BIOL1004 Study Guide - Final Guide: Meristem, Helicase, Beetroot

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5 Jun 2018

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Molecular Genetics

DNA replication

• Primase, DNA polymerase I, ligase needed

RNA

Use:

• Info needs to get where it is needed (usually not the nucleus)

• DNA is single copy → different genes need to be represented in different

copy numbers

• Less stable, more flexible

• However no backup in case of mutation (single strand)

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Translation

Proteins

• Structural

• Regulatory

• Catalytic

Model Organisms

• Research is done to benefit humans

• Research for other organisms is often too difficult (hard to keep alive,

slow reproduction, too large genomes)

Characteristics of model organism

• Representative of many other organisms and processes

• Readily available

• Easy to keep alive

• Reproduces easily and quickly

• Lot of information available

• Genome is sequenced

Modelling

Type of

Name of

Characteristics of

Limitations

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organism

Sub cellular

processes

(does not

require

multi

cellularity)

Prokaryotic

cell

E. Coli

Easily obtained, cultured

and manipulated, not

complex

No ER, Golgi or

mRNA splicing

and

cell wall present

Model

eukaryotic

cell

Saccharomyces

cerevisiae

(yeast)

Domesticated for over

4000 years (we know

what it likes, how to

work with it)

Cell wall present

Parasite

Mycoplasma

genitalium

• Minimal organism-

only has genes that are

crucial for maintaining

life (smallest known

genome)

• First artificial

organism

• Modeling life

Cellular

interactions

(does not

require

tissues)

Slime mold

with uni and

multicellular

life stages

Dictyostelium

discoideum

• Can move, follow

signals and solve

problems

• Eat bacteria → when

there is no bacteria to

eat they become

multicellular

Autotrophic

alga with

uni and

multicellular

life stages,)

Chlamydomonas

reinhardtii

• Can move, follow

signals and solve

problems

Has flagellae,

unlike other plants

and requires a

pyrenoid

(organelle that no

other plant has)

Plants

Unicellular

moss

Physcomitrella

patens

• Grows readily in vitro

• Can be blended and

cultured

MODEL

PLANT

Arabidopsis

thaliana (Thale

cress)

• Fast generation time

• Easy to grow

• Has seeds, flowers,

roots, can model

biological

interactions

• Can be grown in test

tubes, on petri dishes

• Only can’t model

forest growth

A.thaliana has a

small genome-

copy number of

genes is not

representative of

most plants

Annual and fewer

specialised

mechanisms for

interacting with

other species than

trees and

perennials do

Model

nitrogen

Medicago

truncatula

• Fast generation time

• Easy to grow

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Document Summary

Dna replication: primase, dna polymerase i, ligase needed. Use: dna is single copy different genes need to be represented in different. Info needs to get where it is needed (usually not the nucleus) copy numbers: less stable, more flexible, however no backup in case of mutation (single strand) Model organisms: research is done to benefit humans, research for other organisms is often too difficult (hard to keep alive, slow reproduction, too large genomes) Characteristics of model organism: representative of many other organisms and processes, readily available, easy to keep alive, reproduces easily and quickly, lot of information available, genome is sequenced. Sub cellular processes (does not require multi cellularity) organism. 4000 years (we know what it likes, how to work with it: minimal organism- only has genes that are crucial for maintaining life (smallest known genome, first artificial. No er, golgi or mrna splicing and cell wall present.

Related Questions

QUESTION 1. Choose the true statement about prokaryotic and eukaryotic DNA replication.

A.Eukaryotic DNA replication involves less protein factors than does prokaryotic DNA replication.

B. Prokaryotic DNA polymerases replicate DNA 5' to 3', while eukaryotic DNA polymerases replicate DNA 3' to 5'.

C. Eukaryotic DNA replication begins at multiple origins of replication, while prokaryotic DNA replication begins at a single origin of replication.

D. Prokaryotic genomes take longer to replicate than eukaryotic genomes.

QUESTION 2. Bacterial cells use DNA replication to:

A. make back-up copies of their genome in case of a mutation.

B. manifest multiple phenotypes at once.

C. copy their genetic material prior to binary fission.

D. build functional proteins.

QUESTION 3. Choose the true statement about the genetic code.

