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NEUR 2700 - Research Methods > Quiz 2- Lecture 6: A Brief Review of Genes and Proteins > Flashcards

Quiz 2- Lecture 6: A Brief Review of Genes and Proteins Flashcards

1
Q

What is central dogma?

A

The central dogma of molecular biology is a theory stating that genetic information flows only in ONE direction, from DNA, to RNA, to PROTEIN, OR RNA directly to protein

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2
Q

2 major differences between DNA and mRNA

A

DNA is DOUBLE stranded
In DNA, nucleotide THYMINE is used
(ATGC)

mRNA is SINGLE stranded
in RNA, URACIL is used
(AUGC)

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3
Q

What is DNA to mRNA called?

A

Transcription

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4
Q

What is mRNA to Protein called?

A

Translation

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5
Q

Who discovered the DNA double helix and when (3)?

A

Francis Harry Compton Crick, James Dewey Watson, Maurice Hugh Frederick Wilkins

1953 Discovery: DNA Double Helix

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6
Q

When was the Nobel Prize for Physiology or Medicine given?
To who (3)?
For what?

A

The Nobel Prize in Physiology or Medicine was awarded jointly to
Francis Harry Compton Crick, James Dewey Watson, Maurice Hugh Frederick Wilkins
“for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material”

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7
Q

What are the Watson and Crick model’s 4 major features?

A
  1. DNA is double stranded
  2. DNA takes on the shape of a double helix, or twisted ladder
  3. The two strands are complementary to each other due to Chargaff’s Rule
  4. The nitrogenous bases following Chargaff’s Rule always pair up as follows: Adenine (A)-Thymine (T) and Cytosine (C)-Guanine (G)
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8
Q

DNA is a ____ with the ____

A

double-stranded helix, two strands connected by hydrogen bonds

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9
Q

What are A bases (Adenine) always paired with?

What are Cs (Cytosine) always paired with?

This is consistent with and accounts for what?

A

Ts (Thymine)

Gs (Guanine)

Chargaff’s rule

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10
Q

What is DNA?
2 poly… are

A

Antiparallel

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11
Q

A single nucleotide is made up of how many components?
What are they?

A

A single nucleotide is made up of three components
Nitrogen containing base, Five-carbon sugar, Phosphate group

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12
Q

The nitrogen containing base is either…

The five-carbon sugar is either a…

A

Purine or Pyrimidine

Ribose (in RNA) or Deoxyribose (in DNA) molecule

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13
Q

What are possible types of pyrimidines? (3)

What are possible types of purines? (2)

A

Cytosine, Thymine, Uracil (RNA)

Adenine, Guanine

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14
Q

Base + Ribose or Deoxyribose -> ?
What follows?

A

Base + Ribose or deoxyribose -> Nucleoside (base) + Phosphate (P) -> Nucleotide (P and base)

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15
Q

What is another difference between DNA and RNA? (Sugar)

A

DNA- Deoxyribose sugar
RNA- Ribose sugar

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16
Q

What does Deoxyribose mean?

A

Removal of oxygen from ribose sugar

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17
Q

How are Eukaryotic Chromosomes structured?

A

Eukaryotic chromosomes consist of repeated units of chromatin called nucleusomes

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18
Q

How were nucleosomes discovered?

A

Discovered by chemically digesting cellular nuclei and stripping away as much of the outer protein packaging from the DNA as possible

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19
Q

The chromatin that resisted digestion had the appearance of ____ in electron micrographs

What are the beads?

A

“beads on a string”

with the “beads” being nucleosomes positioned at intervals along the length of the DNA molecule

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20
Q

What charge do DNA molecules have?

A

DNA is negatively charged
(because of the presence of phosphate groups in nucleotides)

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21
Q

DNA associates with proteins that are…

A

Positively charged
(Histones are a family of basic proteins that associate with DNA in the nucleus and help condense it into chromatin)
(Histones are positively charged because they contain a very high amount of positively charged amino acids such as lysines and arginines)

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22
Q

Nucleosomes are made up of ____ that has complexed with ____

A

Nucleosomes are made up of double-stranded DNA that has complexed with small proteins called histones

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23
Q

The core particle of each nucleosomes consists of what?
How many of each? What are the different types? (4)

A

The core particle of each nucleosome consists of eight histone molecules,
Two each of four different histone types: H2A, H2B, H3, H4

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24
Q

The structure of histones has been…
What does this suggest?

