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BIOL1007 > MOD 1 > Flashcards

MOD 1 Flashcards

1
Q

What are the key characteristics of Life?

A
  • Cell based
  • Can reproduce
  • Are complex and organised
  • User energy for growth and reproduction * Tend towards homeostasis
  • Change over time
  • Adapt to environment
  • Respond to stimuli
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2
Q

Classify these organisms as prokaryotic or eukaryotic: humans, mushrooms, fish, bacteria, algae, gum trees

A
  • Prokaryotes:
    Eubacteria
    Bacteria
    Archaea
  • Eukaryotes:
    Protests
    Algae (Plants)
    Gum trees
    Fungi (Mushroom)
    Animals (Human, Fish)
  • Virus is neither prokaryotes nor eukaryotes.
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3
Q

What properties of carbon make it central to life as we know it(i.e.carbon-based
life)?

A
  • Can bond with itself
  • Can bond with other elements (4 bonds) in lots of different ways
  • All major biopolymers have a substantially carbon backbone
  • “sweet spot” of stability (stable but not too stable) for forming covalent bonds
  • Carbon bonds often under kinetic control (good for enzymatic regulation)
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4
Q

What are the most common elements in living things,and are they each usually polar or hydrophobic?

A

Common

  • Carbon - C - non-polar / hydrophobic (water hating)
  • Hydrogen - H - heavily influenced by what its near - C/H neutral, O/H polar either polar or non-polar
  • Nitrogen - N - polar / hydrophilic (water liking) - partly (dipoles) or fully charged
  • Oxygen - O - polar / hydrophilic (water liking) - partly (dipoles) or fully charged *

Smaller amounts

Phosphorous - P - polar / hydrophilic (water liking) - partly (dipoles) or fully charged
* Sulfur - S - (sometimes) polar / hydrophilic (water liking) - partly (dipoles) or fully charged either polar to non-polar

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5
Q

True or false: Hydrophobic things like to be in aqueous (water-based) environments.

A

False: hydrophobic is water-hating - don’t like to be in aqueous environments

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6
Q

how do you know if an element is polar or nonpolar

A

Non polar molecules are symmetric with no unshared electrons. Polar molecules are asymmetric, either containing lone pairs of electrons on a central atom or having atoms with different electronegativities bonded.

polar (contains Os, Ns, OH)
non-polar/ hydrophobic (contains lots of Cs and Hs)

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7
Q

What are the five main types of molecules used in Biology and what are their uses?

A
  • Water
  • Carbohydrates / sugars / saccharides
  • Lipids (fats and others)
  • Amino acids
  • Nucleotides
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8
Q

True or False: The only role of Sugars/Carbohydrates is as energy sources?

A

False
* Sugar polymers (long chains of monosaccharides)
* Starch - Storage
* Chitin- Protection
* Cellulose - Structure
* Bacterial cell walls / surrounding coats (complex polymers)

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9
Q

Name three functions of lipids.

A
  • Energy stores (triaglycerols)
  • Signalling molecules (steroids)
  • Protection and waterproofing (waxes)
  • Structure / barriers (phospholipids)
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10
Q

What are the differences between amino acids and nucleotides?

A

Main difference: amino make proteins, nucleotides make nucleic acids Detailed differences: 20 amino acids and 4 types of nucleotides

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11
Q

What chemical properties can different amino acids have (name at least 3)?

A

Think about the side-chains: 20 amino acids
Non-polar (hydrophobic), polar (unchanged), charged (acidic pr basic) flexibility, charge
Aromatic
Size

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12
Q

Match the end to the biopolymer type to indicate the direction.

A

Nucleic acid
* 5’ to 3’ (five prime to three prime)

Protein
* N-terminus (or amino terminus) to C-terminus (or carboxy terminus)

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13
Q

What type of sequence is each of the following (DNA/RNA/Protein)?
A. AATTCGCGCTCTAGCT
B. AAHWYLDDEEPNQGS
C. AAUUCGCGCUCUAGCU

A
  • A: DNA (contains T) * B: Protein
  • C: RNA (contains U)
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14
Q

Which nucleobases base pair with each other (A,C,G,T,U), which are considered to have stronger base pairing and why?

A
  • A = T (U)
  • A and T/U complement each other (2 hydrogen bonds so a bit weaker)
    *C=G
  • Strong base-pairing: C and G complement each other (3 hydrogen bonds so
    stronger binding)
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15
Q

What properties of RNA mean that it is less stable than DNA?

