Exam 5 Study Guide BIO 111

Chapter 16

Describe James Watson and Francis Crick DNA model
- an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA.
What is hereditary information?
- Encoded in DNA and reproduced in all cells of the body
Describe the process of DNA replication and DNA repair.
- DNA is copied during DNA replication, and cells can repair their DNA
What is DNA composed of?
- A polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group.
List the characteristics of the nitrogenous bases.
- Can be adenine, thymine, guanine, or cytosine.
Describe Erwin Chargaff discoveries.
- Reported that DNA composition varies from one species to the next.
  - In any species the number of A and T bases is equal and the number of G and C bases is equal.
What is the antiparallel model?
- When the subunits run in opposite directions, so the backbones of the model are antiparallel.
What is a semiconservative model?
- Predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand.
Define the terms:
- origins of replication - Particular site where replication begins.
- replication “bubble” - Result of two DNA strands separating at the origin(s) or replication.
- replication fork - A Y-Shaped region where new DNA strands are elongated at the end of a replication bubble.
Describe the function of the following enzymes:
- Helicases - Enzymes that untwist the double helix at the replication forks.
- DNA polymerases - Catalyze the synthesis of new DNA at a replication fork and require a primer to which they can add nucleotides.
- Primase - The enzyme that synthesizes the initial nucleotide strand.
  - The strand is a short RNA primer.
- RNA polymerase - Synthesizes RNA by following a strand of DNA.
- DNA Ligase - What Okazaki fragments are joined together by.
- Nuclease - Cuts out and replaces damaged stretches of DNA.
What is the function of a primer?
In which direction DNA replication occurs?
- A new strand of DNA can elongate only in the 5’ to 3’ direction.
How is the leading strand formed? And the lagging strand?
- The leading strand is formed by adding nucleotides to the 3’ end of the growing strand.
  - Synthesized in short fragments that are stitched together.
- The lagging strand is formed by adding nucleotides to the 5’ end of the growing strand.
  - DNA polymerase must work in the direction away from the replication fork.
  - Synthesized as a series of segments (Okazaki fragments).
What are Okazaki fragments?
- A series of segments that the lagging strand is synthesized as. They are joined together by DNA ligase.
DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides
- Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes.
- The usual replication machinery provides no way to complete the 5’ ends, so repeated rounds of replication produce shorter DNA molecules with uneven ends.
  - This is not a problem for prokaryotes, most of which have circular chromosomes.
Describe the process for mismatch repair of DNA.
- Repair enzymes correct errors in base pairing.
- DNA can be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changes.
What is the function of telomeres? What is their importance?
- Special nucleotide sequences at the ends of eukaryotic chromosomal DNA molecules.
- They do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules.
  - Has been proposed that the shortening of telomeres is connected to aging.
What is chromatin?
- DNA is precisely combined with proteins in a complex (called chromatin) in a eukaryotic cell.
What are histones?
- Proteins that are responsible for the first level of packing in chromatin.
Compare euchromatin vs heterochromatin.
- Euchromatin is loosely packed chromatin, mostly in the nucleus during interphase and condenses prior to mitosis.
- Heterochromatin is densely packed which makes it difficult for the cell to express genetic information coded in those regions. Regions of chromatin such as centromeres and telomeres are highly condensed during interphase.