A

The structure of histones has been strongly conserved across evolution, suggesting that their DNA packaging function is crucially important to all eukaryotic cells

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25
Q

What does the diagram of Nucleosome show?

A

Nucleosome, with DNA in orange and histone proteins in blue

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26
Q

The picture here shows…

A

The eight histone proteins as tubes that follow the protein chain, and shows the DNA as thinner tubes that follow the two strands as they circle around the protein octamer

The tails of the eight protein chains, seen extending outward from the center, are actually longer in reality

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27
Q

What is the job of the nucleosome? Why?

What are the two functions?

A

Paradoxical
Requiring it to perform two opposite functions simultaneously

On one hand, Nucleosomes must be stable, forming tight, sheltering structures that compact the DNA and keep it from harm
On the other hand, Nucleusomes must be labile enough to allow the information in the DNA to be used

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28
Q

Polymerases must be…
Why?

A

Allowed access to the DNA
Both to Transcribe messenger RNA for building new proteins and to Replicate the DNA when the cell divides

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29
Q

The methods by which nucleosomes solve these opposed needs is not well understood, but may involve a…

A

Partial unfolding of the DNA from around the nucleosome, one loop at a time, as the information in the DNA is read

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30
Q

What does the diagram with nucleosome doing two functions show?

A

-1 nucleosome, RNAPII, Transcription (Arrow pointing down)

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31
Q

What do Histones do? (2)

A

Histones carry positive charges (Arginine and Lysine rich) and Bind negatively charged DNA in a specific conformation

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32
Q

A. Amino Acids with Electrically Charged Side Chains
Positive (3)

Negative (2)

A

Arginine, Histidine, Lysine

Aspartic Acid, Glutamic Acid

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33
Q

Most amino acids have what structure?

A

O=

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34
Q

Amino acids have lots of what?
It is what charge?

A

Nitrogen (NH2)
Positively charged

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35
Q

B. Amino Acids with Polar Uncharged Side Chains (4)

A

Serine, Threonine, Asparagine, Glutamine

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36
Q

C. Special Cases (3)

A

Cysteine, Glycine, Proline

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37
Q

D. Amino Acids with Hydrophobic Side Chains (8)

A

Alanine, Valine, Isoleucine, Leucine, Methionine, Phenylalanine, Tyrosine, Tryptophan

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38
Q

Apart from their function of ____, nucleosomes also…

A

Safely packaging DNA, Modify the activity of the genes that they store

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39
Q

What is each nucleosome composed of?

A

Eight “histone” proteins bundled tightly together at the center, encircled by two loops of DNA

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40
Q

Unlike most other proteins, how are histone proteins different?
What do they have?

A

Not completely globular
They have long tails, which comprise nearly a quarter of their length

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41
Q

What do histone tails do?

What does the nucleus contain?

In this way, what does the cell do?

A

The tails extend outward from the compact nucleosome, reaching out to neighboring nucleosomes and binding them tightly together

The nucleus contains regulatory enzymes that chemically modify these tails to weaken their interactions

In this way, the cell makes particular genes more accessible to polymerase, allowing their particular information to be copied and used to build new proteins

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42
Q

Why is the slide called Wagging Tails?

A

Histones have a tail

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43
Q

What does genetics mean?

What does epigenetics mean?
Example?
Is it reversible?

What does mutation mean?

A

Inheritance

Changes in genes that are not heritable
^ Ex: Histone modification, add phosphate group to histone tail
Epigenetics is Reversible

Changes in DNA sequence (Hereditary)

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44
Q

What does modified mean?

A

Helps open nucleosomes

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45
Q

A segment of the DNA double helix wraps around each histone core particle how many times?

A

A little less than twice

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46
Q

The exact length of the DNA segment associated with each histone core… BUT

A

Varies from species to species
But most such segments are approximately 150 base pairs in length

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47
Q

What does the end that sticks out from the particle of the histone molecule within the core particle called?
What does it play an important role in?

A

N-terminal tails
Higher-order chromatin structure and gene expression

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48
Q

Each nucleosome is composed of…

A

DNA wound 1.65 times around eight histone proteins

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49
Q

Nucleosomes fold up to form…
Which forms…

A

A 30-nanometer chromatin fiber
Which forms loops averaging 300 nanometers in length

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50
Q

How many chromosomes? How many DNA?

A

A cell with 46 chromosomes has 46 DNA molecules

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51
Q

The 300 nm fibers are compressed and folded to produce what?

A

A 250 nm-wide fiber, which is tightly coiled into the chromatid of a chromosome

52
Q

Diagram:
At the simplest level, what is chromatin?

