PHYSIO - DNA CHAPTER

1. The two forms of nucleic acids are DNA and RNA

2. Nucleic acids are made up of nucleotides

3. Structure of a nucleotides

   1. The structure of a nucleotide includes a 

      1. Sugar that contains 5 carbons

      2. Base that is attached to the #1 carbon of the sugar

      3. Phosphate group that is attached to the # 5 carbon of the sugar

      4. The nucleotide is name according to the (base/phosphate group/sugar)
         

4. Making the nucleic acid strand

   1. Nucleotides form nucleic acids by linking the phosphate group of one nucleotide to the # (1/2/3/4/5) carbon of the sugar of the next nucleotide

   2. The 5’ end of the nucleic acid chain refers to the end that has a free phosphate group

   3. The 3’ end of the nucleic acid chain refers to the end that has a free #3 carbon of sugar
      

5. DNA

   1. DNA is an abbreviation for deoxyribonucleic acid

   2. DNA is organized as 46 chromosomes which are located in the nucleus of the cell

   3. Each cell in our body contains a unique set of DNA molecules (T/F)

   4. Chromosomes

      1. There are 22 pairs of autosomal chromosomes

      2. The X and Y chromosomes are called the sex chromosomes

      3. Females have (two X chromosomes/X and Y chromosomes/ two Y chromosomes)

      4. Males have (two X chromosomes/X and Y chromosomes/ two Y chromosomes)

      5. Y chromosomes are only inherited from fathers to sons

   5. Additional DNA is also present in the (ribosome, mitochondria/ golgi apparatus); this DNA is only inherited from (mothers/fathers) to offspring
      

   6. Structure of DNA

      1. The sugar in DNA is called deoxyribose which has a chemical formula of C5H10O4

      2. The possible bases in DNA are 

         1. Two purine bases: guanine and  adenine

         2. Two pyrimidine bases:  cytosine and thymine

      3. Complementary Base-Pairing

         1. DNA exist as a double strand by forming (hydrogen/ionic/covalent) bonds between the (bases/ugars/phosphate groups)

         2. Guanine is paired with Cytosine by (1/2/3) hydrogen bonds

         3. Thymine is paired with Adenine by (1/2/3) hydrogen bonds

      4. Antiparallel orientation of strands

         1. If one DNA strand is oriented in a 5’ to 3’ direction then the other strand will have a 3 to 5 orientation
            

   7. Genes

      1. Genes are regions of DNA that code for a protein

      2. Human DNA contains approximately 20,000 genes which accounts for only 2% of all the DNA

         1. All of DNA (genes and nongenes) are collectively called the genome

      3. The non-gene portion of our DNA are

         1. Possible remnants  of ancestral genes

         2. Used to control gene expression

         3. Insertions of foreign DNA from viruses

      4. There are approximately 3 billion pairs of DNA nucleotides in all of our chromosomes
         

6. RNA

   1. RNA is the abbreviation for ribonucleic acid

   2. RNA is copied from DNA

   3. Structure of RNA

      1. The sugar of RNA is ribose which has the chemical formula of C5H10O5

      2. The possible bases of RNA are 

         1. Two purines: Guanine and Adenine

         2. Two pyrimidines Cytosine and Uracil

   4. Types of RNA

      1. mRNA contains the codes to make proteins

      2. tRNA binds and transports amino acids throughout the cytoplasm

      3. rRNA acts as an enzyme that form peptide bonds during protein synthesis
         

   5. RNA codons

      1. RNA codons are combination of (2/3/4) RNA nucleotides that code for amino acids 

      2. There are 64 possible RNA codons

      3. The initiator codon is AUG which codes for methionine

      4. The three stop codons are UAA, UGA, and UAG.

      5. There are multiple codons for each amino acid. TRUE
         

Transcription

1. Transcription is the process of copying DNA into RNA.

2. Transcription occurs in the NUCLEUS of the cell

3. Transcription starts when RNA polymerase binds to its promotor which is a region of DNA that is upstream of the (gene/protein/mRNA).

