Chapter 2 & 3

• What are proteins?


  large complex molecules that are the building blocks for structural and function components of a cell. They are made up of amino acids.
• What are nucleic acids

  • DNA & RNA
• Function of amino acids

  • store information in a chemical code (genetic code)
  • Direct the cell on which proteins to produce.
• What are polymers?

  • DNA & RNA are polymers.
  • polymers are made of strings of bonded monomers-nucleotides.
  • monomers are molecules bonded to identical molecules to form polymers.
• What is polymerase?

  • an enzyme that brings about the formation of a particular polymer
• what are nucleic acids composed of?

  • 5 carbon pentose sugar
  • negatively charged phosphate group
  • nitrogen compound (base)
• Proteins


  • Large complex molecules
  • Building blocks for structural and functional components of a cell
  • Made up of amino acids

  
• Amino acid chains

  Make up polypeptide chains
• Polypeptide chains


  Fold up to create proteins

  
• Nucleic Acids


  • DNA and RNA
  • Store information in a chemical code (genetic code)
  • Directs the cell on which proteins to produce
• DNA


  A nucleic acid that is the genetic code for an organism
• Proteins


  • Large complex molecules
  • Building blocks for structural and functional components of a cell
  • Made up of amino acids

  
• Amino acid chains

  Make up polypeptide chains
• Polypeptide chains


  Fold up to create proteins

  
• Nucleic Acids


  • DNA and RNA
  • Store information in a chemical code (genetic code)
  • Directs the cell on which proteins to produce
• DNA


  The genetic code for an organism
• DNA and RNA


  • Are polymers
  • Strings of monomers
  • Nucleotides
• Monomers


  Molecules bonded to identical molecules to form polymers
• Polymers


  Strings of bonded monomers
• Polymerase


  An enzyme that brings about the formation of a particular polymer
• Nucleic Acid Structure


  • DNA and RNA have similar structures
  • Both are made out of nucleotides
• Nucleotides


  Made up of three chemical components: five carbon pentose sugar, negatively charged phosphate group, nitrogen compound (base)
• DNA Structure


  • Made up of nucleotides that have one less oxygen than ribose sugar (deoxyribose)
  • Has four bases: Adenine (A), Thymine (T), Guanine (G), Cytosine (C)
  • A & T bond, and G & C bond
  • Smaller base always bonds with a bigger base, ensures an even distance remains between the strands (complementary base pairing)
  • Thymine and cytosine are the smallest bases (pyrimidines)
  • Adenine and guanine are larger (purines)
  • DNA molecules consist of two polymer strands winding around to form a double helix
  • In each strand, sugar and phosphate alternate, creating a 'back bone' to the DNA (phosphodiester bond)
  • The two DNA strands are tightly bonded in a way that can be 'unzipped' to read genetic information
  • Hydrogen bonds are bonds between bases of each DNA strand, they hold together like rungs of a ladder
  • One strand heads 'upwards' and the other heads 'downwards' (antiparallel)
• Prokaryotic Cells


  • DNA is a single circular chromosomes
  • Sometimes, it may be found as multiple circular pieces of DNA called plasmids
  • Chromosome and plasmids are found in the cytosol

  
• Eukaryotic Cells


  • DNA is linear
  • Its found in the nucleus
  • Histones (proteins) are bound to the DNA to form nucleosomes
  • Nucleosomes are unit 'packages' of DNA
  • They help pack large DNA threads into the nucleus
  • Nucleosomes coil and condense into a fibre, which supercoil to form chromosomes
  • In some organisms, DNA is found in a circular form in mitochondria or chloroplasts
• Genes


  • Complete base sequence of DNA in a haploid set of chromosomes is called genome
  • Segments of DNA are called genes, and certain sequences of nucleotides in DNA of the gene code creates polypeptides (amino acid chains)
  • Two types of genes/regions in DNA: Coding (codes for proteins), Non-coding (does not code for proteins)
  • The sequence of the coding regions determines the sequence of amino acids in a polypeptide, which then determines the protein that is formed
  • Non coding regions of the DNA do not create proteins, but contain regulatory regions for turning DNA on and off
• DNA Copying


  1. The two strands are separated or 'unzipped' by enzymes (action proteins)

  2. The single strands act as templates for the new strands

  3. The new strand is built towards the 3' end

  4. Polymerase (enzyme) moves along the template strand, from 5' to 3' adding complementary nucleotides

  5. This is why double stranded DNA is a long living molecule, as it passes down accurately through generations of cells
• RNA Structure


