LS7A Midterm 2

Name four ways in which pre-mRNA is modified after transcription

- Before translation, pre-mRNA can be extensively altered, unlike bacterial cells in which there is little time for modification since transcription and translation occur simultaneously - Varies modifications: + Addition of a 5' cap + 3' cleavage and addition of poly(A) tail + RNA splicing + RNA editing

Pre-mRNA

- In eukaryotes, pre-mRNA is needed as an intermediate before mature mRNA is formed; it is transcribed first from the DNA and then processed to produce mature mRNA (RNA molecules that are completely processed and ready for translation) - in bacteria, mRNA is transcribed directly from DNA as transcription and translation take place simultaneously

Why was it clear that DNA could not directly encode proteins?

- In eukaryotic cells, DNA resides in the nucleus while protein synthesis takes place in the cytoplasm - Therefore, it was understood early on that there must be some additional molecules that contributes to the transfer of genetic information

pre-mRNA modification: Addition of the 5' Cap

- The 5' cap is a structure that is added at the 5' end - the addition of the cap takes place quickly after the initiation of transcription - functions in the initiation of translation - cap-binding proteins recognize the cap and attach to it, which then allows a ribosome to attach; ribosome moves downstream along mRNA until it reaches the start codon and translation begins! - this cap can also increase stability and influence the removal of introns - The initial step is carried out by an enzyme associated with RNA polymerase II; Thus RNA molecules transcribed by RNA polymerase I & III are not capped)

Codon

- The set of three nucleotides that encodes a specific amino acid in a protein - found on mature mRNA

RNA interference (RNAi)

- a mechanism used by eukaryotic cells to limit the invasion of foreign genes (from viruses and transposons), and censor the expression of the cells own genes - triggered by DOUBLE-stranded RNA molecules

How are tRNA genes processed in the cell?

- all tRNAs are processed in different ways - bacterial tRNAs are usually transcribed together as one large precursor tRNA, which is then cut up into pieces (each containing a single tRNA) + additional nucleotides may then be removed one at a time from the 5' and 3' ends (known as TRIMMING) + eukaryotic tRNAs are processed in a similar manner: large precursors are cleaved, trimmed, and modified to produce mature tRNAs

tRNA structure

- all tRNAs are similarly structured, which is essential to tRNA function - many of the nucleotides in tRNA molecules are complementary to each other by intramolecular hydrogen bonds + This causes tRNA to have a cloverleaf structure, which has 4 major arms

Exons

- coding regions in eukaryotic genes

How many rRNA gene types are in eukaryotic versus bacterial cells?

- eukaryotic cells possess 2 types of rRNA genes: a large gene, and a small gene (encodes different sized rRNA molecules) - bacterial cells contain 3 rRNAs that are all encoded by a single type of gene

Messenger RNA

- functions as the template for protein synthesis - it carries genetic information from DNA to a ribosome and helps assemble amino acids in their correct order

What occurs within the ribosome?

- genetic instructions contained in mRNA are translated into the amino acid sequences of polypeptides - tRNAs help to carry this genetic information to the ribosome

mature mRNA

- made up of codons - both prokaryotic and eukaryotic mRNAs contain three primary regions: + 5' untranslated region + protein-coding region + 3' untranslated region

Introns

- noncoding regions in eukaryotic genes - do NOT code for proteins - also known as "intervening sequences" - after transcription, introns are removed by splicing - common in eukaryotic genes but rare in bacterial genes; more common and longer than exons - the size and number of introns appears to be related to increasing organismal complexity

Describe the structure of the ribosome

- one of the most abundant molecular complexes in the cell - typically contain about 80% of the total cellular RNA - complex structures made up of over 50 proteins and RNA molecules - consists of 2 subunits: large & small ribosomal subunit

Protein-coding region

- one of the primary regions of a mature mRNA - consists of the codons that specify the amino acid sequence of a protein - begins with a start codon and ends with a stop codon