Chapter 17

How is DNA related to specific traits?
- The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins.
What is the link between genotype and phenotype?
- The genotype (genetic makeup) results in the phenotype (physical appearance).
Describe the process of Gene expression.
- Process by which DNA directs protein synthesis, includes two stages: transcription and translation.
What is the main function of the RNA molecule?
- The bridge between genes and the proteins for which they code.
Describe the process of Transcription and Translation?
- Transcription is the synthesis of RNA using information in DNA.
  - Produces messenger RNA (mRNA).
- In a eukaryotic cell, the nuclear envelope separates transcription from translation.
  - Eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA.
- Translation is the synthesis of a polypeptide, using information from the mRNA.
  - In prokaryotes, translation of mRNA can begin before transcription has finished.
What is the function of Ribosomes?
- The sites of translation.
What is the central dogma of cell Biology?
- The concept that cells are governed by a cellular chain of command.
  - DNA → RNA → protein.
How are the instructions for assembling amino acids into proteins encoded into DNA?
- There are 20 amino acids, but there are only 4 nucleotide bases in DNA.
How many nucleotides correspond to an amino acid?
- 3 nucleotides. The nucleotide triplet that encodes an amino acid is called a codon. Each group of 3 encodes one amino acid.
What is a triplet code?
- A series of nonoverlapping, three-nucleotide words.
  - The words are translated into a chain of amino acids, forming a polypeptide.
What is a template strand?
- One of the two DNA strands.
  - Provides a template for ordering the sequence of complementary nucleotides in an RNA transcript.
What is the function of the codons? In which direction the information is read?
- The mRNA base triplets found during translation. They are read in the 5’ → 3’ direction.
What is the function of the RNA polymerase?
- Catalyzes RNA synthesis, which pries the DNA strands apart and joins together the RNA nucleotides.
  - RNA polymerase does not need a primer.
How does RNA synthesis go?
- Follows the same base-pairing rules as DNA, except that uracil substitutes for thymine.
Define the terms:
- Promoter - The DNA sequence where RNA polymerase attaches.
- Terminator - In bacteria, the sequence signaling the end of a transcription.
What is a transcription unit?
- The stretch of DNA that is transcribed.
What are the three stages of transcription?
- Initiation
- Elongation
- Termination
Describe the process of RNA processing in prokaryotes and eukaryotes.
- Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm.
  - During RNA processing, both ends of the primary transcript are altered.
  - Also, in most cases, certain interior sections of the molecule are cut out and the remaining parts splice together.
- Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions.
Compare introns vs exons.
- Introns are noncoding regions, also called intervening sequences.
- Exons are other regions that are eventually expressed and translated into amino acid sequences.
  - Some introns contain sequences that may regulate gene expression.
Define RNA splicing. What is the importance of alternative RNA splicing?
- RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence.
- Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing.
  - That is called alternative RNA splicing, and consequently the number of different proteins an organism can produce is much greater than its number of genes.
What is the function of the transfer RNA (tRNA)?
- Helps a cell translate an mRNA message into protein.
- Transfers amino acids to the growing polypeptide in a ribosome.
- Each tRNA molecule enables a translation of a given mRNA codon into a certain amino acid.
  - Each carries a specific amino acid on one end.
  - Each has an anticodon on the other end.
What is an anticodon?
- Base-pairs with a complementary codon on mRNA.
What is the function of the ribosomal RNA (rRNA)?
- Make up the two ribosomal subunits (large and small) alongside protein.
How can the differences between Bacterial and eukaryotic ribosomes be used in the medical field?
- Bacterial and eukaryotic ribosomes are somewhat similar but have significant differences.
- Some antibiotic drugs specifically target bacterial ribosomes without harming eukaryotic ribosomes.
What are the special codons?
- UAG, UAA, and UGA.
  - They are called stop codons.
- AUG signals the start of translation.
What happens to the protein after translation?
- Often translation is not sufficient enough to make a functional protein.
- Post-translational modifications may be required before the protein can begin doing its particular job in the cell.
List the differences between the two populations of ribosomes?
- Free ribosomes in the cytosol.
  - Mostly synthesize proteins that function in the cytosol.
- Bound ribosomes attached to the ER.
  - Make proteins of the endomembrane system and proteins that are secreted from the cell.
- Ribosomes are identical and can switch from free to bound.
What is a polyribosome (or polysome)?
- The result of multiple ribosomes that can translate a single mRNA simultaneously.
- Enable a cell to make many copies of a polypeptide very quickly.
What are Mutations?
- Changes in the genetic information of a cell.
What is a Point mutation?
- Changes in just one nucleotide pair of a gene.
  - The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein.
What is defined as a genetic disorder or hereditary disease?
- If a mutation has an adverse effect on the phenotype of an organism.
What are the three possible point mutations? Describe the possible results of each mutation.
- Single nucleotide-pair substitutions - Replaces one nucleotide and its partner with another pair of nucleotides.
- Nucleotide-pair insertions - Addition of nucleotide pairs in a gene.
- Nucleotide-pair deletions - Losses of nucleotide pairs in a gene.
- Silent mutations - Have no effect on the amino acid produced by a codon because of redundancy in the genetic code.
- Missense mutations - Still code for an amino acid, but not the correct amino acid.
- Nonsense mutations - Change an amino acid codon into a stop codon.
  - Most lead to a nonfunctional protein.
What is a frameshift mutation?
- Insertion or deletion of nucleotides that may alter the reading frame.
What is a Mutagen? And a carcinogen?
- Physical or chemical agents that cause mutations.
  - Chemical mutagens fall into a variety of categories.
- Carcinogens (cancer-causing chemicals) are mutagens.
  - Most mutagens are carcinogenic.
What is a gene?
- A discrete unit of inheritance.
- A region of specific nucleotide sequence in a chromosome.
- A DNA sequence that codes for a specific polypeptide chain.