Midterm study Flashcards
Human genome
complete set of nucleic acid sequences to code for a human (codes for a human)
3 fundamental discoveries for the human genome
1) Restriction endonucleases
2) Cloning techniques
3) Synthesis of specific probes
Restriction endonucleases:
Enzymes cleave(cut) long DNA strands into many smaller fragments at specific cut sites
Bacteria produces restriction enzymes (EX. EcoRI)when virus adds its DNA into the enzyme
They cut at restriction sites that correspond to the enzyme. 4-6 base pair stretches
Sticky ends: leave some bases without their complementary base pairs making “sticky ends” so that they can re-stick easier
Blunt ends: cut straight down middle
Palindromes:
same back and forth (read same 5’ to 3’ as 3’ to 5’)
Cloning techniques
Combine DNA and introduce to new organism to amplify or increase amount
Introduce a foreign DNA molecule into a replicating cell allowing amplification (make many copies of the foreign DNA that is now tagging along the replication process)
Cloning VECTORS:
a specialized plasmid that has been engineered to act as a carrier or a vehicle that transfers specific foreign genes into the host cells (car that drives the foreign DNA into the host cell)
EX. viral, bacteria, yeast
Cloning techniques STEPS
- Restriction enzyme digests/cuts
- Target gene is joined/connected/stuck to at the cut
- Recombined into plasmid & can now transport into a host cell/put into an environment that can grow !!!!!Either host cell OR pcr!!!!!!
Prokaryotic Plasmids:
smaller circular piece of DNA that naturally exists. extra-chromosomal DNA molecule that replicates independently.
Polymerase Chain Reaction PCR:
where you amplify the specific target gene using science(laboratory technique) (In vitro(in test tube) amplifying technique AKA no host cell required)
Denaturing: template strand is heated up and double DNA strand breaks
Annealing: lower temp & primer is added
Extension: gives proper environment to grow by increasing the temp a bit
Advantages of PCR
Fast
Only need trace amount (a bit) of DNA to make a lot
Disadvantages of PCR
Need to know exact sequence of DNA that you want to amplify
When to use PCR in real life?
Viruses have long latency(showing symptoms) period and are difficult to detect early, can use to see it before symptoms show up
Gel electrophoresis:
- Large molecules travel less because heavy & small molecules travel more because light
- DNA= negatively charged so attracted to positive side which is further away from the probes
- Use stains or probes(markers) to visualize
Synthesis of specific probes
Allow identification and manipulation of specific DNA sequences
Probe:
sequences we made to then stick onto DNA so we can see it, a way to detect if something/a sequence is showing up/appearing
Complimentary to the gene of interest
tRNA
Transfer RNA
what carries the aminoacid and what connects to the aminoacyl site in translation
mRNA
Messanger RNA
What copies the code from the DNA in the nucleus by transcription, and sends the message of the codons to then go through translation
rRNA
Ribosomal RNA
The ribosomal subunits that help in translation
Types of mutations:
- Silent mutation→ the codon (3 letters) that had the change of 1 letter(nucleotide) still codes for the SAME amino acid
- Missense Mutation → the codon (3 letters) that had the change of 1 letter(nucleotide) codes for a DIFFERENT amino acid
- Nonsense Mutation → the codon (3 letters) that had the change of 1 letter(nucleotide) codes for a STOP/TERMINATION codon
Silent mutation
the codon (3 letters) that had the change of 1 letter(nucleotide) still codes for the SAME amino acid
Missense Mutation
the codon (3 letters) that had the change of 1 letter(nucleotide) codes for a DIFFERENT amino acid
Nonsense Mutation
the codon (3 letters) that had the change of 1 letter(nucleotide) codes for a STOP/TERMINATION codon
Trinucleotide repeat expansion
entire codon gets repeated leads to too many copies of the aminoacid that that repeated codon codes for
Splice site mutations
splice site goes into exon(cuts more than needed) OR slice site goes into introns (leaves unneeded things)
Frameshift mutations
addition OR loss of 1 OR 2 nucleotides to mRNA sequence so then it shifts the reading frame for protein production
Wobble hypothesis:
a theory that explains how multiple codons can code for the same amino acid, or how a single tRNA molecule can recognize more than one codon.
