Cell/Molecular Biology Exam 1

What are the main differences between prokaryotes and eukaryotes in terms of the promoter for gene transcription?

In prokaryotes, a sigma factor binds to the RNA polymerase at the promotor on the strand of DNA to being transcribing the RNA. For eukaryotes, there is usually a set of nucleotides called TATA box located about 25 nucleotides upstream of start site.

Explain how the human species can only have 19,000 genes yet be very complex functioning organism?

Genes that code for proteins include exons that can be included or not through alternative splicing. For example, a gene that includes exons A-B-C-D-E-F-G can use all of the exons for one protein and then other combinations of the seven exons to make any other proteins.

Explain the outcome of having a high energy bond on the 3’ end of the transfer RNA. What will be attached at that site?

The high energy bond on the tRNA is “charged” with energy which will used to attach amino acids at the 3’ end

What kind of bonds are presented? What is the value of having this kind of bond between the bases of a DNA molecule?

The bonds are hydrogen bonding which are weak bonds that can easily be broken. The value of this bond here is the ease of separating the two strands of the double helix so the coding strand can be accessed and transcribed.

What are the 3 DNA functions in the context of genetic instructions?

DNA can store, retrieve, and translate genetic instructions

True or False: the flow of genetic information goes from RNA - DNA- protein

False; DNA - RNA - protein

How many codes are illustrated in the mRNA - AUGCUCAGCUUAGCGAUUCCGGAGATG

9 codons

every polypeptide chain synthesized from RNA starts with which amino acid?

Methionine

According to the table of the Genetic Code, changing the second base of the codon

always changes the amino acid that is encoded

Match the following terms with their proper description: terminator, promoter, RNA polymerase, and elongation

The RNA strand growing one amino acid at a time: elongation

Creates an RNA copy of a gene: RNA polymerase

A sequence of bases that determines the end of the gene: terminator

DNA sequence in front of the gene that determines the start of transcription: promoter

if a coding strand of DNA has the sequence AAGCTC, transcription will result in

an mRNA strand with the sequence AAGCUC

if a template strand of DNA has the sequence AAGCTC, transcription will result in

an mRNA strand with the sequence UUCGAG

RNA splicing removes from the mRNA while keeping the

introns; exons

which of the following processes occurs in the nucleus of a cell

All the above - RNA splicing, addition of a 3’ tail, and addition of 5’ cap

true or false: a codon reads AUA. The anticodon that recognizes it is TAT

False; no T’s are in RNA so the anticodon would be UAU

List the key steps of initiation in DNA replication

The mRNA binds to the small ribosomal subunit

The initiator tRNA binds to the P site

The large ribosomal subunit binds to the small ribosomal subunit

starts at origins of replication location where proteins bind to this site recruiting other enzymes like helicase to start the process

List the key steps in unwinding in DNA replication

The helicase enzyme unwinds the double stranded DNA by breaking the hydrogen bonds holding the strands together creating replication forks. Single strand binding proteins bind to the strands together creating keep from rewinding

list the key steps to priming in DNA replication

enzyme primase synthesizes short strands of RNA called primers on the separate DNA strands providing DNA polymerase to begin adding new nucleotides

list the key steps in elongation of DNA replication

DNA polymerase binds to the RNA primers adding new complementary nucleotides to each template strand

leading strand: continuously replicating in direction of replication fork

lagging strand: synthesized dis continuously in short fragments called okazaki fragments moving away from replication fork

list the key steps in proofreading/repair in DNA replication

DNA polymerase correcting errors by detecting and replacing mispaired nucleotides and can fix DNA damage

list the key steps in termination of DNA replication

once entire DNA molecule is copied, replication ends at specific termination sites where RNA primers are replaced with DNA nucleotides by DNA polymerase

list the key steps in ligation of DNA replication

enzyme DNA ligase seals the gaps between newly synthesized fragments (okazaki on lagging strand) forming a continuous DNA molecule

list the 7 steps of DNA replication

1. initiation

2. unwinding

3. priming

4. elongation

5. proofreading/repair

6. termination

7. ligation

Translation converst the information store in into a

RNA; polypeptide

Briefly describe the different kinds of mutation: silent, missense, nonsense, and frameshift

silent - does not change the translation of the protein

missense - changes the amino acid code

nonsense - changes amino acid codon to a stop codon

frameshift - shifts the entire set of codons

Unicellular vs. Multicellular

unicellular - complete and can make colony with division

multicellular - special features; a piece were to wander and get lost can’t reproduce itself

