MCAT DNA Structure and Synthesis

Question 1

Asexual v. Sexual reproduction

Answer 1

Asexual reproduction is genetically identical genetic material that comes from one parent.

Sexual reproduction is genetically distinct and comes from 2 offspring.

Question 2

Describe DNA in prokaryotes v. eukaryotes

Answer 2

In prokaryotes it’s a singular circular chromosome.

In eukaryotes it’s several linear chromosomes.

Question 3

Describe deoxyribonucleotides and ribonucleotides

Answer 3

Both are composed of a sugar group, nitrogenous base, and phosphates. 1 prime carbon contains nitrogenous base, 3 prime carbon contains -OH group , and 5 prime carbons attaches the phosphate groups.

DNA = Deoxyribose sugar
RNA= Ribose sugar

Question 4

What are chargaff rules?

Answer 4

There are equal concentrations of adenine and thymines, guanines and cytosines therefore they bind together in pairs in DNA.

Thymine is turned to uracil in RNA.

Question 5

Describe the structure of DNA?

Answer 5

Sugar- phosphate backbone on the outside ( phosphodiester bonds) while nucleotide pairs are on the inside. Attached to each other via hydrogen bonds.

Strands are antiparallel to each other.

G-C pairs has 3 hydrogen bonds which makes them more stable while A-T pairs has 2.

Question 6

What can RNA bond too?

Answer 6

Can binds to DNA or RNA. When it binds to itself it forms a hairpin structure.

Question 7

Definitions of annealed/ hybridized. Denatured/melt.

Answer 7

Annealed/ hybridized - strands are bonded to each other.

Denatured/melted- strands are separated.

Question 8

What are ways we can denature hybridized strands?

Answer 8

High temperature, urea, change in pH, salt concentrations.

Tm ( melting temperature) is the temperature in which 50% of the DNA strands melted.

When temperature falls below Tm the strands reanneal.

Question 9

How is DNA replication described?

Answer 9

Semiconservative with each new DNA having 1 parental strand and 1 daughter strand.

Question 10

Where does DNA replication begins?

Answer 10

At the ORI ( origin of replication). Enzymes denature DNA strands at these sites.

Once ORI is denatured a replication bubble is formed in which replication happens bidirectionally. Eukaryotes has many ORIs while prokaryotes has one.

Question 11

Describe the steps of DNA replication

Answer 11

1. Helicase unwinds at the ORI and forms replication forks that are bidirectional. Single-strand binding proteins attach to each strand and prevents them from re-annealing.
2. As helicase unwinds it leads to tension ahead of it so topoisomerase create knicks to relive the stress and prevent supercoiling.

3.DNA Polymerase III synthesize new DNA from 5’ to 3’ Requires an RNA primer to attach too this is layed down by primase. Leading strand is make continously while lagging strand is make discontously away from the replication forks via okazaki fragments.
DNA Poly. layes down dNTPs and forms phosphodiester bonds by having a 3’ -OH group attach 5’ phosphate group. Reaction is a condensation reaction and results in a pyrophosphate from being released.

4.DNA polymerase I removes RNA primers and replaces them with DNA. DNA ligase glues the strands together.

Question 12

Which direction is dNTPs added to the growing strand?

Answer 12

Synthesized from 5’ to 3’ and so is new dNTP is attached to the 3’ end.

Question 13

Telomerase

Answer 13

Enzyme that produces repetitive sequences on DNA strand so with each replication cycle the DNA shortens and removes telomeres and not coding DNA.

Question 14

Central dogma

Answer 14

States DNA -) RNA -) Protein

Question 15

Describe where transcription and translation happen in the cell in eukaryotes, prokaryotes?

Answer 15

In eukaryotes, transcription happens in the nucleus while translation happens in the cytoplasm.

In prokaryotes, transcription and translation happens in the cytoplasm.

Question 16

What is a promoter? Upstream and downstream?

Answer 16

Promoter initiates the beginning of a coding region of DNA.

Upstream is the promoter and all the nucleotides before it while downstream is the coding region and the terminator sequence.

Question 17

Describe the steps of transcription?

