Chapter 13 - DNA and Protein Synthesis Flashcards
I get that this is the first part of the first part of unit 6, but I don't feel like dealing with that presently
Go from smol to big - genome, nucleosome, chromosome, histone, gene, base pair, DNA
Genome is all genetic info
Genome is made of chromosomes are made up of nucleosomes are made of DNA around histones, DNA has genes in its segments and contains base pairs
Why did the scientists think proteins could be responsible for heredity?
Have great heterogeneity (diverse) and specificity of function
Also they didn’t know ship about nucleic acids
What is transformation according to Griffith?
Change in geno and pheno due to assimilation of external DNA by a cell
How did Griffith’s experiment prove there’s genetic material in living organisms?
He stuck some S bacteria into a rat with R bacteria and the R bacteria became S bacteria and he tried again with dead S bacteria and it was the same story so there was an inheritable thing that could be picked up
What is a bacteriophage?
Bacteria eating/infecting virus
How did Hershey and Chase label viral DNA protein in their experiment?
Radioactive isotope of sulfur to tag protein, radioactive isotope of phosphorus to tag DNA (bc chons chonp) so they could see what was being tracked and where it was
What were Hershey and Chase trying to find out in their experiment?
Is DNA hereditary material or protein?
What was the Hershey Chase experiment?
Added radioactivity tagged phages to cells to see whether DNA or Protein was incorporated (did 2 runs, added mix, blender to agitate and centrifuge, measured where radioactivity was (in liquid or pellet (cells were in pellet))
What led Hershey and Chase to conclude that DNA was in fact hereditary material (at least in some cells)?
It was incorporated into the cells while the protein (sulfur) stayed out and then the Ecoli released phages containing some radioactive phosphorus, so the DNA had an ongoing role
Who built the first model of DNA and shared the 1962 nobel prize for discovering its structure?
James Watson and Francis Crick
How did Rosalind Franklin and Maurice Wilkins contribute to the discovery of the double helix?
Rosalind Franklin made an X-Ray diffraction image of DNA, Maurice let Watson and Crick use her lab and supplied the image. Watson (or Crick?) looked at it and was like yeah, that looks pretty helical to me
What are nucleotides made of?
5-c sugar (deoxyribose), phosphate, nitrogenous base (which changes between nucleotides - A,T,C,G, sometimes U)
Why do A + T and G + C bind together, structure wise?
Purines must bond with pyrimidines, so if you think of “Cut The Pye” or “PURe As Gold”, you can’t have C+T or G+A. Otherwise, the structure of G and C are made to form 3 h bonds, while A and T only form 2.
What is a purine?
Nitrogen base. Has 2 rings. Pure as gold.
What is a pyrimidine?
Nitrogen base w/ 1 ring. Cut The Pye.
Which base is only found in RNA?
Uracil
If a fly has 23% A dna, what are the other percentages?
23% T, 100-46=54, 27% G 27% C
What does A stand for? (dna)
Adenine
What does T stand for? (dna)
Thymine
What does C stand for? (dna)
Cytosine
What does G stand for? (dna)
Guanine
What makes up the backbone of DNA?
Sugar and phosphate
What makes up the rungs of DNA?
Nitrogenous bases
How to tell A from C from G from T with a picture and no letters?
Pyrimidine or purine
how many bonds does it make
If you don’t see that look for a =O in C and G
How is the 5’ end different from the 3’ end?
5’ has 5th carbon and a phosphate group sticking out, 3’ end has the 3rd carbon and an OH group sticking out
What does it mean if DNA strands run antiparallel to each other?
They go in opposite directions
Describe the Meselson Stahl experiment
They cultured E-coli in a heavy nitrogen isotope then moved it to a lighter nitrogen isotope. Then, after the 1st round of replication, they took a sample and put it in a liquid and it all floated around the middle together. They then took a sample after the 2nd round of replication and put it in liquid and half floated and half sank.
How did Meselson and Stahl use the RESULTS OF THEIR EXPERIMENT to say that DNA replication is semi-conservative?
The DNA was all floating together in the 1st round of replication, so it wasn’t conservative (it would have split if conservative)
Then, it separated during the 2nd round, so it wasn’t dispersive (it would have stayed together if dispersive)
What does DNA semiconservativeness mean at the molecular level?
When DNA is replicated, it’s unzipped and the original strands are used as templates for the new strands, which get added to the old DNA and merge.
Why is prokaryote DNA replication different from Eukaryote DNA replication?
Prokaryote DNA has 1 origin of replication because the DNA is a loop, so no need for leading and lagging strand nonsense (maybe? it does go both ways) There are also no telomeres, because again, it is a circle. Eukaryotes have multiple origins of replication and replication bubbles that expand to meet up and form 2 daughter strands.
