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FSU / Biological Sciences / BSC 2010 / What are the three properties of rna that enable it to function as an

What are the three properties of rna that enable it to function as an

What are the three properties of rna that enable it to function as an


School: Florida State University
Department: Biological Sciences
Course: Biological Science I
Professor: Steven marks
Term: Fall 2015
Tags: BSC2010 FSU
Cost: 50
Name: Study Guide Unit 3 Exam
Description: I have taken the class notes as well as the posted notes and created an easy to remember study guide with highlighted critical test questions. (Includes the charts we need to draw on the exam, as well as other important diagrams)
Uploaded: 11/19/2015
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Unit 3 Exam Study Guide

What are the three properties of rna that enable it to function as an enzyme?

- 6 Seminal lines of inquiry:

i. Griffith- Demonstrations of bacterial transformation  

 (“r” bacteria became “s” permanently, and called this phenomenon transformation, now defined as a change in genotype and phenotype due to assimilation of foreign or external DNA)

ii. Avery McCarty and Macleod- Transforming factor is separable   (announced transforming factor -> acidic; extract from nucleus= DNA; “only DNA works transforming harmless bacteria into pathogenic bacteria” & reductionist biology separates carbohydrates, fats, proteins)

iii. Hershey and Chase- Transforming factor is DNA

 (used T2 phage “35S (proteins) or 32P (DNA) to show that  

It is a stage of transcription that promoters signal the initiation of rna synthesis?

 transforming factor = DNA)

iv. Chargaff- Ratios of DNA within and between species

 (DNA= Nitrogenous base, sugar, phosphate group;  

 30.3% of human DNA = A and 26% of bacteria DNA = A

 A=T and G=C) We also discuss several other topics like What is the difference between the surface and deep structure of sentences?
If you want to learn more check out What is the gateway to the akropolis behind lysistrata in the background?

v. Watson and Crick- DNA structure  

A=T G=C  

The relationship between structure and function is manifest in the double helix If you want to learn more check out What is the difference between lewis acid and lewis base?

Semi-conservative model of replication (each daughter strand has 1 old strand)

vi. Wilkins and Franklin- DNA Structure

vii. Meselson and Stahl- Semi-conservative replication

DNA can be Light/Light, Heavy/Light, or Heavy/Heavy

DNA Replication  

Who are avery mccarty and macleod?

i. Enzymes:  

a. Helicase- untwists the double helix (unzip your genes)  

b. Topoisomerase- relieves the strain of twisting caused by unwinding (breaks swivels and regions bonds)  

c. Primase- Makes a primer (a strating point) for synthesis of a DNA strand. (5’ end of leading strand)

d. DNA Pol III- polymerizes a new strand of DNA by adding nucleotides

i. DNA Pol I- removes RNA and replaces with nucleotides  

e. Ligase- ligates or joins together nucleic acids  

ii. Replication begins at sites called origins of replication, where 2 DNA strands are separated, opening up a replication “bubble”  

iii. Replication proceeds in both directions from each origin, until entire molecule is copied.  

iv. At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating.  We also discuss several other topics like According to erikson’s theory of psychosocial development, what is the main task of the adolescent?

a. Helicases are enzymes that untwist double helix at replication forks  

b. Single-strand binding protein binds to and stabilizes single stranded DNA until it can be used as a template

c. Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands.  

d. DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3’ end. The initial nucleotide strand is a short RNA primer, made by primase.  

Antiparallel Elongation  

a. Enzymes called DNA polymerases catalyze the elongation of new DNA  at a replication fork Don't forget about the age old question of What are the the seven hills of rome?
Don't forget about the age old question of What are the goals of human wildlife conflicts ?

b. Most DNA polymerases require a primer and a DNA template strand c. The rate of elongation is about 500 nucleotides per second in bacteria  and 50 per second in human cells

d. Each nucleotide that is added to a growing DNA strand is a nucleoside  triphosphate

e. dATP, for example, supplies adenine to DNA and is similar to the ATP of energy metabolism

f. The difference is in their sugars: dATP has deoxyribose while ATP has  ribose

g. As each monomer of dNTP joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate

h. The antiparallel structure of the double helix (two strands oriented in  opposite directions) affects replication

i. DNA polymerases add nucleotides only to the free 3' end of a growing  strand; therefore, a new DNA strand can elongate only in the 5' to 3'  direction

j. Along one template strand of DNA, the DNA polymerase synthesizes a  leading strand continuously, moving toward the replication fork

