6. Nucleic acids and protein synthesis Flashcards
What are nucleotides?
the basic units which make up a group of the most important chemicals in all organisms, the nucleic acids.
What are the nucleic acids?
- Ribonucleic acid (RNA)
- Deoxyribonucleic acid (DNA)
The structure of a nucleotide is as follows: (made of THREE components)
- A pentose / 5C sugar represented by a pentagon. (Ribose or deoxyribose).
- A phosphate group represented by circle.
- A nitrogenous organic base. (A, C, G, T, or U).
So, PENTOSE SUGAR + PHOSPHATE GROUP + NITOGENOUS BASE (joined by CONDENSATION RXN) = nucleotide
What are the two groups of bases?
Pyrimidines (C, T, U); 6 sided ring (single ring structure)
Purines (A, G); 6 sided ring joined to 5 sided ring (double ring structure)
Explain the phosphate backbone and phosphodiester bonds?
Nucleotides themselves are joined together via a condensation reaction between the 5C sugar of one nucleotide and the phosphate group of another. The resultant strong covalent bond is a PHOSPHODIESTER BOND.
*Called phosphodiester bond because ONE phosphoester bond between phosphate group and 5’ carbon of pentose sugar and ONE phosphoester bond from same phosphate attached to 3’ carbon of pentose sugar of next nucleotide. Both these bonds from complete phosphodiester bond.
All these phosphodiester bonds joining nucleotides forms phosphate backbone of polynucleotide.
The structure of RNA is as follows:
RNA - a polymer made of repeating nucleotide subunits.
* 5C always ribose
* A, C, G, U (uracil replaces thymine)
Three types of RNA:
- rRNA
ribosomal RNA manufactured in nucleolus.
very large molecule that is complexed with proteins and forms subunits of ribosomes. - tRNA
transfer RNA very small molecule made up of about 80 nucleotides.
makes up 10-15% total RNA in cell.
different types of tRNA each complementary to an amino acid.
three leaf clover shape made of folded single strand. - mRNA (describe this structure)
messenger RNA made in transcription in nucleus (because DNA too big to leave nucleus).
single linear strand; made of thousands of nucleotides.
base sequences and length of mRNA depends on length and sequence of transcribed DNA genes, as well as post-translational modification.
mRNA leaves nucleus via nuclear pores in nuclear envelope and enters cytoplasm then ribosomes for transcription.
broken down quickly; exists temporarily just to fulfil its function.
What is ATP?
ATP (adenosine triphosphate) is a phosphorylated nucleotide. It is the universal energy currency of ALL cells.
What is phosphorylation?
the chemical process of adding a phosphate group to an organic compound, e.g., a protein or a sugar.
What is the structure of ATP?
- adenine molecule (purine; double 6-sided and 5-sided ring)
- ribose molecule (5C sugar)
- three phosphate molecules
Adenine + ribose = adenosine
Adenine + ribose + 1 phosphate = AMP
Adenine + ribose + 2 phosphate = ADP
Adenine + ribose + 3 phosphate + ATP
What is the structure of DNA?
Structure of DNA:
* two nucleotide polymer strands (very long) winding around each other to form double helix.
* For each complete turn of double helix there are 10 base pairs.
* deoxyribose sugar
* nitrogenous bases: A, T, C, G
* sugar-phosphate backbone has “direction” it runs in (5’ to 3’ or 3’ to 5’; refers to carbon atoms on deoxyribose sugars)
* two strands are an equal distance apart (gives stability and strength to molecule) because of complementary base paring between purines and pyrimidines but are ANTIPARALLEL.
* Bases are held together because of hydrogen bonding. C-G have a TRIPLE hydrogen bond but A-T have a DOUBLE hydrogen bond, which is weaker.
Why is DNA able to be passed unchangingly from generation to generation?
DNA able to be passed unchangingly from generation to generation because of extremely stable structure ensured by:
* Double helix (enclosed and protected from outside chemical or physical forces))
* Sum of all hydrogen bonds
* Equidistant base pairing
When does semi-conservative replication occur?
Occurs during synthesis phase of mitotic cell cycle, which is 2nd phase of interphase.
