Chapter 6 - DNA & RNA

Question 1

What are genes composed of? What do they contain?

Answer 1

DNA (Deoxyribonucleic acid) contains information coded in the sequence of its base pairs.

Question 2

What is DNA transcribed into? What happens after?

Answer 2

RNA (ribonucleic acid) which is then translated into a sequence of amino acids (protein).

Question 3

What is DNA essentially called? What does it do?

Answer 3

The blueprint for protein synthesis

- Proteins regulate all life functions

Question 4

Why is DNA replication important?

Answer 4

It can self-replicate which is an essential step in cell visions and reproduction.

Question 5

What is the basis for heredity? Why?

Answer 5

DNA

- It’s ability to self-replicate makes sure that the coded DNA will be passed onto future generations (central dogma)

Question 6

What is important in regard to DNA mutability? What do changes alter? What is the basis of evolution?

Answer 6

It occurs under certain conditions

• The changes alter proteins produced and therefore organisms characteristics
• Changes are usually stable and passed down from generation to generation which is the basis of evolution

Question 7

What is the basic unit of DNA? What is it composed of?

Answer 7

Nucleotide

- Composed of deoxyribose (sugar) bonded to both a phosphate group and a nitrogenous base

Question 8

What 2 types of bases are there? Describe each:

Answer 8

1) Purines
- Include adenine (A) and guanine (G)
- Larger due to double ring N-base

2) Pyrimidines
- Include cytosine (C) and thymine (T)
- Smaller due to 1 ring N-base

Question 9

What is the directionality of DNA?

Answer 9

It is designated by a 3’ and a 5’ naming convention that is based n which carbon of the sugar molecule of the DNA strand is the terminus of the helix.

Question 10

How is DNA found in humans? How are the strands held together?

Answer 10

Typically, it is found in humans as double-stranded helices of complimentary strands with the sugar-phosphate chains on the outside of the helix and the N-bases on the inside
- The strands are held together by H-bonds between the bases oriented towards the center

Question 11

How do purines and pyrimidines link? How is DNA arranged in this pattern? Who discovered this DNA model?

Answer 11

T forms 2H bonds with A, and G forms 3H bonds with C

• One DNA strand will be arranged with the 5’ pointing up and the other strand will also have its 3’ pointing up to give an anti-parallel arrangement
• James Watson and Francis Crick (with the help of Rosalind Franklin) discovered this structure (Watson-Crick DNA Model)

Question 12

Simply put, how does DNA replicate? What does this involve?

Answer 12

DNA must unwind and separate into two single strands
- Involves uncoiling the strands by topoisomerase and breaking the H-bonds between N-bases of each nucleotide by DNA helicase (replication fork)

Question 13

What happens when the H-bonds are broken? What does each new daughter helix contain? What are they identical to?

Answer 13

The single strands can act as a template for complementary base pairing - this allows for synthesis of 2 new daughter cells.

• It contains an intact strand from the parent helix and a newly synthesized strands (semi-conservative)
• Daughter strands from the parent strands are identical to parent strands

Question 14

What does DNA polymerase do? Which direction does it read?

Answer 14

Creates the daughter strands

• Reads the parent DNA and creates complimentary, anti-parallel daughter strand
• Reads the parent strand from 3’ to 5’ to create the daughter strand in a 5’ to 3’ direction

Question 15

What is the difference between the leading and lagging strand?

Answer 15

The leading strand is continuously synthesized by DNA polymerase which attaches nucleotides to the exposed 3’ end of the parents strand and follows the replication fork to the 5’ end.

The lagging strand is synthesized discontinuously because the 5’ end of the parent strand is exposed - therefore DNA polymerase can only read in the 3’ to 5’ direction.
- The short fragments are called Okazaki Fragments which are joined by DNA ligase

Question 16

How are the nucleosides different in RNA?

Answer 16

They are identical such that they have adenine (A), cytosine (C), and guanine (G).

They are difference such that thymine (T) is replaced with uracil (U).

Question 17

What is DNA transcribed into? Then translated into?

Answer 17

mRNA which is then arranged into triplets (codons) which are then translated into amino acids.

Question 18

How many amino acids are there? Formed from what?

Answer 18

20

- Formed from the 4 nucleosides in organized in different combinations

Question 19

How many codons are possible? Why?

Answer 19

64 (based on the triplet code and 4 nucleotides)

- The code consists of synonyms; meaning amino acids have more than one codon for them (redundancy)

Question 20

What is RNA?

Answer 20

Ribonucleic acid

- A polynucleotide that is similar to DNA

Question 21

What are the 3 major exceptions of RNA being similar to DNA?

Answer 21

1) Its sugar is a ribose instead of deoxyribose
2) It contains uracil instead of thymine
3) It is usually single-stranded

Question 22

Where can RNA be found in a cell?

Answer 22

1) Nucleus

2) Cytoplasm

Question 23

What types of RNA is there? What are they involved in?

Answer 23

1) mRNA
2) tRNA
3) rRNA

• All are involved in protein synthesis

Question 24

Describe messenger RNA:

• What does it do?
• What is it made of?
• What does it mean that mRNA is monocistronic?

Answer 24

mRNA carries the compliment of a DNA sequence and transports the compliment from the nucleus to the ribosomes for protein synthesis

• It is made from ribonucleotides complementary to the original DNA
• It means that one mRNA strand codes for one polypeptide

Question 25

Describe transfer RNA:

• What does it do?
• What is its structure?
• What does each amino acid have?
• How many types of tRNA is there for each amino acid?

