STUDY UNION – NEDA Page 1

PLEASE READ*Disclaimer, this may not be all the information you are required to know for your final exam and you should NOT rely on these practice materials alone*

*Chapter 17 is at the beginning as it’s on both exams and 16 is at the end*

CHAPTER 17RNA STRUCTURE

- RNA (Ribonucleic acid): single-stranded nucleic acid that carries out the instructions coded in DNA

- Central Dogma of Biology: The process by which the information in genes flows into proteins: DNA -> RNA -> Protein

- Polypeptide: a chain of amino acids- Codon: a sequence of three nucleotides that corresponds with a specific amino acid or

start/stop signal during translation- Transcription: process during which a DNA sequence of a gene is copied to make an

RNA molecule- Translation: process during which an mRNA molecule is used to assemble amino acids

into polypeptide chains- Mutation: a change in a genetic sequence

NUCLEOTIDE- Composed of three things:

o 5-carbon sugar called riboseo phosphate groupo nitrogenous base

- RNA is generally single stranded- Nitrogenous Bases

STUDY UNION – NEDA Page 2

o Adenine (A) - Uracil (U)o Guanine (G) - Cytosine (C)

TYPES OF RNA- Messenger RNA (mRNA) - carries information from DNA in the nucleus to ribosomes

in the cytoplasm- Ribosomal RNA (rRNA) - structural component of ribosomes- Transfer RNA (tRNA) - carries amino acids to the ribosome during translation to help

build an amino acid chain

- START CODON: AUG- STOP CODON: UAA, UAG, UGA

STUDY UNION – NEDA Page 3

MUTATIONS

Fragile X syndrome *important for Thomas kids for sure*- Most common form of developmental delay- X chromosome (south end), there are genes related to neurological development- more popular in males, 1:1500 males have it- during meiosis, methylation creates repast

o creates an imbalance in chromosomeso imbalance creates a thread hanging and the chromosome becomes unstableo can cause fractured chromosomeso the south end breaks off and neurological problems begin

- Methyl groups wrap around the promoter region of DNA, so RNA polymerase can not bind

Substitution Mutations- silent mutations: do not affect the sequence of amino acids during translation-- nonsense mutations: result in a stop codon where an amino acid should be, causing

translation to stop prematurely- missense mutations: change the amino acid specified by a codon

Insertions and Deletions- insertion: more base added to the DNA sequence- deletion: one or more bases removed from the DNA sequence- frameshift mutations: when inserting or deleting bases interferes with the code

MISCONSEPTIONS- Amino acids are not made during protein synthesis

o amino acids are not being made during translation, they are being used as building blocks to make proteins

- mutations do not always have drastic or negative effects- insertions and deletions that are multiples of three nucleotides will not cause frameshift

mutations

TRANSCRIPTION AND TRANSLATION TERMS- RNA Polymerase: the main transcription enzyme, enzyme that transcribes DNA, making

RNA- Introns: Regions that do not code for proteins- Exons: the remaining codes for proteins after introns are removed during splicing- Polyadenylation: Adds. PolyA (adenine bases) tail to the mRNA; signals the end of

mRNA- TATA box: eukaryotic promoters sequence

o TATA Boxes are the control region in the promoter in front of a gene

STUDY UNION – NEDA Page 4

TRANSCRIPTION

STUDY UNION – NEDA Page 5

- The process in which a gene’s DNA sequence is copied (transcriped) to make an RNA molecule

- the molecule that is directly made by transcription is pre-mRNA, it has a few more steps before it becomes mRNA that are

o addition of the 5’ cap to the beginning of the RNAo addition of the poly-A-tail (tail of A nucleotides) on the end of the RNAo chopping out of introns, or “junk” sequences, ad pasting together the remaining,

good sequences (Exons)- RNA Polymerase is the main transcription enzyme

1. The beginning of transcription is initiation, it occurs when RNA polymerase binds to a region of the gene called the promoter. This tells the DNA to unwind so the enzyme can read the bases in one of the DNA strands. The enzyme is now ready to make a strand of mRNA with a complementary sequence of bases

2. Elongation is the addition of the nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, using complementary base pairs. There is a brief time during this process when the newly formed RNA is bound to the unwound DNA. During this process, A binds to U in the RN

3. Termination is the ending of transcription, and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.

4. The mRNA however is not yet done processing and has a few more steps before it’s ready for translation which includes splicing, editing and polyadenylaiton which allows the gene to be used for more than one protein

STUDY UNION – NEDA Page 6

5. Splicing removes introns from mRNA. Introns are regions that do not code for proteins. The remaining mRNA consists only of regions that docode for proteins, nuclear ribonuclearproteins are involved in pre-mRNA splicing

6. Editing changes some of the nucleotides in mRNA. One form is smaller than the other because editing adds a premature stop signal in the mRNA

