module 8: biology

• gene mutations:

  alteration of base sequences

  occurs in DNA replication

  chances can increase due to mutagenic agents 

  (carcinogens + high energy ionising radiation)
• what does gene mutations result to

  different amino acid sequences

  • modifies tertiary structure (hydrogen and ionic bonds)

  leads to a non-functioning protein
• addition mutation

  DNA nucleotide is added to the sequence

  causes a frame shift

  codes for different amino acids
• substitution mutation

  one base is different

  not as harmful - only one codon would differ

  degenerate (genetic code) - could still coe for the same amino acid
• inversion mutation

  section of bases are inverted

  • results to different amino acids
• deletion mutation

  DNA nucleotide is deleted from the sequence

  causes a frameshift - triplets would be different
• duplication mutation

  one or more bases are duplicated in the base sequence, leading to frame shift
• translocation mutation

  section of bases on a chromosome breaks off and attaches to a different chromosome

  • leads to abnormal phenotypes
• stem cells:

  undifferentiated cells that continually divide and become specialised cells
• totipotent:

  can divide into any type of body cells

  only occurs in the early mammalian embryos

  during development : can translate only one part of DNA - turns specialised
• pluripotent:

  only found in the embryos 

  can become almost any type of cell

  used in research - to treat human disorders (treat damaged cells)

  issues:

  • ethical issues: therapeutic cloning
  • can continually divide to create tumours
• unipotent

  found in mature mammals

  can only differentiate into one type of cell (same type of cell)
• multipotent

  can differentiate into limited number of different cells

  found in the bone marrow
• induced pluripotent stem cells (iPS)

  adult somatic cells DNA manipulated using transcription factors

  • overcomes ethical issues
• advantages of IPS

  • long term
  • won't cause rejection
  • harmless
  • can divide indefinitely
• transcriptional factors:

  transcription of a gene only occurs when a transcriptional factor binds to the base sequence of DNA that came to the cytoplasm to the nucleus

  • creates mRNA which is translated to the cytoplasm to create a protein
• oestrogen

  steroid hormone - lipid soluble - can diffuse through membranes

  • binds to the receptor of transcriptional factor (complementary)
  • changes shape of binding site - 
  • complementary in shape to DNA - activates the transcriptional factors (initiating transcription)
• epigenetics

  heritable change in the gene function without changing the DNA base sequence

  • changes can be caused by environmental changes - inhibits transcription
• environmental changes:

  factors like diet,stress,toxins:

  • adds chemical tags (epigenetics) 

  epigenome (a layer of chemical tags) can impact the shape of the DNA histone complex - whether DNA is tightly coiled or not
• what happens if DNA histone is tightly wrapped

  transcription factors cannot bind - inhibits transcription
• methylation of DNA

  • attaches to cytosine
  • increased methylation - inhibits transcription (prevents transcription factors from binding)
  • attracts proteins and condense DNA-histone complex (tightly coiled together)
• acetylation of DNA

  • decreased acetylation - inhibits transcription
  • histones become more positive and attach to phosphate group - DNA
  • harder for transcription factors to bind
• RNA interference (RNAi)

  translation can be inhibited by RNAi (eukaryotic)

  mRNA is destroyed before it can be used to create polypeptide chain
• process of RNAi

  siRNA combine with another enzyme - siRNA-enzyme complex

  can bind to complementary base sequences of mRNA

  enzymes will cut the mRNA - can not be translated
• tumour-suppressor genes

  genes that maintain normal cell division and prevent the formation by slowing cell division 

  can cause cell death

  eg: mutations in tumour suppressor gene: BRCA1 & BRCA2 - breast cancer
• effect of hypermethylation in tumour-suppressor genes

  causes DNA to be tightly coil

  and gene to be switched off
• proto-oncogenes

  stimulates cell division by producing proteins that make cells divide
• mutations in tumour-suppressor genes

  gene will be inactivated

  • causes cells to uncontrollably divide - leading to a tumour
• mutations in proto-oncogene

  gene will be overactive

  • causing cells to divide uncontrollably - leading to a tumour
• benign tumours:

  non-cancerous tumours:

  grows slowly

  does not spread - doesn't metastase

  non-cancerous

  does not regrow after removal
• malignant tumours

  cancerous tumours:

  grow rapidly 

  can spread - metastasis

  cancerous

  can regrow after removal
• abnormal methylation of tumour suppressor genes

  • occurs in the promoter region
  • leads to the gene becoming inactive
  • transcription in promoter regions are inhibited
  • gene is switched off
  • increases cell division and formation of tumours
• genome

  all the DNA in a cell/organism
• why can't u find the genome in complex organisms

  consists of non-coding DNA and regulatory genes
• proteome

  set of proteins an organism produces?
• methods of producing fragments of DNA

  reverse transcriptase,restriction endonuclease, gene machine
• reverse transcriptase

  reverse transcriptase - joins the DNA nucleotides with the mRNA sequence

  • creates cDNA (complementary DNA)

  DNA polymerase - creates another strand using cDNA and joins it with the template strand to form a complete DNA fragment
• the role of reverse transcriptase in RT-PCR

  Produces (c)DNA using (m)RNA;
• restriction endonuclease

  restriction endonuclease (enzyme) - cuts DNA at staggered ends (recognition sites) to expose bases (sticky ends)

  • sticky ends used to join DNA at complementary bases
• gene machine

  identifies amino acid sequence of protein of interest

  the mRNA sequence is also identified and can find the complementary DNA sequence

  safety check using computer

  oligonucleotides created (small sections of overlapping nucleotides) - joins to DNA fragments