what are proteins? what are the building blocks of proteins? Molecular Biology what type of bond is in The Study of Proteins and Nucleic Acids proteins? Proteins - review hydrogen bonding between functions include: catalysts for reactions, R groups causes folding structure, receptors on membranes, movement structure: ● building block = amino acids ● joined by peptide bonds ● called polypeptides ● 4 levels of structure = primary, secondary, tertiary, and quaternary Amino Acids what are the parts of an amino acid? ● Carbon in the center, w/ a Hydrogen ● amino group = NH2 ● carboxyl group = COOH ● "R" group = varies, determines shape and function what are nucleic acids? what are the building blocks of nucleic acids? what are bases? what do we call the shape of DNA? Nucleic Acids - review Nucleotides Nitrogenous Base functions include: energy currency (ATP), store hereditary information (DNA & RNA) structure: ● building block = nucleotide Sugar - ribose ● nitrogenous bases - A, T, C, G and U Phosphate (RNA) or ● sugar-phosphate backbone deoxyribose ● double helix shape (DNA) what are the base pairing rules? DNA's Double Helix ● nitrogenous bases of nucleotides pair up in a certain manner ● C with G ● A with T ● these base pairs form the steps of a twisted ladder shape Nitrogenous Bases Base-Pairing Rules (Chargaff’s Rule) ● purine always pairs up with pyrimidine 2 kinds: purines and pyrimidines ● adenine with thymine ● Purines - adenine and guanine ● guanine with cytosine ● Pyrimidines - thymine and cytosine ● bases "pair up" by hydrogen bonding DNA is "antiparallel" ends are called: 5' (five prime) http://youtu.be/wdhL-T6tQco and DNA fantastic! music video 3' (three prime) 5' ends - phosphates 3' ends - sugars How do we know DNA has the How do we know DNA has the genetic material? genetic material? Freidrich Miescher (1868) found nuclear material Frederick Griffith (1928) working with to be ½ protein and ½ unknown substance Streptococcus pneumoniae conducted 1890s - unknown nuclear substance named DNA transformation experiments of virulent & nonvirulent bacteria strains Walter Sutton (1902) discovered DNA in Pheobus Levene (1920s) chromosomes determined 3 parts of a nucleotide Griffith’s experiment How do we know DNA has the genetic material? Hershey-Chase experiment ● Alfred Hershey and Martha Chase ● studied bacteriophages, which are made of only DNA and protein ● radioactively labeled the DNA and protein ● see which substance (DNA or protein) moved into infected cells Hershey-Chase experiment Animation http: //highered. mcgraw- hill. com/olc/dl/ 120076/bio 21.swf Hershey-Chase Experiment How do we know the structure of DNA? ● conclusions - proteins did not enter infected cell, DNA did enter infected cell Contributors: ● therefore - DNA must contain genetic code to Erwin Chargaff (1950s) make more viruses ● discovered that every species has different amounts of A, T, C and G ● discovered that the amount of A always equals amount of T ● and amount of C always equals amount of G ● the base pairing rules are aka Chargaff’s rule Rosalind Franklin and Maurice Wilkins the famous x-ray ● Took X-Ray photographs of DNA photograph of DNA ● discovered DNA must have a helix shape taken by Rosalind ● This photograph later inspired the model made by Franklin Watson and Crick called “photo 51” James Watson and Francis Crick you need to know who these people ● figured out 3 dimensional are! structure of DNA was a double helix Friedrich Miescher, Hershey & ● used information discovered by Chargaff, Chase, Frederick Griffith, Rosalind Franklin and Wilkins to Franklin, Maurice Wilkins, Erwin figure it out Chargaff, Watson & Crick DNA Replication using Chargaff’s (base-pairing) rule Replication = process of copying what sequences will be complementary to: DNA ● occurs at many places along ATTCGCTAACGG the DNA molecule simultaneously CGGTTACCGAAT ● happens in both directions ● produces 2 new identical DNA molecules semi-conservative DNA replication DNA Replication DNA replication is called “semi-conservative” because each new DNA molecule contains half of the original molecule Shown by Meselson-Stahl experiment by Matthew Meselson & Franklin Stahl in 1958 http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535:: /sites/dl/free/0072437316/120076/bio22.swf::Meselson+and+Stahl+Experiment DNA replication DNA Replication Step 2: new chains are made by adding/combining complementary nucleotides Step 1: the 2 nucleotide strands are separated by unwinding ● DNA polymerase = enzyme adds nucleotides to new chains ● origin of replication = site where DNA replication begins ● replication fork = where 2 chains separate Animations: http://highered.mcgraw-hill. ● helicase = enzyme breaks