A

Single-stranded: Expose base into aqueous environment; easy break bonds

Ribose vs deoxyribose: The OH group on ribose make it more susceptible to hydrolysis; stop forming B- type double stranded structure

Cytosine deamniation: C>U - lose information

RNA polymerases lacks proofreading activity: Lose information

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16
Q

Match the type of information containing biopolymer to its main role in the central dogma of Molecular Biology:

  • DNA
  • RNA
  • Protein
A
  1. DNA: Doing molecules
  2. RNA: GeneticStore
  3. Protein: Messenger
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17
Q

Considermusclecells,brain cells and skin cells from the same individual .In general terms describe the genome, transcriptome and proteome for each cell type

A
  • Genome
  • Same DNA in all of your cells
  • = complete genetic information
  • Transcriptome
  • Different: micro RNA, small nuclear RNA, messenger RNA, ribosomal RNA, transfer RNA
  • Proteome
  • Different: depends on function given different shape
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18
Q

What are the main differences between genomes and chromosomes from bacteria and eukaryotes?

A
  • Most prokaryotes (bacteria and archea) have circular chromosomes * Tend to be relatively small genomes
  • Eukaryotic genomes have linear chromosomes * Tend to be big
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19
Q

What does semi-conservative replication mean?

A
  • Semi-conservative replication
  • DNA contains one older and one newly replicated strand
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20
Q

What are the main challenges in copying DNA from DNA and how are they overcome?

A

Stopping DNA degradation when ssDNA: ssDNA binding proteins

Pulling the strands apart causes supercoiling, tangling:
topoisomerase/gyrase

Need to pull strands apart: Helicase

Leading and lagging strand: Okazaki fragments Copy small parts and stick
together; copying from 5’ to 3’

How do we start: AT rich sites; fewer H bonds; ORI origins of replication

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21
Q

WhataretherolesofthefollowingproteinsinDNAreplication:DNApolymerase, gyrase, helicase, ligase, primase?

A
  • DNA polymerase: enzyme - make a DNA copy (lots of small fragments) from a DNA template
  • Gyrase: enzyme, that relieves (stops) supercoiling (overwinding DNA)
  • Helicase: enzyme, unwinds DNA
  • Ligase: enzyme, joins pieces of DNA
  • Primase: RNA polymerase that make primers for replication
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22
Q

How are RNA polymerases different from DNA polymerases?

A

DNA polymerases
* Make a DNA copy from a DNA template
* Do need a primer to start
* Use deoxynucleotide triphosphates (dNTPs: dATP, dGTP, dTTP, dCTP) as substrate
* “Proof read” the last nucleotide added; often have 3’ to 5’ exonuclease activity to remove a mismatched nucleotide

RNA polymerases
* Make an RNA copy from a DNA template
* Don’t need a primer to start
* Use ribonucleotide triphosphates (NTPs: ATP, GTP, CTP, UTP) as substrate
* Limited proofreading, no 3’ to 5’ exonuclease activity (make more mistakes)

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23
Q

What are the signals for transcription initiation and termination?

A
  • Transcription initiation * Promoter
  • Transcription termination * Terminator
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24
Q

How can different genes be transcribed into RNA at different rates?

A

Promotor strength
* Strong promoter - more copies
* Weaker promoter - less copies

Repressors
* Makes it easier for binding at promoter

Accelerators
* Blocks the binding of the sigma factor / RNApol complex and therefore RNA polymerase will have no space to bind

25
Q

How do tRNA and amino acylRNA synthetases work together to correctly translate an mRNA sequence translated into a protein/peptide sequence?

A

Aa-tRNA synthetases
* Catalyse the activation of amino acids
* Use ATP hydrolysis to get the energy to make a high energy bond * Attach the correct amino acid to its matched tRNA
* Recognise the anticodon and other parts of the tRNA

26
Q

What roles does the ribosome have in protein synthesis initiation, elongation and termination?

A

Initiation: Binds to mRNA, start codon, recruitment/ binding met-tRNA

Elongation: A site - aa-RNA binding
P site - joins amino acids together - peptidyl transferase activity

Termination: Stop Condon is reached, no tRNA matches and protein release factor binds
Peptide transferase activity adds water

27
Q

True or False: Release Factor is a tRNA that binds to the stop codon to terminate protein synthesis

A

False - not tRNA, it’s protein

28
Q

What are the differences between primary, secondary, tertiary and quaternary structure of proteins?

A
  • Primary: Amino acid sequence
  • Secondary: Local structures, Alpha helix and beta sheet

*Tertiary: Overall 3D arrangement of a polypeptide chain overall fold

-Quaternary: Organisation of subunits

29
Q

What types of bonds and forces hold protein structure held together?