5' untranslated region

- one of the primary regions of a mature mRNA, sometimes call the 'leader' - is a sequence of nucleotides at the 5' end that does not encode any amino acids of the protein - In bacterial mRNA, this region contains a CONSENSUS sequence (Shine-Dalgarno), which is the ribosome-binding site during translation - Eukaryotic mRNA does not have a consensus sequence, instead ribosomes bind to a modified 5' end

3' untranslated region

- one of the primary regions of a mature mRNA, sometimes called the 'trailer' - a sequence of nucleotides at the 3' end not translated into protein - affects the stability of mRNA and the translation of the mRNA protein-coding sequence

Group I introns

- self-splicing because they catalyze their own removal - found in some rRNA genes - lengths vary, but all of these introns fold into a common secondary structure with 9 looped stems

Group II introns

- self-splicing, but mechanism differs from group I introns, similar to spliceosomal-mediated splicing of nuclear genes - found in some protein-encoding genes of mitochondria, chloroplasts, some eubacteria - fold into secondary structures (different from group I secondary structure); splicing generates a lariat (specific structure)

Transfer RNA (tRNA)

- serves as a link between the genetic code in mRNA and the amino acids that make up a protein - each tRNA attaches to a particular amino acid and carries it to the ribosome, where the tRNA adds its amino acid to the growing polypeptide chain + the location on the chain where the tRNA attaches the amino acid is specified by the genetic instruction in the mRNA - each tRNA can only attach to one type of amino acid

Name the three major classes of small RNA molecules - what are their main functions?

- small interfering RNAs (siRNAs) - microRNAs (miRNAs) - Piwi-interacting RNAs (piRNAs) + These are all found in many eukaryotes and are responsible for various functions: regulation of gene expression, defense against viruses, suppression of transposons, and modification of chromatin structure

Describe the rRNA processing in eukaryotic cells

- small nucleolar RNAs (snoRNAs) help to cleave and modify eukaryotic rRNAs and assemble the processed rRNA into mature ribosomes - similar to the snRNAs that take part in pre-mRNA splicing, snoRNAs associate with proteins to form ribonucleoprotein particles (snoRNPs) - the processing of rRNA and ribosome assembly takes place in the nucleolus. Binding occurs in the cytosol

What are the functions of eukaryotic mRNA modifications?

- the removal of introns - takes place in the nucleus before the RNA moves to the cytoplasm (must be done in order for mRNA to move to cytoplasm) - incompletely spliced RNAs remain in the nucleus until splicing is complete or until pre-mRNA is degraded

How do double-stranded RNAs come about?

- the transcription of inverted repeats into an RNA molecule that base pairs with itself to form dsRNA - the simultaneous transcription of 2 different RNA molecules that are complementary to each other, which then pair - by infection by viruses that create dsRNA

How are changes in RNA sequences brought about if the modified sequence doesn't come from a DNA?

- there are a variety of mechanisms - guide RNAs (gRNAs) can sometimes play a crucial role; they contain sequences that are partly complementary to segments of the pre-edited RNA + after pairing up to the mRNA, the mRNA undergoes cleavage and nucleotides are added, deleted, or altered according to the gRNA template - then mature mRNA is released with new sequence - sometimes enzymes can bring about conversions

Transfer RNA introns

- uses another mechanism of splicing different from other 3 groups, and is NOT self-splicing; uses enzymes to cut and reseal RNA - found in tRNA genes

Role of DNA

-Complete instructions for making proteins -Type of molecule: nucleic acid -number of strand: 2 -DNA sugar deoxyribose -found in the nucleus -only one type of DNA(DNA

Primary Structure

-simplest level of protein structure - the sequence of amino acids in a polypeptide chain

DNA Replication steps

1. The strands of he double helix DNA separate 2. Enzymes catalyze the synthesis of new DNA in the 5' to 3' direction, using the original strands as models or templates for the complementary strands 3. Two complete DNA molecules, each an exact cope

How is mRNA template strand of DNA read?