What is the origin of replication?
Place where DNA molecule replication starts and it consists of a specific sequence of nucleotides
What is the difference between the leading and lagging strands during DNA replication?
Leading runs 5’ to 3’ TOWARDS THE FORK (og 5’ is near the helicase)(new strand has 3’ near the helicase) and is made continuously, lagging runs 5’ to 3’ away from the fork and is made in segments
T or F: New nucleotides are added away from the center of the replication bubble
True
How is the lagging strand synthesized?
Added to in segments - primase does a little, then pol 3 does a little, then primase does a little more, and it continues because it can only go in the 5’ to 3’ direction ON THE NEW STRAND REMEMBER ANTIPARALLEL
The segments made by pol3 are called Okazaki fragments
What does primase do?
Adds RNA primer to the new strand of DNA because Pol3 will not add new nucleotides to the strand unless it’s there
What does Topoisomerase do?
relieves tension in the strand by cutting and reattaching because helicase is unwinding and otherwise it would get tangled
What does helicase do?
Unwinds the strand of DNA
What does DNA pol 1 do?
Removes the RNA primer and replaces it with DNA nucleotides
What does DNA pol 3 do?
Running 5’-3’, it adds nucleotides to the new strand as it’s being formed
What does DNA ligase do?
Seals up the Pol1 and pol3
How can DNA polymerase affect repair of DNA?
It can proofread each nucleotide against the template and replace it if it’s wrong
How does Ligase affect repair of DNA?
It can seal free ends of new dna to old dna to make the strand complete
What is mismatch repair?
When DNA is distorted, it’s detected and nuclease cuts out the damaged section, polymerase fills in the missing nucleotides, ligase seals it up
Why is there a short strand of DNA that can’t be repaired or replaced?
There’s no strand on the other end so primase doesn’t go so polymerase doesn’t go so it gets chopped off - overhangs look like damage =========——
What are telomeres and what do they do?
short sections of replicated meaningless dna - these prevent useful genes from getting chopped off/ eroded away
What does telomerase do?
Catalyzes lengthening of telomeres (not meant to go forever but it does in germ cells (I THINK) and cancer cells)
WHat is chromatin?
Uncondensed chromosome (DNA + protein)
Why is packing important in DNA?
Chromosomes can move throughout the cell more easily when packed than unpacked
What is genetic engineering?
Editing genes for practical uses
What is dna cloning?
Making lots of identical copies of specific segments of DNA
What is a plasmid and where does it come from?
Small circular bactewrial DNA molecules with very few genes
What do restriction enzymes do in bacteria?
They act as the bacteria’s immune system and cut up foreign DNA in the bacteria from other organisms/phages
How do scientists use restriction enzymes in genetic engineering?
Used to cut out DNA within a restriction site
What identifies a restriction site?
Palindrome nucleotide sequences
What is the purpose of electrophoresis?
Separate nucleic acids or proteins that differ in size or electrical charge
Which side of an electrophoresis is the DNA loaded into and why?
It’s loaded into the negative side because it’s negatively charged and travels to the positive side
What causes molecules to travel different distances in a gel electrophoresis?
Size and charge (and other stuff?)
How does electrophoresis work? (steps)
Mixtures of dyed DNA molecules of different lengths are placed in wells at the negative end of the gel (agarose)
Current switched on, negatively charged DNA molecules move towards the positive electrode. Small molecules travel faster
After a bit the current is turned off and the DNA is read
How much dna do you share with your parents?
~50% with each
How much dna do you share with your siblings?
~50% with each
How do you use an electrophoresis to tell if someone is a parent or sibling or anything like that?
You should share 50% of your DNA with each parent, and every one of your lines should match up with a parent line.
Siblings should also share 50% of DNA with parents and have every line match up.
Twins should have the same lines (if monozygotic)
What is the denaturation step of PCR?
Heating up the DNA to separate the strands
What is the annealing step of PCR?
Cooling it down and adding primers to highlight the area you want to copy
What is the extension step of PCR?
use a specific DNA polymerase (TAQ because it like heat - comes from thermophile bacteria) to add nucleotides and repeat 40+ times until the DNA says no more
Why is PCR important?
It can make many copies of DNA fragments in a short period of time (in a thermal cycler machine) with only a teeny tiny itty bitty bit of DNA. It’s not too expensive and you can get the DNA from pretty much anywhere, just need to know what you’re isolating
What is next generation sequencing? (if I need to know this I will eat a sock)
Immobilize 1 template strand of DNA
DNA polym. and other reagents added to allow sequencing by synthesis
monitors see the nucleotides that are added, so the sequence can be determined quickly and cheaply (why not just read the og strand? we do now! 3rd gen sequencing is better)
What is DNA sequencing?