A

Hydrophobic effect: Tertiary (quaternary)
Hydrogen bonds: Secondary and tertiary
Covalent bonds: Primary - bonds that holds the polypeptide together
Polar interactions: Tertiary quaternary
Ionic binds/electrostatic / salt bridges: Tertiary quaternary

30
Q

Describe how an element of protein secondary structure can complement dsDNA structure to allow protein-DNA interactions.

A
  • Sidechains must point the right way to recognize either the backbone for general/non- sequence specific binding, or the bases for sequence specific binding
  • α-helixes are a perfect size to fit into the major groove of DNA
  • Single strands of protein Can fit in the minor groove
31
Q

If a reaction is at equilibrium which of the following statements is true?

A

Substrate molecules are probably exchanging with product molecules and vice versa

32
Q

What does it mean if a reaction is under kinetic rather than thermodynamic
control?

A
  • Thermodynamic contorl is about the energy of the reactants / products * Kinetic control is about overcoming activation barrier
  • Kinetically controlled reaction rate can be influenced by enzymes
33
Q

True or False? A reaction (Substrate <-> Product) can be driven to the right by adding more substrate or removing the product.

A

True

34
Q

What are three properties of enzymes that are important for biology and/or medicine?

A
  • Can be regulated
  • Can be localised in certain organelles * Can be organised into pathways
35
Q

How can the hydrolysis of pyrophosphate drive unfavourable interactions?

A
  • Release of energy from ATP to AMP > PP > P + P
  • Gives energy required for overcoming unfavourable thermodynamics * Removes product, driving reaction to the right
36
Q

transcription and translation

A

The process by which DNA is copied to RNA is called transcription, and that by which RNA is used to produce proteins is called translation.

37
Q

mutations: Deletion

A

A deletion changes the DNA sequence by removing at least one nucleotide in a gene.

38
Q

Mutations: insertion

A

An insertion changes the DNA sequence by adding one or more nucleotides to the gene. As a result, the protein made from the gene may not function properly.

39
Q

Frameshift mutation

A

the insertion or deletion of nucleotide bases in numbers that are not multiples of three. rameshift mutations can result in a premature stop codon somewhere in the sequence, truncating the protein

40
Q

silent mutation

A

A silent mutation is a type of substitution mutation (one base is replaced with another). This results in no change to the resulting protein

41
Q

nonsense mutation

A

A nonsense mutation occurs when the substitution results in the formation of a stop codon.

42
Q

substitution mutation

A

Nonsense mutation
Substitution
Substitution
Substitution – when one or more bases in the sequence is replaced by the same number of bases (for example, a cytosine substituted for an adenine

43
Q

missense mutation

A

a DNA change that results in different amino acids being encoded at a particular position in the resulting protein. Some missense mutations alter the function of the resulting protein.

44
Q

point mutation

A

Substitution mutation is when a nucleotide is substituted

45
Q

An example of a sugar polymer is:

A

Chitin

46
Q

“Deoxyribose nucleotides are joined together via _________(i) bonds with the help of a _________(ii) resulting in the release of an H2O by-product.”

A

(i) phosphodiester (ii) polymerase

47
Q

Which of the following statements about protein synthesis is most correct?

A

A nucleotide sequence is effectively converted into an amino-acid sequence

48
Q

Which of the following does not occur in transcription

A

Transcription of the whole genome

49
Q

Which of the following catalyses the formation of peptide bonds

A

Ribosomal RNA

50
Q

Which of the following is not a property of enzymes?

A

They are used up in the reaction

51
Q

Protein sequences are correctly:

A

Defined by the mRNA sequence and tRNAs onl

52
Q

In his famous 1928 experiment, Griffith found that when the “smooth virulent (S strain)” (a deadly bacterial colony) was heat killed, the resulting by-product was mixed with a solution containing the rough non-virulent (R strain) bacteria (a non-pathogenic bacterial colony) and injected into a mouse, what happened to the mouse?

A

The mouse died because the R-strain bacteria was transformed by DNA provided by heat-shocked S-strain bacteria

53
Q

The removal of the –OH group from carbon 2′ of ribose in DNA to make deoxyribose:

A

Prevents the cleavage of the backbone by OH- attack

54
Q

You have two fragments of DNA, one from E. coli and one from mouse liver. They both have 5,000 base pairs and 40 % G+C content. Which of the following parameters is most likely to differ between the two DNA samples?

A

The sequence of the DNA

55
Q

What is the purpose of primase in DNA replication?

A

It synthesises a small sequence of RNA that is used as the starting point of replication

56
Q

What kind of bond is found between two amino acids in a protein?

A

Peptide bond

57
Q

If a reaction has a high activation barrier:

A

The speed of the reaction will be slow

58
Q

Which of the following is most responsible for regulating how often a DNA sequence is transcribed into RNA?

A

Promoter sequences

BIOL1007 (4 decks)

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