Proofreading and repairing DNA  

i. DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides

ii. In mismatch repair of DNA, repair enzymes correct errors in base pairing  

iii. DNA can be damaged by chemicals, radioactive emissions, X-rays, UV light, and certain molecules (ex: Cigarette smoke)  

iv. Nucleotide excision repair, nuclease cuts out and replaces damaged stretches of DNA

Replicating ends of DNA molecules  

a. Limitations create problems for linear DNA  

b. Usual replication machinery provides no completion of 5¢ ends, so repeated rounds of replication produces shorter DNA molecules   c. Eukaryotic chromosomal DNA molecules have end nucleotide sequences called TELOMERES  

d. TELOMERES do not prevent shortening of DNA but postpone erosion of genes near ends of DNA  

 e. Shortening of telomeres is connected to aging  

f. If chromosomes of germs became shorter in every cell cycle, genes would be missing from gametes  

 g. Telomerase catalyzes lengthening of telomeres in germ cells 2

Flow of Genetic information  

- Information content of DNA is in the form of specific sequences of nucleotides - DNA inherited by an organism leads to specific traits by dictating PROTEIN SYNTHESIS

- Proteins are the links between genotype and phenotype  

 - Gene Expression = DNA directs protein synthesis, includes 2 stages: transcription and translation  

i. Archibald Garrod = genes dictate phenotypes through enzymes that catalyze specific chemical reactions; symptoms of inherited disease reflect inability to synthesize certain enzyme

ii. Beadle and Tatum = exposed bread mold to X-rays creating mutants unable to survive on medium as a result of inability to synthesize certain molecules; used crosses to identify 3 classes of arginine deficient mutants; one-gene-one-enzyme hypothesis = each gene dictates production of a specific enzyme (now called one-gene-one polypeptide hypothesis) 

Transcription and Translation

a. RNA is the intermediate between genes and the proteins for which they  code

b. Transcription is the synthesis of RNA under the direction of DNA c. Transcription produces messenger RNA (mRNA)

d. Translation is the synthesis of a polypeptide, which occurs under the  direction of mRNA

e. Ribosomes are the sites of translation

f. In prokaryotes, mRNA produced by transcription is immediately translated  without more processing

g. In a eukaryotic cell, the nuclear envelope separates transcription from  translation  

h. Eukaryotic RNA transcripts are modified through RNA processing to yield  finished mRNA

i. A primary transcript is the initial RNA transcript from any gene j. The central dogma is the concept that cells are governed by a cellular  chain of command: DNA  RNA  protein  

Genetic Code  

i. 20 amino acids; 4 nucleotide bases  

ii. Codons: Triplets of bases  

a. The flow of information from gene to protein is based on a triplet code:  a series of non-overlapping, three-nucleotide words

b. These triplets are the smallest units of uniform length that can code for all the amino acids

c. Example: AGT at a particular position on a DNA strand results in the  placement of the amino acid serine at the corresponding position of  the polypeptide to be produced  

d. During transcription, one of the two DNA strands called the template  strand provides a template for ordering the sequence of nucleotides in  an RNA transcript 


 e. During translation, the mRNA base triplets, called codons, are read in   the 5’ to 3’ direction 

 f. Each codon specifies the amino acid to be placed at the corresponding  position along a polypeptide 

g. Codons along an mRNA molecule are read by translation machinery in  the 5’ to 3’ direction

h. Each codon specifies the addition of one of 20 amino acids

 i. Of the 64 triplets, 61 code for amino acids, 3 triplets are “stop” signals  to end translation 


 k. Genes can be transcribed and translated after being transplanted from  one species to another  

ii. Transcription is the DNA-directed synthesis of RNA 

 a. RNA synthesis is catalyzed by RNA polymerase, which breaks DNA  strands apart and hooks together RNA nucleotides  

b. The DNA sequence where RNA polymerase attaches is called the  promoter; in bacteria, the sequence signaling the end of transcription  is called the terminator

iii. The three stages of transcription:

 a. Initiation 

∙ Promoters signal the initiation of RNA synthesis

∙ Transcription factors mediate the binding of RNA polymerase  and the initiation of transcription