5'-3' 5 prime to 3 prime Ribosome reads it

Tertiary structure

A polypeptide folds into a compact, 3-D shape stabilized by interactions between R groups of amino acids to form a biologically active protein -the shape of a globular protein -disulfide bonds between R groups

Endocytosis

A vesicle can bud off from the plasma membrane, enclosing material from outside the cell and bringing it into the cell interior. Reverse of exocytosis

Provide the complementary sequences of a given sequence of DNA

AT & GC 5'-TGC-3' = 3'-ACG-5' 5'-ATCCG-3' = 5'-CGGAT-3' GATTACA = TGTAATC

Describe how gel electrophoresis separates nucleic acid fragments based on size

As the gel runs, shorter pieces of DNA will travel through the pores of the gel matrix faster than longer ones. After the gel has run for awhile, the shortest pieces of DNA will be close to the positive end of the gel, while the longest pieces of DNA will remain near the wells. By comparing the bands in a sample to the DNA ladder, we can determine their approximate sizes.

Describe the structure and organization of DNA

At the molecular level, there are 4 nucleotide bases: adenine, guanine, cytosine, and thymine, which are all linked to a ribose sugar and phosphate backbone higher levels of organization are necessary, such as the wrapping of DNA around histone proteins, forming a nucleosome core. These nucleosomes are further wrapped around each other to condense into what we call a chromatin fiber. The chromatin fiber condenses into what we identify as a chromosome in eukaryotic cells. This level of condensation only exists during mitosis and meiosis, where it is important that there be no stray bits of DNA floating around. When you move, you make sure to put everything into boxes, and that is exactly what the cell is doing. When it divides, it wants to make sure each daughter cell has the right amount and type of DNA necessary for survival. However, most of the life of the cell is spent outside of mitosis (in interphase), so the levels of packaging are quite variable. Depending on the needs of the cell, certain regions of the chromosome are heavily packaged to silence them and prevent transcription from taking place, while other regions that make important proteins are loosely packaged and open for RNA transcription. This variable packaging process is important for regulating RNA transcription of various genes. Another level of organization in eukaryotic cells is the presence of the nucleus. The fact that all the DNA in the cell is found only in the nucleus, though some exists in the mitochondria Prokaryotic cells, with all due respect, are like our sloppy cousins because they lack the levels of organization that eukaryotes do. They do not have a nucleus, so their DNA, RNA, and ribosomes can all easily interact. In fact, their transcription and translation machinery occurs simultaneously, which potentially leads to damaging consequences if there are any errors in RNA transcription. Their chromosomes are also not tightly packaged because prokaryotes lack histones, and they typically have extrachromosomal plasmids that can integrate into the chromosome or can be removed. It almost seems like prokaryotes were designed to make mistakes because, unlike most eukaryotes, survival of prokaryotes is more heavily biased toward success of the species. Therefore, mutations that lead to death of specific individuals are more tolerated in prokaryotes than in eukaryotes, primarily due to the shorter life span of prokaryotes. Prokaryotes are more accepting of death, like emo vampires.

A particular triplet of bases in the template strand of DNA is 5-'TGA-3'. Which of the following is the anticodon component of the tRNA that binds the mRNA codon transcribed from this DNA? a. 3'ACU5' b.3'AGU5' c.3'UCT5' d.3'UCA5'

B. 3'-AGU-5'

Process of Splicing

Before splicing begins, you have an intron that lies between an upstream exon (towards 5' end) and a downstream exon (towards 3' end) 1. the pre-mRNA is cut at the 5' splice site (between upstream exon and intron) - this frees exon 1 from the intron, and the 5' end of the intron folds back on itself, constructing a LARIAT, attaching to the branch point 2. A cut is made at the 3' splice site (between downstream exon and intron), while simultaneously the 3' end of the upstream exon becomes covalently attached (spliced) to the 5' end of the downstream exon - The intron is released as a lariat + Eventually the intron is degraded by nuclear enzymes + The mature mRNA is then exported to the cytoplasm to be translated

Compare and contrast the structures of DNA and RNA

DNA is a long polymer with deoxyriboses and phosphate backbone. Having four different nitrogenous bases: adenine, guanine, cytosine and thymine. RNA is a polymer with a ribose and phosphate backbone. Four different nitrogenous bases: adenine, guanine, cytosine, and uracil.