What are the 4 building blocks and how are they paired?

Adenine, Thymine, Guanine and Cytosine

AT and GC

What conformation do proteins fold into where free energy, G, is minimized?

lowest free energy

how many stretches of peptides, and length of amino acids is beta sheet?

4-6 stretches; 8-10 amino acids

What bonds are associated with proteins?

hydrogen bonding

What protein activity depends on the ability to bind to other molecules? And what happens to these?

Ligands; proteins have a “pocket” that grabs the ligands and hold tightly

What are the different hydrogen bondings on a DNA strand

Back bone to backbone; Backbone to side chain; side chain to side chain

Explain the central dogma

DNA is transcribed into RNA which is translated to proteins; DNA can replicate itself; with the use of reverse transcriptase enzyme RNA can be transcribed back into DNA

What is the function of DNA in the context of genetic instructions?

To store, retrieve, and transcribe genetic instructions

What happens during condensation reactions also known as dehydration?

A water molecule is lost every time a macromolecule is put together; phosphate group drops the water as well as a sugar base drops a water

Which end (5’ or 3’) carries an unlocked -OH group attached to the 3’ position on the sugar ring?

3’

Which end (5’ or 3’) carries a free phosphate group attached to the 5’ position on the sugar ring

5’

What is a segment of DNA that contains instructions to make a protein or RNA molecule

Gene

What is the total genetic information of a cell/organism

genome

What type of proteins are equal in amount to DNA in forming chromosomes?

Histone and nonhistone proteins

What is the name of the core that has 8 histone proteins?

nucleosome

What is DNA plus both forms of protein?

chromatin

Nucleosomes have high proportion of what kind of charged amino acids (arginine and lysine) to bind tightly to DNA backbone?

positively charged

In the most condensed form, DNA molecule is how many times shorter than its fully extended length?

10,000 times

what form of chromatin is most highly condensed form of interphase chromatin?

heterochromatin

What kind of chromatin is less condensed and more available?

Euchromatin

Most cell types express what percentage of their genes?

30%

In permanent slicing, what is a highly condensed structure due to inactivation of a single X chromosome in females?

Barr body

What enzyme unwinds double stranded DNA by breaking the hydrogen bonds holding them together?

Helicase

What is the origin replication?

where DNA replication process begins forming bubbles with replication forks

What direction is DNA replicated?

5’ to 3’ end

Replication of DNA molecule begins at sites called what which are short stretches of DNA?

origins of replication

what enzyme is a protein that prepares for DNA replication; attaches to DNA at origing of replication and separates the two strands of double helix

Helicase

What enzyme makes primers to start the process of replication?

primase

DNA is the protein that adds nucleotides to the growing DNA molecule

polymerase

DNA ligates (links together); catalyzes phosphodiester bond 3’-OH end and 5’ phosphate end

ligase

Since DNA replication is 5’ to 3’ end direction what direction do daughter strand replicate continuous on?

3’ to 5’ template

What end do DNA polymerases add nucleotides?

3’ end NEVER 5’ end

Replication discontinous on 5’ to 3’ template forming short what kind of fragments (5’ to 3’ stop, 5’ to 3’ stop, etc… until end)?

