Unit 5 Studying DNA Chapter 4 / Proteins Chapter 5 Name:__________________

Chapter 4: DNA Structure and FunctionGene-a section of ________ on a ___________________________ that contains the genetic code of a _______________DNA is composed of subunits called __________________Chemical Structure of a nucleotide

The 4 different Nitrogen bases of Nucleotides composing DNA are:.

Phosphodiester Bonds = A bond that connects ______________________ Hydrogen Bonds (H Bonds)= a bond that connects Nitrogen base to complimentary Nitrogen base.

Facts:Tested by ____________________________________________ in E.coliSemi-conservative ___________________________________________________________________Antiparallel ____________________________________________________________________

DNA replication: happens before Mitosis and uses an enzyme__________________ to unwind the DNA Polymer. Can’t replicate unless unwound.

Variations in DNA in Cells_____________of DNA strands , ___________ in base pairs, the number and type of _____________,The _______________ of the DNA strands:

_______________________chromosomes & ______________________ chromosomes

Prokaryotic DNAE coli: has a ____________________________________ containing ~__________ genes. Plasmids: -__________________________________ (5 to 10) Plasmids are: _________________________________________________________________________________________________

___________________ plasmids may give bacteria a way of “___________________” by gaining new characteristics of survival. Bacteria can “transfer “ plasmids through conjugation or division.When the genes are transferred into cells, the cells would be considered __________________.

Notes from video: Plasmids, Genetics, Biology https://www.youtube.com/watch?v=GNMJBMtKKWU

Eukaryotic DNADNA is ________________Eukaryotes have anywhere between ___________________________

Humans have _______________________________

A lot of DNA is _____________________ or ‘spacer’ DNA (INTRONS) Currently trying to figure out ‘spacer’ DNA’s function

Eukaryotic DNA has _______________________________ that increase the expression of DNA.

These transcription factors turn genes __________________

Eukaryote DNA is made of ______________________________________ sections ___________sections tend to be filler DNA and they are __________________during mRNA processing Before the mRNA leaves the nucleus. Intron means interspersed DNA

Chromosomes coil around proteins called ______________. Histones help to_____________the genes. DNA must be uncoiled by ______________ in order to be transcribed into mRNA and then translated into protein.

GROWING CELLS AND GETTING DNA (Bacterial Cell Culture)Broth: __________________________used for growing cells. Bacteria replicates every _____________.Agar: _________________________ used for growing __________________________________, or other cells. Agar is a mixture of water and __________________________________.Autoclave: creates high _______________ and high _________ to sterilize equipment and media.-this prevents contamination or transmission of microorganisms. Cell concentrations can be checked using a _____________________________.

Mammalian Cell CultureGrowing mammalian cells is ___________________. In order to grow them the substitute environment must be as close as possible to the natural one.

Small scale production: Cells are grown in broth culture tubes and bottles (this is what we will do)Large Scale production: Cells are grown in fermentation tubes/tanks.

Viral DNA (______________________)Viruses are not considered to be _________________; They have no cellular structure Viruses ________________________________________ molecules,_______________________Nonpathogenic viruses are used in biotechnology______________ to carry DNA between cells

_______________________EX: Diabetes & Cystic Fibrosis

Viral vaccine molecules recognize specific viral surfaces and targeting them

Gene Therapy (Pulmozyme)Use modified ______________________ (common cold) to deliver a normal gene into the nasal cells containing defective genes (gene replacement)The Virus acts as a ________________(deliverer)Used to correct genetic defect in Cystic Fibrosis patients

CF: lung infections, breathing problems, CFTR gene defectiveRegulates flow of chloride ions into the epithelial cells lining the respiratory and digestive systems

Chapter 5INTRODUCTION TO STUDYING PROTEINS “DNA is The Flash, but Protein is the cash”

Protein Molecule StructureMade of amino acids. Each has a

central carbon atom carboxyl group amino group different R-group)

_____________________________ are categorized by their R-groups.Proteins are chained together by peptide bonds (between the carboxyl & amino group).Polypeptide chain is called the primary structure.

Amino Acid chain connected by ___________________________between Carboxyl and Amino groups.

Protein Structure: = Protein Function _______________________________is considered to be called the Primary Structure.Polypeptide folds via H-bonding into pleats or helices to create ____________________Structure.

Tertiary strucutre is due to the presence of ______________________, ________________, _________ Charged or uncharged R-bonds and Interactions between polar and nonpolar AA

____________________ is an interaction of tertiary structures and all bonds when 2 or more protein subunits come together. Many proteins are composed of 2 or more subunits.

Production of ProteinsCells are ________________________ and are in continual protein production. The only time cells don’t produce proteins is when?___________________________Similar in both eukaryotic and prokaryotic cells.DNA is the “___________” or __________________________for making proteinsThe ability to modify and synthesize peptides or proteins is crucial to nearly every biotech product.

Steps to protein synthesis: Transcription & TranslationConverting a ____________________ code to an ___________________________ sequence.Protein Synthesis occurs in a 2-step process, _________________________________________.

