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Biochemistry > Chapter 5 - Nucleic Acids > Flashcards

Chapter 5 - Nucleic Acids Flashcards

1
Q

The Structure of the Nucleotide

  1. What is a nucleotide? What 3 things is a nucleotide made of (List the sub-groups for each as well)?
  2. In what two things are ring structures found? How are these two things numbered?
  3. What is a phosphoester bond?
  4. What is the bond between the base and the sugar called? What two things does it link?
A
  1. A nucleotide is the monomer unit (repeating unit) of the long polymers DNA and RNA. Nucleotides consist of
    - Nitrogen containing heterocyclic base (Purine and Pyrimidine). Nitrogen base is attached β to ribose (RNA)
    and deoxyribose (DNA)
    - Five-carbon sugar ring (Ribose and Deoxyribose). The sugar is phosphorylated at carbon 5’.
    - Phosphoryl group
  2. Ring structures are found in both the base and the sugar. Base rings are numbered as usual. Sugar rings numbers are given the designation ( ‘ ) or prime.
  3. Covalent bond between the sugar and the phosphoryl group.
  4. Bond between the base and the sugar is a
    β-N-glycosidic linkage joining the 1’-carbon of
    the sugar and a nitrogen atom of the base.
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2
Q

Major Purine and Pyrimidine Bases

  1. What are Nitrogenous bases? What are two things they consist of?
  2. What do Pyrimidines consist of?
A
  1. Nitrogenous bases are heterocyclic amines.
    - Cyclic compounds with at least 1 N atom in the ring structure
    - Purines: Double ring structure. (A 6-member ring fused to a 5-member ring)
  2. Pyrimidines consist of a single 6-membered ring.
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3
Q 
Adenosine Triphosphate (ATP)
1. What are the names of ATP as sequential phosphoryl groups are added? (Name 1 through 4)
    1. What are the abbreviations for the following:
      - Deoxyadenosine monophosphate
      - deoxyadenosine diphosphate
      - Deoxyadenosine triphosphate
      - Adenosine monophosphate
      - Adenosine diphosphate
      - Adenosine triphosphate
A
  • 1 Phosphoryl group: Adenosine
  • 2 Phosphoryl group: Adenosine monophosphate
  • 3 Adenosine diphosphate
  • 4 Adenosine triphosphate
    • dAMP
      - dADP
      - dATP
      - AMP
      - ADP
      - ATP
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4
Q

The Structure of DNA and RNA

  1. What two things do nucleotides combine to form? What is esterifies to what, and what retains what?
  2. Why is the backbone of the polymer called the sugar-phosphate backbone?
A
  1. Nucleotides combine to form a chain or polymerize in a series of 3’ to 5’ phosphodiester bonds. The 5’ phosphate on one unit esterifies to the 3’ OH on the adjacent unit. The terminal 5’ unit retains the phosphate.
  2. Because it is composed of alternating units of deoxyribose and phosphoryl groups.
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5
Q

Helical Structure of DNA

  1. What is the structure of the two chains in DNA?
  2. What is the structure of the sugar-phosphate backbones? What is the structure of the nitrogenous bases?
A
  1. DNA consists of two chains of nucleotides coiled around one another in a right-handed double helix.
    • Sugar-phosphate backbones of the two strands spiral around the outside of the helix like the handrails on a spiral staircase.
      - Nitrogenous bases extend into the center at right angles to the acids of the helix as if they are the steps of the spiral staircase.
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6
Q

Hydrogen Bonding of the DNA Helix

  1. What is Hydrogen Bonding? Where does hydrogen bonding occur?
  2. How many H bonds does Adenine form and with what? How many H bonds does Cytosine form and with what?
  3. What is the H bonding pattern called?
  4. What is the diameter of a double helix? What is the distance dictated by?
A
  1. A noncovalent attraction aiding in maintaining the double helix structure. Hydrogen bonding occurs between base pairs.
  2. Adenine forms 2 H bonds with thymine A=T. Cytosine forms 3 H bonds with guanine G=C.
  3. Base pairing.
  4. Diameter of the double helix is 2.0 nm. Distance dictated by the dimensions of the purine-pyrimidine base pairs.
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7
Q