7. polyadenyation adds a “tail” to the mRNA. The tail consists of a string of Adenine bases. It signals the end of mRNA. It is also involved in exporting mRNA from the nucleus while the tail protects mRNA from enzymes that might break it down

SUMMARY

- Transcription is the DNA -> RNA part of the central dogma of molecular biology- transcription occurs in the nucleus- during transcription, a copy of mRNA is made that is complementary to a strand of

DNA. In eukaryotes, mRNA may be modified before it leaves the nucleus

TRANSLATION

STUDY UNION – NEDA Page 7

STUDY UNION – NEDA Page 8

STUDY UNION – NEDA Page 9

- During translation, a cell reads information from mRNA and uses this information to build a protein

- builds a polypeptide (chain of amino acids) to make proteins- mRNA is our codon, we got this during our transcription stage- there are 61 different codons for amino acids- we make tRNA from our mRNA that comes in with the amino acid

1.Initiation: in this stage, the ribosome gets together with the mRNA and the first tRNA so translation can begin

-we need two main things for this: ribosomes and mRNA. Here tRNA is the initiator-when these pieces come together, they from the initiation complex

2.Elongation: in this stage, amino acids are brought to the ribosome by tRNAs and linked together to form a chain

-polypeptide chain gets longer-our first methionine-carrying tRNA (UAC; binds to mRNA AUG) starts at the P slot out

of APE. - The A side will be the site for the next tRNA, one whose anticodon is a perfect match

for the exposed codon3.Termination: in the last stage, the finished polypeptide is released to go and do its job in the cell

-occurs when a stop codon (UAA, UAG, UGA) enters the A site. Stop codons are recognized by protiens called release factors (they fit in the P site but are not tRNA).

-after the small and large ribosomal subunits separate form the mRNA and from each other, each element can (and usually quickly does) take part in another round of translation

-our polypeptide that has amino acids still has some work, so polypeptides sometimes need edits. Amino acids can be chemically altered or removed and can fold into a 3D structure to join with other polypeptides, this may use chaperones to control how the polypeptides fold.j

QUESTIONS

For the following question, put the definition of the following in your own words

RNA –

RNA VS DNA –

MRNA -

RRNA –

STUDY UNION – NEDA Page 10

TRNA –

Transcription –

RNA Polymerase –

RNA editing –

Introns –

Exons –

1. The following dna strand is used as a template for transcription:3’ GGC ACT CAT TCA A 5’

a. 5’ CCG TCA GTA AGT T 3’b. 5’ CCG UGA GUA AGU U 3’ c. 5’ GGC ACT CAT TCA A 3’d. 5’ UUA CAG ACG GAA C 3’

2. The following RNA strand was produced:5’ AAA AUG AGU AAG 3’

Which of the following DNA strands could have been the template for this RNA?

a. 3’ UUU TAC UCA UUC 5’b. 3’ AAA ATG AGT AAG 5’c. . 3’ TTT TAC TCA TTC 5’d. 3’ TTT ATG TGC TTC 5’

3. A template strand of DNA in a gene reads:3’ TCT CCA AGC 5’

STUDY UNION – NEDA Page 11

Using the codon chart, what is the sequence of amino acids that is produced after translation?

a. Arg - Gly – Serb. Ser - Gly – Glyc. Arg - Ser – Glyd. Ser - Gly - Leu

4. A sequence of RNA is shown below:5’ AUG GGG AAG UGU UGG 3’

Using the codon chart, what is the sequence of amino acids that is produced when this RNA is translated?

a. Met - Gly - Lys - Cys – Trpb. Met - Gly - Asn - Cys – Tryc. Try - Pro - Phe - Thr – Thrd. Ile - Gly - Lys - Trp - Stop

5. How many bases are there per amino acid?a. 1b. 3c. 6d. 5

6. Which of the following are stop codons?a. UGAb. UAAc. UAGd. All of the abovee. None of the above

7. What process occurs before the other?a. Transcription then translationb. Translation then transcriptionc. transcription then ionizationd. translation and then polymerizatione. translation and then differentiation

8. Messenger RNA (mRNA) can be best described as:a. a good way to rewrite RNAb. The atom that carries information to an RNA templatec. A short lived RNA molecule that carried encoded information, transcribed from

DNAd. A chromosome that is only present in prokaryotes and is involved in DNA

synthesise. A molecule that has no life and translates for the cell

STUDY UNION – NEDA Page 12

9. Just like DNA polymerase, RNA polymerase performs a template directed synthesis in the:

a. 3’ -> 5’ directionb. . 5’ -> 3’ directionc. 5’ -> 5’ directiond. 3’ -> 3’ direction