TranscriptionIn transcription, the genetic code must be “read” and rewritten into an mRNA molecule.The mRNA molecule is ______________________________________________________ in the cytoplasm.The Transcription/Translation Players

mRNA: __________________________________________________________________ tRNA ___________________________________________________________________

TRY IT!DNA T A C A G T A C C A T A A T C mRNA _________________________

amino acid ________________________

Translation : During translation the _________________________is changed into a sequence of amino acids. Each codon corresponds to one of the ______________________. After the polypeptide is made it folds into a 3-D configuration and is considered a ______________________.

Transcription and translation video notes: https://www.youtube.com/watch?v=gG7uCskUOrA

Operon system for Gene Expression in Bacteria:Bacterial cells transcribe and translate DNA into mRNA into Proteins as well…but uses an_______________________________________to determine when to produce proteins. Only when necessary!VERY EFFICIENT!

EX: Lac Operon SystemIf bacterial cells do not have lactose present, they don’t need to have the enzyme lactase, a ___________ ___________________ is always bound to the ______________________after the Promoter, called the __________________ and BLOCKS TRANSCRIPTION of the Lactase gene. No Protein (enzyme) made.

If bacterial cells have the lactose present, they will need to produce the enzyme (protein) Lactase in order to ___________________________________. The REPRESSOR MOLECULE is _____________________________________________ and Transcription of the lactase genes continues and ______________________

Bacteria need to be very efficient due to their small size.

STRUCTURE AND FUNCTION of proteinsWe need to learn about the structure, function, and amino acid sequence of the protein to use them for research. Many times _________________are caused by a defective or lack of proteins.When a protein loses a structure it’s called ______________________________________.Conditions that an enzyme works best at are called ________________________________.

pH, Temp, Salinity We can modify protein _____________________ to change structure and ________________

In Biology …..“It’s Not the Size, It’s the Shape”ENZYMES PROTEIN CATALYSTSThere are two theories that describe enzyme catalysts: Lock and Key Model and Inducted Fit ModelEnzymes are ________________________ meaning 1 Enzyme = 1 SubstrateNeeded in every cell or cells would die ________________________________________________.Biotech companies need significant amounts of enzymes for _______________________________.

Essential Vocab:Enzymes : _______________________________________________________________________

(Speed up rate of reaction by making atoms move faster)Substrate: Any __________________________________________________________________Active Site: _____________________________________________________________________

ENZYME FACTSMost end in “ase” but some end with “in”Work with only certain substrates_______________________________________________________________________________Do not get ______________________ in reactionSpeed up reaction by lowering activation energy; (_________________________________________)

HOW ENZYMES WORKEnzymes attach to substrate Chemical bonds in substrate are formed or broken in the substrate Products of substrate are releasedEnzyme goes back and grabs another substrate, and continues until the substrate is all broken down.Enzymes will also build substrates together into larger products.

How Biotech Really Works!Biotechnology works by merging our knowledge of _________________________________Change the _________________________, change the ________________________ madeRequires Biotech Tools

Restriction Enzyme: an enzyme that cuts DNALigase: an enzyme that pastes DNA back together by reforming the phosphodiester bondGene of Interest: Example Insulin GeneRecipient Genome: E. coli plasmid

Plasmid: Circular DNA that bacteria have in addition to the normal chromosome

Restriction Enzyme: __________________________________________________________________Natural function of restriction enzymes are to: To protect ________________________________________. Digest foreign (e.g. viral) DNA.Restriction enzymes are isolated from bacteria and are used to cut DNA of our making!

HOW IS IT DONE? (________________-______________-__________________-___________)Take a human cell and remove the nucleusExtract the DNA (genome) from the nucleusLocate the Insulin geneCut out the Insulin gene with a restriction enzymeTake a Bacterial Plasmid and cut open with the same restriction enzymePlace the Insulin gene into the bacterial Plasmid; you now have recombinant DNA.Place the recombinant DNA back into a Bacterial Cell (transformation)The Bacteria will now produce insulin.

EcoR1 is a restriction enzyme isolated from E.coliIt specifically cuts DNA at this sequence:

5’….ACTGTACGAATTCGCTA….3’ 3’….TGACATGCTTAAGCGAT….5’

After cutting you are left with sticky ends.

5’….ACTGTACG AATTCGCTA….3’ 3’….TGACATGCTTAA CGAT….5’

If you cut the gene from DNA with this AND also cut the plasmid open with this, then the sticky ends will bond to corresponding bases _____________________will bind the ends!

INSULINThe first commercial product made by genetic engineering (______________).

Insulin is the hormone used to control their ____________________________ in diabeticsFirst sold in _____________________, ( San Francisco)

Recombinant DNA TechnologyRecombinant DNA: used to create new DNA molecules by piecing together different DNA molecules Product is written with an “____” in front of itGenetically engineered: Cells accept ________________ and begin expressing new genes by making _____________________

All products produced from rDNA technology are versions of ____________________________ molecules or organisms that have been ___________________.