A

A double-stranded helical structure of DNA

53
Q

Diagram:
What is the length of a DNA double helix?

A

2 nm

54
Q

What is DNA complexed with to form what?

A

DNA is complexed with Histones to form Nucleosomes

55
Q

Each nucleosome consists of what?
How many times?

A

Each nucleosome consists of Eight Histone Proteins around which the DNA wraps 1.65 times

56
Q

What does a chromatosome consist of?

A

A chromatosome consists of a Nucleosome plus the H1 histone

57
Q

What do the nucleusomes fold up to produce?
What does it form?

A

A 30-nm fiber
That forms loops averaging 300 nm in length

58
Q

What are the 300-nm fibers compressed and folded to produce?

A

A 250-nm-wide fiber

59
Q

What does tight coiling of the 250-nm fiber produce?

A

Tight coiling of the 250-nm fiber produces the Chromatid of a chromosome

60
Q

What are the “beads on a string”?

A

Nucleosome core of eight histone molecules

61
Q

What is the 250-nm-wide fiber coiled into a height of?

A

700 nm

62
Q

What is a chromosome?

A

DNA molecule associated with a lot of protein

63
Q

What is shown on picture of chromatin?

A

A 30-nm fiber of chromatin

64
Q

When are chromosomes Most Compacted?

A

During Metaphase

65
Q

Comparing the length of metaphase chromosomes to that of naked DNA…

What can this be thought of as akin to?

A

The packing ratio of DNA in metaphase chromosomes is approximately 10,000:1 (depending on the chromosome)

Taking a rope as long as a football field and compacting it down to less than half an inch (huge compaction level)

66
Q

How is this level of compaction achieved?

Exactly how this is accomplished is unclear, but what may play a role?

A

This level of compaction is achieved by repeatedly folding chromatin fibers into a hierarchy of multiple loops and coils

Phosphorylation of Histone H1 may play a role

67
Q

What is the difference between neurons and muscle cells?

A

Neurons: don’t have
Muscle cells: Myoglobin expressed in muscle

68
Q

Basic structure of a gene:
Diagram shows what?

A

Intron, Exons, Intron, Exon

69
Q

Basic structure of a gene:
Order

A

Enhancer, Promoter, Exon, Intron, Exon, Intron, Termination Seq.

70
Q

Basic structure of a gene:
Promoter

A

Transcription factor binding and RNA polymerase recruitment

71
Q

What do the Enhancer and Promoter, which are Regulatory Elements, determine? (2)

Examples of both?

A

This sequence elements determine WHEN (time) and WHERE (space) the initiation of mRNA synthesis begins

When: time in organism’s life span, time (age) of individual (ex : child- not expressed at this time, adolescence- sexual characters expressed)
Where: space- ex: neurons and muscle cells (expressed in one cell type and not another)

72
Q

What are exons?

A

Part of the RNA that codes for proteins
“forming RNA”

73
Q

Exons:
The information for the amino acids sequence in the protein is written herein the form of what?

A

Genetic code

74
Q

Introns:

A

Junk sequence?
Removed via RNA Splicing

75
Q

Termination Sequence:

A

This sequence element determines where to stop the mRNA synthesis process
Also determines mRNA stability in the cell

76
Q

Although each codon is specific for only one amino acid (or one stop signal), what is the genetic code described as?
Why?

A

DEGENERATE, or Redundant
Because a single amino acid may be coded for by more than one codon

77
Q

What is the phosphorylation codon?

A

AUG (Met)
Most common start codon and it codes for amino acid Methionine

78
Q

What is the genetic code?
Example of variation?

A

Furthermore, the genetic code is NEARLY UNIVERSAL, with only rare variations reported
For instance, mitochondria have an alternative genetic code with slight variations

79
Q

What are the two “code” diagrams showing?

A

“Universal” code and mtDNA (Mitochondrial) code

80
Q

Does genetic code overlap?
What does this mean?

A

It is also important to note that genetic code DOES NOT OVERLAP,
Meaning that each nucleotide is part of only one codon- a single nucleotide cannot be part of two adjacent codons

81
Q

Table 1: Did the code have commas or not?

A

Non-overlapping code with no “commas” present: CATGAT
Non-overlapping code with comma present (where X is any nucleotide): CATXGAT

82
Q

What is genetic code?

