type of nucleic acid.

what is the central dogma of molecular biology?

The central dogma of molecular biology is that information is transferred from DNA to RNA to protein.

What is transcription?

in which genetic information in a molecule of DNA is used as a template to generate a molecule of RNA. It's tie first step in gene expression

What is translation?

the second step in gene expression; the readout of genetic information in which a molecule of RNA is used as a code for the sequence of amino acids in a protein. The term "translation" is used tio indicate a change of languages, from nucelotides that make

How is the process of transcription and translation regulated?

genes are expressed, or "turned on" only at certain tems and places, and not eexpressed, or "turned off", at other times and places.

How does the flow of genetic informatino from DNA to RNA to protein differ between prokaryotes and eukaryotes?

In prokaryotes, transcrition and translation occur in the cytoplasm. In contrast, in eukearyotes, the two processes are spatially separated from each other, wich transcription occurring in the nucleus and translation in the cytoplasm. The separation of tr

How does the sequence of a molecule of DNA, made up of many monomers of only four nucelotides, encode the enromous amount of genetic infrormation stored in the chromosomes of living organisms?

Just four nucelotides can give rise to the vast divesrity of genetic information because the nucleotides can occur in any order. Any base on a strand of DNA can be followed by any other base (ir the same base), which gives rise to an enormous potential ge

How are the parental strands in a DNA molecule used in DNA replication?

During DNA replication, the two strands of the double helix unwind and separate, disrupting the hydrogen bonds holding the strands together. Each parental strand serves a s a template for a new complementary strand of DNA because of the specific pairing o

Muscle cells make different proteins than nerve cells because they have different sequences of DNa.


Translation is the process by which:

ribosomes suntehsize protein from information in an RNA molecule.

Transcription is the process by which

RNA is syntehsized from DNA

What is the central dogma?

DNA is transcribed into RNA, which is translated into protein

What is the usual flow of genetic information in a cell?

The usual flow of information in a cell is from DNA to RNA to protein.

Key information in DNA specifies the sequence of amino acid subunits that will compose enzymes and other proteins in the cell. Before these proteins can be synthesized, however, what intermediate molecule is synthesized to carry the information coded in t


In eukaryotic cells, where does protein synthesis take place?

in the cytoplasm

What holds the complementary strands of DNA together?

hydrogen bonds

what is the process by which DNa is used a s a template for the synthesis of an RNA molecule?


What is symbolized by the object in the red circle?

an RNA nucleotide

In this figure, what determines which specific unit is added?

it must be the complemet to the base on the DNA strand

A cell that is deficient in ribosomes is unable to complete what process?


in double stranded DNA, the sugar-phosphate backbones are:

on the outside, separated by grooves of unequal size

in a double-stranded DNA molecule, the strands are said to be antiparallel because:

one strand runs in 5' to 3' direction and the other in 3' to 5'.

Which statement is true about the structure of a double-stranded DNA molecule?

The diameter of a DNA molecule is the same along its entire length due to the specific complementary base pairing of the DNA nucleotides

In a DNA strand, successive nucleotides are linked by:

3' - 5' phosphodiester bonds

Which statement about RNA is correct?

the nucleotide at the 5' end of an RNA molecule is typically a nucleoside triphosphate.


protiens are synthesized on these particles. located in the cytoplasm

What are the important differences that distinguish RNA from DNA?

1) the usgar in RAN is ribose
2) the base uracil in RNA replaces thymine in DNA
3) while the 5' end of a DNA strand is typically a monophosphate, the 5' end of an RNA molecule is typically a triphosphate.

What are the physical features that distinguis RNA from DNA?

RNA molecules are usually much shorter than DNA molecules. most RNA molecules in the cell are single stranded, whereas DNA molecules are double stranded

What kind of nucleic acids were present in the earliest cells?

a plausible explanation is that life evolved from an RNA-based world to one in which DNA, RNA, and proteins are specialized for different functions

RNA world hypothesis

the hypothesis that the earliest organisms relied on RNA for both catalysis and information storage

In transcription, ______ is used as a template to make complementrary RNA


What is an RNA transcript?

