Cell Biology Exam 1 Study Guide Part 2

Question 1

3: Know the general packaging of DNA in cells and the chromosome structure related to gene expression (Bacterial and Eukaryotes)

Answer 1

DNA must be packed to fit cells, very long molecules of DNA must be fit into the cell and, in the case of eukaryotes, into the nucleus, Bacterial Chromosomes- Circular chromosome the DNA packaged somewhat similarly to the chromosomes of eukaryotes, the DNA molecules is localized to a region of the bacterial cell called the nucleoid; Eukaryotes package DNA in Chromatin and Chromosomes- chromatin: bound to proteins, DNA is converted, at division chromatin fibers condense in chromosome, Histones bind the DNA to package it, 5 main types of histones, Chromatin contains equal numbers of all these except H1 present in about half the amount of the others

Question 2

3: Chromosome structure related to gene expression (Nucleosomes, Transcription and Packaging)

Answer 2

A histone octamer forms the nucleosome core, histone H1 is not part of the octamer, histone H1 is though to be associated with the linker DNA found between core particles; Transcription- transcriptionally active DNA is less tightly packed than inactive DNA, cells can tightly regulate the portions of chromatin that are active or inactive thorugh altering histones, each histone has a protruding tail that can be tagged by the addition of methyl, acetyl, phosphate, or other groups

Question 3

3: Chromosomal Structure related to gene expression (Histone code, Heterochromatin and Euchromatin)

Answer 3

histone tails can be modified and the pattern of modification governs the activity of the nucleosomes/DNA, acetylation- adds acetyl group to lysine of histone tails relaxing chromatin deacetylation- condenses chromatin by removing acetylated tails from histones, methylation- of histones can activate or repress expression depending on location/pattern, recruitment of other regulatory proteins; Heterochromatin- sections of chromatin so highly compacted they show up as dark spots in micrographs, compacted not expressed, Facultative heterochromatin- can be converted to euchromatin, and vice versa, heterochromatin is permanently compacted , known as constituitive heterochromatin, it serves structural functions within chromosomes, 2 important types of constituitives heterochromatin are centromeres and telomeres; euchromatin- more loosely packed, diffuse chromatin relaxed, active expression

Question 4

3: Structures of chromosomes (Centromeres and Telomeres)

Answer 4

Centromeres appear as constriction of chromosomes, centromere DNA is bound by a complex of proteins and serves important functions, Centromeres maintain sister chromatid cohesion during mitosis and meiosis; Telomeres found at the tips of chromosomes, contain highly repetitive DNA sequences, protect chromosome ends from degradation during each round of DNA replication

Question 5

17: What are consensus sequences?

Answer 5

Sequence varies among bacterial species but contains recognizable similar sequences

Question 6

17: Know the basics of transcription

Answer 6

New DNA molecule derived from parent molecule and other strand is newly synthesized-semiconservative replication, very similar in prokaryotes and eukaryotes, replication forks - replication begins and then proceeds in bidirectional fashion- away from origin, at the origin of replication 2 replication forks synthesize DNA in opposite directions forming replication bubble. DNA helicase, DNA topoisomerase, SSBs, primase DNA polymerase, DNA ligase are proteins invoed in replication, replisome- proteins closely associated in large complex, Replisome moves along DNA it must accomodate the fact that DNA is being produced on both leading and lagging strands, DNA helicase unwinds DNA strands as replication proceeds and it breaks the H bonds between the 2 strands. To stabilize single strands of DNA, SSB binds to unwound regions. Primase synthesize short RNA using DNA as a template, later replaced with DNA sequences, DNA polymerase- enzyme that can copy DNA molecules, can’t start without RNA and the 3’OH, DNA polymerase can add nucleotides only to the 3’ end of an existing nucleotide chain, Incoming nucleotides are added to the 3’ hydroxyl end of the growing DNA chain, so elongation occurs in the 5’ to 3’ direction, DNA synthesized in 5’ to 3’ direction but 2 strands of the double helix are oriented in opposite directions. Lagging strand- synthesized in discontinuous fragments called Okazaki fragments, then joined by DNA ligase to form a continuous new 3’ to 5’ DNA strand, Leading strand synthesized as a continuous chain, RNA primers are replaced with DNA by second polymerase, adjacent fragments are joined together by DNA ligase, Unwinding of helix would create too much supercoiling if not for topoisomerases that break and ligate the DNA to remove supercoiling

Question 7

17: What is polymerase proofreading mechanisms?

Answer 7

Almost all DNA polymerase have a 3’ -> 5’ exonuclease activity which is used as proofreading to correct mistakes during replication. Exonucleases degrade nucleic acids from the ends of the molecule, the exonuclease activity of DNA polymerase allows it to remove incorrectly base-paired nucleotides and incorporate the correct base

Question 8

17: What is the end of replication problem and how is it solved? What strand is involved? What is the general mechanism?