A

“How everything is written in your body”

83
Q

Properties of genetic code (8)

A

(1) Code is a Triplet
(2) The Code is Degenerate
(3) The Code is Non-overlapping
(4) The Code is Comma Less
(5) The Code is Unambiguous
(6) The Code is Universal
(7) Co-linearity (DNA Linear…)
(8) Gene Polypeptide Parity (RNA Linear…- specific)

84
Q

What is Co-linearity?

A

Change in a specific codon in DNA produces a change of amino acid in the corresponding position in the polypeptide
The gene and the polypeptide it codes for are said to be co-linear

85
Q

What is Gene-polypeptide Parity?

A

A specific gene transcribes a specific mRNA that produces a specific polypeptide
On this basis, a cell can have only as many types of polypeptides as it has types of genes
However, this does not apply to certain viruses which have overlapping genes

86
Q

What processes is a gene expressed through? (2)

A

Transcription, Translation

87
Q

What happens during transcription?

Translation?

A

The enzyme RNA polymerase (green) uses DNA as a template to produce a pre-mRNA transcript (pink)

The pre-mRNA is processed to form a mature mRNA molecule that can be TRANSLATED to build the protein molecule (polypeptide) encoded by the original gene

88
Q

Non-Polar Amino Acids: (9)

A

Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Tryptophan (Trp), Phenylalanine (Phe), Proline (Pro)

89
Q

Polar Amino Acids: (6)

A

Serine (Ser), Threonine (Thr), Cysteine (Cys), Tyrosine (Tyr), Asparagine (Asn), Glutamine (Gln)

90
Q

Electrically Charged Amino Acids:
Acidic (2)

A

Aspartic Acid (Asp), Glutamic Acid (Glu)

91
Q

Electrically Charged Amino Acids:
Basic (3)

A

Lysine (Lys), Arginine (Arg), Histidine (His)

92
Q

Levels of Protein Structure: (4)

A

Primary Structure (polypeptide chain), Secondary Structure, Tertiary Structure (most proteins in body), Quaternary Structure

93
Q

What is the Secondary Structure dependent on?

A

Dependent on Hydrogen Bonding

94
Q

What are the two main types of Secondary Structures?

A

a. The a-helix (alpha helix)
b. The b-sheet (beta sheet)

95
Q

What is the a-helix?

A

a-helix is a right-handed coiled strand and the hydrogen bonding is WITHIN the strand (INSTRA-strand)

96
Q

What is the b-sheet?

A

The hydrogen bonding in a b-sheet is BETWEEN strands (INTER-strand)

97
Q

Definition of protein:

A

Bio molecule (big, organic)
Made up of amino acids

98
Q

What is the overall three-dimensional shape of an entire protein molecule?

A

Tertiary structure

99
Q

What occurs under physiologic conditions (normal cellular environment)? (2)

A
  1. The Hydrophobic Side-chains of neutral, non-polar amino acids Buried on the Interior of the Protein Molecule thereby shielding them from the aqueous medium
  2. The Acidic or Basic Amino Acid Side-chains will generally be Exposed on the Surface of the protein as they are hydrophobic
100
Q

What does hydrophilic mean?

A

More charge, Helps them dissolve water

101
Q

What does the diagram show?
Distribution of amino acids in Myoglobin:

A

Hydrophobic in yellow and Charged amino acids in blue

102
Q

“Inside out” amino acid distributions in Porin:
What is the outside covered by?
What about the inside?

A
  1. The outside of Porin (VDAC1) which contacts hydrophobic groups in the membrane is covered largely with hydrophobic residues
  2. Whereas the center Includes a water filled channel lined with charged and polar amino acids
103
Q

What is a Quaternary structure?

A

Spatial arrangement of multi subunit proteins (made of more than one polypeptide chain)

104
Q

Quaternary structure:
Numerous interactions are responsible: (3)

A
  1. Hydrogen bonding
  2. Disulfide bridges (a covalent bond derived from two thiol groups):
    The formation of disulfide bridges happen by oxidation of the sulfhydryl groups on cysteine
  3. Salt bridges (a link between electrically charged acidic and basic groups)
105
Q

What are disulfide bridges?

A

Covalent bond derived from two thiol groups

106
Q

How does the formation of disulfide bridges happen?

A

By oxidation of the sulfhydryl groups on cysteine

107
Q

What are salt bridges?

A

Link between electrically charged acidic and basic groups

108
Q

Who was Richard Phillips Feynman?
What was he known for? (4)

A

American theoretical physicist
Path integral formulation of quantum mechanics, Theory of quantum electrodynamics, Physics of the superfluidity of supercooled liquid helium, and His work in particle physics for which he proposed the Parton model

109
Q

When did Feynman receive the Nobel Prize?