Complementary DNA Strands

  1. The two DNA strands are “complementary” strands. What does this mean?
  2. The two DNA chains run antiparallel. Why?
A
  1. The sequence of bases on one automatically determine the sequence of bases on the other strand.
  2. The chains run antiparallel. Only when the 2 strands are antiparallel can the base pairs form the H bonds that hold them together.
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8
Q

DNA Double Helix

  1. What do the two strands of DNA form?
  2. What rule do the bases in opposite strands hydrogen bond with?
  3. What is the orientation of the 2 strands? Why?
  4. How many nucleotides amount to 1 complete 360° turn of the helix? What is 1 complete turn of the helix in nanometers? What is 1 nucleotide in nanometers?
A
  1. A right-handed double helix.
  2. With A-T/G-C rule.
  3. 2 strands are antiparallel per their 5’ to 3’ directionality.
  4. 10 nucleotides. 1 complete turn is 3.4 nm and 1 nucleotide is 0.34 nm.
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9
Q

Prokaryotic Chromosomes

  1. What are chromosomes?
  2. What are prokaryotes? Do prokaryotes have a nucleus? Why is the helix coiled?
  3. What is the nucleoid?
A
  1. Chromosomes are pieces of DNA that contain the genetic instructions, or genes, of an organism.
  2. Prokaryotes are single chromosomes. No true nucleus. Chromosome is a circular DNA molecule that is supercoiled, meaning the helix is coiled on itself.
  3. At approximately 40 sites, a complex of proteins is attached, forming a series of loops.
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10
Q

Eukaryotic Chromosomes

  1. What are Eukaryotes?
  2. Do eukaryotes have a true nucleus?
  3. What does a Nucleosome consist of? What is a 30 nm fiber? 200 nm fiber?
A
  1. Eukaryotes have a number and size of that chromosomes vary.
  2. Yes. The true nucleus is enclosed by a nuclear membrane.
  3. Nucleosome which consists of a strand of DNA wrapped around a disk of histone proteins – DNA appears like beads on a string.
    - String of beads then coils into a larger structure called the 30 nm fiber. With additional proteins next coiled in to a 200 nm fiber.
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11
Q

RNA Structure

  1. What is the sugar phosphate backbone for ribonucleotides linked by? How are RNA molecules stranded? Does RNA use Ribose or Deoxyribose? In RNA, what replaces Thymine?
  2. Where does base pairing occur? What does this H bonding result in?
A
  1. Just like DNA, also linked by 3’-5’ phosphodiester bonds. RNA molecules usually single-stranded. Ribose replaces deoxyribose. Uracil replaces thymine.
  2. Base pairing between U - A and G - C can still occur. H bonding results in portions of the single-strand that become double-stranded.
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12
Q

DNA Replication

  1. Why must DNA be replicated before a cell divides?
  2. What happens to a cell if it is missing a critical gene?
  3. What is essential in the process of DNA replication? What happens if a mistake occurs in DNA replication?
  4. What does the structure of the DNA molecule suggest?
  5. What does an enzyme reading the nitrogenous bases on one strand of a DNA molecule do? What is the product of this strategy? What is this strategy known as?
A
  1. So that each daughter cell inherits a copy of each gene.
  2. Cell missing a critical gene will die.
  3. That the process of DNA replication produces an absolutely accurate copy of the original genetic information. Mistakes made in critical genes can result in lethal mutations.
  4. Suggests the mechanism for accurate replication.
  5. Adds complementary bases to a newly synthesized strand. Product of this strategy would be a new DNA molecule in which one strand is the original or parent strand, and the other is newly synthesized, a daughter strand. This strategy is known as semiconservative replication.
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13
Q