Answer 25

tRNA is a small RNA molecule found in the cytoplasm that assists in translation of mRNA’s nucleotide code into a sequence of amino acids - It does this by bringing the amino acids coded for in mRNA to the ribosomes during protein synthesis, tRNA recognizes both mRNA codon and corresponding amino acid

• The one end contains a 3-nucleotide sequence (anti-codon) which is complimentary to one of the mRNA codons and the other end is the site of attachment of the corresponding amino acid
• Each amino acid has its own aminoacyl-tRNA synthetase which has an active site that binds to both the amino acid and its corresponding tRNA, catalyzing their attachment to form an aminoacyl-tRNA complex
• At least one, with ~40 know types of tRNA

Question 26

Describe ribosomal RNA:

• What does it do?
• Where is it synthesized?

Answer 26

rRNA is a structural component of ribosomes and is the most abundant of all RNA types - mRNA passes through 2 subunits of rRNA and is translated into amino acids
- rRNA is synthesized in the nucleolus

Question 27

What is transcription?

Answer 27

Transcription is the process through which information coded in the base sequence of DNA is used to direct the synthesis of a strand of mRNA which then leaves the nucleus through the nuclear pores

Question 28

How many different sequences of RNA is formed by each human chromosome? What is true about the length of RNA?

Answer 28

Each human chromosome is a long strand of DNA that is used to make ~1000 different sequences of RNA
- RNA is short in length in comparison to DNA

Question 29

What is the first step of transcription?

Answer 29

Occurs when RNA polymerase binds to the DNA at the promoter region, a short DNA sequence found upstream from the site where transcription of a specific RNA is going to take place (TATA box)

Question 30

What initiates transcription? Describe the rest of the process of transcription:

Answer 30

Transcriptions factors that help RNA polymerase bind to DNA molecule

• RNA polymerase surrounds DNA molecule after it has been opened by DNA helicase and topoimerase
• RNA polymerase recruits and adds complimentary RNA nucleotides based on the DNA sequence
• RNA polymerase reads in 3’ to 5’ direction and creates a new daughter strand in the 5’ to 3’ direction

Question 31

What is the differences between RNA sequence and DNA sequence?

Answer 31

They are in fact complimentary BUT A binds with U instead of T
- RNA also uses a different sugar backbone than DNA (ribose - containing an O on C-2)

Question 32

What occurs after transcription? What is hnRNA? Describe introns vs. exons. What is added to provide protection?

Answer 32

mRNA undergoes post-transcriptional processing

• RNA that has not yet been processed is known has hetero-nuclear RNA (hnRNA) and contains extra nucleotides that are not necessary to create the corresponding proteins
• Introns are the extra sequences and exons are the nucleotides necessary to make the proteins - essentially introns are spliced out by the splice some, leaving the exons behind
• Guanine caps, series of adenines, are added to protect the RNA from enzyme degradation when it leaves the nucleus (poly-A tail)

Question 33

What is translation? Where does it occur?

Answer 33

Translation is the process through which mRNA codons are translated into a sequence of amino acids

• It occurs in the cytoplasm
• It involves tRNA, ribosomes, mRNA, amino acids, enzymes, and other proteins

Question 34

What are the 4 stages of translation? Describe each:

Answer 34

1) Initiation
- Begins when ribosomes binds to mRNA near 5’ end
- Ribosome scans mRNA until it binds to start codon (AUG)
- Initiator aminoacyl-tRNA complex, methionin-tRNA (with the anti-codon 3’-UAC’5’, base pairs with the start codon

2) Elongation
- H-bonds form between mRNA codon in A site of ribosomes and its complementary anticodon on the incoming aminocacyl-tRNA complex
- Peptide bond forms between amino acid attached to the tRNA in the A site and the amino acid attached to the tRNA in the P site of the ribosome
- Ribosome will carry uncharged tRNA to the P site and peptidyl-tRNA in the A site

3) Translocation
- Cycle is completed by this phase
- Ribosome advances 3 nucleotides along the mRNA from the 5’ to 3’ direction
- Concurrent action, uncharged tRNA from P site is expelled and peptidyl-tRNA from A site moves into the P site
- Ribosome now has empty A site read for the entire of the aminoacyl-tRNA corresponding to the next codon

4) Termination
- When one of the 3 special mRNA termination codons (stop codons - UAA, UGA, UAG) arrives at the A site
- Codons signal ribosome to terminate translation - i.e. they do not code for amino acids

Question 35

What occurs after the released of the protein from the ribosome (translation)? What are secondary and tertiary folds determined by? What can polypeptide chains form, and what do they result in?

Answer 35

The protein immediately assumes its characteristic 3-D native confirmation - it is determined by the primary sequence of amino acids

• Secondary and tertiary folds are determined by primary sequence
• Polypeptide chains can form intramolecular and intermolecular crossing bridges with disulphide bonds which results in a functional protein of complex of multiple proteins

Question 36

What are ribosomes composed of? What do they do? Describe their structure:

Answer 36

Ribosomes are composed of two subunits (one small and one big) that consists of proteins and RNA
- They bind together during protein synthesis (translation)

They have 3 binding sites

• A: Aminoacyl-tRNA complex - bind to the next incoming tRNA complex that is transferred to the next site
• P: peptidyl-tRNA dining site - where tRNA contributes to its amino acid to the growing polypeptide chain
• E: exit site - giving up its amino acid and tRNA is released

Question 37

What is the difference between human and bacteria ribosomal sites?

Answer 37

They have different types of subunits that make up their ribosomes
- Ex. Dug manufacturers designing antibiotics = antibiotics target ribosomal structures specific to bacteria, thereby only harming bacterial cells while leaving human cells unharmed