hydrogen bonds com/olc/dl/120076/bio23.swf http://www.stolaf. holding the bases together edu/people/giannini/flashanimat/molgenetics/dna-rna2.swf DNA Replication DNA Replication Step 3: okazaki fragments on the lagging strand are joined together by the enzyme DNA ligase ● leading strand - replication in the direction the DNA molecule is being unzipped happens smoothly ● lagging strand - replication in the other direction is fragmented ● okazaki fragment - fragments on the lagging strand DNA replication results in 2 new identical DNA molecules ● parent strand - part of original DNA molecule ● daughter strand - newly formed strands http://youtu.be/1L8Xb6j7A4w DNA replication music video what is the location of DNA replication? DNA replication location: nucleus enzymes: helicase - unzips DNA what enzymes are involved in the DNA polymerase - adds/combines new nucleotides DNA ligase - combines fragments process? sites: replication fork - where DNA splits leading strand - side where DNA is built smoothly lagging strand - side where DNA is built in pieces okazaki fragments - unconnected pieces of DNA on lagging strand The Language of DNA The Language of DNA ● information in DNA is in the sequence of bases ● DNA's information is expressed as proteins ● a triplet (set of 3) of nitrogenous bases is called a ● each codon codes for an amino acid codon ● each gene codes for a polypeptide ● these are like words in the language of DNA ● DNA never leaves the nucleus ● the code to make proteins is sent to the ribosomes using messenger RNA info goes from DNA --> RNA --> Protein RNA DNA ● stands for RiboNucleic Acid ● ribose instead of deoxyribose Transcription ● uracil (U) instead of thymine (T) RNA Translation Protein 3 types of RNA Transcription ● messenger RNA (mRNA) Transcription = produces RNA from DNA template = carries genetic info from ● begins at regions called promoters (they nucleus to cytosol "promote" the transcription) ● transfer RNA (tRNA) = ● RNA polymerase = enzyme which synthesizes carry amino acids to be RNA built into proteins ● ribosomal RNA (rRNA) = make up ribosomes Transcription ● RNA nucleotides line up along one strand of Animations: DNA following the http://www.concord. Base-Pairing Rules org/~btinker/workbench_web/models/eukTrans cription.swf ● ends at regions called http://www.stolaf. edu/people/giannini/flashanimat/molgenetics/tra termination signals nscription.swf DNA→transcription→RNA→translation → protein what is the sequence of molecules in molecular biology? transcription: location - nucleus enzymes - RNA polymerase describe the language of DNA? what is a sites: promoters - begin process codon? termination signals - end process template DNA strand - used as template to make RNA what is the location of transcription? inactive DNA strand - not used, RNA is single stranded what enzymes are involved in the process? Translation Translation Translation = making proteins from information ● mRNA slides through ribosomes in mRNA ● tRNA brings amino acids to ● occurs on one or more ribosomes ribosomes ● the 'language' of nucleic acids is 'translated' ● tRNA contains sequences called into the 'language' of proteins anticodons which contain 3 bases tRNA complementary to a codon in the mRNA anticodon Translation translation ● always begins at a start codon - AUG on mRNA ● each mRNA codon pairs with tRNA anticodon ● amino acids form peptide bonds together and then detach from the tRNA amino acids tRNA mRNA Translation translation polypeptide new ● ribosome moves along amino the mRNA from codon to acid codon ● new amino acids are brought by tRNAs ● and added to the polypeptide ● the process stops at a stop codon translation Translation Animations: http://www-class.unl. edu/biochem/gp2/m_biology/animation/gene/gene _a3.html http://www.concord. org/~btinker/workbench_web/models/eukTranslati on.swf protein synthesis music video http://youtu.be/JTc18Yh7bSU Protein Processing ● a polypeptide is only the primary shape of a protein ● the R groups of the amino acids will cause the polypeptide chain to fold and bond with other polypeptides ● many proteins also need other compounds added ● for ex. glycoproteins need carbs added ● this is accomplished in the golgi apparatus DNA→transcription→RNA→translation → protein what is the location of translation? translation: location - ribosomes in cytoplasm or on ER what molecules are involved in the enzymes - none, uses tRNA - brings amino acids and rRNA - ribosomes to combine amino acids process? sites: codon - set of 3 nucleotides on mRNA, match up with - anticodon - set of 3 nucleotides on tRNA start codon - begin process what bonds are formed? stop codon - end process binding site on ribosome - where mRNA and tRNA line up.