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CHAPTER 21. NUCLEIC ACIDS AND PROTEIN SYNTHESIS. What Role Do Nucleic Acids Play?. DNA Contained in cell nucleus All information needed for the development of a complete living system Every time a cell divides, cell’s DNA is copied and passed to the new cells. RNA

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chapter 21

CHAPTER 21

NUCLEIC ACIDS AND PROTEIN SYNTHESIS

what role do nucleic acids play
What Role Do Nucleic Acids Play?
  • DNA
    • Contained in cell nucleus
    • All information needed for the development of a complete living system
    • Every time a cell divides, cell’s DNA is copied and passed to the new cells.
  • RNA
    • Part of the process of making proteins from genetic information encoded in DNA
    • RNA transcribes the information contained in the genes and carries the code out to the protein-making machinery
a components of nucleic acids
A. Components of Nucleic Acids
  • DNA and RNA are both nucleic acids
    • Both: unbranched polymers of repeating nucleotide monomers
    • Each nucleotide has three components: a nitrogenous base, a five-carbon sugar, and a phosphate group.
  • Nitrogen-containing bases:
    • Derivatives of pyrimidine or purine.
    • Adenine (A) and guanine (G) are purines, and cytosine C and thymine (T) are pyrimidines. RNA uses the same bases, except that T is replaced by uracil (U).

Nitrogenous Base Structures

ribose deoxyribose
Ribose/Deoxyribose
  • Both RNA and DNA contain 5-carbon sugars.
    • RNA: ribose
    • DNA: deoxyribose
  • The carbons in the sugars are numbered with primes.
nucleosides nucleotides
Nucleosides/Nucleotides
  • Nucleoside: base + sugar
  • Nucleotide: base + sugar + phosphate group

“Tide contains phosphates!”

    • Naming: Adenine + ribose = adenosine

Adenine + deoxyribose = deoxyadenosine

Naming nucleosides of the other bases follows the same pattern.

Naming nucleotides: nucleoside name followed by

5’-monophosphate

ex. Adenosine 5’-monophosphate (AMP) or deoxyadenosine 5’-monophosphate (dAMP)

nucleoside di and triphosphates
Nucleoside Di- and Triphosphates
  • Any nucleoside 5’-monophosphate can bind additional phosphate groups, forming a diphosphate or triphosphate
  • For example, you can form the famous ADP (adenosine 5’-diphosphate) and ATP (adenosine 5’-triphosphate) through the addition of phosphate groups.
  • The same can be done for nucleosides of other bases (ex. GTP, CDP, etc)
let s practice
Let’s practice…
  • Identify each of the following as a nucleoside or a nucleotide:
    • Guanosine

Nucleoside -- “phosphate” not part of the name

    • Deoxythymidine

Nucleoside

    • Cytidine 5’-monophosphate

Nucleotide -- “phosphate” is part of the name

b primary structure of nucleic acids
B. Primary Structure of Nucleic Acids
  • The nucleotides are linked together from the 3’ -OH of the sugar in one nucleotide to the phosphate on the 5’ carbon of the next nucleotide.
  • This phosphate link is called a phosphodiester bond. The chain formed from multiple phosphodiester bonds forms the backbone of a strand of DNA.

Phosphodiester bond formation

  • Sequence of bases in the nucleic acid = primary structure. The sequence is written with 5’ and 3’ ends labeled, for instance -- 5’-ACGT-3’
c dna double helix
C. DNA Double Helix
  • In the 1940’s, it was discovered that the percent of A in an organism = % T. Likewise, %C = %G.

What might this suggest?

  • Base pairing rules: in two complementary strands of DNA, A always base pairs with T, and C always base pairs with G.
  • 1953: DNA discovered to be a double helix (winds like a spiral staircase)

