Week 3: DNA, Gene Expression and Epigenetics Flashcards
Assembling subsets of the exons of a gene, which increases the number and diversity of proteins it encodes.
ALTERNATIVE SPLICING
A three-base sequence on one loop of a transfer RNA molecule that is complementary to an mRNA codon and connects the appropriate amino acid and its mRNA.
ANTICODON
The head-to-toe orientation of the two nucleotide chains of the DNA double helix.
ANTIPARALLELISM
A protein that binds a polypeptide and guides folding.
CHAPERONE PROTEIN
A part of a gene and its corresponding mRNA that encodes amino acids.
EXON
A mutation that alters a gene’s reading frame.
FRMAESHIFT MUTATION
A type of protein around which DNA coils in a regular pattern.
HISTONE
Part of a gene that is transcribed but is excised from the mRNA before translation into protein
INTRON
Pentose sugar + Nitrogenous Base
NUCLEOSIDE
Nucleoside or (Pentose sugar + Nitrogenous Base) + Phosphate Group
NUCLEOTIDE
A unit of chromatin structure consisting of DNA coiled around
an octet of histone proteins.
NUCLEOSOME
This was a quote from which scientist?
“A genetic material must carry out two jobs: duplicate
itself and control the development of the rest of the cell
in a specific way.”
Francis Crick, 1953
DNA is the Genetic Material, can be attributed to who?
Francis Crick, 1953
- Swiss physician and biochemist
- Isolated nuclei from white blood cells in pus
- Found an acid substance with nitrogen and phosphorus
o He called it nuclein (1871)
o Later, it was called nucleic acid
Friedrich Miescher, 1871
- English Physician
- Linked inheritance of inborn errors of metabolism with
the lack of particular enzymes.
Archibald Garrod, 1902
- English microbiologist
- Worked with Streptococcus pneumoniae bacteria,
which exists in two types: - Type S (Smooth) = Enclosed in a polysaccharide capsule
- Type R (Rough) = No capsule
Termed the conversion of one bacterial type into another
as transformation
Frederick Griffith, 1928
Transformation of one bacterial type to another is attributed to which Scientist?
Frederick Griffith, 1928
The virulent type of Streptococcus pneumoniae bacteria according to the experiments of Frederick Griffith in 1928
Type S (Smooth), the polysaccharide capsule defends it from the immune system of the body.
The animal used in Frederick Griffith’s experiments
A rat
- American physicians
- Treated lysed S bacteria with protease and DNase
- Only DNase prevented transformation
- Thus, DNA is the transforming principle
o Can convert type R bacteria into S
Avery, MacLeod and McCarty, 1944
Identified DNA as the transforming principle
Avery, MacLeod and McCarty, 1944
- American microbiologists
- Used E.coli bacteria infected with a virus that consisted
of a protein head surrounding DNA - Blender experiments showed that the virus transfers
DNA, not protein, into a bacterial cell
o Thus, DNA is the genetic material
Alfred Hershey and Martha Chase, 1953
They supported the findings of Francis Crick that DNA is indeed the genetic material
Alfred Hershey and Martha Chase, 1953
- Russian-American biochemist
- Identified the 5-carbon sugars ribose in 1909 and
deoxyribose in 1929 - Revealed chemical distinction between RNA and DNA
o RNA has ribose
o DNA has deoxyribose - Discovered that the three parts of a nucleotide are found
in equal proportions:
o Sugar
o Phosphate
o Base - Deduced that a nucleic acid building block must contain
one of each component
Phoebus Levine, 1909-1929
Discovered the three parts of a nucelotide
Phoebus Levine, 1909-1929
- Austrian-American biochemist
- Analyzed base composition of DNA from various species
and observed regular relationships:
o Adenine (A) + Guanine (G) = Thymine (T) + Cytosine (C)
A = T and C = G
Erwin Chargaff, 1951
- English scientists
- Used a technique called X-ray diffraction
o Deduced the overall structure of the
molecule from the patterns in which the X rays were
deflected - Distinguished two forms of DNA
o “A” form, which is dry and crystalline
o “B” form, which is wet and cellular - It took Franklin 100 hours to obtain “photo 51” of the B-form
of DNA
Rosalind Franklin and Maurice Wilkins, 1952
- Used the earlier research and inferences from model
building with cardboard cutouts to solve the structure of
DNA.
