Central dogma (biology, process)

Question 1

why is DNA semiconservative?

what enzyme is used for replication? what does it require?

Answer 1

semi- conservative replication- parent strand and new strand,
Enzyme: DNA polymerase
• Requires: DNA template
accurate reliability

Question 2

why is the 3’ hydroxyl important and where does the energy for DNA replication from?

Answer 2

incoming strand has three phosphates, important bc u release energy when 2 of the phosphate bond is broken, enzyme converts this energy into new bond between last phosphate and hydroxyl, resulting in extended DNA polymer, and releases pyrophosphate
o DNA polymerase NEEDS a 3’ hydroxyl to add onto

Question 3

what is the central dogma?

Answer 3

• Description of the way info flows in the cell typically. Info is stored in dna, replicated, copied into RNA then to proteins (built from ribosomes)

Question 4

what are genes? what is gene expression?

Answer 4

Gene: a discrete unit of heredity information consisting of a specific sequence of nucleotides in DNA.

Gene expression: the process by which DNA DIRECTS THE SYNTHESIS OF PRODUCTS- when and how much a gene is expressed, all the way to the production of protein (not always)

Question 5

what is transcription?

Answer 5

DNA to RNA,the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA).

Question 6

what is DNA for? RNA?

Answer 6

DNA is long term memory/ information storage

RNA can be the messenger/carrier of this info

Question 7

what is the template for RNA formation?

Answer 7

DNA is template for RNA formation

Question 8

How is DNA replication similar to RNA transcription? How are they different?

Answer 8

Form is different, but the language is the same. DNA and RNA are almost the same molecularly. Both depend on the dna template and base pairing of nucleic acids. Different bc nature of daughter strand, RNA instead of DNA, and Thymine vs uracil.

Question 9

what is the transcription enzyme? template?

Answer 9

Transcription enzyme: RNA polymerase

Transcription template: DNA template, doesn’t need a hydroxyl

Question 10

what is the promoter? start and stop point?

Answer 10

: where enzyme binds, determines direction, always happens 5’ to 3’ prime
• Transcription start point: where new strand starts
• Transcription stop: where it stops

Question 11

what is the transcription unit? promoter? terminator? (eukaryotic)

Answer 11

Transcription unit: the portion of the DNA that is transcribed into RNA

Promoter: Defines the transcription start point

Terminator: defines transcription stop point

Question 12

what are the 3 types of RNA and their functions? (eukaryotic)

Answer 12

mRNA: messenger RNA (only these are translated into proteins)

rRNA: ribosomal RNA

tRNA: Transfer RNA

Question 13

what do eukaryotes do during mRNA processing?

Answer 13

Eukaryotes modify their mRNA before translation

• Possible because: of separation between transcription (in nucleus) and translation (in cytoplasm or ER membrane)

Question 14

what are introns?

Answer 14

The transcription unit of a protein-coding gene—the RNA-coding sequence contains non-protein-coding intervening sequences called introns that interrupt the protein-coding sequence The introns are transcribed into pre-mRNAs but are removed from pre-mRNAs during processing in the nucleus.

Question 15

what are exons?

Answer 15

The amino acid–coding sequences that are retained in finished mRNAs are expressed and therefore called exons.

Question 16

what is splicing?

Answer 16

occurs in the nucleus, removes introns from pre-mRNAs and joins exons

Question 17

what protects the 5’ from exonucleases in eukaryotes?

Answer 17

5’ modified G cap: protects 5’ end from exonucleases and helps with transcription

Question 18

what protects the 3’ end from exonucleases in eukaryotes?

Answer 18

Poly-A tail: a whole bunch of RNA nucleotides which protects the 3’ end from exonucleases (chew up free ends) and helps with delivery

Question 19

what are the ingredients for translation? what do they do?

Answer 19

• mRNA: carries info
• tRNA: connects info from mRNA to the appropriate amino acid
• ribosomes:
• roles of rRNA vs. ribosomal proteins- RNA in ribosome catalyzes the reaction adding the new amino acid to the growing polypeptide. Sequence in the mRNA determines the sequence of amino acids in the protein.

Question 20

what are the three key parts of tRNA?

Answer 20

anticodon, acceptor site, wobble

Question 21

what is anticodon?

Answer 21

complementary to the codon in the mRNA- 3 nucleotide sequence that carries the information

Question 22

what is acceptor site?

Answer 22

where the appropriate amino acid is covalently attached

Question 23

what is wobble?