Answer 17

1. Initiation - RNA polymerase II binds to TATA box in the promoter with help of general transcription factors ( w/o primers) and unwinds strand. Creates two strands: sense ( coding) strand and antisense ( noncoding ) strand.
2. Elongation - RNA polymerase II transcribes RNA in 5’ to 3’ direction using the antisense ( noncoding strand) as template therefore the sense ( coding ) strand would be directly similar to the newly made RNA strand.
3. Termination - Once RNA Poly. reaches the termination sequence:

prokaryotes- RNA poly detaches from DNA. It’s mature RNA.

Eukaryotes - RNA poly transcribes terminator sequence which contains the polyadenylation sequence which codes for proteins to bind and dissociate the complex. Must undergo processing to become mature RNA.

Question 18

Describe pre-mRNA processing in eukaryotes?

Answer 18

5’ cap ( a modified GTP) prevents degradation in cytoplasm and for the ribosome to recognize mRNA.

3’ cap ( poly-A-tail) prevents degradation in the cytoplasm and allows mRNA to exit the nucleus to cytoplasm via nuclear pores.

Question 19

Describe the actions of spliceosome?

Answer 19

Spliceosome ( proteins + snRNAs) removes introns ( noncoding) and keeps exons ( coding).

Spliceosome recognizes introns via the splice donor site ( 5’ end of intron) and splice acceptor site ( 3’ end of intron)

Question 20

Alternative pre-mRNA processing

Answer 20

Introns and exons are removed or kept in in different ways to allow different isoforms of a protein.

Question 21

What is the process of translation?

Answer 21

Process of converting a mRNA strand to a protein using ribosomes.

Sets of 3 nucleotides are called codons and codes for an amino acid.

mRNA is read in the 5’ to 3’ direction.

Start codon is where translation start ( AUG) with the stop codons being UAG, UGA, UAA.

Question 22

Which RNA is responsible for attaching correct amino acid to the correct codon?

Answer 22

transfer RNA ( tRNA)

tRNA contains anticodons which binds to corresponding codons.

Question 23

Third- base wobble

Answer 23

When there is relaxation of watson- crick base pairing rules in the third nucleotide.

Question 24

Aminoacyl tRNA synthetase

Answer 24

Enzyme that attaches amino acid to tRNA via an ester linkage. Once this happens it’s referred to as a charged tRNA.

Question 25

What does it mean when they say the genetic code is degenerate or redundant?

Answer 25

Different codons can code for the same amino acid.

Question 26

Describe the differences between eukaryotic and prokaryotic ribosomes?

Answer 26

Eukaryotic ribosomes are larger being 80s with 60s large subunit and 40s small subunit.

Prokaryotic ribosomes are smaller being 70s with 50s being the larger subunit and 30s being the small subunit.

Question 27

Where are rRNA genes located in the nucleus?

Answer 27

The nucleolus. Appears very dark under the microscope.

Question 28

How does the ribosome catalyze the formation peptide bonds?

Answer 28

Peptidyl transferase enzyme

Question 29

EPA sites of ribosomes

Answer 29

Exit site is where the discharged tRNA leaves.

Peptidyl site has the tRNA that holds the growing polypeptide chain.

Aminoacyl site- site for the incoming charged tRNA.

Question 30

Describe how the translation initiation complex forms?

Answer 30

The small ribosomal subunit binds initiator tRNA ( holds AUG) in the p site.

mRNA than attaches at the 5’ cap and moves in the 5’ to 3’ direction until it reaches the start codon.

When start codon is reached the large subunit binds with the support of protein initiation factors via GTP hydrolysis.

Question 31

Describe the regions of mRNA?

Answer 31

The open reading frame ( ORF) is the section of mRNA that’s translated.

5’ UTR is the region before the start codon.

3’ UTR is the region after the stop codon.

Question 32

Describe the elongation phase of translation.

Answer 32

A- site attaches the incoming charged tRNA.
It moves to the P site where it holds the growing protein chain. Peptidyl transferase in the large subunit catalyze formation of peptide bonds.

It then moves to the E site where the tRNA is released.

Question 33

How does translation initiation complex ends?

Answer 33

Once a stop codon attaches to A- site. Release factors detaches protein from ribosome.

