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 Blank

What is the name of the point that the star shows?

Fill in the Blank

What is the name of the points that the stars show?

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 Blank

What are the orange tips called?

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

Fill in the Blank

What temperature should you incubate cells at? (in Celsius)

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

Fill in the Blank

What colour would milk turn if stained with Haematoxylin?

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

Fill in the Blank

Where does Green Fluorescent Protein come from?

Fill in the Blank

Where does Red Fluorescent Protein come from?

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

Fill in the Blank

What piece of spinning equipment do both alcohol and column DNA purifying require?

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

Fill in the Blank

As of what year has the human genome been analysed to the point of there being no gaps?

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

Fill in the Blank

How many possible codons are there?

Fill in the Blank

How many stop codons are there?

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

Fill in the Blank

How many subunits does the translation ribosome have?

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