DNA Double Helix

  • The strands are antiparallel.
d dna replication
D. DNA Replication
  • Whenever cells divide, the DNA in the cells needs to replicate -- an exact copy of the DNA needs to be passed to the new cells.
  • Replication begins when the enzyme helicase unwinds a portion of the helix by breaking hydrogen bonds between the strands.
  • A nucleoside triphosphate bonds to the sugar at the end of the growing new strand. Two phosphate groups are cleaved (this provides the energy for the reaction)
  • And DNA polymerase catalyzes the formation of the new phosphodiester bond.
dna replication cont
DNA Replication cont.
  • When the entire DNA double helix has been replicated, one strand will be from the original DNA and one will be a newly synthesized strand.
    • This is why the process is called semi-conservative replication
    • Ensures an exact copy of the original DNA through base pairing rules
  • The process of replication has directionality. New nucleotides are only added onto the 3’ end of a growing chain.
    • The chain that grows in the 5’ --> 3’ direction: leading strand. Continuously synthesized.
    • The chain that grows in the 3’ --> 5’ direction: lagging strand.
how is the lagging strand synthesized
How is the lagging strand synthesized?
  • As replication forks (bubbles along the double helix) open up, short fragments of the lagging strand are synthesized in the 5’ --> 3’ direction as space allows. These fragments are called Okasaki fragments.
  • These fragments are eventually joined by DNA ligase to create a continuous strand of DNA.
e rna and transcription
E. RNA and Transcription
  • RNA is similar to DNA, except…
    • Different sugar (ribose instead of deoxyribose)
    • The nitrogen base uracil replaces thymine
    • RNA molecules are single stranded (not double stranded)
    • RNA molecules are much smaller than DNA molecules
three types of rna
Three Types of RNA
  • Ribosomal RNA (rRNA) -- contained in ribosomes, the site of protein synthesis
  • Messenger RNA (mRNA)
    • Carries genetic info from DNA in nucleus to ribosomes in cytoplasm for protein synthesis
    • Is a copy of the gene
  • Transfer RNA (tRNA) -- brings the appropriate amino acid to the ribosome during the process of protein synthesis. Each tRNA contains an anticodon (three bases complementing a three-base segment on the mRNA) which allows for match-up with exact amino acid.
transcription synthesis of mrna
Transcription: Synthesis of mRNA
  • Begins with unwinding of a section of the DNA containing the gene needing to be copied
  • Initiation point (signal) for transcription: TATAAA
  • RNA polymerase moves along the template strand in the 3’ to 5’ direction, allowing it to synthesize RNA adding new nucleotides to the 3’ end of the new strand.
  • When a termination signal is reached, the mRNA is released, and DNA recoils back into its double helix structure.
processing of mrna
Processing of mRNA
  • Happens in eukaryotic cells, but not in prokaryotes
  • Eukaryotic genes contain introns -- sections that do not code for protein -- interspersed with coding sections called exons
  • Prokaryotic genes do not contain exons and introns
  • Prior to leaving the nucleus, the eukaryotic mRNA undergoes processing -- introns get snipped out, or spliced.
regulation of transcription
Regulation of Transcription
  • The cell goes not make mRNA randomly. There are certain proteins which are constantly needed, but not very many.
  • Most mRNA is synthesized in response to cellular needs for a particular protein. Regulation is at the level of transcription.
  • Prokaryotic cells regulate transcription by means of the operon -- more than one gene under the control of the same regulatory center.
    • Control site: promoter (place where RNA polymerase binds) and operator (place where repressor may or may not bind)
f the genetic code codons
F. The Genetic Code: Codons
  • A sequence of three bases is called a codon.
  • Each codon specifies an amino acid in the protein.
  • All 20 amino acids have their own codon -- some amino acids have more than one.
  • Three codons specify the stop of protein synthesis -- they are UAG, UGA, and UAA.
  • AUG signals the start of protein synthesis and also encondes the amino acid methionine.
g protein synthesis translation
G. Protein Synthesis: Translation
  • Occurs at ribosomes, outside of nucleus
  • tRNA are used to translate each codon into an amino acid
  • Anticodon in the bottom loop is a three-base complement to the codon in the mRNA
  • Amino acid is attached to the stem on the opposite end of the tRNA via an aminoacyl-tRNA synthetase..
initiation of protein synthesis
Initiation of Protein Synthesis
  • Both ribosomal subunits and an mRNA combine, recognizing the start codon on the mRNA
  • The appropriate tRNA binds to the codon
  • Next, the appropriate tRNA binds to the second codon on the mRNA; a peptide bond is formed between the two neighboring amino acids.
    • The first tRNA dissociates
    • The ribosome shifts down the mRNA chain, allowing space for the next tRNA down the line to float in and bind
  • This process continues until a stop codon is reached.
termination of protein synthesis
Termination of Protein Synthesis
  • When the ribosome reaches a stop codon, protein synthesis ends.
  • The entire complex dissociates, and the peptide is released. The peptide can fold.
h genetic mutations
H. Genetic Mutations
  • Mutation = change in DNA sequence, altering the amino acid sequence as well
  • Causes of mutation: radiation (X rays/UV light), chemicals called mutagens, perhaps viruses
  • Mutation in somatic cell: body cells resulting from division contain the mutation
    • Could lead to tumor/cancer
  • Mutation in germ cell (egg or sperm): offspring will contain mutation
  • Mutations can affect function of important enzymes
types of mutations
Types of Mutations
  • Replacement of one base with another: substitution mutation
    • May or may not change the individual amino acid, but no downstream effect
  • Frameshift mutation: base is added to, or deleted from, the sequence. Changes reading frame.
    • The amino acid in question is affected, as well as all downstream amino acids (out of frame)
effect of mutations
Effect of Mutations
  • If an enzyme, may completely lose activity
    • Does the mutation change the active site directly?
    • If not, does it alter the 3D shape of the protein enough so that the substrate can no longer bind?
  • A defective protein (due to mutation) may result in genetic disease.
practice
Practice…