The RNA sequence synthesized from a DNA template

What is RNA polymerase?

the enzyme that carries out polymerization of ribonucleoside triphosphates from a DNA template to produce an RAN tanscript

Describe the 3 stages of transcription

A. Initiation: After RNA polymerase binds to the Promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the DNA Template Strand. Start Codon is AUG.
B. Elongation: The polymerase moves downstream, unwinding DNA

Transcription along a stretch of DNA.

promoters include 5'TATAAA-3' sequence known as a TATA box. transcription takes place about 25 nucleotides downstream of the TATA box, and elongation occurs as teh RAN plymerase moves along the template strand in the 3'-5' direction until it encountars te

How does bacteria regulate transcription?

promoter recognition is mediated by a protein called sigma factor, which associates with RNA polymerase and facilitates its binding to specific promotes. Once transcription is initiated, the sigma factor dissociates and the RNA polymerase continues transc

What are general transcription factors?

A set of proteins that bind to the promoter of a gene whose combined action is necessary for transcription

What is a transcriptional activator protein?

A regulatory protein that binds to a DNA sequence (enhancer) to enable transcription to begin.

what is an enhancer?

a specific DNA sequence necessary for transcription

what is a mediator complex?

a complex of proteins that interacts with the Pol II complex and allows transcription to begin.

What does pol II do?

The RNA polymerase complex responsible for trancription of protein-coding genes.

What is the eukaryotic transcription complex?

What 3 steps make up eukaryotic mRNA processing?

synthesis of a primary transcript

Which of the following reads the nucleotide sequence of a gene and synthesizes the corresponding primary transcript?

RNA polymerase

The primary transcript is _____ to the DNA template strand. Select all that apply.
A. identical
B. complementary
C. antiparallel

B. complementary
C. antiparallel

Which of the following mRNA processing events occurs in the nucleus of human cells? select all that apply.
A. 5' cap addition
B. excision of introns
C. splicing of exons
D. ply-A tail addition

all of the above

Where is the transcription bubble?

within the RNA polymerase, the two strands of DNA separate and the growing RNA strand forms a duplex with the DNA template.

What is the polymerization reaction that allows the RNA transcript to be elongated?

What does transcription require to take place?

template DNA, a supply of ribonucleoside triphosphates, and RNA polymerase

What are four differences between the structure of DNA and RNA?

1) The sugar in RNA is ribose, wherease the sugar in DNA is deoxyribose
2) The base thymine in DNA is replaced by uracil in RNA.
3) DNA molecules are double stranded, whereas RNA molecules are single stranded
4) DNA molecules are typically very long, wher

A segment of one strand of a double-stranded DNA mplecule has the sequence 5'-ACTTTCAGCGAT-3'. what is the sequence of an RNA molecule synthesized from this DNA template?


What is the consequence for a growing RNA transcript if an abnormal nucleotide with a 3'-H is incorporated rather than a 3'-OH? How about a 2'-H rather than a 2'-OH?

The incorporation of a nucelotide with a 3'-H group rather than a 3'-OH group will stop subsequent elongation because the 3'-H group is necessary to attack the high-energy phosphate bond of the incoming nucleoside triphosphate. The incoporation of a nucle

What is the name of the enzyme that forms at the start of transcription?

RNA polymerase

What genetic material is made during the process of transcription? select all that apply

all of the above

If the first nucleotide after the promoter on the top DNA strand is changed from G to T, what would the resulting nucleotide be on the mRNA?


If you made a change in the promoter sequence in the DNA, what would happen at the RNA level?

the RNA polymerase would not be able to recognize and bind the DNA, so no RNA would be made.

Which example correctly lists the components necessary for eukaryotic transcription?

RNA polymerase, DNA template, general transcription factors, and RNA nucleotides

Whichever DNA strand is transcribed, the RNA polymerase reads the template strand from 3' to 5'


In eukaryotes, where do activator proteins bind?


In eukaryotes, where do general transcripion initiation factors bind?


Transcription continues until:

a terminator sequence is encountered

Gel Electrophoresis

Procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel

Gel electrophoresis is a technique used to separate nucleic acids by their _____/


Denaturation of DNA is a necessary step in Souther blotting procedure because it separates double stranded DNA into single stranded DNA


In gel electrophoresis, DNA fragments migrate toward the negative pole of the electric field


A southern blot is a technique that relies on hybridization of

a nucleic acid probe to a complementary DNA.