∙ The completed assembly of transcription factors and RNA  

polymerase II bound to a promoter is called a transcription  

initiation complex 

∙ A promoter called a TATA box is crucial in forming the initiation  complex in eukaryotes 

 b. Elongation 

∙ As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time

∙ Transcription progresses at a rate of 40 nucleotides per second  in eukaryotes

∙ A gene can be transcribed simultaneously by several RNA  


 c. Termination 

∙ The mechanisms of termination are different in bacteria and  eukaryotes

∙ In bacteria, the polymerase stops transcription at the end of the terminator

∙ In eukaryotes, the polymerase continues transcription after the  pre-mRNA is cleaved from the growing RNA chain; the  

polymerase eventually falls off the DNA

i. Eukaryotic cells modify RNA after transcription  

a. Enzymes in the eukaryotic nucleus modify pre-mRNA before the  genetic messages are dispatched to the cytoplasm

b. During RNA processing, both ends of primary transcript are altered 4

c. The 5’ end receives modified nucleotide 5’ cap (modified guanine  nucleotide)

d. The 3’ end gets a Poly-A tail (50-250 adenine nucleotides)

i. This facilitates export of mRNA  

ii. Protects mRNA from hydrolytic enzymes  

iii. Help ribosomes attach to 5¢ end

e. Introns and Exons splicing:  

i. Noncoding regions = Introns (intervening sequences)  

ii. All other regions = Exons (eventually expressed, translated into  amino acid sequences)  

iii. Sometimes RNA splicing is carried out by SPLICEOSOMES  

iv. Spliceosomes = consist of proteins and ribonucleoproteins 

(snRNPs) that recognize splice sites  

 v. Proteins often have modular architecture consisting of discrete  regions called domains 

 vi. Exon shuffling can result in new proteins 

vii. Ribozymes  

a. Catalytic RNA that functions as enzyme and splice RNA

b. 3 properties of RNA enable it to function as enzyme:  

1. Forms three-dimensional structure because of  

ability to base pair with itself  

2. Some bases in RNA have functional groups  

3. RNA may hydrogen-bond with other nucleic acid  


ii. Synthesis of a polypeptide

 a. A cell translates an mRNA message into protein with the help of  transfer RNA (tRNA) 

b. Molecules of tRNA are not identical:

i. Each carries a specific amino acid on one end

ii. Each has an anticodon on the other end; the anticodon base pairs with a complementary codon on mRNA

c. A tRNA molecule consists of a single RNA strand that is only about 80  nucleotides long

d. Flattened into one plane to reveal its base pairing, a tRNA molecule  looks like a cloverleaf

 e. Because of hydrogen bonds, tRNA actually twists and folds into a  three-dimensional molecule 

f. tRNA is roughly L-shaped

g. Accurate translation requires two steps:

i. First: a correct match between a tRNA and an amino acid, done  by the enzyme aminoacyl-tRNA synthetase

ii. Second: a correct match between the tRNA anticodon and an  mRNA codon

h. Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon

Building a Polypeptide  

a. The three stages of translation:

i. Initiation

ii. Elongation

iii. Termination

 b. All three stages require protein “ factors ” that aid in the translation process 


 c. Initiation 

iv. The initiation stage of translation brings together mRNA, a tRNA  with the first amino acid, and the two ribosomal subunits

v. First, a small ribosomal subunit binds with mRNA and a special  initiator tRNA

vi. Then the small subunit moves along the mRNA until it reaches the  start codon (AUG)

vii. Proteins called initiation factors bring in the large subunit that  completes the translation initiation complex

 d. Elongation 

viii. During the elongation stage, amino acids are added one by one to  the preceding amino acid

ix. Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and  


 e. Termination 

x. Termination occurs when a stop codon in the mRNA reaches the A  site of the ribosome

xi. The A site accepts a protein called a release factor

xii. The release factor causes the addition of a water molecule instead  of an amino acid

xiii. This reaction releases the polypeptide, and the translation  assembly then comes apart