   1. Common promotor sequences are TATATA and TATAA

   2. The promotor is located on the (sense/antisense) strand of the DNA

4. RNA polymerase opens the DNA and makes (a complementary/the same exact) copy of the DNA stand

   1. As an example, a DNA sequences of GCCATTC will be copied to a RNA sequence of CGGUAAG.

5. Transcription ends when the RNA polymerase reaches the terminator sequence.

6. Several RNA polymerases can simultaneously transcribe the DNA into RNA (T/F)
   

7. Splicing

   1. The RNA that is initially transcribed contains coding regions called exons and noncoding regions called introns.

      1. This type of RNA is called (pre-mRNA/mRNA)

   2. During splicing, enzymes are used to remove (introns/exons) from the RNA

   3. The remaining (introns/exons) are joined together to create (mRNA/tRNA)

      1. The intron/exons can be joined in (a single/multiple) arrangements

      2. This is called alternative splicing

      3. This allows for a single gene to code for (a single/several) proteins

   4. After splicing the mRNA is exported to the cytoplasm where it is used to form a (DNA strand/protein)
      

Translation

1. Translation is the process of synthesizing proteins based on the codons contained in RNA

2. Translation primarily occurs in the (nucleus/cytoplasm)

3. Steps of Translation

   1. The 3 stages of translation are initiation, elongation, and termination.

   2. Initiation

      1. The small ribosomal unit (SRU) slides along the mRNA until it recognizes AUG which is called the START codon

      2. Next, a tRNA that is attached to methionine amino acid with an anticodon sequence of UAC forms temporary (covalent/hydrogen/ionic) with the AUG codon

         1. This tRNA is called the (terminator tRNA/initiator tRNA)

      3. Next, the large ribosomal unit (LRU) attaches to the SRU such that the initiator tRNA is in the (E/A/P) site

         1. The E and A sites of the LRU remain unoccupied.

   3. Elongation

      1. A second tRNA enters and bind to the codon in the (A/P/E) site

         1. This tRNA will be bound to an amino acid that is appropriate for the (anticodon/codon) that is currently sitting in the (A/P/E) site

      2. The amino acid in the P site is transferred to and bounded to the amino acid in the A site by a (peptide/hydrogen) bond.  This bond is formed by rRNA which acts as an enzyme

      3. The entire ribosome complex will slide by (1/2/3) codon in a direction that is (away from/toward) the start codon 

         1. The sliding will move 

            1. the tRNA from the A site into the P site and

            2. the tRNA from the P site into the E site

            3. After sliding, the A site will be vacant

      4. A new tRNA with its amino acid will bind to the codon in the now vacant A site

      5. Next, the dipeptide in the P site will be transferred and bound to the amino acid in the A site

      6. The ribosome will slide again and another tRNA will enter the A site to lengthen the peptide by one amino acid

      7. The process of sliding followed by tRNA entry followed by peptide bond formation will repeat until ribosome reaches a STOP codon.

   4. Termination

      1. When a codon of UAA, UGA or UAG enters the A site of the ribosome, an  enzymes cuts the bond between the growing polypeptide and the tRNA in the P site. 

      2. Afterwhich, the ribosome separates into LRU and SRU.  

      3. Several ribosomes may simultaneously translate the same mRNA codon (T/F);  this is called a polyribosome.

Replication

1. DNA replication occurs during the S phase of (interphase/mitosis)

2. DNA replication is used to copy single chromosomes into duplicated chromosomes which contain two sister chromatids.  This is a necessary preparation step for (cell division/ATP synthesis/Translation)

3. Steps of DNA replication

   1. DNA helicase unwinds and separates a portion of the DNA strand 

      1. The replication fork is the region of exposed DNA that is (ahead of/behind) the DNA helicase

   2. DNA polymerase attach to each exposed strand and synthesize a (identical/complementary) DNA strand

      1. Each DNA polymerase must synthesize the new strand in a (3’-5’/5’-3’) direction

      2. As a result, each newly built strand is synthesized in (the same/opposite) direction

      3. The DNA strand that is synthesized in the direction of the replication fork is called the (leading/lagging) strand

      4. The DNA strand that is synthesized in the direction that away from the replication fork is called the lagging strand.  This strand is made in pieces called Okazaki fragments which are joined by an enzyme called ligase.

      5. The leading and lagging strands are paired with (each other/a complementary strand from the original DNA)

   3. Semi-Conservative Replication means that at the end of replication, 

      1. One DNA molecule will contain both of the original strands of DNA and the other DNA molecule will contain two new strands (T/F)

         1. Each DNA molecule will contain an old strand and a new strand (T/F). 

   4. Multiple DNA Polymerase work on each strand simultaneously (T/F)

   5. DNA polymerase can work at a rate of 100 base/sec

   6. It takes approximately 6-8 hours to copy all of the chromosomes in a cell

   7. The error rate of DNA polymerase is 1 error in 1 billion.