Pierce's Genetics: Chapter 10

colinearity

genes and proteins are colinear—that there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein

poly(A) tail

the addition of 50 to 250 adenine nucleotides at the 3 end of pre-mRNA, forming a poly(A) tail. These nucleotides are not encoded in the DNA but are added after transcription

upstream

where transcription starts, promoter region

ribonucleoside triphosphate (rNTP)

A nucleoside that contains ribose as its sugar component. triphosphate + ribose sugar + base substrates for RNA synthesis 2 phosphates cleaved

Concept 6

A promoter is a DNA sequence adjacent to a gene and required for transcription. Promoters contain short consensus sequences that are important in the initiation of transcription.

Concept 16

A ribosome is a complex organelle consisting of several rRNA molecules and many proteins. Each functional ribosome consists of a large and a small subunit. Ribosomal RNAs in both bacterial and eukaryotic cells are modified after transcription.

Transposable

DNA moves around in the genome

Transcription Requirements

DNA template Substrates to build new RNA Apparatus-proteins to catalyze synthesis

ribosomal RNA (rRNA)

Ribosomal RNA (rRNA) along with ribosomal protein subunits make up the ribosome, the site of protein assembly. Where protein synthesis occurs.

ribozyme

catalytic RNA molecules can cut out parts of their own sequences, connect some RNA molecules together, replicate others, and even catalyze the formation of peptide bonds between amino acids.

exon

coding regions (want in final RNA)

initiation

apparatus assembles on promoter and begins RNA synthesis (transcription initiation complex)

protein-coding region

comprises the codons that are translated specify the amino acid sequence of the protein begins with start codon and ends with stop codon

large ribosomal subunit and small ribosomal subunit

consists of one or more pieces of RNA and a number of proteins.

CRISPR RNAs (crRNAs)

degrade foreign DNA (prokaryotic)

Concept Check 6 If a splice site were mutated so that splicing did not take place, what would the effect be on the protein encoded by the mRNA? a. It would be shorter than normal. b. It would be longer than normal. c. It would be the same length but would have different amino acids.

b. It would be longer than normal.

Concept Check 1 Which class of RNA is correctly paired with its function? a. Small nuclear RNA (snRNA): processes rRNA b. Transfer RNA (tRNA): attaches to an amino acid c. MicroRNA (miRNA): carries information for the amino acid sequence of a protein d. Ribosomal RNA (rRNA): carries out RNA interference

b. Transfer RNA (tRNA): attaches to an amino acid

Accessory proteins

bind to RNA polymerases and affect their functions

polymerase

binds and adds bases

long noncoding RNAs (lncRNA)

function in gene expression regulation

Pre-mRNA must undergo processing to splice out the non-coding regions

Contain both introns and exons, introns must be spliced out and exons joined to make mature mRNA

Elongation

RNA polymerase (usually II) changes conformation so no longer bound to promoter or other transcription factors, moves along DNA (lets transcription go away)

alternative processing

a single pre-mRNA is processed in different ways to produce alternative types of mRNA, resulting in the production of different proteins from the same DNA sequence

transcription unit

a transcription unit are three critical regions: a promoter, an RNA-coding sequence, and a terminator

RNA-coding region

a sequence of DNA nucleotides that is copied into an RNA molecule. (Pre-mRNA)

terminator

a sequence of nucleotides that signals where transcription is to end DNA sequence that ends transcription, after terminator itself has been transcribed

Concept 4

RNA is synthesized from ribonucleoside triphosphates.Transcription is 5 3: each new nucleotide is joined to the 3-OH group of the last nucleotide added to the growing RNA molecule.

Not all DNA is transcribed all the time

(insulin production) only one or a few genes copied at a time, as needed not all products needed by every cell all the time much DNA is non-coding

Concept Check 5 Which region of mRNA contains the Shine-Dalgarno sequence? a. 5 untranslated region c. 3 untranslated region b. Protein-coding region d. All three regions

5 untranslated region

Processing 3 main steps

5' cap, poly (A) tail, RNA splicing

microRNA (miRNA)

A class of very small and abundant RNA molecules, termed microRNAs (miRNAs) RNA interference, inhibits translation of mRNA

RNA polymerase IV

A fourth RNA polymerase, named RNA polymerase IV, has been found in plants. It functions in the nucleus and transcribes siRNAs that play a role in DNA methylation and chromatin structure.