For the following mRNA sequence:

5’-ACA-UCA-CGG-GUA-3’

If a mutation changes UCA to ACA, what happens to the protein?

What happens if the first U is removed from the sequence?

genetic diseases
Genetic Diseases
  • Result of a defective enzyme, resulting from a mutation
  • Example -- albinism
    • An enzyme normally converts tyrosine to melanin (pigment causing hair/skin color)
    • If this enzyme is defective, no melanin produced = albinism
j recombinant dna
J. Recombinant DNA
  • “Cutting and pasting” DNA from the same organism, or from different organisms
  • The resulting DNA is called recombinant
  • Has allowed for the production of human insulin, interferon, human growth hormone…
preparing recombinant dna
Preparing Recombinant DNA
  • Using E. coli (prokaryotic) as an example… some bacteria contain circular DNA called plasmids.
  • Plasma membranes are dissolved and plasmid DNA isolated
  • A restriction enzyme (recognizes a certain DNA sequence and cuts) cuts through the plasmid
  • Another piece of DNA can be placed into the cut plasmid, and ends sealed
  • The recombinant plasmids can be placed into cells
the point of recombinant dna
The Point of Recombinant DNA…
  • If you have a cell containing your recombinant plasmid… when the cell multiplies, each new cell will contain this plasmid
  • If your recombinant plasmid contains a gene (protein) of interest following a promoter, you can stimulate the cells to make large amounts of your protein of interest
polymerase chain reaction
Polymerase Chain Reaction
  • If you only have one copy (or a few copies) of one gene, this is a method to amplify (make a lot of copies) the gene quickly.
  • Three steps:
    • Heat your DNA of interest -- the double strands will separate
    • Primers (short sequence complementary to each end) are added -- they anneal to the end of your single strands
    • The addition of DNA polymerase and free nucleotides extends along the single strand, filling in until each double strand is complete.
k viruses
K. Viruses
  • Cannot replicate without a host cell
  • Invades the host cell, taking over materials necessary for protein synthesis and growth
  • Viral infection:
    • Virus inserts its genetic material (DNA or RNA) into host cell
    • Material is replicated into DNA form
    • The viral DNA is used to make viral proteins via transcription and translation
    • In some cases, the host cell will lyse, releasing new viral particles
reverse transcription
Reverse Transcription
  • Viruses that use RNA as their genetic material must make viral DNA once inside the host cell
  • It does so via the enzyme reverse transcriptase.
  • A virus which contains RNA and uses this process is called a retrovirus.
aids hiv a retrovirus
AIDS/HIV: A Retrovirus
  • HIV destroys helper T cells (important in the immune response)
  • Thus, AIDS is defined by opportunistic infections
  • Treatments for AIDS?
    • Nucleoside analogs: transcription enzymes put false nucleotides into strands, proteins can’t be made
    • Protease inhibitors: HIV protease “chops” the final viral peptide into useable form. If protease blocked, viral proteins are nonfunctional