Cellular Control

Annotations:

• Genes are lengths of DNA DNA can be found in mitochondria and on Chromosome, DNA is made of nucleotides Genes code for a polypeptide made of amino acidsPolypeptides code for protenins such as enzymes like atpase, proteaseGenes are found on loci of a chromosome DNA is a macromolecule formed when the single molecules called nucleotides polymerise into nucleic acids
• The human genome comprises some three gigabases (three million base pairs), from genes within DNA. Most of the DNA is kept within the cell nucleus, but some DNA can be found in the mitochondrion

1. Chromosomes

   Annotations:

   • genes are found on chromosome 
2. Proteins

   Annotations:

   • genes code for proteins including enzymes e.g. atpase 
3. made of dna

   Annotations:

   • a polynucleotide = mad of lots of nucletoides joined together, each nucleotide has a pentose sugar, a phosphate group and a nitrogenase base, the sugar is a deoxyribose sugar, 

1. Definition

   Annotations:

   • Genetic code: the three letter code that by which infom,ation is contained in DNA molecule; a group of three bases specifies a particular amino acid to be added to a growing polypeptide chainBecayse genes code for the enzymes that are in control of all metabolic pathways
2. Universal

   Annotations:

   • The same DNA triplets code for the same amino acids in nearly all organismsThis indicates is eveolved very early on in the evolution of the earthNot 100% universal are some variations
3. Triplets

   Annotations:

   • One triplet of bases codes for one amino acid. Degenerate Code: More than on triplet can code for one amino acid There are 20 different amino acidsOne DNA strand is used to code for proteins this is the reference strand

1. 1. Transcription

   Annotations:

   • Only a gene/one part of gene (cistron) is transcribed, this is a small part of the DNA molecule Genes are in nuclease, proteins are made in the cytoplasm on the ribosomes (protin synthesis) Double stranded DNA is too large to fit through nuclear envolope pores to reach the ribosome so single stranded mRNA needs to be made
   1. 1.DNA Unzips

      Annotations:

      • This is done by the enzyme DNA helicase which breaks the Hydrogen bonds betweeen the bases on a geneA-TC-G have a template stand - the strand where nucleotides for H bonds and a coding strand which is the strand identical to the new mRNA strand, No H bonds with this
   2. 2. Free Nulceotides Join

      Annotations:

      • Free activated RNA nucleotides from cytoplasm join the exposed base RNA don't have a thymine so A-binds to uracil and thymine on coding strand binds to A Pair up with complementary bases   
   3. 3. RNA polymerase

      Annotations:

      • !!RNA!! (not DNA) polymerase moves along the template causing condensation reactions between adjacent RNA nucletides, building up the sugar phosphate back bone    also making sure that all the new nucleotides are complementary based paired to the template strand This creates the mRNA strand  
      1. exam q

         Annotations:

         • why is something classified as an amino acid  contains an amino group and a carboxyl group
   4. 4. Stop Triplet

      Annotations:

      • The RNA polymerase will reach a triplet of bases that code for an amino acid which signals the RNA polymerase to stop  and the mRNA can now break offMay stay unzipped or be zipped back up mRNA now guided out of nuclear pores to ribosomes in nuclease
2. 2. Translation

   Annotations:

   • mRNA is now used to line up amino acids to make a polypeptide chain each group of three bases is called a codon, one codon codes for one amino acids there are also stop and start codons involved tRNA that has 2 bidning sites on for an anticodon (binds to/complementary to codon on mRNA) and other biding site for amino acid
   1. 1.Held in Ribo Cleft

      Annotations:

      • The mRNA molecule is held in the cleft of the ribosome (either free in cyto or bound to endoplasmic reticulum) so that only 6 RNA bases are exposed, 3 codons
   2. 2.tRNA bind x3

      Annotations:

      • 1st) a Trna molecule with a complementary anti codon to the first codon binds bringing with it a particular amino acide that
      • 2nd) another tRNA molecule binds to the 2nd codon, complementary & amino acid etc The amino acids are held next to each other and a peptide bond, via a condensation forms between the two of then
      • 3rd) the mRNA moves through the cleft of the ribosome so that another codon is visible, a trna complementary to it binds and condesation reaction causes peptide bond between the amino acid = 3 amino acids Meanwhile the first t rna is completed and breaks away leaving the AA behind it can then go to cyto where it is reloaded with different/same amino acid and anti codon
   3. trna transferase

      Annotations:

      • specific enzymes load specific amino acids on to specific trna molecules. there is a different kind for each kind of trna 
3. Exam Q

   Annotations:

   • how does rna interface effect gene expression stops translation stops mrna binding with ribo stops protein syntheis

Annotations:

• Mutations occur during DNA replication Meiosis - mutation will usually be inherited Mitosis - mutation is not passed on to offsprin but may contribute to ageing process/cancer
• natural selection = proteins behavouir in particular way and mutation can have huge effect but can be beneficial

1. Deletion

   Annotations:

   • If one base pair goes missing = codes for a different amino acid and triplets all read differently Less likely to make large difference if in 3x tabel becuase only effects one or two amino acids not all in sequenceVery likely to have big changePostive or negaticve effectCauses frame shiftWill usually be affective mutation nut can be netural if organisms does not gain adv or disadv
2. Substitution

   Annotations:

   • is the addition of new pair of bases, replacing old ones, often called point mutation not cause fram shift becuase the dna code is degenerate (each amino acid is coded for by moer than one triplet  usually silent
   1. Sickle Cell Anemia

      Annotations:

      • substion of one base in the gene that codes for one of the polyp chains in heamoglobin  inherited  mutation in the B chain cuases sickle cell anemia  base sequence changes from ctt to cta and this binds to a different amino acid
      • when the four chains (a and b) form tertiary sturture they have very specise 3d shape some aa have hydrophilic side chains and others have hydrophobic chains  Polyp curls up so hydrophobic on outside and hydrophilic on inside the old amino acid before the subsitution  had a hydrophilic side chain (outside) the new one has hydrophobic chain, that goes outside, effects that make the heamoglobin less soluble and water and this amino acid can also form bonds with themselves so can stick amino acids together  cause a biconcave shape = not oxygen carried and canot pass through cappiklarys so get stuck
   2. point mutation
3. Insertion

   Annotations:

   • addition of a new base pair always causes frame shift can be pos or neg usually affective or neautral like deletoion
4. exam q

   Annotations:

   • name the process that has given rise to coat colour varaitons in cats Mutation

Annotations:

• some proteins are activated by chemicals, like cyclic amp that, like atp, is a nucletoide derivative (Nucleotide derivatives are necessary for life, as they are building blocks of nucleic acids and have thousands of other roles in cell metabolism and regulation.). it acitves proteinns be chinaging their 3d shape so tat their shape is a better fit to their complementary molecules

1. exam q

   Annotations:

   • describe the events that occur after adrenaline reaches the cell surface membrance that then results in changes in the metbolism inside the cell cytoplasm: adrenaline binds to receptor, complementary fit, activates g protein, adenyl cylase activates, atp converted to cyclic amp, camp activates enzymes that alter 3d strucutre
   1. adrenaline binds to receptor - complementary
      1. activates a g protein
         1. adeyle cyclase is activated
            1. atp converted cyclic amp
               1. cyclic amp activates enzymes which alter the 3d shape

Annotations:

• Found in Ecoli that often respires glucose but will respire lactose if it present and break it down into glucoase and galactose operon: a length of dna control sites and structual genes

1. 4th5th)Structual Genes

   Annotations:

   • Z structual gene code for B galactosidease Y structual gene codes B galactoside permease Only transcribed if lactose present
2. 3rd) Operator Region

   Annotations:

   • binding site for repressor proteindetermines wheather  the structual gene is on or off when repressor bind to operator also covers promotor so rna poly can bind
3. 1st) Regulator Gene

   Annotations:

   • Code for repressor protein, DNA polymerase transcribes it when no lactose present repressor has 2 binding sites one to lactose and one for the operator region, when lactose binds to the protein it changes the shape so it can no longer bind to the operator region and rna poly can bind to promoter region
   1. codes for Transcription factor

      Annotations:

      • which turns genes on or off by increasing or decreasing the amount of transcription 
4. 2nd) Promotor Region

   Annotations:

   • Where DNA polymerase binds to transcribe structual genes if lactose is present. RNA polymerase can only bind if no repressor on the operator region
5. When Lactose is absent

   Annotations:

   • when lactose is absent the regulator gene is expressed and rna polymerase transcribes the gene and mRNA is translated into a repressor protein the repressor protein bind to the operator region so rna poymerase cannot bind to the promotor region and cannot transcribe the z and y sites  2 enzymes are not synthesised
6. When Lactose is present

   Annotations:

   • regulator gene expressed so repressor protein present inducer molecule lactose binds to repressor protein to alter its shape so that its other binding site will not fit on the operon the rna polymerase therefore is able to bind to the promotor region and transcribe z and y into the enzymes so lactose can be brought into the cell and respired

Annotations:

• genes that determin how an organisms body developes as it grows from a zygote into a complete organism, thye determine the organisms body plan homeobox gene contain a homeobox sequence that codes for particular part of protein called the homoedomain the hemeodomain binds to specific sites of dna enabling the protein to work as a transcription factor protein binds to start or end of dna supressing or activating transcrription

1. Development

   Annotations:

   • Proteins control the development of body plans  Proteins are coded for by genes called homeostatic genes (homeobox genes) have different genes for different body parts 
   1. Exam Q

      Annotations:

      • list two cellular process that must occur during the devlopment from a tad pole to a frog apoptosis, respiration, dna replication, mitosis, protein synthesis
   2. exam q

      Annotations:

      • explain why there has been little mutation in the homeobox genes; they are very important it would lethal and would have a very large effect
   3. altering the proteins involved in development
2. Universal

   Annotations:

   • similarity between homeobox genes in animals plants and fungi all homeobox genes are homologuose with each other  barley changed over millions of years highly conserved = activitiy is fundemental to development 
   1. highly conserved
   2. homologuouse
3. 2x Exam Q

   Annotations:

   • state what is meant by a homeobox gene control body development, switch genes on and off, contain homeobox sequence that codes for homeo domain, binds to dna
   • explain why there has been very little change by mutation in these genes Important, change would be lethal, bug effect, change many genes 
4. details

Annotations:

• programmed cell death highly controlled in proper way is cell nerosis which is usually caused by external factors

1. Process

   Annotations:

   • all cells contain genes that code and inhibit apoptosis during the developmet different genes are activated 1. enzymes (caspases) break down the cells cytoskeleton 2. the cytoplasm densly packed as organelles begin to bundle 3. Plama membrance contains blebs and looks flaccid 4. Nuclear envelope disappears 5. Breaks into nuclear fragments 6.Cell packages into vesicle 7. vesicles engulfed by phagocytes and digested
2. Why

   Annotations:

   • mitosis and differentiation make the bulk and apoptosis refines it by removing any unwanted structures  tad poles fingers and toes