A. A cell's mRNA code is read four nucleotides at a time to specify a single amino acid.

B. The genetic code encodes 64 amino acids, one for each of the 64 corresponding codons.

C. The genetic code is redundant, with multiple codons specifying a single amino acid.

D. The genetic code varies widely among organisms, with each having a different set of codons for a corresponding amino acid.

QUESTION 4. Of the following enzymes, which are correctly matched with their function? To be marked correct, you'll need to select all correctly matched statements, as there may be more than one correct answer.

A. Helicase, relieves torsion stress as DNA unwinds

B. Ligase, covalently bonds adjacent Okazaki fragments

C. Primase, removes RNA primers

D. DNA polymerase III, builds most of the DNA on the leading and lagging strand

QUESTION 5. Which of the following contributes to DNA replication accuracy? To be marked correct, you'll need to select all true statements, as there may be more than one correct answer.

A. The capacity to proofread improves DNA replication accuracy.

B. A slow rate of DNA replication contributes to accuracy.

C. The use of primase improves DNA replication accuracy.

D. DNA replication accuracy is improved thanks to complementary base pairing rules.

Which of the following did Erwin Chargaff observe?

A)	Base composition changes as the organism ages.

B)	Base composition of DNA does not vary from one species toanother.

C)	In all species the number of adenines equals the number ofguanines.

D)	In all species A + T = G + C.

E)	DNAs isolated from different tissues of the same species havethe same base composition.

The melting temperature (Tm) of a DNA duplex is:

A)	the temperature at which double-stranded nucleic acids degradeinto free nucleotides.

B)	the temperature at which double-stranded DNA is toosingle-stranded to ever renature back to double strands.

C)	the temperature at which double-stranded DNA is completelymelted.

D)	the temperature at which double-stranded DNA has become 50%single-stranded.

E)	the temperature at which double-stranded DNA begins to melt.

Given your knowledge and the descriptions of each of thesemethods, which of the following does NOT rely on the ability ofnucleic acids to hybridize with each other?

A)	Southern blotting for the detection of specific DNA fragmentsthat have been separated by gel electrophoresis.

B)	Colony blot hybridization to identify a specific sequence from acollection of sequences that have been inserted into bacteria.

C)	Northern blotting for the detection of specific RNA fragmentsthat have been separated by gel electrophoresis.

D)	A DNA oligonucleotide microarray incubated with probes made fromcDNA.

E)	Western blotting for the detection of specific proteins thathave been separated by gel electrophoresis.

Which of the following is a possible reason why DNA uses thymineinstead of uracil?

A)	Cytidine is deaminated to uracil so it would be difficult forany repair mechanism to differentiate between uracil that belongsin the sequence and uracil that resulted from deamination.

B)	Adenine is deaminated to uracil so it would be difficult for anyrepair mechanism to differentiate between uracil that belongs inthe sequence and uracil that resulted from deamination.

C)	When uracil is bound to a deoxyribose it will become morereactive, forming covalent bonds with other bases.

D)	None of the above.

Which of the following is an enzyme used in cloning to breakcovalent bonds?

A)	DNA ligase

B)	Restriction endonuclease

C)	Reverse transcriptase

D)	DNA polymerase I

E)	Alkaline phosphatase

Which of the following could you use to remove the 5' phosphatesafter cleavage of a plasmid with a single type of restrictionenzyme to ensure that the plasmid would not simply fuse backtogether upon addition of ligase?

A)	Reverse transcriptase

B)	Alkaline phosphatase

C)	DNA ligase

D)	DNA polymerase I

E)	Restriction endonuclease

Which of the following would you use to create a cDNA librarythat you would not use for a genomic library?

A)	Alkaline phosphatase

B)	Reverse transcriptase

C)	Restriction endonuclease

D)	DNA ligase

E)	DNA polymerase I

A plasmid vector typically has which of the followingfeatures?

A)	An origin of replication

B)	A selectable marker to ensure that the only bacteria growingcontain the intact or recombinant vector.