Answer 23

: where the third position of the codon can potentially be 1, 2, 3, or even all four nucleotides.

Question 24

what are key things that happen for the ribosome? (translation)

Answer 24

• Subunits assembled in nucleus (specifically nucleolus) – made separately
• Exist separately in cytoplasm
• rRNA recognizes mRNA
• two halves are assembled separately, shipped out of the nucleus, then interact with mRNA to create a protein.

Question 25

what are the three sites in ribosomes? APE

Answer 25

• aminoacyl, peptidyl, exit

Question 26

what are the steps of initiation? (translation)

Answer 26

* 1. initiator tRNA starts in A site (small subunit only), determined by the sequence in the mRNA upstream (5’) from the AUG in prokaryotes * 2. carries methionine, AUG in mRNA * not all mature proteins have methionine so it may get cleaved later * 3. Large subunit binds to initiator, bumps tRNA Met (initiator) into P site (middle) * Now A site is open and ready for next tRNA

Question 27

what are the seven steps of elongation? (translation)

Answer 27

1. New codon in mRNA is in A site 2. rRNA catalyzes peptide bond formation- covalent bond between the amino acid (or peptide) in the P slot with the incoming amino acid. This involves breaking the covalent bonds between the peptide and the tRNA in the p slot. Remember, the incoming or charged tRNA is covalently bonded to its amino acid. 3. Now the peptide is bigger by one amino acid, and the ribosomal proteins bump the newly emptied tRNA into the E slot. 4. This happens at the same time as they bring the tRNA from the A into the P slot with its growing peptide chain 5. Happens in tandem with the mRNA getting shuffled over by one codon 6. Empty tRNA in the E slot exits 7. A new tRNA comes in and the cycle continues

Question 28

what are the six steps of termination? (translation)

Answer 28

1. A stop codon comes into the A slot 2. The peptide is finished and needs to be cut loose 3. There are 3 stop codons and none are recognized by tRNAs, but instead by the termination factor 4. The termination factor is a protein that looks similar to tRNA 5. Breaks covalent bond between peptide and last tRNA in the P slot 6. the ribosome dissociates and components are released

Question 29

how is translation done in prokaryotes?

Answer 29

* no modification of mRNA as the mRNA is available to the translation machinery even as its being transcribed * Nucleotide interaction is important. It doesn’t happen in eukaryotes bc its process is more complicated * Bacteria: starts translating at first AUG codon after ribosome binding site Prokaryotic translation initiation: can start before transcription is finished bc the ribosomes recognize a specific sequence in the mRNA: the ribosome binding site which corresponds with a sequence in one of the rRNAs

Question 30

how is translation done in eukaryotes?

Answer 30

Water-soluble protein used in the cytoplasm: • finished and modified mRNA is exported from nucleus to cytoplasm -two possibilities after: 1. resulting water-soluble protein is needed in cytoplasm. For these, ribosomes attach and translation begins 2. the protein will be water Insoluble and function in the membrane or Water-soluble protein to be exported. • In either of these cases, once a ribosome recognizes the mRNA, it brings it to the rough ER and docks in the membrane. • then the peptide is translated into the lumen or directly into the membrane. • Once translation is done the ribosome dissociates and the other halves go off to find another mRNA • The docking is directed by a signal recognition particle (SRP), it binds to the ribosome after the formation of the ribosome. – blocks translation until docking is complete. • Cant have further translation until docked properly in the membrane, then SRP leaves, and translation is continued.

Question 31

what is reading frame?

Answer 31

* Reading frame: the way the ribosome groups the nucleotides of the mRNA into groups of three. It is critical that the ribosome has the right reading frame or else nonsense comes out. It uses it for the rest of the transcript. * Reading frame is determined by the first AUG codon (start). The first one depends on prokaryotes or eukaryotes.

Question 32

what is frame shift?

Answer 32

• Frame shift, and effect of frame shift: A frameshift mutation is a type of mutation involving the insertion or deletion of a nucleotide in which the number of deleted base pairs is not divisible by three.

Question 33

what is the genetic code/ codon table?

Answer 33

• Code which allows translation from “language” of nucleic acids to “language” of amino acids

Question 34

what is the start codon? what are stop codons?

Answer 34

* Start codon: AUG- ONLY CODON FOR METHIONINE * Stop codons: UAA, UAG, UGA * Stop codons are recognized by the termination factor.