Honors Bio - Ch. 10 Structure of DNA

Viruses

Viruses

-Bind to receptors on a host cell

-Inject viral genetic material into the host cell

-Hijacks the host cell’s own equipment to produce new copies of the virus

-Ultimately cause the host cell to be destroyed when the new viruses are released

Unique characteristics of DNA and RNA in viruses

They can have double stranded DNA and RNA like a typical cell, or they could have single stranded RNA (which is an exception to certain scientific rules)

True/False: Viruses are generally considered alive.

False; they are NOT generally considered alive because they are not cells and cannot reproduce on their own.

True/False: Because of their simplicity, viruses are used to study the functions of DNA.

True

Until the 1940s, it was believed that _________ were genetic material.

proteins

Main reason that scientist used to believe proteins were genetic material

Proteins are made from 20 different amino acids, while DNA has only 4 bases

Molecular biology

The study of heredity at the molecular level; this field was led up to by the studies of bacteria and viruses

True/False: The study of bacteria and viruses revealed the role of DNA in heredity.

True

Bacteriophages

A virus that infects bacterial cells; sometimes just called a phage for short

Examples of Nucleic Acids

DNA and RNA

Polynucleotide

A nucleotide polymer (chain)

Nucleotides are composed of…

-A nitrogenous base

-Five carbon sugar

-Phosphate groups

Sugar-phosphate backbone

This is what joins nucleotides together

True/False: DNA and RNA are polymers of nucleotides.

True

DNA nucleotides have a different nitrogen-containing base, including…

adenine, cytosine, thymine, guanine

Shape of DNA

double helix

Pyrimidines

Single ringed, thymine and cytosine

Purines

Double ringed, adenine and guanine

RNA

Ribonucleic acid

RNA has ___________ instead of deoxyribose, and _________ instead of thymine.

ribose, uracil

James D. Watson and Francis Crick

Deduced the secondary structure of DNA using x-ray crystallography data of DNA from the work of other scientists

Rosalind Franklin and Maurice Wilkins

Created x-ray crystallography data of DNA that eventually ended up helping Watson and Crick

Chargaff’s Rule

-The amount of adenine = the amount of thymine

-The amount of guanine = the amount of cytosine

Watson and Crick discovered…

-DNA consisted of two polynucleotide strands wrapped into a double helix

-The sugar-phosphate backbone is on the outside

-The nitrogenous bases are perpendicular to the backbone in the interior

-Specific pairs of bases give the helix a uniform shape

Specific pairs of bases that give the helix a uniform shape are…

Adenine + Thymine = two hydrogen bonds

Guanine + Cytosine = three hydrogen bonds

Some types of DNA models are…

Ribbon model, partial chemical structure model, and computer model

True/False: Watson, Crick, Wilkins, and Franklin all received the Nobel Prize for their work in discovering the structure of DNA.

False; Watson, Crick, and Wilkins all received the prize in 1962, however, Franklin had died from cancer in 1958 and so she never received the award (Nobel Prizes are never awarded posthumously/after death).

DNA replication follows a _______ model

semiconservative

Semiconservative model

-The two DNA strands separate

-Each strand is used as a pattern to produce a complementary strand, using specific base pairing

-Each new DNA helix has one old strand with one new strand

DNA Replication (step 1)

DNA helicase unzips the double stranded DNA.

DNA Replication (step 2)

SSBP (single stranded binding proteins) stabilize the open template strand

DNA Replication (step 3)

Leading strand is synthesized continuously in the 5’ to 3’ direction by DNA polymerase

DNA Replication (step 4)

Primase beings to synthesize RNA primer for Okazaki fragments

DNA Replication (step 5)

DNA polymerase is completing synthesis of the next fragment when it reaches the primer. It detaches and begins adding DNA nucleotides to the 3’ end of the next fragment.

DNA Replication (step 6)

DNA Polymerase I removes the primer from the 5’ end of the fragment, replacing it with DNA nucleotides added one-by-one to the 3’ end of the fragment

DNA Replication (step 7)

DNA ligase joins the 3’ end of one fragment to the 5’ end of another fragment

True/False: DNA Helicase, DNA polymerase, and ligase are all examples of sugars.

False; they are examples of enzymes (-ase is enzyme, -ose is sugar)

DNA replication begins…

At the origins of replication; where DNA unwinds to produce a “bubble,” and then replication proceeds in both directions until products from the bubbles merge with each other

Direction of DNA replication

5’ to 3’

Replication is continuous on the ________ template

3’ to 5’

Replication is discontinuous on the _________ template

5’ to 3’

Discontinuous replication forms short segments called __________

Okazaki fragements

Analogy for DNA ligase

Tape or glue (because it joins small fragments into a continuous chain)

Function of DNA polymerase

-Adds nucleotides to a growing chain

-Proofreads and corrects improper base pairings

Enzymes that repair DNA that was damaged by harmful radiation and toxic chemicals

DNA polymerase and DNA ligase (this is their secondary function)

DNA replication ensures that all somatic cells of a multicellular organism…

Carry the same genetic information

Reason that old people will have shorter chromosomes with less genes

With each round of mitosis, the telomeres start to chip away. This causes the chromosomes to shorten and therefore cuts away some of the genes. Ultimately can result in cancer and other diseases

