BBoL weeks 1-4

Building blocks weeks 1-4

​Lectures include:

1. What is life?

2. Intro to ancestry and phylogeny

3. Cell culture and microscopy

4. Genetic manipulation techniques

5. Genome structure

6. Information flow from DNA to protein

​This was the order I took down the lectures in, but the schedule they planned was different. I don't know who is correct, if I am not, then one of the lectures may be from week 5.

Disclaimer:

Lets begin the quiz!

These are week 1 questions :)

Multiple Choice

Which one of these is NOT a requirement to be considered alive?

• Be metabolically active

• Be separated from the outside environment by a boundary e.g. membrane

• Be evolved through natural selection

• Be able to move on its own (independently)

Multiple Choice

What is an amyloplast?

• A plant plastid that forms and stores starch

• A lysozyme

• A single membrane inside a plant cell

• Another name for any molecule containing starch

Multiple Choice

What macro are cell membranes mostly made of?

• Protein

• Lipid

• Carbohydrate

• Sugar

Multiple Choice

What percentage of genes are necessary for life?

• 100%

• 96.4%

• 1%

• 9.2%

Multiple Choice

What is LUCA?

• Last Universally Claimed Ancestry

• Less Uncommon Corroboration Aseptic

• Last Universal Common Ancestor

• Least Universal Community Attributes

Multiple Choice

Who created the first nested hierarchy?

• Darwin

• Linnaeus

• Mendel

• Charnia

Multiple Choice

How many animals and plants did the first nested hierarchy include?

• 7000 plants, 5000 animals

• 10,000 plants, 5500 animals

• 7500 plants, 8250 animals

• 6000 plants, 4200 animals

Multiple Choice

Which of these does NOT provide evidence for common descent?

• Biochemical

• Taxonomic

• Biogeographical

• Palaeontology

• Convergent evolution

Fill in the Blanks

Fill in the Blanks

These are week 2 questions

Multiple Choice

What is cell senescence?

• When the cell enters the S phase

• The end point of a cells life

• The division of cells

• When cells are cancerous

Multiple Choice

What phase are senescent cells stuck in?

• G0

• G1

• G2

• S

Fill in the Blanks

Multiple Choice

Why are cancer cells immortal?

• They have telomerase which rebuilds telomeres

• They skip the G2 phase

• They multiply 50x faster

• They remain in the mitotic phase

Multiple Choice

What does a typical cell culture contain?

• 1. Water

  2. Salts

  3. Sugar

• 1. Salts

  2. Protein

  3. Fatty acid

  4. Sugars

  5. Starch

• 1. Salts

  2. Amino acids

  3. Vitamins

  4. Glucose

  5. Phenol red dye

• 1. Salts

  2. Protein

  3. Phospholipids

  4. Radioactive markers

Multiple Choice

What does trypsin do?

• Adheres cells to the disc

• Detaches cells from the disc

Multiple Choice

What 2 cells can be grown in suspension? (rather than adhered to plate)

• Stem cells

  Red blood cells

• Skin cells

  Muscle cells

• Sperm cells

  Skin cells

• Blood cells

  Leukaemia cells

Multiple Choice

Why do we use laminar flow cabinets?

• Keep harmful gases away from us

• Keep a fresh supply of oxygen to cells

• Keep aseptic conditions

• For fun ;)

Multiple Choice

What does the stain haematoxylin do?

• Stains acidic substances purple

• Stains basic substances purple

• Stains cell red

• Stains cells orange

Multiple Choice

What does the stain Eosin do?

• Stains acidic substances purple

• Stains basic substances purple

• Stains basic substances pink

• Stains eukaryotes only

Multiple Choice

What colour would Azan Trichrome stain the nucleus?

• Red

• Blue

• Green

• Purple

Multiple Choice

What colour would Azan Trichrome stain the membrane & collagen?

• Red

• Blue

• Green

• Purple

Multiple Choice

What colour would Azan Trichrome stain the muscle & red blood cells?