The Products of DNA Replication / Bacterial DNA Replication

  1. What does semiconservative replication generate? How many helixes are formed from 2 DNA strands?
  2. What is a bacterial chromosome? How many nucleotides are in bacterial chromosome?
  3. In Bacterial chromosomes, where does DNA replication begin?
  4. How does bacterial DNA replication move? At what rate?
  5. What is the replication fork? What happens to the replication fork as DNA synthesis moves bidirectionally?
A
  1. Semiconservative replication generates 2 new DNA helices. Each helix has 2 DNA strands. One strand is from the parental DNA (purple). The other strand is newly synthesized (blue).
  2. Bacterial chromosome is a circular molecule of DNA. Approximately 3 million nucleotides.
  3. DNA replication begins at a unique sequence, the replication origin.
  4. Replication moves bidirectionally, 500 nucleotides per second.
  5. Position where new nucleotides are added to the growing daughter strand is the replication fork. As DNA synthesis moves bidirectionally, there are two replication forks moving in opposite directions.
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14
Q

The Initiation of DNA Replication

  1. What is the first step of DNA replication? How is this accomplished?
  2. What is positive supercoiling the result of? How is it relieved?
  3. What happens once supercoiling is relieved?
  4. What does Primase catalyze?
A
  1. First step is the separation of the strands. Accomplished by helicase, which breaks the hydrogen bonds between base pairs.
  2. Positive supercoiling results when hydrogen bonds are broken, this is relieved by topoisomerase.
  3. When supercoiling is relieved, single-strand binding protein binds to the separated strands to keep them apart.
  4. Primase catalyzes synthesis of a 10-12 base piece of RNA to “prime” the DNA replication.
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15
Q

DNA Polymerase Reaction

  1. What does DNA polymerase III do?
  2. What occurs during the polymerization reaction?
  3. What is the polymerization referred to as?
A
  1. After the first initiation step is completed, DNA polymerase III “reads” the parental strand or template, catalyzing the polymerization of a complementary daughter strand.
  2. A pyrophosphate group is released as a phosphoester bond is formed between the 5’-phosphoryl group of the nucleotide being added, and the previous 3’-OH of the nucleotide in the newly synthesized daughter strand.
  3. Based on the bond formed in the polymerization this is referred to a 5’- 3’ synthesis.
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16
Q

Leading Strand DNA Replication

  1. Where are RNA primers produced?
  2. What does DNA polymerase III continuously catalyze?
A
  1. A single RNA primer is produced at the replication origin.
  2. DNA polymerase III continuously catalyzes the addition of nucleotides in the 5’- 3’ direction.
17
Q

Lagging Strand DNA Replication

  1. How are many RNA primers produced?
  2. In what direction does DNA polymerase III catalyzes the elongation of the new strand?
  3. What happens as the new strand encounters a previously synthesized new piece? When does the process repeat?
  4. What 3 things occur during the final step?
A
  1. Many RNA primers are produced as the replication fork moves along the molecule.
  2. In the 5’ - 3’ direction.
  3. As the new strand encounters a previously synthesized new piece synthesis stops at that site. The process repeats with another primer made at a new location of the replication fork.
    - The process repeats with another primer made at a new location of the replication fork.
    • The removal of the RNA primers – DNA polymerase I
      - Filling in the gaps – DNA polymerase I
      - Sealing the fragments into an intact strand of DNA – DNA ligase
18
Q

The Replication Fork

1. In what two ways do DNA polymerase III read?

A
  1. Discontinuously and in the opposite direction.
19
Q

Eukaryotic DNA Replication

  1. What is the size difference between a eukaryotic chromosome and a bacterial chromosome?
  2. Where does DNA replication begin and move in eukaryotes?
A
  1. One eukaryotic chromosome may be 100 times larger than a bacterial chromosome.
  2. In eukaryotes, DNA replication begins at many replication origins and moves bidirectionally along each chromosome.
20
Q

Information Flow in Biological Systems

  1. What does the Central Dogma tell us?
  2. What is transcription?
  3. What is translation?
A
  1. Central Dogma tells us that “in cells the flow of genetic information contained in DNA is a one-way street that leads from DNA to RNA to protein”.
  2. Transcription is the process by which a single-strand of DNA serves as a template for the synthesis of an RNA molecule. Think of making a copy.
  3. Translation converts the information from one language of nitrogenous bases to another of amino acids. Think of TRANSLATING into another language.
21
Q

