AP Bio Unit 6 (2)

DNA

A type of nucleic acid that is genetic material for all living organisms

Purpose of DNA

Involves the storage, transfer, and expression of heritable information

Protein synthesis

The process of expressing genes

Central dogma of genetics

DNA➡RNA➡Proteins (Phenotype)

Monomer of nucleic acids

nucleotides

Nucleotide structure

1 phosphate group

1 pentatose (5 carbon) sugar

1 nitrogenous base

What two more unique do nucleotides have?

Nitrogen and phosphorous

What carbon is the phosphate group bonded to?

5 carbon

What carbon is the nitrogenous bonded to?

1 carbon

DNA vs. RNA

DNA: deoxyribose sugar, thymine, double strand

RNA: ribose sugar, uracil, single strand

How does the phosphate group of one nucleotide form covalent bonds with the sugar of another nucleotide?

Dehydration synthesis

What does the process of dehydration synthesis and creating the sugar phosphate back bone make?

A single strand of DNA

How do two sperate strands of DNA come together?

By forming hydrogen bonds between nitrogenous bases

Purines

Double ringed nitrogenous bases (guanine, adenine)

Pyrimidines

Single-ringed nitrogenous bases (cytosine, thymine, uracil)

Adenine pairs with...

Thymine (DNA)

Uracil (RNA)

Guanine pairs with...

Cytosine (ALWAYS)

When you add the percentages of guanine, adenine, thymine, and cytosine, what should it equal?

100%

What is the structure of DNA?

The two DNA strands run antiparalell

One strand runs 5' - 3'

The second strand runs 3' - 5'

What are chromosomes like in prokaryotes?

Prokaryotes have a single chromosome made of a double strand of DNA that is circular

Where do prokaryotes store their genetic info?

In the nucleoid region

What are chromosomes like in eukaryotes?

Longer than prokaryotes and linear

Where is DNA stored in eukaryotes?

In the nucleus

What is the nucleus the site of?

The site of DNA replication, transcription, and RNA processing

Nucleosome

each bead of chromatin (histone protein wrapped with DNA)

Chromatin

Complex of DNA + histone proteins

Plasmids

Small circular DNA molecules that are seperate from the chromosomes. They ARE NOT necessary, but do provide advantageous traits

DNA replication

The process by which a variety of enzymes work together and make a copy of each chromosome

What does DNA replication in the S phase produce?

Two exact copies of DNA that serve as a template for new copies

Semiconservative

Each of the original parent strands is used as a template to synthesize two new "daughter" strands using the base-pair rule "conserving"

What are the benefits of semiconservative DNA?

This makes mistakes easier to repair

And increases accuracy and efficiency

Origin of replication

The particular sites in DNA where replication begins

Replication bubble

a region of DNA, in front of the replication fork, where helicase has unwound the double helix

The percentage of ______ equals the percentage of adenine

thymine (DNA) uracil (RNA)

The percentage of ______ equals the percentage of guanine

cytosine

Helicase

Untwists the double helix structure creating a replication bubble

How by helicase untwist the DNA strand?

By breaking the hydrogen bonds that held the nitrogenous bases a part

Topoisomerase

Prevents the DNA from coiling and getting into a knot

RNA primase

Places down a primer that prepares for DNA polymerase to

DNA polymerase

Adds DNA nucleotides onto the chain, following the complementary base pairing rules

Can DNA polymerase start a DNA chain?

NO it can only extended the DNA chain

What direction does DNA polymerase add nucleotides?

5'-3'

Elongation

The rate of adding new nucleotides

How does DNA polymerase form covalent bonds between new nucleotides and old nucleotides?

Dehydrattion synthesis

Leading strand

The strand that runs from 3'-5' and its synthesized continuously

Lagging strand

The strand that runs from 5'-3' and is synthesized in fragments

Why can't DNA polymerase run continously on the lagging strand?

Because DNA polymerase must run in the 5'-3' direction, so it cannot directly follow helicase as it unzip the DNA strand.

Okazaki fragments

The fragments created on the lagging strand due to DNA polymerase jumping around on the strand

Ligase

Forms covalent bonds between nucleotides and "glues" them together

Mutation

Any change in the sequence of DNA

What causes mutations?

