Quiz 2- Lecture 6: A Brief Review of Genes and Proteins Flashcards
What is central dogma?
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
2 major differences between DNA and mRNA
DNA is DOUBLE stranded
In DNA, nucleotide THYMINE is used
(ATGC)
mRNA is SINGLE stranded
in RNA, URACIL is used
(AUGC)
What is DNA to mRNA called?
Transcription
What is mRNA to Protein called?
Translation
Who discovered the DNA double helix and when (3)?
Francis Harry Compton Crick, James Dewey Watson, Maurice Hugh Frederick Wilkins
1953 Discovery: DNA Double Helix
When was the Nobel Prize for Physiology or Medicine given?
To who (3)?
For what?
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”
What are the Watson and Crick model’s 4 major features?
- DNA is double stranded
- DNA takes on the shape of a double helix, or twisted ladder
- The two strands are complementary to each other due to Chargaff’s Rule
- The nitrogenous bases following Chargaff’s Rule always pair up as follows: Adenine (A)-Thymine (T) and Cytosine (C)-Guanine (G)
DNA is a ____ with the ____
double-stranded helix, two strands connected by hydrogen bonds
What are A bases (Adenine) always paired with?
What are Cs (Cytosine) always paired with?
This is consistent with and accounts for what?
Ts (Thymine)
Gs (Guanine)
Chargaff’s rule
What is DNA?
2 poly… are
Antiparallel
A single nucleotide is made up of how many components?
What are they?
A single nucleotide is made up of three components
Nitrogen containing base, Five-carbon sugar, Phosphate group
The nitrogen containing base is either…
The five-carbon sugar is either a…
Purine or Pyrimidine
Ribose (in RNA) or Deoxyribose (in DNA) molecule
What are possible types of pyrimidines? (3)
What are possible types of purines? (2)
Cytosine, Thymine, Uracil (RNA)
Adenine, Guanine
Base + Ribose or Deoxyribose -> ?
What follows?
Base + Ribose or deoxyribose -> Nucleoside (base) + Phosphate (P) -> Nucleotide (P and base)
What is another difference between DNA and RNA? (Sugar)
DNA- Deoxyribose sugar
RNA- Ribose sugar
What does Deoxyribose mean?
Removal of oxygen from ribose sugar
How are Eukaryotic Chromosomes structured?
Eukaryotic chromosomes consist of repeated units of chromatin called nucleusomes
How were nucleosomes discovered?
Discovered by chemically digesting cellular nuclei and stripping away as much of the outer protein packaging from the DNA as possible
The chromatin that resisted digestion had the appearance of ____ in electron micrographs
What are the beads?
“beads on a string”
with the “beads” being nucleosomes positioned at intervals along the length of the DNA molecule
What charge do DNA molecules have?
DNA is negatively charged
(because of the presence of phosphate groups in nucleotides)
DNA associates with proteins that are…
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)
Nucleosomes are made up of ____ that has complexed with ____
Nucleosomes are made up of double-stranded DNA that has complexed with small proteins called histones
The core particle of each nucleosomes consists of what?
How many of each? What are the different types? (4)
The core particle of each nucleosome consists of eight histone molecules,
Two each of four different histone types: H2A, H2B, H3, H4
The structure of histones has been…
What does this suggest?
The structure of histones has been strongly conserved across evolution, suggesting that their DNA packaging function is crucially important to all eukaryotic cells
What does the diagram of Nucleosome show?
Nucleosome, with DNA in orange and histone proteins in blue
The picture here shows…
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
What is the job of the nucleosome? Why?
What are the two functions?
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
Polymerases must be…
Why?
Allowed access to the DNA
Both to Transcribe messenger RNA for building new proteins and to Replicate the DNA when the cell divides
The methods by which nucleosomes solve these opposed needs is not well understood, but may involve a…
Partial unfolding of the DNA from around the nucleosome, one loop at a time, as the information in the DNA is read
What does the diagram with nucleosome doing two functions show?
-1 nucleosome, RNAPII, Transcription (Arrow pointing down)
What do Histones do? (2)
Histones carry positive charges (Arginine and Lysine rich) and Bind negatively charged DNA in a specific conformation
A. Amino Acids with Electrically Charged Side Chains
Positive (3)
Negative (2)
Arginine, Histidine, Lysine
Aspartic Acid, Glutamic Acid
Most amino acids have what structure?
O=
Amino acids have lots of what?
It is what charge?
Nitrogen (NH2)
Positively charged
B. Amino Acids with Polar Uncharged Side Chains (4)
Serine, Threonine, Asparagine, Glutamine
C. Special Cases (3)
Cysteine, Glycine, Proline
D. Amino Acids with Hydrophobic Side Chains (8)
Alanine, Valine, Isoleucine, Leucine, Methionine, Phenylalanine, Tyrosine, Tryptophan
Apart from their function of ____, nucleosomes also…
Safely packaging DNA, Modify the activity of the genes that they store
What is each nucleosome composed of?