James Watson and Francis Crick
In the year 2008 this scientist had his genome sequenced
James Watson
Discovered that DNA transmits killing ability in bacteria
Oswald Avery, Colin MacLeod and Maclyn McCarty, 1940
4 scientists that discovered DNA components, proportions, and positions
Phoebus Levine, Erwin Chargaff, Maurice Wilkins and Rosalind Franklin (1909-early 1950’s)
A section of a DNA molecule.
Gene
Building block of DNA
Nucleotide
Sequence of building blocks specifies the sequence of amino acids in a particular protein.
Gene
Sugar found in DNA
Deoxyribose
Phosphorus atom bonded to four oxygen atoms
PHOSPHATE GROUP
Information containing parts of DNA because they form sequences.
NITROGENOUS BASE
Enumerate the Purines
Adenine and Guanine
Enumerate the Pyrimidines in DNA
Cytosine and Thymine
Enumerate the Pyrimidines in RNA
Cytosine and Uracil
are the informational parts of nucleotides.
DNA bases
Each composed of a 6-membered and 5-membered ring.
Purines
Have only a single six-membered ring
Pyrimidines
created when Phosphodiester bonds form between the deoxyribose sugars and the phosphates which causes nucleotides joint into Polynucleotide chains
Sugar Phosphate Backbone
Form between the deoxyribose sugars and the phosphates which causes nucleotides joint into Polynucleotide chains
Phosphodiester bonds
A chain of nucleotides
Polynucleotide chains
MODIFIED TRUE OR FALSE
DNA consists of two chains of two polynucleotide chains in an
PARALLEL configuration
FALSE, Antiparallel
- Derives from the structure of sugar-phosphate backbone.
- One-half of the double helix runs in a 5’ to 3’. The other half
runs in a 3’ to 5.
ANTIPARALLELISM
TRUE OR FALSE
Antiparallel nature of the DNA double helix becomes apparent when the carbons in the sugar are numbered
TRUE
TRUE OR FALSE
Carbons are numbered from 1 to 5 in deoxyribose.
TRUE
MODIFIED TRUE OR FALSE
DNA is IRREGULAR
FALSE, DNA IS DIRECTIONAL
TRUE OR FALSE
These are your complementary base pairs in DNA:
Adenine = Uracil
Guanine = Cytosine
FALSE, Adenine = Thymine
The key to the constant width of the double helix is the specific pairing of purines and pyrimidines via
Hydrogen Bonds
form frameworks that guide DNA strands.
Scaffold Proteins
The DNA coils around proteins called ________ , forming a bead-on-a string-like structure.
histones
The bead part in in the DNA coiled histone is called
Nucleosome
DNA wraps at several levels, until it is compacted into a
Chromatid
Chromosome substance is called
Chromatin
HYPOTHESIS ON DNA REPLICATION
- Watson and Crick: Envisioned the 2 strands of the DNA
double helix
unwinding and separating. - One old strand & one new strand
Semiconservative Hypothesis
HYPOTHESIS ON DNA REPLICATION
- Entirely new DNA molecule
Conservative Hypothesis
HYPOTHESIS ON DNA REPLICATION
- Max Delbruck
- Replication involves a break in the DNA backbone
every 10 nucleotide and attaches the old strand to the
new one.
Dispersive Hypothesis
ended their report on the structure of DNA with the
statement:
“It has not escaped our notice that the specific pairing we
have postulated immediately suggests a possible copying
mechanism for the genetic material.”
Watson and Crick
Semiconservative Replication was demonstrated by ______ and ______, using a series of ______ experiments
Matthew Meselson and Franklin Stahl, Density Shift
A series of Density Shift experimentation were conducted by these 2 scientists
Matthew Meselson and Franklin Stahl
This was observed in a series of Density Shift experiments, what type of DNA replication does this prove?
The two daughter double helices are identical
to the original parental double helix in DNA
sequence. However, the light blue helix
halves of the daughter DNA molecules
indicate that each consists of one strand of
parental DNA and one strand of newly
replicated DNA.