In a population of organisms, beneficial and harmful random mutations are retained or eliminated through the process of A.) Conservation. B.) Folding. C.) Expression. D.) Translation. E.) Selection.

E.) Selection

Transcription in Eukaryotes

Occurs in the nucleus does not occur simultaneously because the mRNAs must be exported from the nucleus before ribosomes can get at them. Eukaryotes have 3 RNA polymerase that handles transcription and is way more complex than prokaryotes In eukaryotes, the RNA polymerase itself can't actually initiate transcription. Instead, a variety of other proteins and transcription factors are required to help recruit the RNAP to the promoter (this is partly because eukaryotic DNA is coiled around histones so needs to be "opened up" for a polymerase to bind it). B/c of the variety of factors at play, regulation is also much more complex. In eukaryotes, termination is dictated by a terminator sequence and a poly-A signal. Eukaryotic Pol II is made up of 10 subunits

Transcription of Prokaryotes

Prokaryotic transcription occurs in the cytoplasm (by virtue of the fact they don't have a nucleus). Transcription and translation often occur simultaneously in prokaryotes. Prokaryotes have one RNA polymerase that handles all transcription.The prokaryotic RNA polymerase is much simpler structurally than the eukaryotic polymerases. Transcription initiation is also much simpler in prokaryotes. Prokaryotes have different proteins called σ factors which bind to promoter sequences and start transcription (they are part of the RNA polymerase, which is often considered as its "core" polymerase + a σ factor). Different σ factors bind different promoters and are responsible for a different set of genes, often functionally related. Expression is highly regulated at this level. Prokaryotic termination is relatively simple with only two different mechanisms, Rho-dependent and Rho-independent termination.

Exocytosis & Endocytosis

Provide a way to move material into and out of cells without passing through the cell membrane.

Secondary structure

The alpha helix, beta-pleated sheets, or triple helix forms by hydrogen bonding between the atoms in the peptide bonds along the chain -beta-pleated sheet

Discuss the central dogma of molecular biology

The central dogma of molecular biology describes the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein. Transcription is the synthesis of an RNA copy of a segment of DNA. The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes. The central dogma states that the pattern of information that occurs most frequently in our cells is: From existing DNA to make new DNA (DNA replication?) From DNA to make new RNA (transcription) From RNA to make new proteins (translation).

Splicesosome

The large molecular complex where splicing takes place - consists of five RNA molecules (snRNPs) and about 300 proteins! - RNA components are small nuclear RNAs (snRNAs), which associate with proteins to form small ribonucleoprotein particles (snRNPs) + key catalytic steps in splicing process are carried out by snRNAs + Each snRNP contains a single snRNA molecule and multiple proteins

Role of RNA

Transfer info Protein production -Type of molecule: nucleic acid - 1 strand -RNA Sugar: ribose - found in nucleus and cytoplasm -mRNA/tRNA/rRNA

Quaternary structure

Two or more protein subunits combine to form a biologically active protein -a protein with two or more peptide chains

Exocytosis

When a vesicle fuses with the plasma membrane and depositing its contents into the extracellular space is referred to as

Template DNA 5'TGA3' Whats the mRNA? tRNA?

mRNA 3'-ACU-'5 tRNA 5'-UGA-3'

Operon

multiple gene or coding sequences in mrna molecule in prokaryotes