DNA Structure, Replication, Manipulation

Genome

the genetic complement of a cell or virus

10³ base pairs

kilobase (kb)

10^6 base pairs

megabase (Mb)

DNA is a linear polymer of four ____.

deoxyribonucleotides

Nucleotides are composed of…

2'- deoxyribose (a five-carbon sugar), phosphoric acid, and the four nitrogen-containing bases denoted A, T, G, and C

Purines

double-ring structure (A,G)

Pyrimidines

single-ring structure (T, C)

Nucleotides are joined to form a ____ _____.

polynucleotide chain

What is in a polynucleotide chain?

the phosphate attached to the 5' carbon of one sugar is linked to the hydroxyl group attached to the 3' carbon of the next sugar in line

phosphodiester bonds

chemical bonds by which the sugar components of adjacent nucleotides are linked through the phosphate groups

The duplex molecule of DNA consists of two polynucleotide chains twisted around one another to form a ____ _____ ____ in which the bases form ____ ____.

right-handed helix, hydrogen bonds

Adenine pairs with ____

Thymine

Guanine pairs with ____

Cytosine

A hydrogen bond is a ___ bond.

weak

Collectively, hydrogen bonds are ____.

strong

C and G base pairs form ____ H-bonds

three

A and T base pairs form ___ H-bonds

two

The backbone of each strand consists of deoxyribose sugars ____ with phosphate groups that link 5' carbon of one sugar to the 3' carbon of the next sugar in line

alternating

The two polynucleotide strands of the double helix run in opposite directions. The paired strands are said to be _____.

antiparallel

Hydrogen bonds between DNA bases break to allow ___ ____.

strand separation

Each DNA strand is a _____ for the synthesis of a new strand

template

Template strand is also called…

parental

New strand is also called…

daughter

Template (parental) strand determines the sequence of bases in the new strand (daughter)

complementary base pairing rules

DNA replication is semiconservative

The parental strands remain intact and serves as a template for a new strand

The linear DNA duplex in a eukaryotic chromosome also replicates ____

bidirectionally

_____ _____ is a means of reducing the total replication time

Multiple initiation

One strand of the newly made DNA, ___ ____, is synthesized continuously

leading strand

Lagging strand is made in…

small precursor fragments (Okazaki fragments)

DNA must always be synthesized in….

the 5’ to 3’ direction

Template strand is “read”

3’ to 5’ direction

DNA sugar

deoxyribose

RNA sugar

ribose

RNA contains the pyrimidine _____ in place of thymine

uracil

DNA is _____-stranded

double

RNA is _____-stranded

single

Short RNA fragment serves as a ____ to initiate DNA synthesis at origins of replication

primer

Gyrase

topoisomerase II

introduces a double-stranded break ahead of the replication fork and swivels the cleaved ends to relieve the stress of helix unwinding

topoisomerase II

unwinds DNA at replication fork to separate the parental strands

Helicase

stabilizes single strands of DNA at replication fork

Single-strand binding protein (SSB)

What initiates strand synthesis by forming RNA primer?

primosome

The multi enzyme complex called primosome (contains the enzyme _____)

primase

The enzyme ____ _____ forms the ______ _____ between adjacent nucleotides in a new DNA acid chain in 5’ to 3’ direction

DNA polymerase, phosphodiester bond

DNA polymerase has a _____ _____ that corrects errors in replication.

proofreading function

DNA ligase catalyzes…

the formation of the final bond connecting the two precursor fragments

Two DNA strands can be separated by heat without breaking phosphodiester bonds

DNA denaturation

DNA renaturation is also called…

hybridization

____ ____ cleave double stranded DNA at specific nucleotide sequences

Restriction enzymes

The nucleotide sequence recognized for cleavage by a restriction enzyme is called the ____ _____ of the enzyme

restriction site

A DNA sequence with this type of symmetry is called a _____

palindrome

Each end of the cleaved site has a single-stranded overhang that is complementary in base sequence to the other end

sticky ends

Some restriction enzymes cleave symmetrically— at the same site in both strands. They yield DNA fragments that have ____ ____

blunt ends

Because of the sequence specificity, a particular restriction enzyme produces a unique set of ____ _____ for a particular DNA molecule

restriction fragments

A map showing the unique sites of cutting of a particular DNA molecule by restriction enzyme

restriction map

a radioactive fragment of DNA or RNA

probe

____ ____ ______ is used to detect very small amounts of DNA or to identify a particular DNA band by DNA-DNA or DNA-RNA hybridization

Southern blot analysis

Hybridization

formation of hydrogen bonds between complementary base pairs

____ ___ ___ makes possible the amplification of a particular DNA fragment

Polymerase chain reaction (PCR)

Oligonucleotide ____ that are complementary to the ends of the target sequence are used in repeated rounds of denaturation, annealing, and DNA replication

primers

The number of copies of the target sequence ____ in each round of replication, eventually overwhelming any other sequences that may be present

doubles

____ ____ isolated from bacterial thermophiles that can withstand high temperature used in procedure

Taq polymerase

The dideoxy sequencing method employs DNA synthesis in the presence of small amounts of fluorescently labeled nucleotides that contain the sugar ______ instead of ______

dideoxyribose, deoxyribose