Okazaki

What does DNA proofreading do and which direction does it occur?

detect and correct mismatched nucleotides in the new synthesized DNA strand before mutations can become permanent. It occurs 3’ to 5’

DNA connects adjacent fragments where ATP is required to connect the phosphate backbone

ligase; Okazaki

Explain what happens in Topoisomerase I

one strand is clipped and passes the other through to relief stress

Explain what happens in Topoisomerase II

both strands are clipped and a double strand is passed through

Long repetitive sequences are called?

telomeres

What are agents that cause mutations to DNA called?

mutagens

Does the most DNA damage due to chemical reactions occur inside or outside the cell?

inside

Correction of DNA damage is immediate due to what?

DNA repair

A point mutation in DNA that substitutes a pyrimidine for another pyrimidine or a purine for another purine and can result in a silent mutation? A transition or transversion?

Transition

A point mutation that substitutes a pyrimidine for a purine and can result in damage to the genetic code for proteins? transition or transversion?

transversion

Spontaneous DNA damage is caused by what?

water

What happens during deamination?

An amine is taken away; cytosine is change to uracil which binds to guanine (point mutation)

What happens during depurination?

a purine structure is taken away; water comes in taking this purine; frameshift mutation (missing teeth) and can be repaired with base excision method

What is a nonhomologous end joining?

A double stranded pieced back together to avoid drifting fragmenets; repair enzymes clean up broken ends and even digest nucleotides; repair can cause a small deletion

What strand is a segment of DNA that codes for a protein?

coding

what strand is COMPLEMENTARY base pairs with the coding strand?

template

The resulting mRNA will be an exact copy of coding strand except what base will be replaced with what base?

Thymine will be replaced with Uracil

What is a dissociable subunit of RNA polymerase and is only used in what

sigma factor; prokaryotes

what kind of box is a feature of many eukaryotic promoters?

TATA box

In eukaryotes, what is the name for the coding regions? Introns or exons?

exons

In eukaryotes, what is the name for the noncoding regions? Introns or exons?

introns

What percentage of human genes undergo alternative splicing?

90%

What kind of mRNA is initially transcribed?

pre mRNA

what mRNA is the final trancripted mRNA?

mature mRNA

In human genome, about what x 10 to the what bases of DNA (haploid)

3.2 × 10^9

What are the 4 letters of nucleic acid language?

A G C T

What is the term for the 20 letter amino acid language?

genetic code

What is the term for three consecutive nucleotides that specify amino acids?

codon

What is the term for when most amino acids have more than one codon?

redundant

What are the 3 stop codons?

UAA, UGA, and UAG

What is the role of transfer RNAs (tRNAs)?

to transfer amino acid to the mRNA molecule

What is responsible for charging the correct amino acid to a specific tRNA and uses nucleotide sequences in the anticodon and acceptor arm of tRNA?

aminoacyl tRNA synthetases

What does the acceptor arm do?

carries the tRNA

Explain the 4 step cycle of translation

1. a charged tRNA carrying an amino acid enters the A site of the ribosome and the anticodon of the tRNA must be complementary to the codon on the mRNA

2. the ribosome catalyzes a peptide bond between the amino acid on the A site and growing polypeptide chain attach in the P site; the chain is transferred to the tRNA in the A site

3. ribosome shifts codon down the mRNA and the tRNA in the P site moves to the E site (exit site) and the tRNA in the A site that is carrying the peptide chain moves to the P site

4. the uncharged tRNA in the E site is released from the ribosome; A site is empty and ready to accept the next tRNA and to repeat

When does translation end?

Once a stop codon is created the polypeptide is terminated and released; ribosome dissociated and used to process another protein

What is the name of the sequence where a ribosomal binding site is about 8 base pairs upstream from the AUG start site in bacterial and archael mRNA (prokaryotes)?

Shine-Dalgarno

What is the starting codon?

AUG

What kind of mRNA that encodes two or more proteins in prokaryotes?

polycistronic

What is the term for covalent attachment of chain of small proteins for protein degradation?

ubiquitin

What is a silent mutation?

a change where a base pair is altered but there is no change in the polypeptide

What is a missense mutation?

a change in one of the codons; now coding for a different amino acid