Answer 8

Telomeres solve the DNA End-replication problem, linear DNA molecules have a problem in completing DNA replication on the lagging strand because primers are required, Each round of replication would end with the loss of some nucleotides from the ends of each linear molecule, Eukaryotes solve this problem with telomeres- highly repeated sequences at the ends of chromosomes, a polymerase called telomerase can catalyze the addition of repeats to chromosome ends, This enzyme-bound RNA acts as a template for adding the DNA repeat sequence to the telomere ends, Telomere capping proteins bind to the exposed 3’ end to protect from degradation, In multicellular organisms, telomerase function is restricted to stem and germ cells, telomerase has been detected in almost all types of human cancers

Question 9

17: What are some examples of mutations in the DNA and their effects?

Answer 9

Several mechanisms are in place to ensure minimal mistakes on DNA: Accuracy- Incorporation of correct nucleotide (complementary base pairing), Immediate proofreading- DNA polymerase proofreading mechanisms, Post-replication repair- Mismatch, Double strand Breaks; Trinucleotide repeats, which are susceptible to strand slippage, in this process DNA polymerase replicates a short stretch of DNA twice due to repeats matching with each other. Strand slippage; Errors remaining after DNA replication are repaired by excision repair- abnormal nucleotides are removed and replaced, a protein detects the mismatch, a repair endonuclease introduces a nick in the new strand, an exonuclease removes the incorrect nucleotides from the nicked strand, and these are replaced with the correct sequence, DNA ligase seals the DNA backbone; Double-strand breaks cleave DNA into 2 fragments, two pathways re used: nonhomologous end-joining and homologous recombination; Nonhomologous end joining- uses a set of proteins that bind to ends of broken DNA fragments and join them together, this is error prone because nucleotides can be lost from the broken ends and there is no way to ensure the correct DNA fragments are joined; Homologous recombination- the process of crossing over, genetic exchange between DNA molecules with extensive sequence similarity, If DNA molecule from one chromosome is broken the homologue is available as a template to guide accurate repair

Question 10

18: What is the central dogma of molecular biology?

Answer 10

The principle of directional information flow from DNA to RNA to protein

Question 11

18: What is needed for Transcription? What are the steps?

Answer 11

Genetic code- the relationship between the DNA base sequence and the linear order of amino acids in the protein products, coded info of DNA is used to guide production of RNA and protein molecules, there are 4 DNA bases and 20 amino acids, A triplet code- combinations of 3 bases specify amino acids would have 64 possible combinations, more than enough for all 20 amino acids, the synthesis of RNA molecules is called transcription, DNA serves as template for the synthesis of RNA molecule then directs the synthesis of protein product, Translation is synthesis of proteins using the information in RNA

Question 12

18: What are the differences between Prokaryotes and Eukaryotes? Make a table

Answer 12

Bacteria (prokaryotes)- don’t have nuclear envelope, translation of mRNA can begin before its transcription is completed; Eukaryotes- compartmentalization leads to spatial separation of transcription and translation

Question 13

18: What are promoters?

Answer 13

RNA polymerase binds to a DNA promoter site- sequence of several dozen base pairs that determine where RNA synthesis will start, the terms upstream and downstream refer to sequences located toward the 5’ to 3’ end of the transcription unit respectively, the promoter is upstream of the transcribed sequence

Question 14

18: What are some types of RNA in the cell? Are they all translated? What are their functions?

Answer 14

mRNA-translated into protein, rRNA- integral component of ribosome, tRNA- molecules serve as intermediaries brining amino acids to the ribosome (functional RNA)

Question 15

18: What is the genetic code? What are some of its characteristics?

Answer 15

gene is written in language of 3 letter words, inserting or deleting a nucleotide causes the rest of the sequence to be read out of phase- this is a shift in the reading frame, Frameshift mutation- mutations that cause insertion or deletion of a nucleotide causing a shift on the reading frame; 64 combinations of nucleotide triplets and only 20 amino acids, genetic code is degenerate- particular amino acid can be specified by more than 1 triplet, unambiguous- every codon has 1 meaning; nonoverlapping- reading frame advances 3 nucleotides at a time

Question 15

18: What is the genetic code? What are some of its characteristics?

Answer 15

gene is written in language of 3 letter words, 64 combinations of nucleotide triplets and only 20 amino acids, genetic code is degenerate- particular amino acid can be specified by more than 1 triplet, unambiguous- every codon has 1 meaning; nonoverlapping- reading frame advances 3 nucleotides at a time

Question 16

18: What is the reading frame? How do you identify the reading frame?

