BIO 412 EXAM #1

What is the central dogma of molecular biology and what is an exception to it? [lecture #1]

the flow of genetic information, DNA is transcribed into RNA and mRNA is translated to proteins. An exception to it is introns.

what is molecular biology

the study of the structure and function of organic macro molecules

what are the four main types of macromolecules and their monomers

1. nucleic acids: nucleobases

2. proteins: amino acids

3. lipids; fatty acids

4. carbohydrates; sugar residues

What are the three components of nucleotides?

1. a nitrogenous base

2. a phosphate group

3. a five carbon sugar

Which ribose molecule is used for DNA and which is used for RNA?

for DNA deoxyribose for RNA ribose

what type of bonds are used to form nucleic acid polymers?

phosphodiester bonds are used to join together nucleotides

what nitrogenous bases are purines? what do purines have?

guanine and adenine, purines have two rings

what nitrogenous bases are pyrimidines? what do they have?

Thymine, cytosine, uracil, they have one ring

What is the meaning of 5’ and 3’ and how are they important when
nucleotides are joined together in a chain to form nucleic acids?

The 5’ end is the one with the phosphate group while 3’ is the downstream region of the strand. Nucleotides are added to the 3’ end of the chain to form nucleic acids. the phosphate bridges the 5’ carbon of one nucleotide to the 3’ carbon of the next nucleotide.

how would you know if a nucleotide is used in DNA or RNA? 

If it were used in RNA there would be an OH group on the 2’ carbon. If it were used in DNA there would be a lack of OH on 2’ and instead a hydrogen on 2’

which bases pair together between the two strands of double stranded DNA? What type of bonds link these pairs together?

adenine pairs with thymine and they form two hydrogen bonds

cytosine pairs with guanine and they form three hydrogen bonds

What are transcription and translation?

transcription is when the DNA is used a template to make RNA

translation is when the RNA is used as a template to make protein

what are phenotypes and what determines them?

they are observable traits. Our genetic code and environment determines them

What is the most common type of genomic variation? What are two of
the less common types of genomic variation

the most common type of genomic variation is single nucleotide polymorphisms

two of the less common ones are copy number variants and sequence repeats

How many chromosomes do most humans have?

23 chromosomes, 22 are homologous autosomal chromosomes and 1 is sex chromosome

define homologous chromosomes

when you have two copies of a each chromosome one from your mom and one from your dad

the complete human genome encompass what

genomic DNA and mitochondrial DNA

What is recombination? How does it make the chromosomes we
receive from our parents a bit different than theirs?

when homologous chromosomes swap genetic material during meiosis

define a gene

a chromosomal region that is capable of making functional transcript.

define exon

sequences that are encoded as RNA and code for the final product

define intron

regions that are spliced out of the RNA before the final product is made

define the promoter region

the promoter region is the 5’ end where RNA polymerase binds to initiate transcription

define enhancer

segment of DNA that can be bound by proteins called activators that increase the transcription of a gene

define silencer

segment of a gene that prevents transcription by binding to repressor proteins that bock RNA polymerase

define open reading frame

the region of DNA from start to stop of a gene

definen the poly A cap

it is the addition of a poly(A) tail to the 3’ end of mRNA, it is made of a bunch of adenosine monophosphates

What is the most common conformation of the DNA double helix
called? name two traits

B-form DNA,

1. it is a right handed double helix the base pairs form a ladder on the interior of the helix

2. it has a hydrophilic sugar phosphate backbone

In B-DNA the helix forms what two things

1. a major groove

2. a minor groove

what are two other confirmations of DNA and breifly describet hem

1. A-DNA: a right handed helix but the grooves are more evenly sized

2. Z-DNA: a left handed helix which results from methylation of cytosine

What does it mean that DNA replication is “semi-conservative”? [Lecture #2]

when a cell copies the DNA , a new helix contains one original parental strand and one new synthesized strand.

why is replication fast in bacteria compared to humans

1. human DNA is more difficult to access

2. human DNA undergoes a lot of proof reading and repair during replication

how can DNA mutations be detrimental to an individual organism?

a mutation can interfere with a cells function.

when might mutations be benficial to a specieis?

when a mutation can create genetic diversity that allow a species to adapt to changing environments.