• Red/orange

• Blue

• Orange

• Green

Multiple Choice

What goes in the red box?

• Condenser lens

• Detector

• Graticule

Multiple Choice

What goes in the yellow box?

• Objective

• Detector

• Graticule

• Eye piece

Multiple Choice

What goes in the blue box?

• Slide

• Condenser

• Graticule

• Eye piece

Multiple Choice

What does a fluorophore do?

• Emits all wavelengths of light

• Emits 3 different wavelengths of light

• Absorbs specific wavelength of light and emits a lower one

• Absorbs specific wavelength of light and emits a higher wavelength

Multiple Choice

Why did they mutate red and green fluorescent proteins to make a whole colour spectrum of them?

• They support the LGBTQ

• To visualise multiple proteins at once

• To find which colour alleles are heritable

Multiple Select

Select ALL that are uses for fluorescent proteins:

• Transgenic animals

• Making humans fluorescent

• Locating diseases on a disc

• Sub-cellular localisation (e.g. glow in the dark mitochondria)

Multiple Choice

Limitations of fluorescent proteins: What is photobleaching?

•  Destruction of the protein by high intensity laser light

• Destruction of the protein by white light

• Destruction of the protein by red light

Multiple Choice

Limitations of fluorescent proteins: What is phototoxicity?

•  Destruction of the protein by high intensity laser light

• Free radical formations caused by high intensity laser light

• Radiation from UV

Multiple Choice

Limitations of fluorescent proteins: What is overexpression?

•  When tagged genes are expressed highly, excess protein may be handled differently by the cell

• When untagged genes are expressed highly

• When the protein causes overexpression in all genes

Multiple Choice

Limitations of fluorescent proteins: protein folding?

• Proteins may affect other protein folding, causing denaturation

• Protein may affect folding of fusion protein, affecting function

Multiple Choice

Limitations of fluorescent proteins: what is cellular distribution? (GFP = green fluorescent protein)

• Large GFPs may alter distribution of tagged proteins

• Large GFPs cause destruction of tagged proteins

Week 3 is next, sorry it's so long D:

Multiple Choice

Studying and modifying nucleic acids and proteins = ?

• Molecular biology

• Molecular biotechnology

• Cloning

Multiple Choice

What is cloning / genetic manipulation?

• Studying macromolecules and the macromolecular mechanisms

• Studying and modifying nucleic acids and proteins

• Taking a piece of DNA and placing it into a new organism where it had never been

• Using DNA and micromolecules to create a brand new organism

Multiple Choice

Purifying DNA using alcohol involves what steps?

• 1. freeze and crush

  2. detergent

  3. shake with beads

• 1. freeze and crush

  2. heating to 100C

  3. filtering

• 1. heating to 100C

  2. filtering

  3. drying

• 1. filtering

  2. centrifuge and discard pellet

  3. filter again

Multiple Choice

DNA purifying with a column involves what steps

• 1. same as alcohol

  2. resin/mineral binding

  3. wash excess out

  4. elute

• 1. same as alcohol

  2. heat

  3. bind to membrane

  4. elute

• 1. same as alcohol

  2. crystallise

  3. wash away excess liquid

  4. pass through lime water

Multiple Choice

EcoRI cleaves DNA asymmetrically so leaves sticky ends

• True

• False

Multiple Choice

What is used to transport foreign DNA into the host genome?

• DNA ligase

• EcoRI

• mRNA

• Plasmid vector

Multiple Choice

In gel electrophoresis, shorter molecules are slowed down less so will move further through the gel.

• True

• False

Multiple Choice

Which of these is NOT a type of cloning vector?

• Plasmid

• Lamda phage

• Plantiophage

• Cosmid

• Expression

Multiple Select

Why are cloning vectors easy to use? Select all reasons

• Easy to introduce to bacteria

• Multiply rapidly

• Don't breakdown when exposed to light

• Easily maintained

Multiple Select

Most common host cells:

• Mammalian

• Bacteria

• Yeast cell

• E.coli

Multiple Choice

When choosing a host cell, the host enzymes should not impact your decision.

