Lecture 1- The Structure and Function of Nucleic Acids + Chromatin and Chromosomes

Question 1

What are the 5 types of DNA?

Answer 1

1. ) Chromosomal DNA in nucleus.
2. ) Mitochondrial DNA
3. ) Chloroplast DNA
4. ) Viral DNA
5. ) Bacterial DNA

Question 2

What are the 8 types of RNAs and their functions?

Answer 2

1. ) mRNA- translated into polypeptides.
2. ) rRNA- an integral part of ribosomes.
3. ) tRNA- transfer amino acids to form polypeptides.
4. ) small nuclear RNAs- play a role in processing pre-mRNAs into mature mRNAs.
5. ) Small nucleolar RNAs- help process and assemble ribosomal RNAs.
6. ) Ribozymes- function like enzyme proteins (cleave RNAs)
7. ) Antisense RNAs-
   (a. ) Some interfere with protein production:
   
   • Interfering RNAs (microRNAs and Small interfering RNAs)
     (b. ) Some enable protein production-
   • Piwi-interacting RNAs and CRISPR RNAs.
8. ) Long Noncoding RNAs- Some act as molecular decoys binding up proteins that would otherwise destabilize chromosomes and others cause changes in the structure of chromosomes, inhibiting gene expression.

Question 3

What are the requirements for the molecule of inheritance?

Answer 3

1. ) Must carry all the information for the function and traits of the organism.
2. ) Must be stable in general, but should not cause harm to the organism if changed in some way.
3. ) Must be found on chromosomes based on the theory of inheritance.

Question 4

What were the three candidates of the theory of inheritance and describe who was the favorite/nonfavorite?

Answer 4

• DNA, protein, and RNA were the three candidates.
• RNA was eliminated because it is not found on chromosomes (requirements for the theory of inheritance).
• Protein was the favorite because scientist knew that there needed to be variation between individuals and protein has 20 different amino acids while DNA has only 4 different nucleic acids.

Question 5

What did Rosland Franklin and Maurice Wilkins discover using X-Ray diffraction?

Answer 5

1. ) DNA was in a double helix.
2. ) Each helix was 10 B.P. per turn
3. ) It was 10 angstroms in diameter (2 nm)

Question 6

What did Watson and Crick immediately suggest due to the complementary base pair concept?

Answer 6

• They suggested a mechanism for DNA replication.

Question 7

Why does RNA have Uracil while DNA has Thymine?

Answer 7

• Uracil is less energetically expensive than thymine and since there are a lot of mRNA strands being made this could save a lot of energy.

Question 8

What is the most likely base pair mutation to occur and why? And where does it occur most in and why? What are the repercussions?

Answer 8

• Cytosine is easily converted to Uracil is base pair mutation because this mutation does not need an enzyme for this to happen.
• If there are too many C to U changes then this could cause a disease in an organism.
• The C to U change usually occurs in the DNA strand which means you will make an RNA with an A base pair when it should really be a G.
• This does not usually happen in RNA because RNAs are usually short-lived and there is not enough time for Cs to change to Us.

Question 9

Where are new nucleotides added to form strands of molecules?

Answer 9

• New nucleotides are added on the phosphate group on the 5’ end and the O on 3’ end.
• This means there are 5’ front ends and a 3’ OH tails

Question 10

What are the three different configurations of DNA?

Answer 10

1. ) B- form: “normal” right-handed double helix.
2. ) A-form: A right-handed double helix but under high salt concentrations it is shrunken.
3. ) Z-form: A left-handed double helix- seen in short DNA with alternating purine/pyrimidine base pairs.

Question 11

Is RNA single stranded or double stranded? Can it be both? How?

Answer 11

• RNA is typically single-stranded but can have double-stranded elements.
• Complementary base pairs can fold and bind to one another resulting in hairpins, double helicases, bulges, internal loops, etc.

Question 12

Which organism contains something other than double-stranded DNA and single-stranded RNA?

Answer 12

• Viruses can have both double-stranded or single-strand DNA OR RNA.

Question 13

How do HIV and other diseases stay alive in the body and what is a therapy to stop this from occurring?