DNA synthesis is catalyzed by what?

DNA polymerase, It catalyzes the addition of dNTPs to the 3’-OH end of a polynucleotide chain. Can only synthesize in the 5’ to 3’ direction

DNA synthesis is driven by what

a large favorable free energy change caused by the release of pyrophosphate

what is a DNA replication fork?

when the two strands of the double helix separate a region of replication that moves along the parental DNA helix is called the replication fork.

Why can’t DNA replication proceed in the same direction on the
two two strands of template DNA at a replication fork? what is the cells solution to this problem?

DNA replication can not proceed in the same direction because of the antiparallel orientation of the two DNA strands. DNA polymerase can only synthesize in the 5’ to 3’ direction. To solve this the cell uses okazaki fragments.

what are the leading and lagging strand?

1. the leading strand is the strand the allows continuous replication in the 5’ to 3’ direction

2. the lagging strand is in the wrong direction to allow continuous 5’ to 3’ replication

how does replication proceed in the lagging strand

1. Primase creates RNA primers to start DNA synthesis at intervals

2. DNA polymerase (DNA pol alpha) synthesizes DNA starting from one primer to the next creating okazaki fragments

3. Nucleases that recognize RNA hybrids remove the RNA primers

4. Repair DNA polymerase fills in the primer space with DNA

5. ligase connects the fragments

what are okazaki fragments

the short synthesized pieces of DNA on the lagging strand

define fidelity of replication

how accurate the daughter strands of DNA are made using the parental DNA as a template.

What is EXONUCLEOLYTIC PROOFREADING

it is how DNA polymerase removes incorrect nucleotides during DNA replication. After nucleotide binding , DNA polymerase undergoes a conformational change which makes its grip tighten around the active site. This occurs more readily with the correct base pairing, this feature allows DNA polymerase to double check before adding another nucleotide The mismatched nucleotide is excised by the exonuclease domain of polymerase and replaced with the correct pair.

what two proteins denature the double helix and stabilize the single strands

1. DNA helicase

2. single stranded DNA binding proteins

how does helicase denature

Helicase hydrolyzes ATP when they are bound to single strands which causes a shape change of the protein, helicase uses this to propel itself along a DNA single strand. when it reaches a double helix region it continues to pry apart the helix.

how do single strand DNA binding proteins stablize single strands

single strand DNA binding proteins stabilize by coating and straightening out the regions of single stand DNA to prevent hairpin helices that can prevent DNA synthesis

what keeps DNA polymerase firmly on the DNA when its moving

a clamp protein (PCNA), it keeps DNA polymerase firmly on the DNA until a double helix region is reached

What is the “winding problem” that arises during DNA replication
and how do cells solve the problem?

It is when tension builds up in the front of the replication fork as it becomes overwound. To try and relieve some tension DNA becomes super coiled. DNA topoisomerase adds itself to the DNA backbone phosphate and breaking the phosphodiester bond in the DNA strand. it then re forms the bond as the protein leaves.

what does topoisomerase also prevent

the severe tangling problems that would arise during replication

What problem arises in DNA replication at the ends of linear
chromosomes? What is the cell’s solution to this problem?

The final RNA primer synthesized on the lagging strand can not be replaced by DNA because it lacks the 3’-OH needed for polymerase, this would lead to DNA lost from the ends of all chromosomes each time the cell divides. A solution is telomeres, repetitive sequences that cap the ends of chromosomes.

what does telomerase do

They are able to recognize telomere DNA sequences and replenish the sequence each time the cell divides.

how is telomere length regulated

in most somatic cells, telomeres gradually shorten, preventing the unlimited proliferation of cell in adult tissues.

what are some similarities and differences between RNA and DNA

RNA contains the base uracil DNA uses thymine

RNA has an OH group on the 2’ position DNA has H on its 2’ position

RNA polymer stability is much lower than DNA

what is the RNA world hypothesis

The idea that life on earth started with RNA not DNA. That early life used RNA to store genetic information like how DNA does now and to catalyze chemical reactions like proteins do now. RNA was both the gene and the enzyme in the very first life.