(allows for fewer tRNA molecules to be required for the translation process, enhancing efficiency)
Ribosomal subunit
- rRNA responsible for peptide bond formation
- reads the mRNA 5’-3’ direction
- NOT a protein bound enzyme
Ribosomal tRNA binding sites
A- Aminoacyl
P- Peptidyl
E- Exit site
Peptidyl transferase:
an enzyme that catalyzes the formation of peptide bonds between amino acids during protein synthesis
How does the immune system defend?
Antibodies TAG/mark an antigen for destruction
Antibodies:
proteins produced by immune system to recognize and bind to foreign molecules (proteins) called antigens
Antigens:
protein on surface of a foreign molecule EX. bacteria, viruses, fungi
SDS-PAGE
electrophoresis of proteins (separate proteins based on their molecular weight.)
Denatures proteins making it stretch out giving it a negative charge
WESTERN BLOT
- On a GELL plate using gel electrophoresis with proteins
- Add primary antibody then secondary antibody that has the direction signal on it
(Size and amount)
ELIZA
- In WELLS put proteins
- Add antibody thens secondary antibody with the signal
(Amount QUANTITATIVE)
Titration curve & buffering region
Buffers:keep steady and maintain equilibrium
Buffering region: always 1 greater and 1 less than pK
Peptide bonds have…
a partial double bond character
(Planar, Rigid, Fixed and a Little shorter than a single bond)
CIS:
Molecules close together (not preferred because will be repulsion)
TRANS:
Molecules far apart (prefered because reduces steric hinders AKA clashes)
Primary structure:
Linear sequence/ polypeptide chain
- Peptide bond made between aminoacids using dehydration synthesis reaction
- Read: N terminal (NH3+) → C terminal (COO-)
- Sickle cell anemia: disorder results in protein with altered aminoacid
In what way to do read polypeptides?
N terminal (NH3+) → C terminal (COO-)
Secondary protein structure: 2 TYPES
Alphahelix
Beta pleated sheet
Alphahelix
- Pepetide bonds coil & R groups stick out
- H bonds run parallel to axis (vertically)
Helix breakers
Proline: doesnt fit/bend that way due to benzine ring because of secondary amide group
Clumps of charged reside: ionic attraction or repultion
Too many bulky aminocids: due to longer side chain, need more space
Beta pleated sheet:
- Peptide bonds involved in H bonds
- 2 or more peptide side chains that form the beta strands
- H bonds run perpendicular to polypeptide (horizontaly)
- Can be parallel or anti parallel
Super secondary structure
combination of Alpha helix & Beta pleated sheet
Tertiary protein structure
- Folding into final 3D structure
- The folds depend on domains of the protein (the fundamental function)
- Polar stay out (where water is) & Non-polar stays in (where no water bc scared of it)
- Hydrophobic interactions are the primary driving folding force
- H-bonds (O,N,F)
- Ionic interactions (neg charge R groups(acids) interact with Pos charge R groups(bases))
- Disulfide bonds: Covalent link between two cystines
Globular proteins and EXAMPLE:
Globby
EX: Myoglobin & Hemoglobin
Quaternary protein structure
- Binding 2 or more chuncks/peptide chains
- Monomer, dimer, Trime ect.
Myoglobin
- O2 Storage
- Reversable binding of O2
- Heme is bound to pocket lined with nonpolar aminoacids
- Keeps steady affinity for O2
Hemoglobin
- O2 transportation
Deoxygemoglobin= no O at heme
Oxygemoglobin= yes O at heme - Only red blood cells
- Transport O2 from lungs to capilitlies in tissues
- 4 peptide chains (2a & 2b)
(each chain similar to myoglobin)
Cooperative binding: (T →R state)
Cooperative binding: (T →R state)
- When o2 binds, causes confirmational change/change in shape
- Iron shifts into pane of heme and pulls histidine and helix with it
- Twists into place
- Changes binding to high affinity site!
Myoglobin O2 Affinity?
high
good at storing but also good at giving away when needed
Chart line closer to Y axis
Hemoglobin Affinity
low
pick up from lungs because needs high [ ] to pick up
releases intensely and doesn’t take back easy
Fiberous proteins
Not globy, in a line
Functions: for structure, like skin, hair, connective tissue