Concept 3

A transcription unit is a piece of DNA that encodes an RNA molecule and the sequences necessary for its proper transcription. Each transcription unit includes a promoter, an RNA-coding region, and a terminator.

modified base

A unique feature of tRNA is the presence of rare modified bases. All RNAs have the four standard bases (adenine, cytosine, guanine, and uracil) specified by DNA, but tRNAs have additional bases, including ribothymine, pseudouridine (which is also occasionally present in snRNAs and rRNA), and dozens of others.

small nuclear ribonucleoprotein (snRNP)

Additional classes of RNA molecules are found in the nuclei of eukaryotic cells.

Concept 15

All tRNAs are similar in size and have a common secondary structure known as the cloverleaf. Transfer RNAs contain modified bases and are extensively processed after transcription in both bacterial and eukaryotic cells.

anticodon

At the 3' end attached to the amino acid. At the 5' end of the tRNA is a set of three nucleotides that make up the anticodon, which pairs with the corresponding codon on the mRNA during protein synthesis to ensure that the amino acids link in the correct order

Concept 5

Bacterial cells possess a single type of RNA polymerase, consisting of a core enzyme and other subunits that participate in various stages of transcription. Eukaryotic cells possess three distinct types of RNA polymerase: RNA polymerase I transcribes rRNA; RNA polymerase II transcribes pre-mRNA, snoRNAs, and some snRNAs; and RNA polymerase III transcribes tRNAs, small rRNAs, and some snRNAs.

RNA-induced silencing complex (RISC)

Both siRNA and miRNA molecules combine with proteins to form an RNA-induced silencing complex

downstream

End of transcription

Concept 13

Eukaryotic pre-mRNAs are processed at their 5 and 3 ends. A cap, consisting of a modified nucleotide and several methyl groups, is added to the 5 end. The cap facilitates the binding of a ribosome, increases the stability of the mRNA, and may affect the removal of introns. Processing at the 3 end includes cleavage downstream of an AAUAAA consensus sequence and the addition of a poly(A) tail.

5 splice site and 3 splice site

One end of the intron is referred to as the 5 splice site, and the other end is the 3 splice site

Concept 14

Introns in nuclear genes contain three consensus sequences critical to splicing: a 5 splice site, a 3 splice site, and a branch point. Splicing of pre-mRNA takes place within a large complex called the spliceosome, which consists of snRNAs and proteins.

pre-messenger RNA (pre-mRNA)

Large precursor molecules, which are termed pre-messenger RNAs (pre-mRNAs), are the immediate products of transcription in eukaryotic cells. Modified in nucleus to become whatever we transcribe (amino acids)

Concept 10

Many eukaryotic genes contain exons and introns, both of which are transcribed into RNA, but introns are later removed by RNA processing.The number and size of introns vary from gene to gene; they are common in many eukaryotic genes but uncommon in bacterial genes.

messenger RNA (mRNA)

Messenger RNA (mRNA) carries the coding instructions for polypeptide chains from DNA to the ribosome template for assembling amino acids. Shuttles from nucleus

Concept 12

Messenger RNA molecules contain three main regions: a 5 untranslated region, a protein-coding region, and a 3 untranslated region. The 5 and 3 untranslated regions do not encode any amino acids of a protein.

4 steps of initiation

Promoter recognition by transcription factors, which recruit RNA polymerase Formation of transcription bubble by one of these transcription factors in the complex creation of the first bonds between rNTPs Escape of apparatus from promoter (sequence polymerase binds to, adjacent to transcription start site) apparatus will disengage

Concept 1

RNA differs from DNA in that RNA possesses a hydroxyl group on the 2-carbon atom of its sugar, contains uracil instead of thymine, and is normally single stranded. Several classes of RNA exist within bacterial and eukaryotic cells.

Concept 17

Small interfering RNAs and microRNAs are tiny RNAs produced when larger double-stranded RNA molecules are cleaved by the enzyme Dicer. Small interfering RNAs and microRNAs participate in a variety of processes, including mRNA degradation, the inhibition of translation, the methylation of DNA, and chromatin remodeling.

small nucleolar RNA (snoRNA)

Small nuclear RNAs (snRNAs) combine with small protein subunits to form small nuclear ribonucleoproteins (snRNPs, affectionately known as "snurps") Process RNA

spliceosome

Splicing takes place within a large structure called the spliceosome, which is one of the largest and most complex of all molecular complexes. The spliceosome consists of five RNA molecules and almost 300 proteins Complex of snRNA molecules and proteins combined to make snRNP

Concept 11

The discovery of introns forced a reevaluation of the definition of the gene. Today, a gene is often defined as a DNA sequence that encodes an RNA molecule or the entire DNA sequence required to transcribe and encode an RNA molecule.

template strand

The nucleotide strand used for transcription is termed the template strand.

nontemplate strand

The other strand, called the nontemplate strand, is not ordinarily transcribed.