A ribosome has three binding sites for tRNA:

i. The P site holds the tRNA that carries the growing polypeptide chain ii. The A site holds the tRNA that carries the next amino acid to be added to  the chain

iii. The E site is the exit site, where discharged tRNAs leave the ribosome Completing and Targeting Proteins  

i. Translation is not sufficient to make a functional protein  

ii. Polypeptide chains are modified after translation  

iii. Protein Folding and Post-Translational modifications:

a. During and after synthesis, polypeptide chain spontaneously  coils and folds into three-dimensional shape  

iv. Two populations of ribosomes are evident in cells: Free ribosomes  (cytosol) = synthesize proteins; and bound ribosomes (attached to  ER)= make proteins of endomembrane system and secreted from cell  v. POLYPEPTIDE SYNTHESIS ALWAYS BEGINS IN CYTOSOL  

*** Mutations  

i. Changes in genetic material of a cell or virus  

ii. POINT MUTATIONS= chemical changes in one base pair of gene  iii. SILENT MUTATIONS= no affect on amino acid produced by a codon  because of redundancy of genetic code  

iv. MISSENSE MUTATIONS= still code for an amino acid but not the right  one  

v. NONSENSE MUTATIONS= change amino acid codon into stop codon,  leading to nonfunctional protein  

vi. FRAMESHIFT MUTATIONS= insertion or deletion of nucleotides alter the  reading frame; additions or losses of nucleotide pairs in a gene  vii. Mutagens = physical or chemical agents that can cause mutations  Gene Expression  


i. Prokaryotes and Eukaryotes alter gene expression in response to  changing environment  

ii. Gene expression regulates development and is responsible for  differences in cell types  

iii. Bacteria respond to environmental change by regulating transcription iv. A cell can regulate the production of enzymes by feedback inhibition or by gene regulation

v. Gene expression in bacteria is controlled by the operon model:

1. Operons  

 a. A cluster of functionally related genes can be under coordinated   control by a single on-off “ switch” 

b. The regulatory “switch” is a segment of DNA called an operator usually positioned within the promoter

 c. An operon is the entire stretch of DNA that includes the operator, the  promoter, and the genes that they control 

d. Repressors ****

i. The operon can be switched off by a protein repressor 

ii. The repressor prevents gene transcription by binding to the  operator and blocking RNA polymerase 

iii. The repressor is the product of a separate regulatory gene 

iv. The repressor can be in an active or inactive form, depending on the presence of other molecules 

v. A corepressor is a molecule that cooperates with a repressor  protein to switch an operon off 

vi. For example, E. coli can synthesize the amino acid tryptophan Negative Gene Regulation  

i. Repressible and Inducible Operons – Two Types of Gene Regulation  a. Repressible Operon = ON; binding of a repressor to the operator  shuts off transcription. (TRP Operon)  

b. Inducible Operon = OFF; inducer molecule inactivates the  

repressor and turns on transcription. (LAC Operon)  

c. TRP Operon =  

i. by default, is on; genes for tryptophan synthesis are  


ii. Tryptophan binds to TRP repressor which turns operon OFF 

iii. Repressor only active in the presence of its corepressor  

tryptophan; thus the TRP operon is turned off (repressed)  

if tryptophan levels are high.  

d. LAC Operon =  

i. Inducible operon, contains genes for the code for enzymes 

used in the hydrolysis and metabolism of lactose  


ii. By itself the lac repressor is active and switches the lac  

operon off 

iii. An INDUCER inactivates the repressor to turn the lac  

operon on 

e. Repressible and Inducible Operons  

i. INDUCIBLE enzymes function in CATABOLIC pathways;  

synthesis is induced by chemical signal

ii. REPRESSIBLE enzymes function in ANABOLIC pathways;  

synthesis is repressed by high levels of the end product.

iii. Regulation of TRP and LAC involves negative control of  

genes because operons are switched off by active  


- Some operons are also subject to positive control through a stimulatory  protein, such as CATABOLITE ACTIVATOR PROTEIN (CAP), an activator of  transcription

- When glucose is scarce, CAP is activated by binding with cyclic AMP - GLUCOSE IS A PREFERRED FOOD SOURCE OF E.COLI 

- Activated CAP attaches to the promoter of the lac operon and increases the  affinity of RNA polymerase, thus accelerating transcription 

- When glucose levels increase, CAP detaches from the lac operon, and  transcription returns to a normal rate 

