Bio AS: Nucleic acid and protein synthesis

• Macromolecule and its types

  Giant molecule that has three types:

  1. polysaccharides
  2. protein(polypeptides)
  3. Nucleic acids
• Nucleic acid( DNA or RNA)

  They are polymers made from monomers known as nucleotides.

  DNA and RNA are therefore polynucleotides.
• Nucleotides are made from three smaller components name them

  1) Phosphate group (negatively charged)

  2) Pentose sugar: deoxyribose in DNA and ribose in RNA

  3) Nitrogen-containing base

  .The three units are linked together by condensation reaction.
• There are five types of nitrogenous bases name the ones in DNA and the ones in RNA.

  Each DNA has four nitrogenous bases: adenine, thymine, guanine, cytosine

  Each RNA has four nitrogenous bases: adenine, uracil, guanine, cytosine.
• Adenine is always paired with Thymine in DNA and Uracil in RNA
• In DNA, there are two strands held together by hydrogen bonds between complementary pairs of bases. This structure is called double helix.
• There are two types of bases name them and each type in them:

  They are the purine bases and the pyrimidine bases.

  The purine bases can be remembered from the phrase PURE AS GOLD: adenine and guanine in which is has two helical ring structures.

  The pyrimidine bases are: Thymine, Cytosine, Uracil. Have one helical ring structure.
• What’s the difference between ribose and deoxyribose

  The difference is that deoxyribose has one less oxygen atom in its molecule.
• What does ATP stand for

  Adenosine triphosphate molecule
• what is ATP made of

  It is a phosphorylated nucleotide, made from ribose as its Pentose sugar, adenine as its nitrogen base forming adenosine, and can be combined with one, two, or three phosphate groups. If it’s combined with one phosphate group it will be called adenosine monophosphate(AMP), if combined with two phosphate groups it will be called adenosine diphosphate(ADP), if it combined with three phosphate groups it will form the Adenosine triphosphate(ATP).
• What is ATP

  A universal energy currency of cells as it is:

  1. Small and water soluble so it can easily diffuse between cell organelles.
  2. Immediate energy donor as it is easily hydrolyzed to ADP to release energy in the presence of water.
• Uses of ATP

  1)Cell division

  2)Muscle contraction

  3) Maintenance of body temperature

  4) Anabolic reactions such as protein synthesis

  5) Nerve impulse transmission.
• how is a polynucleotide formed

  It’s formed during interphase, where many nucleotides are linked together by a condensation reaction forming a phosphodiester bond between the phosphates of one nucleotide and the carbon 3’ of another nucleotide. Thus the phosphodiester bond links the 5-carbon of one sugar with the 3-carbon of another. This forms a sugar phosphate backbone with its bases at one side, so the polynucleotide strand is said to have 3’ and 5’ ends.
• The structure of a DNA molecule: 1)Two polynucleotide strands.

  2) They are running in opposite directions meaning there are anti parallel

  3) Held by hydrogen bonds between between the nitrogenous bases

  4) Where the bases pair together according to a complementary base pairing rule where in each base pair there is a purine and pyrimidine.

  5) Each strand has a sugar phosphate backbone with phosphodiester bonds.

  6) The two strands twist forming a double helix
• Explain the importance of the hydrogen bonding between the 2 strands of DNA

  1)Holds the two polynucleotide strands together.

  2)Important inc contributing to the 3D structure of DNA molecule where the hydrogen bonds between the bases stabilize the a-helix structure.

  3)Many hydrogen bonds give stability

  4) H-bonds are more easily broken than covalent bonds.

  5)H-bonds only formed between specific bases so few mistakes.

  6) H-bonds can easily reform without chemical reaction.
• why DNA should stay stable

  1)So the sequence won’t spontaneously change thus decreasing the chances of mutation.

  2) Maintains all genetic information through out the life of cell so the same genetic information is passed on to daughter cells(offspring)

  3) Maintains size so still enclosed within the nucleus.
• What is semi-conservative replication?

  Each old parental strand acts as a template to form a new complementary strand producing two genetically identical molecules where the new DNA molecule has one old and one new strand(This occurs during the S phase of the cell cycle)
• What forms the sugar phosphate backbone?

  When the carbon-3 is linked to the carbon-5
• Steps of DNA replication

  1)The DNA double helix unwinds

  2) The hydrogen bonds between the complementary bases get broken by an enzyme called DNA helicase forming a replication fork. 3)The free activated nucleotides formed 4) Both DNA strands act as templates. Where each of the bases of activated DNA nucleotides pair up with its complementary base on each of the old DNA strand by hydrogen bonds….DNA polymerase then adds nucleotides one by one to the growing DNA chain forming new complementary strand of DNA.(Leading strand and Lagging strands are formed).
• Second part of steps of DNA replication

  6) Producing two genetically identical DNA molecules. 7) Replication is semi-conservative where each newly formed DNA molecule contains one original and one newly synthesized DNA strand.