Eight “histone” proteins bundled tightly together at the center, encircled by two loops of DNA
Unlike most other proteins, how are histone proteins different?
What do they have?
Not completely globular
They have long tails, which comprise nearly a quarter of their length
What do histone tails do?
What does the nucleus contain?
In this way, what does the cell do?
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
Why is the slide called Wagging Tails?
Histones have a tail
What does genetics mean?
What does epigenetics mean?
Example?
Is it reversible?
What does mutation mean?
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)
What does modified mean?
Helps open nucleosomes
A segment of the DNA double helix wraps around each histone core particle how many times?
A little less than twice
The exact length of the DNA segment associated with each histone core… BUT
Varies from species to species
But most such segments are approximately 150 base pairs in length
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?
N-terminal tails
Higher-order chromatin structure and gene expression
Each nucleosome is composed of…
DNA wound 1.65 times around eight histone proteins
Nucleosomes fold up to form…
Which forms…
A 30-nanometer chromatin fiber
Which forms loops averaging 300 nanometers in length
How many chromosomes? How many DNA?
A cell with 46 chromosomes has 46 DNA molecules
The 300 nm fibers are compressed and folded to produce what?
A 250 nm-wide fiber, which is tightly coiled into the chromatid of a chromosome
Diagram:
At the simplest level, what is chromatin?
A double-stranded helical structure of DNA
Diagram:
What is the length of a DNA double helix?
2 nm
What is DNA complexed with to form what?
DNA is complexed with Histones to form Nucleosomes
Each nucleosome consists of what?
How many times?
Each nucleosome consists of Eight Histone Proteins around which the DNA wraps 1.65 times
What does a chromatosome consist of?
A chromatosome consists of a Nucleosome plus the H1 histone
What do the nucleusomes fold up to produce?
What does it form?
A 30-nm fiber
That forms loops averaging 300 nm in length
What are the 300-nm fibers compressed and folded to produce?
A 250-nm-wide fiber
What does tight coiling of the 250-nm fiber produce?
Tight coiling of the 250-nm fiber produces the Chromatid of a chromosome
What are the “beads on a string”?
Nucleosome core of eight histone molecules
What is the 250-nm-wide fiber coiled into a height of?
700 nm
What is a chromosome?
DNA molecule associated with a lot of protein
What is shown on picture of chromatin?
A 30-nm fiber of chromatin
When are chromosomes Most Compacted?
During Metaphase
Comparing the length of metaphase chromosomes to that of naked DNA…
What can this be thought of as akin to?
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)
How is this level of compaction achieved?
Exactly how this is accomplished is unclear, but what may play a role?
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
What is the difference between neurons and muscle cells?
Neurons: don’t have
Muscle cells: Myoglobin expressed in muscle
Basic structure of a gene:
Diagram shows what?
Intron, Exons, Intron, Exon
Basic structure of a gene:
Order
Enhancer, Promoter, Exon, Intron, Exon, Intron, Termination Seq.
Basic structure of a gene:
Promoter
Transcription factor binding and RNA polymerase recruitment
What do the Enhancer and Promoter, which are Regulatory Elements, determine? (2)
Examples of both?
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)
What are exons?
Part of the RNA that codes for proteins
“forming RNA”
Exons:
The information for the amino acids sequence in the protein is written herein the form of what?
Genetic code
Introns:
Junk sequence?
Removed via RNA Splicing
Termination Sequence:
This sequence element determines where to stop the mRNA synthesis process
Also determines mRNA stability in the cell
Although each codon is specific for only one amino acid (or one stop signal), what is the genetic code described as?
Why?
DEGENERATE, or Redundant
Because a single amino acid may be coded for by more than one codon
What is the phosphorylation codon?
AUG (Met)
Most common start codon and it codes for amino acid Methionine
What is the genetic code?
Example of variation?
Furthermore, the genetic code is NEARLY UNIVERSAL, with only rare variations reported
For instance, mitochondria have an alternative genetic code with slight variations
What are the two “code” diagrams showing?
“Universal” code and mtDNA (Mitochondrial) code
Does genetic code overlap?
What does this mean?
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
Table 1: Did the code have commas or not?
Non-overlapping code with no “commas” present: CATGAT
Non-overlapping code with comma present (where X is any nucleotide): CATXGAT
What is genetic code?
“How everything is written in your body”
Properties of genetic code (8)
(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)
What is Co-linearity?
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
What is Gene-polypeptide Parity?
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
What processes is a gene expressed through? (2)
Transcription, Translation
What happens during transcription?