• True

• False

Multiple Choice

Used to look at gene structure and compare genomes = ?

• cDNA library

• Genomic library

• Cloning library

• rDNA library

Multiple Choice

Used to identify genes encoding proteins in a specific tissue = ?

• cDNA library

• Genomic library

• Cloning library

• rDNA library

Multiple Choice

A DNA probe is a single-stranded sequence of DNA or RNA used to search for its complementary sequence in a sample genome.

• True

• False

Multiple Choice

What is stringency?

• How well DNA strands break apart

• How well DNA strands bind

• How well DNA strands stick together

• How well DNA strands separate in solution

Multiple Choice

What happens if stringency is too high?

• Probe doesn't bind to target

• Probe binds to unrelated targets

Multiple Choice

What happens if stringency is too low?

• Probe doesn't bind to target

• Probe binds to unrelated targets

Multiple Select

Select all ways to increase stringency:

• Increase salt concentration

• Decrease salt concentration

• Increase temperature

• Decrease temperature

Multiple Choice

What is southern blotting used for?

• To look at gene expression in a complex mixture

• To look for a specific DNA sequence in a complex mixture

• To look for a specific DNA sequence in a tissue

Multiple Choice

In southern and northern blotting, after gel electrophoresis, how is the DNA fixed to the membrane?

• Heat/UV

• DNA ligase

• Nitrocellulose

• Autoradiography

Multiple Choice

What is the difference between southern and northern blotting?

• Southern uses DNA, Northern uses RNA

• Southern uses RNA, Northern uses DNA

• Southern uses heat/UV, northern uses freezing

• Southern uses freezing, northern uses heat/UV

Multiple Choice

What is northern blotting used for?

• To detect a specific DNA sequence in a complex mixture

• To transfer DNA to a new organism

• To look at gene expression in a tissue / size of transcripts

Multiple Choice

What is fluorescence in situ hybridisation (FISH) used for?

•      to identify and characterize abnormalities in chromosomal structure or numerically

• to hybridise the probe

Multiple Select

Select the 3 stages of PCR:

• Replication

• Denaturation

• Primer annealing

• Extension

Multiple Choice

PCR is useful for when DNA is degraded

• True

• False

Multiple Choice

PCR is not sensitive to small amounts of contamination

• True

• False

Multiple Choice

If you start with 1 copy of a DNA strand, after 4 cycles of PCR how many copies will you have?

• 2

• 4

• 8

• 16

Multiple Select

Select all applications of PCR:

• Detect small amounts of DNA quickly

• Amplify a target sequence

• Modify sequences of DNA

• Paternity testing

• Detection of rare species in aqueous habitats

Multiple Select

Dideoxy sequencing requires what?

• Deoxynucleotides

• DNA polymerase

• Oligonucleotide primer complementary to a short stretch of the DNA

• Many identical copies of the DNA to be sequenced

• Chain-terminating nucleotides

Multiple Choice

In DNA sequencing, what happens at 96C?

• Strands separate

• Terminator bases stop chains

• Primers anneal to strand

• Polymerase builds new strands

Multiple Choice

In DNA sequencing, what happens at 60C?

• Strands separate

• Terminator bases stop chains

• Primers anneal to strand

• Polymerase builds new strands

Multiple Choice

In DNA sequencing, what happens at 50C?

• Strands separate

• Terminator bases stop chains

• Primers anneal to strand

• Polymerase builds new strands

Week 3 had to be summarised a lot as i had 6 pages of notes

Make sure you don't only use this quiz as revision for week 3

Week 4 questions :)

Again this is 5 pages of notes it is very simplified

Multiple Choice

Karyotype = ?

• number of sets e.g. diploid is two

• number of chromosomes in the cell

• wrong number of chromosomes

Multiple Choice

Ploidy = ?