Classes RNA Molecules

  1. What is mRNA? What does mMRNA do? What does mRNA have?
  2. What is rRNA? What does it form and how? How many types in prokaryotes? How many types in eukaryotes?
  3. What is tRNA?
A
  1. Messenger RNA - A complimentary copy of a gene. mRNA directs the amino acid sequence of proteins.
    It has the codon for an amino acid in a protein.
  2. Ribosomal RNA - Structural functional component of the ribosome. Forms ribosomes by reaction with proteins. 3 types in prokaryotes, 4 types in eukaryotes.
  3. Transfer RNA - Transfers amino acids to the site of protein synthesis.
22
Q

tRNA

  1. What is necessary for each amino acid to be incorporated into a protein?
  2. What is the structure of tRNA? How many nucleotides?
  3. What is the overall structure of tRNA known as?
  4. What two things does intrachain hydrogen bonding occur to give?
  5. What does the 3’-OH group of the terminal nucleotide do?
  6. What do 3 nucleotides at the base of the cloverleaf serve as?
A
  1. There is at least one tRNA for each amino acid to be incorporated into a protein.
  2. tRNA is single-stranded with typically about 80 nucleotides.
  3. A cloverleaf.
    • Regions called stems with an α-helix
      - A type of L-shaped tertiary structure
  5. Covalently bind the amino acid.
  6. 3 nucleotides at the base of the cloverleaf serve as the anticodon, which forms hydrogen bonds to a codon on mRNA.
23
Q

Transcription

  1. What is transcription catalyzed by? What does transcription produce?
  2. What are the 3 stages of transcription?
A
  1. Transcription is catalyzed by RNA polymerase. Produces a copy of only 1 DNA strand.
      1. Initiation binds RNA polymerase to the promoter region at the beginning of the gene.
          1. Chain elongation then occurs forming a 3’-5’ phosphodiester bond, generating a complementary copy. - 3. Termination is the final step of transcription when the RNA polymerase releases the newly formed RNA molecule.
24
Q

Post-transcriptional Processing of mRNA

  1. What do prokaryotes release at the end of termination? Why?
  2. What is a primary transcript that must be processed in post-transcriptional modification? What 3 steps are involved in this process?
A
  1. Prokaryotes release a mature mRNA at the end of termination for translation.
  2. Eukaryote mRNA is a primary transcript which still must be processed in post-transcriptional modification.
    - A 5’ cap structure is added, required for efficient translation of the final mRNA. (Guanosine methylated at N-7).
    - A 3’ poly(A) tail (100 to 200 units) is added by poly(A) polymerase. Poly(A) tail protects the 3’ end of the mRNA from enzymatic digestion. This prolongs the life of the mRNA.
25
Q

RNA Splicing

  1. What is RNA Splicing?
  2. Bacterial chromosomes are “continuous”. What does this mean?
  3. Eukaryotic chromosomes are “discontinuous”. What does this mean? What are introns? What does the presence of introns do?
  4. What are exons? What eventually happens to both inrons and exons?
A
  1. The removal of portions of the primary transcript that are not protein coding.
  2. Continuous meaning all DNA sequence from the chromosome is found in the mRNA.
  3. Discontinuous meaning there are extra DNA sequences within the genes that do not encode any amino acid sequence called introns or intervening sequences. Presence of introns makes direct translation to synthesize proteins impossible.
  4. Exons are coding sequences. The introns are cut out and the exons are spliced together.
26
Q

RNA Splicing Details

  1. What must RNA splicing be? What happens if an incorrect number of nucleotides are removed? What do signals mark?
  2. What 2 things do spliceosomes help? What are they composed of?
A
  1. RNA splicing must be very precise. Removing an incorrect number of nucleotides will destroy the code for the protein. Signals mark the intron boundaries.
    • Recognize intron-exon boundaries
      - Stabilize the splicing complex
      - They are composed of small nuclear ribonucleoproteins (snRNPs, “snurps”)
27
Q