The process of determining the nucleotide sequence in a gene
What was the DNA sequencing method used before next gen sequencing?
Sanger method
DNA vs RNA sugar
DNA has Deoxyribose, RNA has Ribose (not Oxyribose because then it would be ONA)
Dna vs Rna number of strands
Dna has 2, Rna has 1
Dna vs Rna location in cell
Dna in the nucleus, Rna in the nucleus and cytoplasm (dna is stuck, rna is not)
Dna vs Rna nitrogen bases
Dna has Adenine, Thymine, Cytosine, Guanine, RNA has Adenine, Uracil, Cytosine, Guanine
What are the elements & monomers of DNA and RNA?
CHONP
Nucleotides
What are the monomers and elements of protein?
CHONS
Amino Acid
Nucleotide vs Nitrogenous base vs Nucleoside
Nitrogenous base is just the A, T, C, G, or U
Nucleoside is nitrogenous base + sugar
Nucleotide is nucleoside + phosphate group
What is gene expression?
How DNA controls protein/RNAs-that-aren’t-related-to-protein making
What conclusion did Beadle and Tatum come to after completing their experiment?
They concluded that the function of a gene is to dictate the production of a specific enzyme that catalyzes a particular reaction
beetles are buff and like to wear jeans
ta tum chhhh
What exceptions are there today to the Beadle Tatum conclusion?
Some genes encode stuff that’s not enzymes, like different proteins or subunits of proteins or not proteins (RNA)
Template for transcription
Preexisting DNA
Product synthesized by transcription
mRNA
Where does transcription happen?
in the nucleus
Template for translation
mRNA
Product synthesized by translation
Amino acid chains (that fold to form proteins)
Where does translation happen in the cell
Cytoplasm
What is the triplet code?
A genetic info sequence in which a series of nonoverlapping 3-nucleotide-long words specifies a sequence of amino acids for a polypeptide chain
3 nucleotides that can code for an amino acid
What is meant by “genetic code is universal”?
All diverse forms of life share a common genetic code due to shared ancestry, so DNA from 1 species can affect another (and make it produce specific proteins)
How many nucleotides are required to code for an amino acid?
3 (per codon)
What is another name for the coding strand?
Non-template strand (this one matches the RNA)
AGUCCCGGUACG
What is the first codon?
AGU which codes for idk but they’ll give us a chart so it’ll be fine
T or F: All codons code for amino acids
False, UAA, UAG, and UGA are stop codons
What is the start codon?
AUG with Met(hionine)
How is genetic code REDUNDANT?
Multiple codons can specify 1 amino acid
How is genetic code NOT AMBIGUOUS?
each codon specifies only 1 amino acid
Similarities between protein synthesis in prokaryotes and eukaryotes
Ribosomes make proteins, transcription and translation, inherited info flows DNA –> RNA -> Protein
Differences between protein synthesis in prokaryotes and eukaryotes
Proks - No mRNA processing (no need to protect it from leaving the nucleus because there is no nucleus)
Make multiple proteins at once by translating immediately to get all sorts of different proteins (different lengths)
What adds RNA nucleotides to exposed DNA bases?
RNA polymerase
What helps RNA polymerase recognize and bind to the promoter region?
Transcription factors
What is the beginning of a gene called?
Initiation sequence
What is the region of dna where RNA polymerase binds and transcription begins?
Promoter region
What is the end of a gene called?
Termination sequence
What is the short sequence in the promoter region where the transcription factor binds?
TATA box
T or F: During protein synthesis, helicase does the unzipping
False, RNA pol takes care of it
What is the little strand of mRNA you make during protein synthesis called before it’s premRNA?
RNA transcript
When does the RNA polymerase let go in transcription?
Termination sequence
Which direction does RNA polymerase go in transcription?
5’ to 3’ (downstream)
What makes up the transcription initiation complex?
WHOLE COMPLEX of promoter + transcription factors + RNA pol (2) bound to the promoter
During RNA processing, what happens to the 5’ end?
A methylated (5’) cap is added
During RNA processing, what happens to the 3’ end?
The poly-a(denine) tail is added (proteins bind to speed it up)
3 functions of 5’ cap and poly-a tail
- Protect mRNA from degradation by hydrolitic enzymes
- Facilitate export of mature mRNA from the nucleus (POLY A)
- Help ribosomes attach to the 5’ end of mRNA (5’ CAP) (once it reaches the cytoplasm) (but APPARENTLY that’s not necessary because the prokaryotes are just fine without this one)
Are introns or exons spliced out of premRNA?