• number of sets e.g. diploid is two

• number of chromosomes in the cell

• wrong number of chromosomes

Multiple Choice

Aneuploidy = ?

• number of sets e.g. diploid is two

• number of chromosomes in the cell

• wrong number of chromosomes

Multiple Choice

Genes exist arranged as what in prokaryotes?

• Operons

• Plasmodiums

• Double helix

• Chromosomes

Multiple Choice

Genes exist arranged as what in eukaryotes?

• Operons

• Plasmodiums

• Double helix

• Chromosomes

Multiple Choice

What is a metagenome?

• all the DNA of a population

• all the genes in a single organism

• all of the genomes of a species

• all the genes present in a particular environment

Multiple Choice

Which of the following is NOT a way to find genes?

• CpG islands

• Predicted ORFs

• RNA sequencing

• Homology

• Southern blotting

Multiple Choice

93% of diversity is within races not between

• True

• False

Multiple Choice

How many base pairs do we have?

• 3000

• 1 million

• 3 billion

• 10 billion

Multiple Choice

What is nanopore sequencing?

• A technique used to measure the width of a nuclei nanopore

• Monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore

• Monitoring changes to an electrical current as water is passed through a protein nanopore

Multiple Choice

What is the central dogma?

• information can only be passed between

  nucleic acids or from nucleic acids to proteins

• all the gene sequences in a single genome

• information passes more easily when there is current applied

• information can only be passed through DNA and not RNA

Multiple Choice

What kind of replication is this?

• Linear

• Theta

• Alpha

• Hoop

Multiple Choice

What kind of replication is this?

• Linear

• Theta

• Alpha

• Hoop

Multiple Choice

The leading DNA strand is synthesised continuously

• True

• False

Multiple Choice

What enzyme catalyses the elongation of DNA?

• DNA ligase

• DNA polymerase

• Primase

• Protease

Multiple Choice

The lagging strand is synthesised continuously in Okazaki fragments

• True

• False

False - The lagging strand is synthesised discontinuously in Okazaki fragments

Multiple Choice

DNA is always elongated in what direction?

• 3' to 5'

• 5' to 3'

• 1' to 5'

• 5' to 1'

Multiple Choice

The stretch of DNA being transcribed = ?

• Gene

• Leading strand

• Transcription unit

• Regression model

Multiple Choice

Promoter = ?

• where the strands separate

• where primase attaches the primer

• where RNA polymerase attaches

• I hate revision this is killing me yall

Multiple Choice

Terminator = ?

• sequence signalling end of transcription in bacteria

• the enzyme that cuts off the DNA being transcribed

• a stop codon

• the last codon in a sequence

Multiple Select

Select the 3 stages of transcription (they are the same stages for translation too)

• Elongation

• Binding

• Termination

• Promotion

• Intiation

Multiple Choice

Introns are important because they may contain sequences that regulate gene expression

• True

• False

Multiple Choice

What enzyme mediates translation?

• Primase

• Aminoacyl-tRNA synthetase

• tRNA

• Codon-mediated synthase

Multiple Select

Select which of the following are NOT properties that allow RNA to be tRNA

• Base-pair with itself

• Some bases contain functional groups that may participate in catalysis

• May hydrogen bond with other nucleic acid molecules

• tRNA is not polar so is not reactive to nearby nucleotides

• Always has an anticodon

Multiple Choice

Proteins are modified during AND post-translation

• True

• False

Multiple Choice

What are mutations sources of?

• 1. variation

  2. diseases

  3. disorders

• 1. diseases

  2. cancer

  3. premature babies

• 1. variation

  2. chromosomes

  3. proteins

• 1. disorders

  2. allele imbalance

  3. death

Multiple Choice

Oncogene = ?

• any gene that plays a role in introns

• any gene that encodes a stem cell to differentiate

• any gene that encodes a mutant protein

• any gene that encodes a protein able to induce cancer

That is weeks 1-4 done congrats! :3