# Chapter 9 Outline

Chapter 9 Molecular Biology

9.1: The Structure of DNA

1. The building blocks of DNA are ________________________ which are made up of three parts:
1. ___________________ a five-carbon sugar,
2. _____________________________, and a
3. _____________________________
1. The four types of nitrogenous bases in DNA are
1. _____________ (A) and ______________(G) are double-ringed purines.
2. _______________(C) and ______________ (T) are single-ringed pyrimidines.
3. Check for understanding:
1. T or F: Each nucleotide is named according to the nitrogenous base it contains?
1. The DNA molecule is made up of two strands  of nucleotides that are twisted around into a ____________  ______________.
2. Base-pairing takes place between a _____________ and pyrimidine.
1. An  ____ binds with a T, and C binds with a ________.
2. Chargaff’s rule states that: ______________________________________________________________________________________________________________________________________________________________________________________________________
3. Adenine and thymine are connected by _____ hydrogen bonds, whereas C and G are connected by ________ hydrogen bonds.
4. Check for understanding:
1. T or F: The diameter of the DNA double helix is uniform throughout because a purine always base-pairs with a pyrimidine which makes the combined lengths equal.
1. The Structure of RNA
1. There is a second nucleic acid in all cells called __________ or ribonucleic acid.
2. Like DNA each of the nucleotides in RNA is made up of a ________________ ________, a _________ - __________ sugar, and a _______________ group.
3. How does the five-carbon sugar ribose differ from deoxyribose? See figure 9.5
1. ______________________________________________________________________________________________________________________
1. How DNA is Arranged in the Cell
1. Stretched end-to-end, the DNA molecules in a single human cell would be ______________  _____________ long.
2. Which cell has the larger genome? Human cell or a bacterial cell?
3. Outline the packing strategy that eukaryotes utilize in organizing the DNA inside the nucleus. Use figure 9.7 as a guide
1. At the most basic level:  ______________________________________________________________________________________________________________________
2. Nucleosomes stack compactly to form a ___________________________________________________________
3. During which stage of mitosis are the chromosomes at their most compact.

9.2: DNA Replication

1. DNA replication occurs during the _______ phase of interphase.
2. The two strands of the DNA molecule are said to ___________________ to one another.
3. The model that is used to explain the process of DNA replication is called the ___________________________ model. In this model each DNA molecule is a combination of one parental strand and one new daughter strand.
4. Check for understanding: See figure 9.9 in the textbook
1. T or F: When two DNA copies are formed, they have an identical sequence of nucleotide bases and are divided equally into two daughter cells.
1. DNA replication in eukaryotes
1. Specific nucleotide sequences called _______________ of _______________ at which replication begins.
2. Certain proteins called ___________ unwind and open up the DNA helix.
3. As the DNA helix opens Y-shaped structures called ________________ __________________ are formed.
1. How many replication forks are formed at each origin of replication?
2. T or F: There is only one origin of replication on the eukaryotic chromosome
1. An enzyme called _____________________________ adds nucleotides to the ______’ end of the template.
2. A ____________ sequence of complementary RNA nucleotides is added to provide the starting point for DNA replication. This primer is removed later with the RNA nucleotides replaced by DNA nucleotides.
3. The strand that is complementary to the parental DNA strand is synthesized continuously toward the replication fork. This is called the ___________________ strand.
4. The second new strand is synthesized in short pieces called ________________  ______________________. This strand is known as the __________________ strand.
5. The enzyme that seals the gaps between the fragments is called _________________________.
6. The ends of linear chromosomes are known as _______________, the enzyme that maintains the ends is called _________________.
7. T or F: telomerase is not active in adult somatic cells. The shortening of telomeres in these cells is associated with aging.
1. DNA Replication is Prokaryotes
1. How does the prokaryotic chromosome differ from a eukaryotic chromosome?
1. ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
2. Fill in this table with the differences between prokaryotic and eukaryotic replications.
1. DNA Repair
1. DNA polymerase-Proofreading during elongation of the DNA molecule.
2. Mistakes such as wrong bases  paired together are corrected by the ______________  ____________________ mechanism.
3. In _______________ ____________________  ____________________ the incorrect bases are removed  and replaced with the correct bases with the help of DNA polymerase. This type of repair is important in correcting thymine dimers.
4. Mistakes in DNA replication that are not corrected may result in a ____________________

9.3 Transcription

1. The two functions of DNA are:
1. _________________________________ and
2. _________________________________
1. In transcription DNA is read or transcribed into a ______________ molecule.
2. The Central Dogma: DNA Encodes RNA; RNA Encodes Protein
1. Transcription: from DNA to mRNA
1. Initiation
1. The region of unwinding is called a ___________________ __________________
2. The DNA sequence which initiates transcription is called a __________________________
1. Elongation
1. Transcription always proceeds along this DNA strand, the_________________________ strand
2. The other DNA strand that is not involved in transcription is called the ________________________________ strand
3. The enzyme involved in transcription is _____________________________________
1. The end of transcription is called _____________________.
1. In prokaryotes, upon termination, the process of transcription is (complete/incomplete).
2. T or F: Only in prokaryotes can transcription and translation proceed together at the same time.
3. What prevents simultaneous transcription and translation occurring in eukaryotic cells?
1. Eukaryotic RNA Processing
1. Eukaryotic genes are composed of protein coding sequences called ______________ and intervening, non-protein coding sequences called _________________.
2. The removal of introns and reconnecting exons is called RNA __________________, which only occurs in the (nucleus/cytoplasm).

9.4: Translation

1. The Protein Synthesis Machinery
1. List the required inputs for translation.
1. _______________________________
2. _______________________________
3. _______________________________
1. Ribosomes are in the ___________________ in prokaryotes and in the ___________ and endoplasmic reticulum of ________________________.
2. Ribosomes are composed of two _________________, the large subunit binds ___________________ whereas the small subunit binds __________________.
1. The Genetic Code
1. Protein sequences consist of ___________ commonly occurring amino acids.
2. Each amino acid is coded for a three-nucleotide sequence called   the ________________
3. The relationship between a codon and its corresponding amino acid is called the ________________________  ____________________.
4. There is a total of __________ codons. Three of these codons are ___________ codons, they do not code for any amino acid.  Therefore, __________ codons code for amino acids.
1. Check for understanding: T or F: Many amino acids may be encoded by more than one codon?
1. One codon _____________ is the start codon. Its code is for the amino acid _________________. This codon sets the reading frame for translation.
2. Translation consists of the following three steps
1. ________________________________________ which involves the small RNA subunit, the mRNA template,  initiation factors and special initiator tRNA.
2. ________________________________________ is the bringing of amino acids to be joined together to form a growing polypeptide.
3. _________________________________________ occurs when a stop codon is reached.

9.5: How Genes are Regulated

1. Prokaryotic vs Eukaryotic Gene Regulation
1. In prokaryotes gene regulation occurs at the transcriptional level
1. Lac Operon - _________________________________________________________________________________________________________________________________________________________________________________
2. In eukaryotes gene regulation occurs at several levels:
1. When DNA is uncoiled and loosened from nucleosomes to bind transcriptional factors:
1. __________________________
1. When the RNA is transcribed ___________________________
2. When RNA is processed and then transported to the cytoplasm
1. ________________________________________
1. Or after the protein has been made: ______________________________________

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