Lecture 2 - 3 (Ch 7) Flashcards by Seong Im Hong

The 5 types of RNA and their function are ___

mRNA will be translated to proteins at the ribosome 2. rRNA forms part of the ribosome 3. tRNA carries AA to ribosomes 4. retrovirus RNA uses reverse transcriptase to produce complementary DNA 5. micro-RNA regulate gene expression in plants and animals

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DNA coding strand and mRNA transcript have the ___ polarity

same

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Transcription/gene expression is regulated in 3 different ways; these are ___

promotor, termination sequence, and exon/introns

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Promotors help to regulate the transcription by ___; it is ___ to the process and is the ___

initiating transcription; essential; the most common method of regulating gene expression

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Termination Sequence helps to regulate the transcription by ___; it is (same/different) according to eukaryote, prokaryote, and individual genes

signaling the end of transcription; different

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Exons and introns are found in ___; the coding information is found in ___, while ___ is removed

eukaryotes; exon; intron (Eukaryotes have Exons)

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In bacteria, 1 transcript leads to ___ protein; this RNA transcript (can/can’t) be translated straightaway because ___

multiple protein; can; The RNA transcript is mRNA because there is no need to process it. It also does not have a nucleus that has a separate mechanism of translation.

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In eukarya, 1 transcript leads to ___ protein; this RNA transcript (can/can’t) be translated straightaway because ___

1 protein; can’t; the RNA transcript is called pre-mRNA because it has introns, which must be excised.

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Describe the relationship between the promotor region, the 5’ untranslated region, coding region, termination region, 3’ UTR and the transcribed region in coding sequence of the bacteria. How will it look different within eukaryotes?

5’ –[Promotor] { [5’ UTR][Coding][3’ UTR] } [Termination]–3’ Promotor signals beginning of transcribed region; Transcribed region contains 5’ UTR, coding seq, and 3’ UTR; Termination signals end of transcription, and is not transcribed; In eukaryotes, there will be intermittent exons and introns between 5’ and 3’ UTR

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Upstream of gene refers to ___; downstream of gene refers to ___

the area of the template DNA before start of mRNA transcription; the area after the end of mRNA transcription; upstream 5’—->3’ downstream —————————————————- downstream 3’ upstream

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Translation ___; it takes place at the ___

converts genetic message carried by mRNA into sequence of AA joined together by covalent peptide bond; ribosome

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The result of translation is ___

Polypeptide

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The relationship between polypeptide and protein is ___

polypeptide folds to make up all or part of a protein (i.e. folded polypeptide from gene 1 + folded polypeptide from gene 2 = protein)

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Why is polpeptide called a POLYPEPTIDE?

peptide indicate 2 - 5 AA; polypeptide indicate many more AA

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The start codon is ___, and (is/isn’t translated)

AUG; is translated to Met

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The bond between AA is ___

covalent peptide bond

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DNA is antiparallel but isn’t ___

a palindrome

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In most genome, a given region of DNA can be transcribed and then translated into protein in (one/both) directions; the notable exception is

one; restriction enzyme sites

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Restriction enzymes are also called restriction endonucleases because ___

the enzyme goes into the DNA at the MAJOR groove, read it, and then cut it at the palindromic sequence

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Translation begins when mRNA ___

attaches to the ribosome in a manner that places the start codon (AUG) in the correct position

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DNA, RNA, and polypeptides add in 5’->3’ direction because ___

they all use the same rnx.

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Peptide Bond: Compare the P-site and the A-site of the ribosome

P-site: peptide already added; A-site: next AA will be brought in

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Peptide Bond: At the A-site during elongation, what factors are present before and after peptide bond is formed? What are released/changed?

Before, AA-tRNA-EFtu*-GTP complex is at the A-site (EFtu is Elongation Factor) After, AA-tRNA EFtu is released and recycled; GTP is hydrolyzed

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Peptide Bond: When tRNA is at both P and A-site, peptide bond is formed by ___ at ___;

peptidyl transferase; large ribosomal subunit

Peptide Bond: The two steps of peptidyl transferase are \_\_\_

at the P-site, fMET and tRNA bond is broken; at the A-site peptide bond between fMET and next AA is formed, causing elongation of the AA

Peptide Bond: Peptidyl transferase is a \_\_\_, called \_\_\_\_.

catalytic RNA molecule called ribozyme

Translocation: After peptidyl transferase activity, the P-site contains \_\_\_; the A-site contains \_\_\_

uncharged tRNA (w/o AA); tRNA bound to fMET-AA

Translocation: The next step is translocation of the ____ to the ___ sites, which is initiated by \_\_\_

uncharged tRNA at P-site and tRNA bound to fMET-AA at A-site, to E-and P-site respectively; EFtu and GTP hydrolyzing

Translocation: The integrity of condon frame during translocation is ensured by the ___ ; this unit is rejected when \_\_\_

EF-GDP unit; when the tRNA bound to fMET-AA is bound correctly to the P-site

The sites of large ribosomal subunit are \_\_\_

E-P-A

tRNA reads mRNA in a ___ direction; it has an ____ sequence

5'-\>3'; tRNA has anticodon (3'-\>5') sequence

Codons have 3rd nucleotide "wobble"/redundancy because \_\_\_\_

the 3rd nucleotides are often silent mutations; even with the mutation, the expression of the gene (AA sequence) is conserved

What are the 3 stop codons?