  • Made up of nucleotides bonded by phosphodiester bonds
  • RNA contains ribose sugar (one more oxygen atom than deoxyribose sugar)
  • Contains uracil (U) instead of thymine (T)
  • Is single stranded with many folding patterns
  • Ranges in size
  • Various types and functions

  
• RNA Functions


  • Degrades rapidly by cells
  • Has multiple functions regulating protein production
  • 3 main types: mRNA, tRNA, rRNA
• mRNA


  • Messenger RNA
  • Carries DNA code from nucleus to ribosome
  • Contains instructions for protein synthesis
  • Found in nucleus and cytosol in eukaryotes and cytosol in prokaryotes
• tRNA

  • Transfer RNA
  • Delivers amino acids to ribosomes for protein synthesis
  • Found in cytosol in eukaryotes and prokaryotes
  • Leaf shape
• rRNA

  • Ribosomal RNA
  • Ribosome component, associates with proteins in order to form ribosomes
  • Found in ribosomes in prokaryotic and in endoplasmic reticulum or cytoplasm in eukaryotic
  • 3D fold
• Prokaryotic DNA


  • Single circular chromosome in the cytosol OR
  • Circular plasmids in cytosol
• Eukaryotic DNA


  • Linear chromosomes in nucleus OR
  • In mitochondria OR
  • In chloroplasts in plant cells
• Gene Transcripts


  Transfer of DNA code to ribosomes in cytosol to produce a gene product via transcription and translation
• Transcription

  1. DNA is too large to leave nucleus via nuclear pore, mRNA is small enough to pass in and out

  2. mRNA copies information on DNA

  3. Copying this DNA to produce an RNA molecule is called transcription

  4. Pre-mRNA is synthesised by polymerase

  5. Exons are coding for amino acids in polypeptide formation

  6. Introns are non coding regions in DNA
• Transcription Steps

  1. DNA in the region of the gene needing to be transcripted unwinds and unzips with the help of helicase

  2. Exposes the nucleotide bases of both DNA strands

  3. Polymerase begins to synthesise pre-mRNA with complementary base pairing using the template strand

  4. The promoter region (a DNA sequence) signals the start of the gene to be copied

  5. Transcription begins when polymerase is positioned by proteins onto the DNA promoter region

  6. The template strand will be transcribed (copied with complementary base pairing) in the 5' to 3' direction

  7. A nucleotide sequence signals the end of the gene and to stop transcription

  8. The mRNA releases itself as a single strand of pre-mRNA and the DNA rezips and coils back up

  9. Pre-mRNA is not yet in full mRNA form as it still contains introns and exons

  10. Introns are cut out, and exons are rejoined to mRNA by splicing mature RNA strands

  11. In some cases, some exons and introns may be cut out or included to produce mRNA of different length (alternative splicing)

  12. Methyl (CH3) is added to the 5' end of the mRNA (methylated cap)

  13. 100-200 adenine bases are added to the 3' end of the RNA to prevent degradation (poly-A tail)

  14. The pre-mRNA is now mature mRNA. It leaves the nucleus through a nuclear pore into the cytosol towards a ribosome
• Alternative Splicing


  • When pre-mRNA keeps various introns to make mRNA if various lengths and sequences from the same RNA makeup
  • Knows what to include and exclude by either proteins protecting the exons from removal or looping introns together to protect and exon from being detected, and the exon is cut out
• Ribosomes


  • In eukaryotes, rRNA combines with special proteins to form ribosomes made out of two subunits (40S and 60S)
  • Subunits move from the nucleolus and combine to create functional ribosomes for mRNA translation
  • In prokaryotes, ribosomes are found in the mitochondria and chloroplasts and are smaller than eukaryotic ribosomes
  • Free ribosomes create proteins that are to be used for cell structure and functioning
  • Some ribosomes are bound on the endoplasmic reticulum, forming the rough endoplasmic reticulum
  • Ribosomes may form chains called polyribosomes or polysomes which bind to a single mRNA strand, allowing many different polypeptides to be formed from a single mRNA strand faster than a single ribosome could
• tRNA


  • Exist as free floating molecules within the cytosol
  • tRNA molecules all carry one of 20 amino acids, and one of 64 codon combinations
  • tRNA is in a four 'clover' leaf shape, and at the bottom, contains one codon that is uncoded, mainly used to bind to mRNA, called the anticodon
  • tRNA also contains an amino acid acceptor site, which is where the amino acid is bound to