CELL BIO EXAM 3- Evan Kaplan

Info in cells

encoded in the sequence of nucleotides that make up the DNA

Gene

a segment of DNA that directs the production of a specific protein or functional RNA molecule

properties and function of a protein

determined by the sequence of amino acids in its peptide chain - also true with functional RNA molecules

unique amino acid sequence

dictates how the chain will fold to form a molecule with a distinctive shape and function

polypeptide chain

nonfunctional; direct product of translation

genetic information

The flow of __________ _______________ is the same regardless of the organism.

transcription, translation

__________________ and ________________ are two steps involved in the flow of genetic information.

Transcription

- occurs in the NUCLEUS/ where DNA is located

-genetic region of DNA---> mRNA

-product is transferred to the CYTOPLASM

Translation

-occurs in the CYTOPLASM/ where ribosome is located

-RNA---> polypeptide

-RNA molecule is used to determine the amino acid sequence of the polypeptide

Central Dogma of Molecular Biology

DNA -> RNA -> Protein-- (Replication-> Transcription-> Translation)-- (Crick, 1958)

Gene expression

process by which a gene produces its product and the product carries out its function (functional gene product)

Proteins, tRNA, rRNA

Forms of functional gene products include _____________ and and functional RNA molecules such as __RNA and __RNA

DNA, RNA

In transcription the ________ nucleotide sequence of a gene is used to determine the sequence of an _______ molecule

RNA, protein

In translation the nucleotide sequence of the ______ molecule is used to the determine the amino acid sequence of the __________.

RNA

-comprised of 4 nucleotides A,G,C,U

-nucleotides contain ribose sugar

-has the N-base uracil

-SINGLE STRANDED MOLECULE (polynucleotide strand)

methyl

Uracil is similar to thymine but it LACKS a ________ group.

RNA folding

-RNA can fold into a variety of shapes (like proteins) and make base-paired segments

-stem-loop structures- hairpins and simple loops

-narrow major groove- not accessible to most proteins

-There will be local regions of base-pairing but there will NEVER be base pairing within the entire RNA molecule

transcription

the first step in the process of gene expression

DNA

the sequence/series of ______ nucleotides dictates the production of the RNA and ultimately the PROTEIN.

Transcription

-chemically and enzymatically similar to DNA replication

-only ONE STRAND of the DNA is used as the TEMPLATE

-the new polynucleotide strand is in the form of RNA nucleotides

-selectively copies only certain regions of DNA, the GENES

RNA polymerase

enzyme complex that synthesizes a new polynucleotide strand (made up of RNA nucleotides) that is complimentary to the RNA template strand

-has helicase abilities (separation)

-does NOT need a primer

-can start FROM SCRATCH

3'-5'

RNA polymerase travels along the template strand in the _______________ direction.

less

Transcription is _______ accurate than replication.

-one mistake for every 10,000 nucleotides added

T

(T or F) RNA molecules and proteins can be broken down.

RNA molecules

-NOT permanent

-constantly remade as needed

-this is why errors are NOT typically lethal

RNA base pairs

A=U

G---C (triple bond)

mRNA

"go between" between DNA and protein

-used in translation to make a protein

rRNA

make up large complexes that forms ribosomes

tRNA

pick up and deliver amino acids to ribosomes

other forms of RNA

act as regulator molecules involved in gene expression

-non-coding

Ribozymes

RNA molecules that function as enzymes

-contain an active site and possibly a bonding site for allosteric molecules

Ribosomes

(example of a ribozyme) a large complex of RNA and proteins involved in the translation of mRNA into protein

snRNA

(example of a ribozyme) involved in the splicing process of removing introns from pre-mRNA

RNase P

(example of a ribozyme) a ribonuclease molecule involved in generating tRNA molecules from larger precursor RNA molecules

initiation, elongation, termination

the three steps of Transcription are ____________, ______________, and ___________________.

Initiation

-starts transcription

-RNA polymerase and associated transcription factors bind to a sequence of DNA located at the start of a gene-> THE PROMOTER

-MOST IMPORTANT FOR GENE EXPRESSION REGULATION

transcription bubble

the region of locally unwound DNA that allows for transcription of mRNA

-REMEMBER- only one strand of the DNA is used as the template

Promoter

A specific nucleotide sequence in DNA that binds RNA polymerase and indicates the beginning of a gene aka where to start transcribing RNA.

promoter region

around 40-60 nucleotides in length

(set of DNA sequences required for transcription initiation)

Regulatory sequences

-bind regulatory proteins involved in activating or repressing transcription

-mostly located upstream (before) of the promoter

Elongation

-2nd phase of transcription

-RNA polymerase adds RNA nucleotides to the growing chain of RNA based and complementation to the template strand of DNA

-as the RNA polymerase moves through the template it UNWINDS the DNA ahead of it while REANNEALING the DNA behind it.

dissociates

The RNA molecule being made from transcription (specifically elongation) ____________ from the DNA template as it moves along.

Proofreading

RNA polymerase has a __________ ability

-REMEMBER: all of RNA pol's abilities lie in ONE molecule instead of the different ones involved in replication.

Termination

-3rd step of transcription

-upon completion of transcribing the gene, RNA polymerase STOPS and RELEASES the RNA product

terminator

(stop site) specific nucleotide sequences on the gene that RNA polymerase does not go past.

E. Coli

a lot of our understanding of transcription and translation comes from studying the model organism _______________.

I, III

RNA pol __ and ___ are involved in transcribing specialized RNA such as rRNA and tRNA.

II

RNA pol __ is the MAIN RNA POLYMERASE, it is involved in transcribing most protein-coding genes and miRNAs.