C)	Unique restriction sites for insertion of DNA.

D)	Small size to facilitate entry into the cell and biochemicalmanipulation of the DNA.

E)	All of the above are features of plasmid vectors.

Which of the following is FALSE of genomic or cDNAlibraries?

A)	Genes represented in cDNA libraries include control sequencesthat direct transcription.

B)	cDNA libraries contain cDNAs made from mRNA.

C)	Genomic libraries contain fragments of genomic DNA that aregenerated by partial digests with restriction enzymes.

D)	Genomic libraries usually contain large fragments and are likelyto be constructed in YAC or BAC vectors.

E)	cDNA libraries contain sequences from expressed genes only.

Which of the following is NOT a typical component of apolymerase chain reaction (PCR)?

dNTPs

B)	DNA containing the sequences to be amplified

C)	DNA ligase to connect the fragments together

D)	Primers complementary to each end of the sequence to beamplified

E)	Heat stable Taq polymerase

How can a fusion protein be formed?

A)	Site-directed mutagenesis where a fragment is replaced with asynthetic sequence containing the altered DNA sequence.

B)	Two proteins can recombine in the bacterial cell to form a newhybrid protein.

C)	Portions of two different genes are ligated together to create anew hybrid gene. When expressed the gene product is a fusion of thetwo gene products.

D)	Using oligonucleotide-directed mutagenesis to introduce specificmutations that cause the expressed protein to fuse to otherproteins.

E)	A portion of the gene can be removed to form a shorter gene andtherefore a shorter protein.

Why is green fluorescent protein (GFP) so useful in visualizingfusion proteins in eukaryotes?

A)	The GFP protein recognizes and binds to fusion proteins allowingthe location of the fusion protein to be determined.

B)	The reaction is only dependent on the presence of GFP and oneother cofactor.

C)	It is easily cloned and expressed in bacterial cells.

D)	The presence of just a few molecules of GFP fusion proteins canbe sufficient for observing the proteins microscopically allowingthe study of its location and movements in the cell.

E)	It is derived from fire flies, which are easy to cultivate inthe lab.

You wish to determine the cellular location of a protein butunfortunately it is not particularly antigenic (can t develop astrong antibody response). How could you solve this problem?

A)	Create a fusion protein with an epitope tag that can bevisualized by incubation with fluorescently tagged antibody to theepitope.

B)	Create a fusion with green fluorescent protein (GFP).

C)	Express the protein as a fusion with biotin. The addition of GFPwill cause fluorescence.

D)	A and B might work.

E)	A, B, and C might work.

F)	None of the above will work.

A positive result for the yeast two-hybrid analysis means thefollowing:

A)	The proteins that you are studying can be made into fusionproteins, but do NOT interact with each other within the nucleus ofyeast.

B)	A fusion protein containing the Gal4p activation domain, hasbound to RNA polymerase resulting increase transcription ofnumerous genes, including the reporter gene, and formation ofcolonies.

C)	Two fusion proteins, one containing the Gal4p binding sitedomain and one containing the Gal4p activation domain, haveinteracted through their Gal4p domains resulting in transcriptionof the reporter gene.

D)	Two fusion proteins interact with each other and because of theGal4p binding site domain and the Gal4p activation domain containedin each fusion protein, the reporter genes are activated and thecells die resulting in no colonies.

E)	The colonies growing are expressing the two fusion proteins, butthe two proteins have not interacted with each other.

Which of the following is the approximate size of the humangenome?

3 Gm

300 Kb

3 Mb

3 Gb

3 Mm

Which of the following is correct about the structure orlocation of genes?

Question 22 options:

A)	Prokaryotic genes typically possess their own regulatorysequences that only control expression of a single gene.

B)	Eukaryotic genes often encode introns that are spliced outbefore translation.

C)	Eukaryotic genes are mostly located at the telomeres and thecentromeres of chromosomes.

D)	Eukaryotic genes are typically arranged in operons.

E)	Prokaryotic genes often encode exons that are spliced out beforetranslation

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BIOL1004 Study Guide - Final Guide: Meristem, Helicase, Beetroot

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