A

For contributions to the development of quantum electrodynamics, Feynman received the Nobel Prize in Physics in 1965 jointly with Schwinger and Tomonaga

110
Q

What are prions?

A

Prions are infectious proteins which replicate without going through DNA or RNA intermediates
(Particularly notable example of exception to the theory)

111
Q

What disease are prions responsible for?
What does the disease cause?

A

Prions are responsible for the rare but devastating neurological disease, Creutsfeldt-Jakob, which is a uniformly lethal disease that
Causes degeneration of the nervous system

112
Q

What is scrapie?
What is it classified as?

What can inflected flocks experience?

A

Fatal, degenerative disease affecting the central nervous system of sheep and goats
Transmissible spongiform encephalopathies (TSE)

Significant production losses

113
Q

What are clinical signs of scrapie?

A

Due to damage to the nervous system, Affected animals often show behavior changes, such as nervousness or aggression, intense rubbing, and locomotor incoordination that progresses to recumbency and death

114
Q

Infectious proteins:

A

The concept of an infectious protein, or prion, was proposed in the 1960s to explain scrapie infection

115
Q

What did researchers find out about scrapie?
What did they propose?

A

Researchers found that the infectious agent that transmits scrapie is resistant to ultraviolet radiation (which typically destroys nucleic acids)
They proposed that this agent was actually protein based

116
Q

Why was the idea that proteins could be infectious by themselves highly controversial?

A

Because it appeared to challenge the central dogma of molecular biology

117
Q

How did Prusiner show that proteins can indeed be infectious?
What was he awarded?

A

Eventually, Stanley B. Prusiner and his team purified the prion protein responsible for scrapie
Prusiner was awarded the Nobel Prize in Physiology or Medicine in 1997

118
Q

What are prions also responsible for? (3)

A

Transmissible spongiform encephalopathies (TSE) that include infectious diseases such as scrapie in sheep
Bovine spongiform encephalopathies (mad cow disease) whose infective form can cause Creutzfeldt-Jakob disease in humans
Kuru, the only epidemic human prion disease known to

119
Q

What is mad cow disease caused by?

A

Prions that misfold and aggregate

120
Q

Prions are proteins that can adopt which two forms?
Why may this not seem unusual?

A

A Normal form and a Misfolded form
Since many proteins are flexible and adopt different shapes

121
Q

What is another unusual characteristic of prions?
In this way, what happens?

Example?

A

The misfolded form of the prion can force normal prions to change into the misfolded shape
A few misfolded prions can corrupt a whole population of normal prions, converting them one-by-one into the misfolded shape
(This can have deadly consequences, as the levels of misfolded proteins build up)

Misfolding of the PrP prion causes fatal neural diseases in humans and other mammals

122
Q

Misfolded prions are…

A

Infectious, so a small dose of misfolded prions can infect and corrupt an entire organism

123
Q

What happens when the normal form of prion protein PrP changes into its misfolded shape?

When does infection occur?

A

It aggregates into long fibrils that clog up the normal functioning of the brain

Infection occurs when a little bit of misfolded protein is eaten or accidentally gets into the blood through an injury

124
Q

What does the Prion Protein (PrP) have?

A

A lipid attached at the bottom, which normally anchors the protein to the surface of nerve cells, and two carbohydrate chains (all shown in orange)
The rest of the protein chain is largely flexible

(PrP still holds many mysteries. It is found on nerve cells, but its precise function is still a matter of conjecture)

125
Q

What is misfolding produced by?

A

An incorrect folding process that results in the formation of a protein with a different conformation from its native fold

126
Q

Protein misfolding can occur by several reasons: (6)

A

1) Somatic mutations in the gene sequence leading to the production of a protein unable to adopt the native folding
2) Errors on the processes of transcription or translation leading to the production of modified proteins unable to properly fold
3) Failure of the folding and chaperone machinery
4) Mistakes on the post-translational modifications or trafficking of proteins
5) Structural modification produced by environmental changes or
6) Induction of protein misfolding by seeding and cross-seeding mechanisms

127
Q

Healthy (PrPc) vs Prion disease (PrPSc)

A

Healthy (PrPc):
- monomeric
- high a-helix

Prion disease (PrPSc)
- multimeric amyloid fibril
- parallel in-register architecture
- high b-sheet

NEUR 2700 - Research Methods (18 decks)

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