RNA pol. III

transcribes tRNA genes, SS RNA genes for many other small RNA molecules, and other noncoding RNAs (like those of the spliceosome.

RNA pol I

transcribes most rRNA genes

crabclaw

RNA polymerase has a ___________________ structure.

between the claws

active site of the "crab-claw" structure

claws

part of the "crab claw" that holds the DNA

GTFs (general transcription factors)

specific types of proteins required to LOCATE the promoter and bring it into the RNA polymerase

-aid in "unwinding" the double-stranded DNA and "pushing" RNA polymerase II into the elongation phase.

2

various GTFs will bind to their appropriate sequences in the promoter and RECRUIT RNA pol ____.

transcription initiation complex

transcription factors+ RNA polymerase II

TATA box

The transcription initiation complex forms at the ______________ region of the promoter.

TFIID

-recognizes and binds to TATA box

-begins the formation of the transcription initiation complex

T

(T or F) TFIID is composed of subunits.

TBP subunit

(TFIID subunit) involved in binding with the TATA box

-OTHER subunits recognize and bind to other promoter regions

TATA box

Upon binding the structure of the ____________ is altered. This causes the recruitment of additional transcription factors followed by RNA pol II.

TFIIH binding

causes the UNWINDING of the promoter DNA

Phosphorylation

"activates" RNA polymerase II in order to begin transcription

10

Once RNA pol II makes a transcript longer than ____ nucleotides in length, it is said to have escaped the PROMOTER and transitions into the ELONGATION phase.

chromatin remodeling complexes

proteins that allow for transcription to occur in the presence of histones by removing nucleotides from the nucleosome as the RNA pol II complex approaches them and then puts the histones back as the protein passes by

3

As RNA is transcribed it will undergo ___ main RNA processing steps before leaving the nucleus.

RNA capping

methylated guanine nucleotides get added to the 5' end of the RNA transcript

-this occurs as soon as it exits the RNA polymerase II complex

-stabilizes the 5' end by prevent exonuclease degradation, stimulates translation, and facilitates nuclear transport

Polyadenylation

the addition of several hundred adenines (A) to the 3' END of the RNA transcript

poly-A tail

addition of the ____________ provides a similar function as capping. It is associated with the cleavage of the RNA transcript, degradation of the remaining RNA associated with RNA pol II, and termination of transcription.

Eukaryotic

In _______ cells the coding sequence is periodically interrupted by stretches of non coding sequences.

-the nucleotides that make up a gene are NOT all used to code for a protein.

Exons

Coding segments of a eukaryotic gene.

~150 nucleotides in length

Introns

A noncoding, intervening sequence within a eukaryotic gene.

~ vary in length but are generally very long ( several hundred kilobases)

F

(T or F) The number and length of introns and exons does not vary from one gene to another

Splicing

introns (non-coding segments) get cut out and removed from the transcript and exons (coding regions) are sealed together.

introns and exons

The pre-mRNA transcript is made up of ________ and ________.

T

(T or F) when a protein is being made the translation machinery CANNOT distinguish between introns and exons.

Introns

The _________ (non coding sequences) must be REMOVED BEFORE TRANSLATION.

pre-mRNA

specific nucleotides within the __________________ molecule determine the locations of introns and exons and where splicing should occur.

splicesosome

complex made up of small nuclear RNAs (snRNAs) and other proteins called small nuclear ribonucleoproteins (snRNPs) by which splicing occurs

alternative splicing

some pre-mRNAs can be spliced in more than one way, generating alternative mRNAs

-result: one gene can produce more than one mRNA/protein

95

___% of human genes undergo alternative splicing

F

(T or F) Transcription in prokaryotic cells is more complex

Transcription, Translation

In prokaryotes, ____________ and ____________ occurs simultaneously.

cytoplasm

one the mRNA has been processed, it is transported out of the nucleus and into the ________ where it will be translated into a PROTEIN.

cap and tail

various protein bin to the _____ and ______ regions and aid in not only stability but also transport.

Exportins

identify the molecule as being mRNA destined for export out of the nucleus

-other proteins: label the mRNA to not be exported and possibly degraded.

-some are involved in transport through the nuclear pores while other are involved with transport through the ribosome.

nuclear pore complexes

-act as gates that connect the nucleoplasm to the cytosol

-controls what enters and leaves the nucleus

active transport

RNA molecules require energy to pass through the nuclear membrane, this is considered _____ (transport.)

protein

Once the mRNAs have been transported into the cytosol, they can be translated into __________.

T

(T or F) mRNAs have a life span and will eventually be degraded.

amino acids

In translation the genetic info that is within the order of mRNA nucleotides and is translated into the linear sequence of ____________ _________ in proteins.

mRNAs

provides the genetic info (template) to be translated into amino acids.

tRNAs

provides the interface between the mRNA and their corresponding amino acids

aminoacyl-tRNA synthetases

An enzyme that joins each amino acid to the appropriate tRNA.

Ribosomes

-coordinates recognition between the mRNA and corresponding tRNA

-catalyzes peptide bond formation between tRNA associated amino acids

F (only some)

(T or F) In translation all of the mRNA is decoded

Codons

The protein coding region of mRNA consists of an ordered series of three consecutive nucleotide units called ___________> they specify the order of amino acids that from the protein.

open reading frame (ORF)

A contiguous non-overlapping string of codons

-starts and ends at internal sites within the mRNA

5', 3'

translation starts at the _______ end of the ORF, proceeds one codon at a time, and ends at the _______ end of the ORF.

5'-3'

translation occurs along the ORF in the _____ (to) _____ direction.