Introns (some of the exons sometimes but always the introns)
T or F: Lots of spliceosomes bind together to make a snRNP
False, lots of snRNPS (snurps) bind together to make a spliceosome
What are snurps made of?
Small Nuclear RiboNucleoProteins - Protein and RNA
How do spliceosomes work?
Snurps within the spliceosome base pair with nucleotides at specific sites within the intron. Next, small spliceosome RNAs catalyze the cutting of pre-MRNA and splicing together of the exons, releasing the intron (which gets degraded)
What is alternative mRNA splicing? How could this be important for an organism?
This is what happens when different combinations of introns and exons are spliced out so that genes can make more than one type of polypeptide - number of proteins produced can be more than the number of genes (and ups diversity)
T or F: Alternative splicing of a pre-mRNA with exons 1, 2, and 3 could give you protein 123 or 13 but never 32
True, the order doesn’t change
What are some evolutionary advantages to mRNA splicing?
Intron mutations don’t harm the cell, you can make lots of proteins from 1 gene
Step 1 of transcription
Transcription factors bind to promoter region of a gene (specifically the tata box)
Step 3 of transcription
RNA pol untwists and opens a short segment of DNA
Step 4 of transcription
RNA polymerase adds nucleotides to the 3’ end of the elongating strand of RNA
Step 5 of transcription (final)
RNA polymerase reaches the termination site, transcription stops, RNA released
mRNA function
Is read by tRNA and rRNA (but mostly tRNA) to make proteins
tRNA description
Transfer RNA - it has a specific amino acid at one end and an anticodon at the other end
tRNA function
Transfers amino acids from itself to the growing polypeptide chain being created (they also use their anticodon to read the codon because they don’t just bond willy nilly)
………O
…..|=|
…..|=|
__………__ This is the top half of a tRNA. What are the equals signs?
Hydrogen bonds
Which way is the anticodon going?
3’ to 5’ (but don’t really mind this because it just needs to match up with the codon whatever way it’s read)
How is complementary base pairing important in the anticodon?
the t-RNA anticodon base pairs with the codon and adds the appropriate amino acid whenever that codon appears - you need the right base pairing to get the right amino acid
What is the difference between prokaryote and eukaryote ribosomes, and why is that medically significant?
Eukaryote ribosomes are alittle bigger and have slightly different molecular compositions
This means antibiotic drugs can inactivate bacterial ribosomes without affecting the ability of eukaryotic ribosomes to make proteins, which lets them combat bacterial infections
3 stages of transcription and translation
Initiation, elongation, termination
What happens during translation initiation?
smol ribosomal subunit binds to mrna/mRNA attaches to the ribosome starting with the 5’ cap, 1st tRNA attaches and releases the Met (first codon will always be Aug with Methionine)(this is called the translation initiation complex because biology wants to confuse me and me specifically)
What happens during translation elongation?
Anticodon of incoming tRNA base pairs with complementary mRNA codon, peptide bond forms (which rRNA catalyzes) between the new and old amino acid + polypeptide
Translocation - the RIBOSOME shifts over to the next codon
What happens during translation termination?
When a stop codon is reached on the mRNA, the A site accepts a release factor (instead of aminoacyl tRNA) which promotes hydrolysis of the bond between the tRNA in the P site and the last amino acid of the polypeptide
Then everything falls apart
What are the 3 ribosome sites?
E, P, and A (in that order)
What are some post-transcriptional modifications?
Adding on sugars, lipids, phosphate groups, the works
Removing 1 or more amino acids from the leading end of the polypeptide chain (so Met isn’t always the first in a finished protein)
The chain may be cleaved into 2 or more pieces or 2 separately synthesized polypeptide chains may come together
What does the signal peptide do?
Determines where the protein/ribosome thingy goes
What is a mutation in terms of molecular genetics?
A change in the sequence of nucleotides
What is a point mutation?
Substitution of one or more nucleotides
What is a frameshift mutation?
Addition or deletion of one or more nucleotides
What is a silent mutation?
A point mutation where the nucleotide that is replaced still codes for the same amino acid and therefore doesn’t really change anything
What is a missense mutation?
A point mutation where the nucleotide that is replaced causes the codon to code for a different amino acid
What is a nonsense mutation?
A point mutation where the nucleotide replaced causes the codon to code for a stop codon, ending the protein early
What is a mutagen?
Endo or Exogenous agents that increase genetic mutation probability (or just straight up cause mutations bc why not)