  8) Where each of the two strands, the old and new complementary one will wind together forming two DNA helices genetically identical to each other and to their mother.
• Leading strand

  DNA polymerase adds nucleotides one by one to the new growing DNA strand in 5’ to 3’ direction only forming the leading strand which is formed continuously from 5’ to 3’.
• Lagging strand 


  Is formed by DNA Polymerase forming Okazaki fragments from the 5’ to 3’ direction then the ligase enzyme which is responsible for the formation of phosphodiester bonds between the Okazaki fragments, joins the Okazaki fragments together on the lagging strand.
• Why is the lagging strand formed in this way?

  DNA Polymerase can only copy in the 5’ to 3’ direction along each strand. Where in case of the template strand running from 5’ to 3‘, so the lagging strand has to be made from 3’ to 5’ Where DNA polymerase has to copy an unwound piece of DNA and then go back and copy the next piece of unwound DNA…. it keeps repeating this process resulting in short fragments of copied DNA called Okazaki fragments... forming the lagging strand.
• Function of DNA polymerase

  1)Adds nucleotides one by one to the new growing DNA chain/ strand allowing the formation of a polynucleotide chain.

  2)It allows the complementary base pairing rule.

  3) Where the nucleotides holding on the parents strand with hydrogen bonds

  4) Repairs mismatching base pairs.
• what is a gene 


  A gene is a length of DNA that contains a specific sequence of bases that codes for a specific sequence of amino acids to form a specific protein, giving a particular phenotype/characteristic.
• The template strand

  It’s the strand of a DNA molecule that codes for the manufacture of proteins in a cell.
• The non-template strand

  Is the other strand in the DNA molecule which is used to stabilize the DNA molecule and allow its replication.
• How many sequences of bases of the DNA code for one amino acid.

  A sequence of 3 bases in the template strand.
• what codes for one amino acid in a protein.

  Triplet code is called a genetic code that is made of three nucleotides which code for one amino acid in the protein.
• Examples:What does CAA code for and what does TTT code for and what does GAA code for and what does CCC code for?

  CAA:codes for the amino acid valine

  TTT:codes for the amino acid lysine

  GAA:codes for the amino acid leucine

  CCC:codes for the amino acid glycine.
• what is a codon

  A codon is a sequence of three bases (nucleotides).
• Properties of the genetic code

  1)Universal: The same triplet genetic code, codes for the same amino acid in all living organisms.

  2)Degenerate: It is possible for different codons to specify the same amino acid, 61 possible codons for 20 amino acids( 3 stop codons ), so more than one codon specifies an amino acid.

  3)Not overlap: No base of a given triplet enter to be a part of the adjacent triplet.
• state the differences between DNA and RNA

  DNA:1- It‘s double stranded (forms a double helix).

  RNA:1- It’s a single strand

  DNA:2- Contains the sugar deoxyribose.

  RNA:2- Contains the sugar ribose

  DNA:3- Contains thymine and no uracil.

  RNA:3- Contains uracil

  DNA:4- Has hydrogen bonds between the complementary bases.

  RNA:4- No hydrogen bonds

  DNA:5- Has only one type

  RNA:5- Has many types( tRNA, rRNA, and mRNA)
• How many stages in protein synthesis?

  Two stages:

  1. Transcription
  2. Translation
• How RNA is made simple video

  https://youtu.be/gG7uCskUOrA?si=sN5DwWj5_i8ufWjL
• How DNA is replicated simple video

  https://youtu.be/gG7uCskUOrA?si=sN5DwWj5_i8ufWjL
• what is transcription

  Transcription occurs in the nucleus.

  1. Part of the DNA will unwind and unzip due to the breaking of hydrogen bonds between the bases.
  2. The sense strand acts as a template, where free activated RNA nucleotides line up alongside the template strand according to the complementary base pairing rules.
  3. The free activated nucleotides are joined together by RNA polymerase.
  4. mRNA is spliced by a splicesome to remove the non-coding part of mRNA and join the coding parts called exons by the splicesome enzyme.
• What is translation

  1)The triplet code in mRNA is called a codon, where each codon codes for a particular amino acid

  2) The mRNA attaches to a ribosome.

  3) Ribosomes are made from rRNA and some proteins.

  4) tRNA has an anticodon which is complementary to a particular codon on the mRNA

  5) And at the other end of the tRNA there is a site where a specific amino acid can attach under the control of a specific enzyme and with energy from ATP forming tRNA-amino acid complex. The tRNA molecule carries this amino acid to the ribosome.
• There are three Stop codons name them.

  UAA UAG UGA
• what is a gene mutation

  A change in the nucleotide( base) sequence of DNA so a new allele is formed.