Then protein release factors separate ribosome subunits via GTP hydrolysis.

Question 34

How does finished proteins know which cellular destination to go to?

Answer 34

Contains a signal peptide sequence within the N-terminus.

Question 35

What are some of the post- translational modifications of proteins?

Answer 35

Chaperone proteins aid in folding it into a 3D shape.

Add chemical modifications:
- Lipidation = adding a lipid group.
- Ubiquitination = adding a protein.
- Glycosylation = adding a carbohydrate group.

Proteolysis of the inactive part of the protein ( removing of zymogen).

Question 36

Mutagens and carcinogens

Answer 36

Mutagens are agents ( chemical, physical, or biological) that can cause mutations in DNA.

Carcinogens are mutagens that cause cancer.

Question 37

What types of mutations are passed down?

Answer 37

In eukaryotes only germline mutations ( mutations of germ cells ) can be passed down not somatic cells.

In prokaryotes all mutations are passed down.

Question 38

Point mutations

Answer 38

Mutations that effects one nucleotide therefore effecting the pairing nucleotide.

Question 39

What are the three point mutations?

Answer 39

Missense mutation- mutation that changes an amino acid in the protein, can disrupt function.

Nonsense mutation - mutation that leads to a premature stop codon, shortening the protein, can disrupt protein function.

Silent mutation - mutation that doesn’t change the amino acid, no disruption in the function of the protein.

Question 40

Frameshift mutation

Answer 40

Insertion or deletion of nucleotides leads to disruption in the reading frame, often leads to dysfunctional protein.

Question 41

In- frame mutations

Answer 41

insertion or deletion of a codon which leads to an additional amino acid or taking away an amino acid from protein. This can lead to nonfunctional protein but the protein is intact.

Question 42

Each cell in the body contains the same genome but has different functions why?

Answer 42

The cells participate in selective transcription of genes that’s important for their function.

Only a subset of genes are constitutively ( always) made, they’re called housekeeping genes and are responsible for general maintenance of the cell.

Question 43

Histone acetylases v. Histone deacetylases

Answer 43

Histone acetylases add acetyl group to histone tails and lead to euchromatin as DNA + histone binding is loosen.

Histone deacetylases remove acetyl group for tails which leads to heterochromatin as DNA + histone binding is tighten.

Question 44

DNA methyltransferases

Answer 44

Adds methyl groups to histone tails or cytosine bases causing DNA + histone tightening and heterochromatin.

DNA methyl enzymes that remove methyl groups loosen the bond and leads to euchromatin.

Question 45

Epigenetic inheritance

Answer 45

DNA methylation and acetylation patters are passed from parent to offspring this leads to genomic imprinting in mammals.

Unlike mutations these can be removed.

Question 46

How can regulation of proteins happen at the level of transcription?

Answer 46

Transcription factors bind to enhancers ( speed up transcription). They can be close to the gene or far away or even located within an intron.

Multiple enhancers for a gene controls expression variably.

Activators = speed up transcription
Repressors = decrease transcription

Question 47

What are the domains of transcription factors?

Answer 47

DNA binding domain which binds to the enhancer and the activation domain which binds to other proteins to help with transcription initiation.

When transcription factor’s activator site is bound to the enhancer the DNA strand loops around so that the activator site interacts with the transcription initiation complex.

Question 48

How does transcription repressors work?

Answer 48

They decrease process of transcription by either competing with activators for enhancer site, block activators from binding to enhancers, or bind to enhancers to prevent activators from binding.

Bind to silencers

Question 49

How are proteins broken down in the cell when they’re not wanted anymore?

Answer 49

via polyubiquitination in which multiple ubiquitin proteins covalently bonded to each other on the protein marks it for destruction by protesomes.

The proteosome breaks them down into oligonucleotides and spits them out into cytoplasm where they are further broken down into amino acids.

Question 50

Role of noncoding RNAs ( ncRNAs) ?

Answer 50

They bind to mRNA and attract other proteins to form a complex and either lead protein to degradation or just silence it.

Two types of ncRNAs are microRNAs ( miRNA) and small interfering RNAs ( siRNA)