The Genetic Code

  1. What is genetic code? What are the 4 characteristics of the genetic code?
  2. How many codons are there? What do each code for? What are the codes/amino acids for the 1 start and 3 stop signals?
  3. What do multiple codes for an amino acid tend to have? What does this do?
  4. How are codons written?
A
  1. The message on DNA that has been translated to mRNA.
    - Degenerate: more than one three base codon can code for the same amino acid.
    - Specific: each codon specifies a particular amino acid.
    - Nonoverlapping and uninterrupted: None of the bases are shared between consecutive codons. No noncoding bases appear in the base sequence.
    - Universal: all organisms use the same code
  2. 61 code for amino acids. Three code for the “stop” signal.
    - AUG (Methionine) = START
    - UGA, UAG, UAA = STOP
  3. Multiple codes for an amino acid tend to have two bases in common. Makes the code mutation resistant.
  4. Codons are written in a 5’ -> 3’ sequence.
28
Q

Protein Synthesis

  1. What is protein synthesis referred as? Where is it carried out?
  2. Where does protein synthesis occur? What is a polysome?
  3. In protein synthesis, what does tRNA bind and what is it aided by? What does tRNA recognize?
A
  1. Translation. Carried out on ribosomes, complexes of rRNA and Proteins.
  2. Protein synthesis occurs in multiple places on one mRNA at a time.
    - Polysome: mRNA plus the multiple ribosomes.
  3. Binds a specific amino acid aided by aminoacyl tRNA synthetase. Recognizes the appropriate codon on the mRNA.
29
Q

Ribosomes

  1. What are ribosomes? What 2 things is each ribosome made up of and what are their contents?
  2. What do many ribosomes on 1 mRNA comprise a polysome with?
A
  1. Ribosomes are complexes of rRNA and proteins. Each ribosome is made up of 2 subunits, Small Ribosomal Subunit and Large Ribosomal Subunit. Small ribosomal subunit contains 1 rRNA and 33 proteins. Large ribosomal subunit contains 3 rRNA and about 49 proteins.
  2. Many ribosomes on 1 mRNA comprise a polysome with many copies of the protein made simultaneously.
30
Q

The Role of Transfer RNA

  1. What are tRNA molecules?
  2. What must each tRNA covalently bind? Where is the binding site for covalent attachment? What does enzyme aminoacyl tRNA synthetase covalently link?
  3. What must the tRNA be able to recognize? What is this process mediated by? What is complementary to what in this process?
A
  1. tRNA are molecules that decode information on mRNA into the primary structure of the protein.
  2. Each tRNA must covalently bind one, only one, specific amino acid. Binding site for covalent attachment of amino acid at 3’ end. Enzyme aminoacyl tRNA synthetase covalently links the proper amino acid to the tRNA = aminoacyl tRNA.
  3. The tRNA must be able to recognize the appropriate codon on the mRNA that calls for that amino acid. This process is mediated by the anticodon located at the bottom of the tRNA cloverleaf. The anticodon is complementary to the codon on the mRNA.
31
Q

The Process of Translation

  1. What 5 things come together together in the initiation phase of translation? What sites do ribosomes have to bind tRNA?
  2. What are the 3 steps in the process of Chain elongation?
  3. What does translocation achieve? What does chain elongation require?
A
  1. Initiation factors (proteins), mRNA, initiator tRNA, and small and large ribosomes come together. Ribosome has two sites to bind tRNA: P-site binds to the growing peptide. A-site binds the aminoacyl tRNA.
      1. An aminoacyl tRNA binds to A-site.
          1. Peptide bond formation occurs catalyzed by peptidyl transferase.
          1. Translocation (movement) of ribosome down the mRNA chain next to codon.
  3. Shifts the new peptidyl tRNA from the A-site to the P-site. Chain elongation requires hydrolysis of GTP to GDP.
32
Q

Termination of the Translation Process

  1. What prompts the termination of the translation process? What is hydrolyzed in the termination of translation?
  2. Will the protein that is released be in its final form? Provide 3 examples as to why or why not.
A
  1. Upon finding a “stop” codon, a release factor binds the empty A-site. The bond between the last amino acid and peptidyl tRNA is hydrolyzed releasing the protein.
  2. The protein released may not be in its final form. Post-translational modification may occur before a protein is fully functional:
    - Cleavage
    - Association with other proteins
    - Bonding to carbohydrate or lipid groups

Biochemistry (9 decks)

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