10. Transcription is:a. A word your professor made up to confuse the noodle out of youb. The synthesis of RNA from a DNA templatec. The synthesis of proteins from information on the mRNAd. The synthesis of polydiester linkages from an Econe. The synthesis of brain cells by neuro kinetic means

11. To understand the strupture of RNA polymerase, researches employed what technique to view this enzyme?

a. X-ray crystallographyb. Gas chromatographyc. El electrophoresisd. PCR amplificatione. Hardy-Weinberg equilibrium

12. ——— is the bridge between genes and the proteins for which they code?a. Polypeptideb. DNAc. RNAd. Chaperonin

13. What is the site of translation?a. the rough Endoplasmic reticulumb. The nucleus c. The nucleolusd. Ribosomes

14. (T/F) Genes build proteins directly.a. Trueb. False

15. Messenger RNA carries information from the —— to the ——- manufacturing components .

a. Anticodon, codonb. Ribosomes, nucleusc. Translation, transcriptiond. DNA, proteins

STUDY UNION – NEDA Page 13

16. Eukaryotic RNA transcripts ———-a. Keep their initial transcripts and move their mRNA to translationb. Become primary transcriptsc. Are modified through RNA processing to yield the finished mRNAd. To form pre-mRNA

CHAPTER 16DNA STRUCTURE

- DNA (Deoxyribonucleic acid): nucleic acid that transmits genetic information form parents to offsprings and codes for the production of proteins

- Nucleotide: building block of nucleic acid- Double Helix: structure of two strands, looks like a twisted ladder- DNA replicaiton: when a double stranded DNA molecule is copied to produce two

identical DNA molecules- Base Pairing: nitrogenous bases match specifically with one another

NUCLEOTIDE- composed of 3 things:

o 5-carbon sugar called deoxyriboseo phosphate groupo nitrogenous base

- Nitrogenous bases

o Adenine (A) - Thymine (T) held together with 2 hydrogen bonds in DNA

o Guanine (G) - Cytosine (C) together with 3 hydrogen bonds in DNA

o ^ Also called Chargaff’s ruleo A and G are purineso T and C are pyridines

DNA IS:

- Antiparallel : two strands of the helix run in opposite directionso 5’ -> 3’o 3’ -> 5’o DNA replicates in the 5’ -> 3’ direction

- Semiconservative: each new strand of DNA has half of the parent strand

STUDY UNION – NEDA Page 14

DNA REPLICATION IN PROKARYOTES

1. DNA opens with helicase, tropoisomerase making sure it doesn’t stretch too much2. Primase (after helicase)(begins process of replication) primase puts down a starter piece

of RNA (which gets peeled off eventually)(primer: a little piece of RNA begin replication)(Primase: enzyme that puts down RNA). RNA is necessary to begin 5’-3’

- All DNA enzymes have the requirement of an open 3’ group- No DNA can work on a 5’ group because of the phosphate (that’s why you

add primer (RNA))3. DNA polymerase III does not work in number order (work in number they were founded)

- DNA polymerase III is the main DNA synthesizing / DNA making enzyme for prokaryotes

- Hops on 3’ group and makes DNA4. DNA polymerase I goes into DNA strand and picks of read RNA replaces with DNA5. DNA is not nice and neat out end. You add DNA polymerase I and it needs to connect

- DNA ligase seals hole in backbone of DNA and makes a covalent bond6. DNA backbone is made with covalent bond b/w phosphate and sugar7. DNA polymerase II checks for mistakes in DNA replication8. Then you have a new strand of DNA

- Prokaryotes can have multiple replication bubbles at once

QUESTIONS:

1. A Gene is:a. A piece of clothing that is placed upon the bipedal legs of humanb. A chromosome carrierc. A section of DNA that codes for a protein or RNA moleculed. A regulatory sequencee. An exon

2. What type of bond forms between Complementary base pairs?a. Hydrogenb. Covalentc. Ionicd. Interkinetic

3. What 3 things does each nucleotide contain?

4. Where is DNA located?

STUDY UNION – NEDA Page 15

5. What are the 4 nitrogenous bases?

6. What is a virus?

7. What are the monomers that make up polymer DNA?

8. Describe Eukaryotes:

9. What is molecular diversity?

10. What is Chargaff’s rule?

11. Why do we match purine (A, G) to Pyrimidine (T, C)?

12. DNA and RNA are polymers, what does that mean?

13. How many hydrogen bonds are between A-T? How many hydrogen bonds are between C-G?

14. What seals the hole in the backbone of DNA with covalanet bonds?

STUDY UNION – NEDA Page 16

15. What is the only enzyme involved in transcription?

16. What 3 things are needed for translation?

17. What is the use for m-RNA, r-RNA and t-RNA?

18. What are codon and anticodon?

19. What does it mean that DNA is antiparallel?