Environmental factors or errors in DNA replication

How can DNA polymerase help with preventing mutations?

It can go back and correct any errors that occurred during DNA replication

Are mutations in somatic cells passed down to the next generation?

No

Are mutations in gametes passed down to the next generation?

Yes

What is the primary source of genetic variation?

Mutations

Are mutations always negative?

No, mutations can be positive, negative, or have no effect

Genetic Engineering

The direct analysis and manipulation of genes for practical purposes

Locus

The location of a gene on a specific chromosome

What can be used to determine the loci of specific genes?

Recombination frequencies and DNA sequencing

DNA cloning

Preparing well-defined segments of DNA in multiple identical copies

Step 1 in DNA cloning

Isolating the desired DNA fragment

Restriction enzymes

DNA cutting enzymes that make cuts in DNA, are used in this step

Step 2 in DNA cloning

Inserting desired DNA into a cloning vector

Cloning vector

a small piece of DNA—usually a plasmid—used as a "vehicle" to carry foreign genetic material into a host cell

Step 3 in DNA cloning

Introducing this recombinant DNA into a host organisms where it can replicate multiple copies and/or express the desired gene

Recombinant DNA

DNA containing the newly inserted DNA from cloning and the organism's previous DNA

Transgenic bacterium

A microorganism whose genetic material has been artificially altered by introducing foreign DNA

Gene cloning

The organism can reproduce itself through cell division, creating another organism with both foreign and native DNA

What is the purpose of cloning

Making multiple copies of a particular gene (amplifying it)

Producing a specific protein product from that gene

Bacterial transformation

Introducing foreign DNA into bacteria

Do all organisms share the same genetic code?

Yes

Genetically modified organisms (GMOs)

Any organisms that has had their DNA altered in some way

Transgenic

When one organisms contains genetic materials from a completely unrelated organism

Gel electrophoresis

Technique that allows for the separation of DNA fragments by molecular size and charge

Whats the purpose of Gel electrophoresis?

To create a visualization and comparison of the fragments

Step 1 of Gel electrophoresis

Samples of DNA are placed into wells at one end of the gel

Step 2 of Gel electrophoresis

An electric current runs through the gel

What charge are DNA molecules?

Negative

What direction do the DNA molecules move in gel electrophoresis?

From the negative end to the positive end

Which DNA fragments move further through the gel?

shorter fragments

DNA ladder

A sample used in gel electrophoresis with known base pair lengths

What does the more band mean in gel electrophoresis?

The more related two individuals are

Polymerase chain reactions (PCR)

Makes billions of copies of DNA super fast

Used to amplify a small sample of DNA

Step 1 of PCR

Denaturing: The DNA is heated to separate the two strands

Step 2 of PCR

Annealing primers: The DNA is cooled allowing complementary DNA primers to attach to the 3' ends of the target sequence

Step 3 of PCR

Extending: A unique DNA polymerase is heat tolerant preventing it from becoming denatured during denaturation

Does PCr require a large amount of DNA?

No

DNA sequencing

Used to determine the exact sequence of nucleotides in a particular gene

CRISPR-Cas9

A protein system that can cut DNA anywhere

Why is CRISPR-Cas9 needed?

because restrictions enzymes are limited in where they can cut DNA

What directs the Cas9 protein to cut anywhere?

an RNA guide

Purpose of CRISPR Cas9

helps treat genetic disorders, reduces insect-borne diseases, targeted cancer therapies, and simpler creation of DNA

Gene expression

The process by which DNA is used to direct the synthesis of proteins

Messenger RNA (mRNA)

A single-stranded transcript of the DNA nucleotide sequence from a gene

Ribosomal RNA (rRNA)

Makes up the structure of ribosomes that synthesize the proteins by reading the mRNA

Transfer RNA (tRNA)

Transfers amino acids (monomers) from the cytoplasm to the ribosome as the polypeptide chain continued to grow

Transcription

Transcribing DNA nucleotides into a strand of complementary mRNA nucleotides

Where does transcription occur?

In the nucleus of eukaryotes

What determines the bases of mRNA?

The sequence of DNA nucleotide bases

Template strand

The strand being used to build the mRNA strand