proteins and nucleic acids

• The primary structure is the sequence of amino acids.
• Monomers are small building blocks or molecules, while polymers are long repeated chains of molecules
• Polymers have different properties from their monomers depending on the way they are bonded together
• Bonds are chemical interactions between molecules allowing them to stick together, with different types providing different strengths of attraction
• When bonds are formed, energy is released, and when bonds are broken, energy is also released
• Types of bonds:

  • Covalent: atoms share an electron
  • Ionic: electrons transferred between atoms with opposite charge
  • Hydrogen: bond between a hydrogen atom and another bonded atom
  • Disulfide: sulfate + cysteine side chains
• Nucleic acids:

  • Two types: DNA (double-stranded, deoxyribose sugar, bases: thymine) and RNA (single-stranded, ribose sugar, bases: uracil, 5’ and 3’)
• Types of RNA:

  • Messenger RNA (mRNA): copy of DNA, carries genetic messages to ribosome
  • Transfer RNA (tRNA): carries specific amino acids to ribosome
  • Ribosomal RNA (rRNA): together with proteins, makes up the ribosome
• Ribosome: structure where proteins are made, with an amino acid being the monomer of a protein
• Amino acids have three groups: amino group, carboxyl group (acid group), and rest group (r group), with peptide bonds connecting them
• Four levels of protein structure:

  • Primary structure: sequence of amino acids, held together by strong covalent peptide bonds, determines protein type
  • Secondary structure: formed from hydrogen bonds, can be alpha helix or beta pleated sheets
  • Tertiary structure: maintained by ionic attraction, interactions between hydrophobic r groups, and covalent disulfide links, giving the protein a 3D shape
  • Quaternary structure: two or more polypeptide chains interact to form a protein
• Transcription is the process in which gene structure includes coding region (introns + exons), promoter region, and terminator region
• RNA polymerase is the enzyme responsible for synthesizing a DNA strand into an RNA strand, with non-template strands being coding strands (3’ to 5’) and template strands being non-coding strands (5’ to 3’)
• Tertiary structure involves interactions between different parts of the protein molecule that result in its overall shape.
• DNA manipulation involves swapping bases or changing the DNA sequence
• Restriction enzymes are used to cut DNA at specific recognition sites
• Blunt ends are created when the restriction enzymes cut the two strands of DNA directly opposite each other
• Sticky ends are formed when the restriction enzymes cut the two strands of a DNA molecule at one point but cut the second strand at a point that is not directly opposite
• If a specific recognition site is present in DNA, the DNA molecule will be cut into two or more fragments
• The length of the fragments depends on the relative position of the recognition sites
• In some cases, multiple restriction enzymes will be added to a DNA sample to cut at different sites
• Ligase is an enzyme that can stick different DNA pieces together by forming strong covalent bonds at the sugar-phosphate backbone
• Both sticky and blunt ends can be joined using ligase
• Polymerase chain reaction (PCR) allows millions of copies of a specific DNA sequence to be produced
• PCR involves denaturation, annealing, and extension steps to amplify DNA
• Gel electrophoresis is a technique for sorting DNA fragments of different lengths based on their size
• DNA fragments move down the gel towards the positive electrode in gel electrophoresis due to the electrical current passing through the gel
• Shorter DNA fragments move faster in gel electrophoresis, while longer DNA fragments move slower
• Mistakes during gel electrophoresis can include inserting electrodes the wrong way, using the wrong voltage, or leaving the electrophoresis on too long
• Ethidium bromide dye is commonly used to stain DNA fragments for analysis after gel electrophoresis
• DNA profiling can use nuclear or mitochondrial DNA, with differences in inheritance and mutation rates
• Short tandem repeats (STRs) found in nuclear DNA can uniquely identify a person
• Hypervariable regions found in the non-coding regions of mitochondrial DNA are used for identification when nuclear DNA is not available
• Living relatives are needed to provide mitochondrial DNA for comparison in DNA profiling
• Issues with DNA profiling include concerns about DNA databanks, familial searching, legal, and ethical concerns, and predictive testing