Answer 16

inserting or deleting a nucleotide causes the rest of the sequence to be read out of phase- this is a shift in the reading frame, Frameshift mutation- mutations that cause insertion or deletion of a nucleotide causing a shift on the reading frame;

Question 17

18: Do all codons code for amino acids?

Answer 17

Only 61 of them specify the addition of specific amino acids to a growing polypeptide chain, 1 of them AUG- start codon, 3 of them UAA, UAG, UGA- stop codons, terminate polypeptide synthesis and don’t code for amino acids

Question 18

18: What is the key difference between DNA replication and mRNA synthesis (Transcription)

Answer 18

In mRNA synthesis only 1 DNA strand is copied- template strand, used as a template to make the mRNA; coding strand- the genetic information is the same as the mRNA except that T in the DNA are U in the mRNA

Question 19

18: What differences and similarities do RNA and DNA have? What are the key carbon in each molecule?

Answer 19

RNA is chemically similar to DNA but contains ribose instead of deoxyribose, also has base uracil instead of thymine; RNA is usually single stranded

Question 20

18: What is RNA processing? In what organisms does it happen? What is the purpose for each? Know the general mechanisms for each.

Answer 20

primary transcript or pre-mRNA- newly produced RNA molecule, must undergo RNA processing- chemical modification before it can function in the cell, eukaryotic transcripts must be exported from the nucleus to be translated, substantial processing occurs in the nucleus before export, pre-mRNAs are processed by removal of sequences and addition of 5’ caps and 3’ tails, the C-terminal domain of one of the subunits of RNA polymerase 2 acts as a platform for protein complexes involved in processing

Question 21

18: How is termination in general different in prokaryotes and eukaryotes?

Answer 21

Prokaryotes (bacteria): Intrinsic termination is most common, RNA molecules contain short G-rich sequence followed by several U’s at the end of the transcript, The GC region in the RNA form a hairpin loop pulling the RNA molecule away from the DNA, Then the weaker bonds between the U’s and A’s of the template strand break releasing the RNA; Eukaryotic: RNA polymerases move along the DNA synthesize complementary RNA, for RNA polymerase 2, transcripts are cleaved at specific site before transcription ceases, the cleavage site is 10-35 nucleotides downstream of a AAUAAA sequence in the RNA, the cleavage site of polymerase 2 transcripts it also the site for addition of poly (A) tail, this is a string of adenine nucleotides added to the 3’ end of most eukaryotic mRNAs, RNA cleavage is more important than termination of transcription in determining the 3’ end of the transcript

Question 22

19: What are the main players in translation?

Answer 22

Ribosomes carry out the process of polypeptide synthesis, 4 sites: mRNA-binding site, the A site, the P site, the E site; tRNA molecules align the amino acids in the correct order; Aminoacyl-tRNA synthetases attach amino acids to their appropriate tRNA molecules

Question 23

19:What are the sequences within a mRNA and role in translation?

Answer 23

Sequence of codons in mRNA directs the order of amino acids in the polypeptide, mRNA must first be exported from the nucleus to the cytoplasm, the 5’ end of the message 5’UTR is an untranslated sequence that aids in mRNA interaction to the ribosome

Question 24

19: What are the differences between monocistronic and polycistronic mRNAs?

Answer 24

Monocistronic- most mRNAs in eukaryotes encode just 1 polypeptide; Polycistronic- in bacteria and archaea encoding several polypeptides usually with related functions. These polycistronic transcription units are called operons

Question 25

19: What are the general steps of transcription and what are the 3 phases?

Answer 25

mRNA is read by ribosomes the 5’ to 3’ direction, translation begins at the N-terminus of the polypeptide and adds amino acids to the growing chain until the C-terminus is reached. 3 stages: initiation, elongation, termination

Question 26

19: How is the peptide bond made? Between which sites? Who does the bond?

Answer 26

During elongation- binding of aminoacyl tRNA to the ribosome A site brings new amino acid into position, Peptide bon formation links amino acid to the growing polypeptide. the polypeptide is transferred from the P-site to the A-site where polypeptidyl transferase makes the peptide bond

Question 27

19: What drives the movement of the ribosome? In what direction?

Answer 27

Translocation- the ribosome move the 3’ of the mRNA advancing 3 nucleotides through. The A site is bound by factors that assist on the translocation; the tRNA with the polypeptide moves to P; the uncharged tRNA moves to E to exit

Question 28

19: What drives the end of translation?

Answer 28

Codons are read on the mRNA one after the other until a stop codon arrives at the A site, stop codons are recognized by protein release factors rather than tRNAs, once release factors bind to the stop codons, translation is terminated through release of the completed polypeptide

Question 29

19: What are polyribosomes?

Answer 29

a cluster of such ribosomes, these maximize the efficiency of mRNA utilization

Question 30

19: What are some mutations that affect polypeptides? What do they do? Be ready to identify them given a sequence?