 - CAP helps regulate other operons that encode enzymes used in catabolic  pathways 

i. Eukaryotic gene expression can be regulated at ANY stage  a. ALL organisms MUST regulate which genes are expressed 24/7 b. In multicellular organisms, gene expression is essential for cell  specialization 

c. Differences between cell types result from differential gene  expression, the expression of different genes by cells with the same genome 

ii. Regulation of Chromatin Structure  


b. Chemical modifications to HISTONES and DNA of chromatin influence  structure and gene expression  

c. HISTONE ACETYLATION= acetyl groups attached to + charged lysines in  histone tails

- Loosens chromatin structure – promotes initiation of transcription - METHYLATION (adding methyl groups) condenses chromatin - PHOSPHORYLATION (adding phosphate groups) NEXT TO METHYLATED  AMINO ACIDS can loosen chromatin 

 - HISTONE CODE HYPOTHESIS = specific combinations of modifications  help determine chromatin configuration and influence transcription d. DNA METHYLATION  

- Addition of methyl groups to certain bases of DNA  

- Methylation can reduce transcription (some species)  

 - Can cause long-term inactivation of genes in cellular differentiation - GENOMIC IMPRINTING -- methylation regulates expression of maternal  and paternal alleles of certain genes at start of development


- Inheritance of traits not involving the nucleotide sequence


e. Regulation of Transcription Initiation

- Chromatin-modifying enzymes—initial control of gene expression— make region of DNA more or less able to bind the transcription  


- CONTROL ELEMENTS = segments of noncoding DNA that help regulate transcription by binding certain proteins 

^^ critical to precise regulation of gene expression  

- to INITIATE TRANSCRIPTION, eukaryotic RNA polymerase requires  assistance of proteins called TRANSCRIPTION FACTORS  

- Transcription factors essential for transcription of all protein-coding  genes

 - EUKARYOTES –- high levels of transcription of particular genes depend  on control elements interacting with specific transcription factors   -Enhancers and Specific Transcription Factors: *********

1. Proximal control elements located close to promoter 

2. Distal control elements (enhancers) are far away from gene;  

sometimes located in an intron 

3. ACTIVATOR = protein that binds to enhancer and stimulates  


4. BOUND ACTIVATORS cause mediator proteins to interact with  proteins at promoter 

5. some transcription factors function as repressors, inhibiting  

expression of gene  

6. some activators and repressors act indirectly by influencing  

chromatin structure to promote or silence transcription 

f. Post- Transcriptional Gene Regulation  

- RNA Processing:  

 a. Alternative RNA splicing—different RNA produced from same  primary transcript, depending on which RNA segments are exons or introns  

- mRNA Degradation

a. life span of mRNA in cytoplasm is key to determining protein  synthesis  

b. Eukaryotic mRNA lives longer than Prokaryotic mRNA

c. mRNA lifespan determined by sequences in leader/trailer regions - INITIATION of TRANSLATION

 a. Initiation of translation of mRNAs can be blocked by  

REGULATORY PROTEINS that bind to sequences or structures of  mRNA 

 b. Translation of all mRNAs regulated simultaneously  

EX: Translation Initiation Factors simultaneously activated in an  egg after fertilization  

- Protein Processing and Degradation

a. AFTER TRANSLATION protein processing (cleavage & adding  chemical groups) are subject to control

b. PROTEASOMES = giant protein complexes that bind molecules  and degrade them 

g. Non-coding RNA role in gene expression  

- Significant amount of genome can be transcribed into noncoding  RNAs


 - Noncoding RNAs regulate gene expression at 2 points: mRNA  TRANSLATION and CHROMATIN CONFIGURATION 

 - miRNA = MICRO RNA = small single-stranded RNA that can bind to  mRNA – they can degrade mRNA or block translation 


a. Inhibition of gene expression by RNA molecules is called RNA  interference (RNAi)  

b. RNAi caused by siRNA 

c. siRNA play role in HETEROCHROMATIN FORMATION and block  large regions of chromosome 

d. siRNA and miRNA similar but form different RNA precursors 

Charts and Diagrams

Schematic Model Showing Binding Sites  10

 ** Know how to draw this:  


Amino Acid  

binding site 5

Hydrogen bonds’ between paired  



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