Answer 13

• These diseases use reverse transcriptase to replicate there DNA fast.
• Therapies use a 5’ OH phosphorylated group which looks enough like a usual 5’ end. The disease incorporates this nucleotide (Nucleic acid derivatives) into its replicated DNA.
• But the 3’ group which usually has an OH attached to it is different from this, so no more nucleotides can be added to the chain, replication ends, and the organism dies.

Question 14

Are chloroplasts and mitochondrial DNA circular?

Answer 14

Yes.

Question 15

Over evolution, where have genes transferred from (Two answers)?

Answer 15

1. ) From mitochondria to the nucleus

2. ) From chloroplast to the mitochondria

Question 16

What has a higher melting point: A sequence with high G-C content or one with high A-T content? Why?

Answer 16

• A high C-G content has a higher melting point because there are stronger bonds between them; 3 H bonds vs. the 2 H bonds between A-T.

Question 17

How is DNA in a bacteria situated?

Answer 17

• Bacteria does not have its DNA in the form of chromosomes, rather DNA is in the form of supercoiled loops attached/anchored to DNA binding proteins.

Question 18

What do topoisomerase and nucleoid-associated proteins do to bacterial DNA?

Answer 18

• Topoisomerase negatively coils the DNA while nucleoid-associated proteins make sure it stays in its proper configuration.

Question 19

What are the two ways in which bacterial DNA can be coiled?

Answer 19

1. ) Positively

2. ) Negatively

Question 20

What is a plasmid? Is it needed?

Answer 20

• A plasmid is a circular piece of DNA which is independent form the main DNA of the bacteria and it independently replicates.
• It can be transferred from on bacteria to another through a process known as conjugation.
• It is not necessarliy needed in order to survive but it can contain genes that encode for protein that can give it an advantage in its environment.

Question 21

What is the process of supercoiling DNA in eukaryotes?

Answer 21

1. ) Topoisomerase temporarily cuts the DNA and rotates the ends to be coiled.
2. ) The DNA is then wrapped around 8 histone proteins to form a nucleosome.
3. ) The Histone 1 protein (H1) makes sure the DNA stayed attached to the histone protein to form a chromatosome.
4. ) Linker DNA connects chromatosomess and coils the DNA.
5. ) Scaffold proteins help hold the coils together.
6. ) Protein and DNA together in this form is called chromatin.

Question 22

How is DNA loosened for transcription to occur?

Answer 22

• DNA is negatively charged due to its phosphate group while histones are positively charged due to lysin. This forms a tight grip between the DNA and histone proteins.
• Histone acetyltransferase places Acetyl groups on the histone proteins (-) charge which neutralizes the histone (+) charge, loosening its grip on the DNA.

Question 23

How is a chromosome in Eukaryotes shaped and labeled?

Answer 23

• They are usually linear and the top half (above the centromere) is known as the p region while the lower half ( below the centromere) is known as the q region.

Question 24

What are the four different types of chromosomes and what do they look like?

Answer 24

1. ) Metacentric: regular chromosomal shape
2. ) Submetacentric: p region shortens while q region lengthens
3. ) Acrocentric: p region shortens even more and q regions lengthen even more.
4. ) Telocentric: p region barely exists while the q region is fully lengthened.

Question 25

WHat are polycentric chromosomes?

Answer 25

• Chromosomes have more than one centromere throughout it.

Question 26

How could you determine where the centromere is on a piece of chromosome with just looking at the base pair?

Answer 26

• The centromere has repeated sequences that span hundreds to thousands of b.p. long.

Question 27

What is the kinetochore? Where is it located and what is its function?

Answer 27

• The kinetochore is a protein coat surrounding the centromere on chromosomes.
• Spindle fibers attach to the kinetochore during anaphase of mitosis and meiosis form sister chromatids to be pulled apart.

Question 28

What is a telomere? Why does a telomere need to be stabilized and how does it get stabilized?

Answer 28

• A telomere is found at the ends of chromosomes.
• Telomeres need to be stabilized to protect the chromosome from being degraded.
• It does this by forming a t-loop which is where one DNA strand is longer than the other at the end of the telomere, projects beyond the other, and binds to its complementary sequence forming a t-loop.
• The longer strand (which binds to itself) has a G- rich single-stranded overhang.

Question 29

What is shelterin and what does it do?

Answer 29

• Shelterin is a protein which binds telomeres together so they do not get replicated.