Answer 30

Silent: change codon on mRNA but still codes for original amino acid due to flexibility of genetic code, applies for substitution by similiar amino acids that does not change gene product function; Missense: change codon on mRNA codes for different amino acid that in the mRNA, effect depends on change can go from no function to lower or higher function; Nonstop: change stop codon to amino acid codon, longer transcript is made, effect depends on change can go from no function to lower or higher function; Nonsense: change amino acid codon to stop codon, shorter transcript usually nonfunction of the new gene product; Frame shift mutations: Changes the reading frame of the message, arise from base-pair insertions or deletions, or a combination of these; Nonsense, nonstop, and missense codons can also arise from frameshift mutations

Question 31

19: How is nuclear import and export regulated?

Answer 31

Each protein released to cytosol has localization signals specific to the destination, Nuclear pores are specialized channels in the nuclear envelope where inner and outer membranes are fused, They provide direct contact between the cytosol and the nucleoplasm (interior nuclear space), They are lined with a protein structure called the nuclear pore complex (NPC) , The NPC is built from about 30 different proteins called nucleoporins; the transporter is likely involved in moving molecules across the nuclear envelope

Question 32

20: How do operons work in general?

Answer 32

Operon- gene located contiguously on a stretch of DNA and are under the control of one promoter to which the RNA polymerase bind to initiate transcription; Inducible operons- gene expression is off unless activated, repressible operons- gene expression is on unless repressed

Question 33

20: How do distal regulators influence promoters?

Answer 33

Silencer- DNA sequence capable of binding transcription regulation factors called repressors, Repressors- DNA or RNA binding protein that inhibits the expression of one or more genes; Enhancer- DNA sequence that can be bound by proteins to increase the transcription of a particular gene; Activators- DNA binding proteins that bind to enhancers or promoter-proximal elements to increase gene transcription; Insulators- sometimes employed to prevent an enhancer or silencer from affecting the wrong genes

Question 34

20: How does chromatin modifications affect gene regulation?

Answer 34

dramatically affect gene expression, many transcriptional activators recruit Histone Acetyl transferases which adds acetyl groups resulting in euchromatin, many transcriptional repressors recruit histone deacetylases which remove acetyl groups resulting in heterochromatin

Question 35

20: How do differentiated cells are similar and different to each other?

Answer 35

distinguish from each other based on difference in appearance and protein products, indicate differential gene expression plays a central role in creating differentiated cells, acquire unique sets of regulatory proteins specific to that cell type, combination of these tissues specific regulators is ultimately what controls differential gene expression, alterations in tissue specific regulatory proteins can change differentiated cells into other cell types

Question 36

20: How does cell memory work?

Answer 36

Differentiated cells give rise to cells of the same cell type, a transient signal signal induces differentiation of the parent cells, that signal induces expression of regulator protein, regulator protein enhances expression of its own expression in addition to tissue specific gene expression, this ensure that the regulator protein will continue to be expressed in daughter cells without the initial signal

Question 37

20: What is epigenetics and how can it control gene expression?

Answer 37

stable alterations in gene expression transmitted from 1 generation to the next without any change in DNA sequence; DNA methylation: methylation of cytosine nucleotides of DNA recruit proteins that generally inhibit translation, Methylation patterns are copied to newly synthesized strands during DNA replication by maintenance methyltransferase; Histone code: modification of histones through acetylation and deacetylation, half parental histones are inherited on new strand following replication, carrying parental histone code, code copied to new histones nearby, reestablishes chromatin structure new daughter cells

Question 38

20: How can mRNA expression be regulated by other RNAs (siRNA and miRNA)?

Answer 38

A cytoplasmic ribonuclease called Dicer cleaves the double-stranded RNA into short fragments about 21–22 bp long, The resulting fragments are called siRNAs (small interfering or silencing RNAs), The siRNAs combine with a group of proteins to form an inhibitor of gene expression called RISC (RNA-induced silencing complex), in this case called the siRISC, One of the strands is degraded, and the remaining one binds the siRISC to a target mRNA by complementary base pairing , If pairing between siRNA and the mRNA is a close (or perfect) match, mRNA is degraded; MicroRNAs (miRNAs) are produced by genes found in almost all eukaryotes, These bind to and regulate expression of genes that are separate from the genes that produce the miRNAs

Question 39

20: What are some examples of Post-translational gene expression control?

Answer 39

Protein Stability- Ubiquitination and targeted degradation; Protein Activity- Modifications induce conformational changes that affect protein function

Question 40

20: Remember this summary of eukaryotic gene regulation

Answer 40

Genomic control, transcription control, RNA processing and nuclear export, Translational control, posttranslational control