Molecular BiologyThe Study of Proteins and Nucleic Acids

what are proteins?what are the building blocks

of proteins?what type of bond is in

proteins?

Proteins - reviewfunctions include: catalysts for reactions, structure, receptors on membranes, movementstructure:● building block = amino acids● joined by peptide bonds● called polypeptides● 4 levels of structure = primary, secondary,

tertiary, and quaternary

hydrogen bonding between R groups causes folding

what are the parts of an amino acid?Amino Acids● 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 - reviewfunctions include: energy currency (ATP), store hereditary information (DNA & RNA)

structure:● building block = nucleotide● nitrogenous bases - A, T, C, G and U● sugar-phosphate backbone● double helix shape

NucleotidesNitrogenous Base

Sugar - ribose (RNA) or deoxyribose (DNA)

Phosphate

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 Bases2 kinds: purines and pyrimidines● Purines - adenine and guanine● Pyrimidines - thymine and cytosine

Base-Pairing Rules (Chargaff’s Rule)● purine always pairs up with pyrimidine● adenine with thymine● guanine with cytosine● bases "pair up" by hydrogen bonding

DNA is "antiparallel"ends are called:5' (five prime)and3' (three prime)

5' ends - phosphates3' ends - sugars

http://youtu.be/wdhL-T6tQcoDNA fantastic! music video

How do we know DNA has the genetic material?

Freidrich Miescher (1868) found nuclear material to be ½ protein and ½ unknown substance1890s - unknown nuclear substance named DNAWalter Sutton (1902) discovered DNA in chromosomes

How do we know DNA has the genetic material?

Frederick Griffith (1928) working with Streptococcus pneumoniae conducted transformation experiments of virulent & nonvirulent bacteria strainsPheobus Levene (1920s) 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

Animationhttp://highered.mcgraw-hill.com/olc/dl/120076/bio21.swf

Hershey-Chase Experiment● conclusions - proteins did not enter infected cell,

DNA did enter infected cell● therefore - DNA must contain genetic code to

make more viruses

How do we know the structure of DNA?

Contributors:Erwin Chargaff (1950s)● 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● Took X-Ray photographs of DNA● discovered DNA must have a helix shape● This photograph later inspired the model made by

Watson and Crick

the famous x-ray photograph of DNA taken by Rosalind Franklincalled “photo 51”

James Watson and Francis Crick● figured out 3 dimensional

structure of DNA was a double helix

● used information discovered by Chargaff, Franklin and Wilkins to figure it out

you need to know who these people are!

Friedrich Miescher, Hershey & Chase, Frederick Griffith, Rosalind Franklin, Maurice Wilkins, Erwin Chargaff, Watson & Crick

using Chargaff’s (base-pairing) rule

what sequences will be complementary to:

ATTCGCTAACGG

CGGTTACCGAAT

DNA ReplicationReplication = process of copying DNA● occurs at many places along

the DNA molecule simultaneously

● happens in both directions● produces 2 new identical DNA

molecules

DNA Replication

DNA replication is called “semi-conservative” because each new DNA molecule contains half of the original moleculeShown by Meselson-Stahl experiment by Matthew Meselson & Franklin Stahl in 1958http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120076/bio22.swf::Meselson+and+Stahl+Experiment

semi-conservative DNA replication

DNA Replication

Step 1: the 2 nucleotide strands are separated by unwinding● origin of replication = site where DNA

replication begins● replication fork = where 2 chains separate● helicase = enzyme breaks hydrogen bonds

holding the bases together

DNA replicationStep 2: new chains are made by adding/combining complementary nucleotides● DNA polymerase = enzyme adds

nucleotides to new chains

Animations: http://highered.mcgraw-hill.com/olc/dl/120076/bio23.swfhttp://www.stolaf.edu/people/giannini/flashanimat/molgenetics/dna-rna2.swf

DNA Replication DNA ReplicationStep 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/1L8Xb6j7A4wDNA replication music video

what is the location of DNA replication?

what enzymes are involved in the process?

DNA replicationlocation: nucleusenzymes: helicase - unzips DNADNA polymerase - adds/combines new nucleotidesDNA ligase - combines fragments

sites: replication fork - where DNA splitsleading strand - side where DNA is built smoothlylagging strand - side where DNA is built in piecesokazaki fragments - unconnected pieces of DNA on lagging strand

The Language of DNA● information in DNA is in the sequence of bases● a triplet (set of 3) of nitrogenous bases is called a

codon● these are like words in the language of DNA

The Language of DNA● DNA's information is expressed as proteins● each codon codes for an amino acid● each gene codes for a polypeptide

● DNA never leaves the nucleus● the code to make proteins is sent to the ribosomes

using messenger RNAinfo goes from DNA --> RNA --> Protein

DNA

RNA

Protein

Transcription

Translation

RNA● stands for RiboNucleic Acid● ribose instead of deoxyribose● uracil (U) instead of thymine (T)

3 types of RNA● messenger RNA (mRNA)

= carries genetic info from nucleus to cytosol

● transfer RNA (tRNA) = carry amino acids to be built into proteins

● ribosomal RNA (rRNA) = make up ribosomes

TranscriptionTranscription = produces RNA from DNA template● begins at regions called promoters (they

"promote" the transcription)● RNA polymerase = enzyme which synthesizes

RNA

● RNA nucleotides line up along one strand of DNA following the Base-Pairing Rules

● ends at regions called termination signals

Transcription

Animations:http://www.concord.org/~btinker/workbench_web/models/eukTranscription.swfhttp://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.swf

what is the sequence of molecules in molecular biology?

describe the language of DNA? what is a codon?

what is the location of transcription?

what enzymes are involved in the process?

DNA→transcription→RNA→translation → protein

transcription: location - nucleusenzymes - RNA polymerasesites: promoters - begin processtermination signals - end processtemplate DNA strand - used as template to make RNAinactive DNA strand - not used, RNA is single stranded

TranslationTranslation = making proteins from information in mRNA● occurs on one or more ribosomes ● the 'language' of nucleic acids is 'translated'

into the 'language' of proteins

Translation● mRNA slides through ribosomes● tRNA brings amino acids to

ribosomes● tRNA contains sequences called

anticodons which contain 3 bases complementary to a codon in the mRNA

anticodon

tRNA

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

mRNA

amino acidstRNA

translation

translation Translation● ribosome moves along

the mRNA from codon to codon

● new amino acids are brought by tRNAs

● and added to the polypeptide

● the process stops at a stop codon

polypeptide new amino acid

translation TranslationAnimations:http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a3.htmlhttp://www.concord.org/~btinker/workbench_web/models/eukTranslation.swf

protein synthesis music videohttp://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

what is the location of translation?

what molecules are involved in the process?

what bonds are formed?

DNA→transcription→RNA→translation → protein

translation: location - ribosomes in cytoplasm or on ERenzymes - none, uses tRNA - brings amino acidsand rRNA - ribosomes to combine amino acidssites: codon - set of 3 nucleotides on mRNA, match up with -anticodon - set of 3 nucleotides on tRNA start codon - begin processstop codon - end processbinding site on ribosome - where mRNA and tRNA line up