Purpose of DNA Transcription

Makes mRNA

Location of DNA Transcription

Cell nucleus

DNA Transcription (step 1)

RNA polymerase binds to the DNA (called initiation)

DNA Transcription (step 2)

RNA polymerase adds RNA nucleotides together (called elongation)

DNA Transcription (step 3)

RNA polymerase will release the DNA and mRNA when it reaches a termination sequence (called termination)

Purpose of DNA Translation

Making a protein

Location of DNA Translation

Ribosome (loose or attached to RER)

DNA Translation (step 1)

mRNA binds to the small subunit of ribosome

DNA Translation (step 2)

A tRNA brings the first amino acid to the ribosome

DNA Translation (step 3)

The large subunit attaches to the small subunit

DNA Translation (step 4)

The ribosome reads the mRNA in triplets called codons (codon recognition)

DNA Translation (step 5)

Elongation of the polypeptide chain (elongation + peptide bond formation)

DNA Translation (step 6)

The whole “unit” moves over (translocation)

DNA Translation (step 7)

When the ribosome reads the stop codon, it lets go of the mRNA and the polypeptide chain, and the 2 subunits come apart.

Peptide bonds are only found between 2 ________

amino acids

The molecular chain of command is from…

DNA in the nucleus to RNA and RNA in the cytoplasm to protein

What analogy can be used to describe transcription and translation?

DNA = cookbook, RNA = copy of specific recipe (chocolate cookies), Ribosome = kitchen, Protein = final cookies that were baked

What an organism looks like is based on…

it’s genotype

One Gene - One Polypeptide hypothesis recognizes that…

Some proteins are composed of multiple polypeptides

The sequence of nucleotides in DNA provides a coe for __________

constructing a protein

Protein construction needs…

Conversion of a nucleotide sequence to an amino acid sequence

Transcription rewrites…

DNA code into RNA, using the same nucleotide “language”

Gene to protein is based on _______

Triplet code

Triplet code:

The genetic instructions for the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of nonoverlapping three-base “words” called codons

____ codons are possible

64

True/False: Some amino acids have more than one possible codon

True

Characteristics of the genetic code

Three nucleotides specify one amino acid:

-61 codons correspond to amino acids

-AUG codes for methionine and signals the start of transcription

-3 “stop” codons signal the end of translation

The genetic codes is…

Redundant, unambiguous, nearly universal, without punctuation

Redundant

more than one codon for some amino acids

Unambiguous

any codon for one amino acid does not code for any other amino acid

Nearly universal

the genetic code is shared by organisms

Without punctuation

no gaps in between codons

Job of Messenger RNA (mRNA)

-Encodes amino acid sequences

-Conveys genetic messages from DNA to the translation machinery of the cell

Difference between location of translation machinery in prokaryotes and eukaryotes

Prokaryotes - occurs in the same place that mRNA is made (nucleoid region)

Eukaryotes - mRNA must exit the nucleus via nuclear pores to enter the cytoplasm

Eukaryotic mRNA has…

Introns and exons

Introns

Interrupting sequences that separate (think of the “i” in “intron,” stands for “in the way”)

Exons

Coding regions of mRNA (think of the “e” in “exon,” it stands for “expressed”)

RNA splicing

-Eukaryotic mRNA must undergo this process before leaving the nucleus

-Removes introns and joins exons to produce a continuous coding sequence

-A cap and tail of extra nucleotides are added to the ends of the mRNA

Reason a cap and tail of extra nucleotides are added to the ends of mRNA

-Help the export of the mRNA from the nucleus

-Protect the mRNA from attack by cellular enzymes

-Help ribosomes bind to the mRNA

Spliceosomes

Enzyme used for RNA splicing

Transfer RNA (tRNA) molecules function as __________

language interpreters (specifically, they convert the genetic message of mRNA into the language of proteins)

How tRNA performs its task

-Pick up the appropriate amino acid

-Use a special triplet of bases, called an anticodon, to recognize the appropriate codons in the mRNA

True/False: Ribosomes coordinate the functioning of mRNA and tRNA, and ultimately, the synthesis of sugar

False; polypeptides

True/False: RIbosomes have two subunits: small and large

True

Each subunit is composed of __________

Ribosomal RNAs and proteins

Ribosomal subunits come together during _____

translation

True/False: Ribosomes have binding sites for mRNA and tRNA

true

tRNA binding sites

P (peptidyl) Site, A (arrival) Site

sometimes: E (exit) Site

Gene mutations

Affect a single gene by changing its base sequence, resulting in an incorrect, or nonfunctional, protein being made

Substitution mutation

Occurs where one nucleotide base is replaced by another; they are often called “point mutations” because a single base is changed at one point in the gene

Two types of substitution mutations

Missense and Nonsense

Missense mutation

Replacement of a single nucleotide, resulting in the incorrect amino acid, which may produce a malfunctioning protein (ex. sickle cell anemia)

Nonsense Mutation

Replacement of a single nucleotide that accidentally results in a “stop” codon, shortens the protein