Why is it known as semi-conservative DNA replication?
Known as semi-conservative because each new DNA molecule contains one parent strand and one daughter strand.
Note: Energy demands
Anabolism = energy required
Catabolism = energy released
How does semi-conservative replication work overview:
- Opening and unwinding DNA double helix
- Assembling leading strand
- Assembling lagging strand
- Removing wrongly coded DNA
How does step 1 of semi-conservative DNA replication (opening and unwinding DNA double helix) work?
• DNA helicase (enzyme) breaks hydrogen bonds between base pairings to unwind helix. Unwinding occurs at a number of points (each called a replication origin) and forms replication forks (like a zipper).
• Each exposed strand acts as a template to which free DNA nucleotides can bind.
Note: These nucleotides were activated by the addition of two phosphate molecules (now have 3, much like ATP – because anabolism requires energy).
Note: In eukaryotic cells there are many replication origins with many sections of DNA being unwound and replicated at the same time. These “open” sections are called replication bubbles. In prokaryotic cells there is only one replication origin because less DNA.
How does step 2 of semi-conservative DNA replication (assembling the leading strand) work?
• Activated nucleotides joined one at a time to form new polynucleotide strand of DNA.
• DNA polymerase (enzyme) facilitates building of new DNA strand.
• This is a continuous process.
• Occurs in 5’-3’ direction (only direction that DNA polymerase works in).
How does step 3 of semi-conservative DNA replication work? (Assembling the lagging strand)
• Lagging strand is antiparallel and runs in 3’-5’ direction.
• DNA polymerase builds up short sections of lagging strand in 5’-3’ section simultaneously.
• Short sections known as Okazaki fragments.
• Okazaki fragments are then linked by DNA ligase (enzyme) to from phosphodiester bonds.
Note: Ligase only functions on lagging strand because it is the only strand containing Okazaki fragments.
How does step 4 of semi-conservative replication work? (removing wrongly coded DNA)
• Sometimes errors occur during DNA replication, e.g., incorrect nucleotide being added.
• DNA polymerase performs DNA proofreading to check for errors and repair them.
• Proofreading is highly accurate but is rarely uncorrected, this leads to mutations.
• Mutations are basis for genetic variation.
Note: DNA polymerase only ADDS nucleotides to EXTEND a chain; it cannot start one.
What are the other three proteins involved in DNA replication, and what are their functions?
• Topoisomerase (enzyme); temporarily causes a break in one strand to release tension and rejoins strand after unwinding has occurred.
• RNA primase; (enzyme) catalyses synthesis of short strands of RNA (known as RNA primers) on DNA strand in order to allow DNA polymerase to begin polypeptide synthesis. Lengths of RNA replaced by DNA nucleotides before replication completes.
• Single-stranded DNA-binding proteins; bind to DNA after unwinding to help keep strands apart and protect them until replication process is complete.
What are the three possible theories for DNA replication?
• Conservative model: separate parental DNA and daughter DNA
• Semi-conservative: one strand original, one strand new per each DNA molecule
• Dispersive model: parental DNA broken down and nucleotides replicated then randomly dispersed throughout new molecules. Not necessarily equal amounts old and new material in each molecule.
Describe the experiment of Meselson and Stahl that proves theory of semi-conservative DNA replication?
To figure out correct theory of DNA replication need a way to “mark” original DNA then track its distribution.
1. Cells grown on N14 medium. 1st control.
2. Some of cells transferred to heavier isotope N15. N15 in form of ammonium chloride.
3. Bacteria grown using nitrogen from N15 isotope. 2nd control.
4. After many generations DNA was exclusively heavy type.
5. Samples of heavy DNA then transferred to medium of N14.
6. Bacteria grown long enough for cells to divide once.
7. Sample removed, DNA extracted, placed in solution of caesium chloride and centrifuged.
8. Caesium establishes density gradient. DNA molecules sink in density gradient and float at certain level. N15 heavier than N14 and sinks to lower level.
9. Bacteria sinks to density mid way between light N14 and heavy N15, meaning it contains one strand N14 and one strand N15. Acts as evidence fro semi-conservative replication.