Translation?
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
Non-Polar Amino Acids: (9)
Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Tryptophan (Trp), Phenylalanine (Phe), Proline (Pro)
Polar Amino Acids: (6)
Serine (Ser), Threonine (Thr), Cysteine (Cys), Tyrosine (Tyr), Asparagine (Asn), Glutamine (Gln)
Electrically Charged Amino Acids:
Acidic (2)
Aspartic Acid (Asp), Glutamic Acid (Glu)
Electrically Charged Amino Acids:
Basic (3)
Lysine (Lys), Arginine (Arg), Histidine (His)
Levels of Protein Structure: (4)
Primary Structure (polypeptide chain), Secondary Structure, Tertiary Structure (most proteins in body), Quaternary Structure
What is the Secondary Structure dependent on?
Dependent on Hydrogen Bonding
What are the two main types of Secondary Structures?
a. The a-helix (alpha helix)
b. The b-sheet (beta sheet)
What is the a-helix?
a-helix is a right-handed coiled strand and the hydrogen bonding is WITHIN the strand (INSTRA-strand)
What is the b-sheet?
The hydrogen bonding in a b-sheet is BETWEEN strands (INTER-strand)
Definition of protein:
Bio molecule (big, organic)
Made up of amino acids
What is the overall three-dimensional shape of an entire protein molecule?
Tertiary structure
What occurs under physiologic conditions (normal cellular environment)? (2)
- 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
- The Acidic or Basic Amino Acid Side-chains will generally be Exposed on the Surface of the protein as they are hydrophobic
What does hydrophilic mean?
More charge, Helps them dissolve water
What does the diagram show?
Distribution of amino acids in Myoglobin:
Hydrophobic in yellow and Charged amino acids in blue
“Inside out” amino acid distributions in Porin:
What is the outside covered by?
What about the inside?
- The outside of Porin (VDAC1) which contacts hydrophobic groups in the membrane is covered largely with hydrophobic residues
- Whereas the center Includes a water filled channel lined with charged and polar amino acids
What is a Quaternary structure?
Spatial arrangement of multi subunit proteins (made of more than one polypeptide chain)
Quaternary structure:
Numerous interactions are responsible: (3)
- Hydrogen bonding
- Disulfide bridges (a covalent bond derived from two thiol groups):
The formation of disulfide bridges happen by oxidation of the sulfhydryl groups on cysteine - Salt bridges (a link between electrically charged acidic and basic groups)
What are disulfide bridges?
Covalent bond derived from two thiol groups
How does the formation of disulfide bridges happen?
By oxidation of the sulfhydryl groups on cysteine
What are salt bridges?
Link between electrically charged acidic and basic groups
Who was Richard Phillips Feynman?
What was he known for? (4)
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
When did Feynman receive the Nobel Prize?
For contributions to the development of quantum electrodynamics, Feynman received the Nobel Prize in Physics in 1965 jointly with Schwinger and Tomonaga
What are prions?
Prions are infectious proteins which replicate without going through DNA or RNA intermediates
(Particularly notable example of exception to the theory)
What disease are prions responsible for?
What does the disease cause?
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
What is scrapie?
What is it classified as?
What can inflected flocks experience?
Fatal, degenerative disease affecting the central nervous system of sheep and goats
Transmissible spongiform encephalopathies (TSE)
Significant production losses
What are clinical signs of scrapie?
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
Infectious proteins:
The concept of an infectious protein, or prion, was proposed in the 1960s to explain scrapie infection
What did researchers find out about scrapie?
What did they propose?
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
Why was the idea that proteins could be infectious by themselves highly controversial?
Because it appeared to challenge the central dogma of molecular biology
How did Prusiner show that proteins can indeed be infectious?
What was he awarded?
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
What are prions also responsible for? (3)
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
What is mad cow disease caused by?
Prions that misfold and aggregate
Prions are proteins that can adopt which two forms?
Why may this not seem unusual?
A Normal form and a Misfolded form
Since many proteins are flexible and adopt different shapes
What is another unusual characteristic of prions?
In this way, what happens?
Example?
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
Misfolded prions are…
Infectious, so a small dose of misfolded prions can infect and corrupt an entire organism
What happens when the normal form of prion protein PrP changes into its misfolded shape?
When does infection occur?
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
What does the Prion Protein (PrP) have?
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)
What is misfolding produced by?
An incorrect folding process that results in the formation of a protein with a different conformation from its native fold
Protein misfolding can occur by several reasons: (6)
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
Healthy (PrPc) vs Prion disease (PrPSc)
Healthy (PrPc):
- monomeric
- high a-helix
Prion disease (PrPSc)
- multimeric amyloid fibril
- parallel in-register architecture
- high b-sheet