UGA, UAG, UAA

Locate AUG, UGA, UAG, and UAA within this model of the coding DNA: 5' --[Promotor] { [5' UTR][Coding][3' UTR] } [Termination]--3'

5' --[Promotor] { [5' UTR][\*Coding][^3' UTR] } [Termination]--3' \*AUG is translated! ^UGA/UAG/UAA is NOT translated.

DNA replication mechanism and DNA as molecule of heredity is ___ across life forms

conserved

Life-forms differ from one another due to \_\_\_

differing quantity and sequence of DNA

Relate evolution, natural selection, and mutation:

Evolution is a theory that all organisms are related by a common ancestor that have diversified over time via natural selection acting on spontaneously occuring mutation

Phenotypic variation and allele variation are related because \_\_\_

Phenotypic variation indicate allele variation

DNA Polymerase uses (dNMP/dNTP), which contain \_\_\_

dNTP, which contain deoxyribose, nitrogenous base, and tri-phosphate group

In DNA replication, __ is released

PPi (2 phosphate groups)

Why must the DNA be a helix?

If the diameter of 3.4 A is constant, but the bond length between bases vary (A-T v. C-G), DNA must be a helix

3 attributes of DNA replication shared by all organisms are:

1. Each strand of parental DNA molecule remains INTACT during replication, 2. Each parental strand serves as a template for ANTIPARALLEL and COMPLEMENTARY daughter strand, 3. Results in formation of two identical daughter duplexes with 1 PARENTAL + 1 DAUGHTER STRAND (semiconservative)

How was the semiconservative replication of DNA empirically discovered? What trait of N was exploited? What was the assay?

Meselson and Stahl; 15N is heavier than 14N, which is naturally occurring; 1. Gen 0: 15N medium so all DNA had 15 N; following Gen in 14 N medium; 2. DNA samples from each generation spun to form a gradient by weight 3. DNA analysis by weight

Meselson and Stahl: Describe the bands for t0 Describe how each alternative models of DNA replication (conservative, semiconservative, dispersive) were proven/disproven.

at t0, all heavy at first cycle, conservative was ruled out because all bands indicated hybrid (15N-14N) DNA. If conservative, then there will be 1:1 ratio of heavy to light. at second cycle, dispersive was ruled out because there was 1:1 light to hybrid band. If dispersive, then all bands will remain hybrid.

To figure out number of origin of replication in plasmids, what property of T was exploited? What was the assay?

Radioactive T (T\*) emits weak light; At various time points, take e- micrograph.

What about the e- micrograph picture indicated that there was 1 ori in plasmids?

there was always a bubble where DNA seemed to come apart that was indicated by T\*

In unidirectional replication model, the ori will be \_\_\_. In bidirectional replication model, the ori will be \_\_\_

right adjascent to the termination site vs. away from the termination site

In eukaryotes, multiple "bubbles" were visible with T\* e- microscopy. That suggests \_\_\_

multiple ori

According to different cell types in Eukaryotes, ori fire at \_\_\_

different priorities according to gene expression

Replisomes are \_\_\_; they assemble at the \_\_\_

CONSERVED enzymes and proteins involved in DNA replication; replication fork

7 parts of the replisome are \_\_\_

1. Helicase that binds to the origin and unwind dsDNA 2. SSB that binds to ssDNA and keeps it ss 3. Primase that syntheizes RNA primer 4. DNA Polymerase that adds dNTP to 3' end of RNA primer & the DNA strand 5. Sliding Clamp that anchors DNA Polymerase to DNA for high processivity 6. 5'-3' exonuclease and polymerase degrades RNA primer and replaces rNTP to dNTP 7. Ligase makes ss gap between Okazaki fragments and between adjascent lagging/leading strand fragments with P-d bond

Problem during replication specific to the bacteria is \_\_\_; to compensate, the bacteria uses ____ to

supercoiling while unwinding the circular DNA helix; topoisomerase to cut, rotate to unwind, and then rejoin DNA

Steps to processing RNA primer in lagging strand (mention when nucleoside triphosphate and nucleoide is used):

1. DNA Pol I binds to ss gap between DNA and RNA primer and replaces RNA with DNA by using nucleoside tri-phosphate 2. DNA Ligase replaes pol I at DNA-RNA ss gap and binds them together with p-d bond

DNA Ligase works only in lagging strands to anneal Okazaki fragments. T/F?

F. Gap btw lagging and leading at ori also important

DNA proofreading occurs with \_\_\_'s ____ activity; 3 steps to the process are\_\_\_

DNA polymerase 3'-5' exonuclease activity; 1. DNA plymerase makes an error 2. Exonuclease removal of mismatched base pair 3. Daughter strand resumes DNA synthesis

Consensus sequence's function is to \_\_\_\_\_; they are conserved in their ___ (state why); the bases themselves are \_\_\_

serve as recognition sequences for protein binding in replication (but promoter itself is the binding site); presence upstream of the promotor (b/c essential for replication initiatino), and spacing (b/c provides physical space for proteins to bind to DNA template); similar but variable

In yeast, multiple replication origins are called ___ and have ___ DNA sequence

Antunomously Replicating Sequences (ARS); conserved

In bacteria, comparison of single replication origin found consensus sequences called ___ and \_\_\_

13-mer (TATA box) and 9-mer

In eukaryotes besides yeast, replication origins have ____ DNA sequence; this means that DNA is "marked" for replication via \_\_\_, rather than \_\_\_

non-conserved; chromatin modification, rather than consensus sequence