RNA splicing

The other major type of modification of eukaryotic pre-mRNA is the removal of introns by RNA splicing

promoter

The promoter is a DNA sequence that the transcription apparatus recognizes things needed to be transcribed and binds. tells which strand to read, what direction to go, which nucleotide to start with, and not transcribed itself

5' untranslated region - sometimes called the leader

a sequence of nucleotides at the 5 end of the mRNA, does not encode any of the amino acids of a protein. functions in initiation of translation In bacterial mRNA, this region contains a consensus sequence called the Shine-Dalgarno sequence, which serves as the ribosomebinding site during translation

codon

a set of three nucleotides

Concept Check 3 What is the function of the sigma factor?

The sigma factor recognizes the promoter and controls the binding of RNA polymerase to the promoter.

Concept Check 2 What is the difference between the template strand and nontemplate strand?

The template strand is the DNA strand that is transcribed into an RNA molecule, whereas the nontemplate strand is not transcribed.

RNA polymerase

a single enzyme—RNA polymerase— carries out all the required steps of transcription but, on closer inspection, the processes are actually similar different for bacteria; large multi-part enzymes, more than a dozen subunits

5 cap

This capping consists of the addition of an extra nucleotide (guanine) at the 5 end of the mRNA and methylation by the addition of a methyl group (CH3) to the 5' end of pre-mRNA, functions to initiate translation (7 methyl guanosine)

Concept 8

Transcription ends after RNA polymerase transcribes a terminator. Bacterial cells possess two types of terminator: a rho-independent terminator, which RNA polymerase can recognize by itself; and a rho-dependent terminator, which RNA polymerase can recognize only with the help of the rho protein.

Concept 7

Transcription is initiated at the start site, which, in bacterial cells, is set by the binding of RNA polymerase to the consensus sequences of the promoter. No primer is required. Transcription takes place within the transcription bubble. DNA is unwound ahead of the bubble and rewound behind it.

Concept 9

When a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein, the two are said to be colinear. In eukaryotes, not all genes are colinear with the proteins that they encode.

Concept 2

Within a single gene, only one of the two DNA strands, the template strand, is usually transcribed into RNA.

RNA interference (RNAi)

a powerful and precise mechanism used by eukaryotic cells to limit the invasion of foreign genes (from viruses and transposons) and to censor the expression of their own genes

hairpin

a secondary structure that forms when sequences on the same strand are complementary and pair with one another.

Transcription process is 3 steps

initiation, elongation, and termination

DNA transcription direction

is always a 5'to 3' (identical to DNA replication

small nuclear RNA (snRNA)

join with small nuclear proteins to form small nuclear ribonucleoproteins. Used in RNA processing

small interfering RNA (siRNA)

microRNAs (miRNAs) and small interfering RNAs (siRNAs), are found in eukaryotic cells and carry out RNA interference (RNAi), a process in which these small RNA molecules help trigger the degradation of mRNA or inhibit their translation into protein.

intron

noncoding regions (inverting sequences)

Termination

recognize the end of transcription unit and serration of RNA from DNA template (in prokaryotes, inverted repeats from hairpin loop)

topoisomerase

relives strain so DNA doesn't break in half

Repressors

sequences where proteins bind that decrease the rate of transcription

Enhancers/Activators

sequences where proteins bind that increase rate of transcription can be far from the promoter easy to forget DNA has a 3D structure

transfer RNA (tRNA)

serves as the link between the coding sequence of nucleotides in the mRNA and the amino acid sequence of a polypeptide chain. brings an amino acid to the ribosome during translation and hooks it into the polypeptide chain (reads and translates)

gene

set of nucleotides that code for amino acids to make a protein

consensus sequence

short stretches of common nucleotides important regulatory regions

3 untranslated region

sometimes called a trailer,don't code for a protein, increase stability, helps in splicing a sequence of nucleotides that is at the 3 end of the mRNA and not translated into protein

piwi-interacting RNAs (piRNAs)

suppress expression of transposable elements

alternative splicing

the same pre-mRNA can be spliced in more than one way to yield multiple mRNAs 60% of all human genes alternative splices

RNA polymerase II

transcribes pre-mRNAs, snoRNAs, some snRNAs

RNA polymerase I

transcribes rRNA

RNA polymerase III

transcribes small RNA molecules—specifically tRNAs, small rRNA, some miRNAs, and some snRNAs

Transcription

transfer of information from a double-stranded template DNA molecule to a single-stranded RNA molecule First step in the transfer of genetic info from DNA to protein (genotype to phenotype), occurs throughout cell cycle