what are some inspiration to RNA world

1. RNA is capable of storing genetic information and is self replicating

2. RNA is capable of acting like an enzyme- some RNA called ribozymes can catalyze chemical reactions

Describe the three RNA motifs

1. sequence motifs: linear stretches of RNA sequence that act as binding sites for proteins or other RNAs

2. secondary structural motifs: different shapes formed by short regions of base paired RNA within stretched of unpaired RNA

3. tertiary structural motifs: 3D confirmations of secondary structural motifs

What are chaperones?

RNA binding proteins that help resolve misfolded structures or prevent misfolding. They do this by lowering the energy barrier needed to go form a nonstable to stable confirmation.

what are 3 factors contribute to RNA instability?

1. The OH group on RNAs 2’ position makes RNA susceptible to hydrolysis under alkaline conditions.

2. there are also RNAses that degrade RNA

3. the 2’ OH group can cause spontaneous cleavage

About how much of a cell’s total RNA is mRNA (by number, not by
mass)

1~5% of total cellular RNA

what do rRNA do and about how much of cells RNA is rRNA by mass

they are found in the ribosomes and assist with translation, about 80%

what does tRNA do

they provide amino acids to ribosomes for translation of mRNA into protein. This is done in the cytoplasm where translation takes place.

what does mRNA do

RNA that codes for protein

what does telomerase RNA do

it acts as a template for the telomerase enzyme that extends the ends of chromosomes

what does gRNA do

guide RNA, it is a synthetic RNA meant to find a target sequence for CRISPR

What are some similarities and differences between the RNA for
protein coding genes and for non-protein coding genes?

Protein coding genes contains enhancer, silencer, promoter, 5’UTR, 3’ UTR, terminator, exons and introns

non protein coding genes contains enhancer, silencer, promoter, terminator, exons some get a 5’ cap and poly A tail

what 3 diseases that result from defects in RNA

1. spinal muscular atrophy: mutations affecting splicing of SMN1 gene lead to non functional protein

2. myotonic dystrophy 1 and two: expansion of a non- coding repeat creates a toxic RNA that make protein non functional

3. MELAS: mutations in mitochondrial gene for tRNA make them unable to synthesize protein

what does this mutation mean N501Y

N is the original amino acid 501 is the specific position of the amino acid and Y is the muted amino acid

With 4 distinct bases (A, C, T, G) there are 64 possible 3-letter
codons. Why only 20 amino acids?

there is redundancy many different codons code for the same amino acids, there are also stop and start codons

Name 3 different types of proteins and their functions give example

1. structural proteins: provide physical support - collagen

2. enzymes: help catalyze reaction- DNA polymerase

3. Defense: protect from pathogens - antibodies

protein folding is driven by what

hydrophobic interactions, hydrophobic residues associate and exclude water molecules.

commonly occuring secondary protein structures are called what

domains or motifs

how do abberant proteins create and maintain a disease state

the mutations may lead to over-expression, gain of function, non functional or absence

what can cause double stranded DNA breaks

1. ionizing radiation like x-rays or sunlight

2. replication errors

3. oxidizing agents

what is the best way for doube stranded breaks to be repaired?

homologous recombination is the best way to repair double stranded break. If the break occurs in only one of two duplicated DNA double helices after replication has occurred, the undamaged double helix can be used as a template to repair the damage. This is the best way because it accurately repairs the damage at that specific site.

why homologous recombination not always available and what is the next best method what problems does this method give?

Homologous recombination is not always available because it requires sister chromatids. the next best method is non homologous end joining which sticks two broken sections together, this usually mean nucleotides are lost

How might a mutation in a gene involved in each of these
processes cause disease:
• Nucleotide excision repair

causes skin cancer

How might a mutation in a gene involved in each of these
processes cause disease:
Homologous recombination repair

breast cancer

How might a mutation in a gene involved in each of these
processes cause disease:

mismatch repair

colon cancer