Semiconservative Replication
E. coli was labeled with a dense, heavy form of NITROGEN, and traced the pattern of replication
Density Shift Experiments
STEPS IN DNA REPLICATION
G1 –> S —> G2 —> Mitosis
Pre-DNA Synthesis part of Interphase
G1 (Gap 1)
Post-DNA Synthesis part of Interphase
G2 (Gap 2)
DNA Synthesis part of Interphase
S (Synthesis)
Mitosis lasts for about?
1hr
Gap 1 of Interphase lasts for about?
10hrs
Gap 2 of Interphase lasts for about?
4hrs
DNA Synthesis or S Phase of Interphase lasts about?
9hrs
The steps in DNA replication are as follows:
1.) Parent DNA molecule.
2.) Parental strands unwind and separate at several points.
3.) Each parental strand provides a template for DNA polymerase to bind complementary bases, A with T and G with C.
4.) Sugar-phosphate backbones of daughter strands close.
Site where DNA is locally opened, resembling a fork.
Replication Fork
Also known as the Continuous strand
Leading strand
Also known as the Discontinuous strand
Lagging strand
The unwinding protein
Helicase
Proteins that keep strands apart and stabilized, they actually do not bind but they maintain the separation, hence they are Misnomers
Binding Proteins
attracts complementary RNA nucleotides to build a
short piece of RNA called RNA primer to be added to the template strand.
Primase
A short piece of RNA
RNA primer
adds DNA nucleotides to the RNA primer, also binds nucleotides to form new strands.
DNA Polymerase (DNAP)
is an enzyme that build a polymer which is a chain
of chemical building blocks
Polymerase
engages in proofreading activity check and replaces incorrect bases.
* Excising mismatched bases
* Inserting correct bases.
DNA Polymerase (DNAP)
Continuous strand synthesis continues in this direction.
5 to 3
Discontinuous synthesis produces these fragments
Okazaki fragments
This is the reason why the growing fork proceed in one
direction when both parental strands replicate and run in
opposite direction.
Discontinuous synthesis
removes RNA primers.
Enzymes
rewinds to the sections of the strand that remain unwound.
Annealing helicase
“backstitched“ fragments that form your
lagging strand.
Okazaki Fragments
seals sugar-phosphate backbone and joins Okazaki Fragments
Ligase
- The sites of replication resemble bubbles that coalesce as
the double helices form. - Significance: DNA replication can accomplish 100 quadrillion
times faster compared to only one point of replication.
DNA REPLICATION BUBBLES
A DNA amplification technique that uses DNAP to rapidly replicate a specific DNA sequence in a test tube.
o Significance: To identify a specific DNA sequence in a
virus
Polymerase Chain Reaction (PCR)
In the PCR process this is the variation of temperature that can separate the strands
Temperature shift
When Primers hybridize due to base complementarity
Hybridization
In the PCR Process this step equals to 2n, where n is the number of temperature cycles.
Amplification
The PCR Process:
- Preparation
- Temperature shift
- Hybridization
- Amplification
invented a way to determine the base sequence of a small piece of DNA.
Frederick Sanger
Sanger sequencing uses an approach called
Chain Termination
This describes a step in DNA sequencing
First synthesizes an RNA molecule that is complementary to one strand of the DNA double helix for a particular gene. The RNA copy is taken out of the nucleus and into the cytoplasm.
Transcription
This describes a step in DNA sequencing
Uses the information in the RNA to manufacture a protein by aligning and joining specified amino acids. Finally, the protein folds into a specific three-dimensional form necessary for its function.
Translation
_______ —> ______ —> ________
Some of the information stored in DNA is copied to RNA (transcription), some of which is used to assemble amino acids into proteins translation). DNA replication perpetuates genetic information.
DNA, RNA, PROTEIN
contains the genetic information that was replicated in cell nucleus mRNA carries the protein encoding information going to ribosome for translation process
DNA
Stores RNA- and protein encoding
information, and transfers information to daughter
cells
DNA
Carries protein-encoding information,
and helps to make proteins
RNA
Cannot function as an enzyme
DNA
Can function as an enzyme
RNA
Maintains protein-encoding
information
DNA
Carry protein-encoding information
and controls how information is used
RNA
Double-stranded
DNA
Single-stranded
RNA
Bridge between gene and protein
RNA
A type of RNA whose base sequence complements
that of the strand of the double helix
Template strand
The enzyme that builds an RNA molecule
RNA Polymerase
The non-template strand of the DNA double helix
Coding strand
The process of folding of RNA into a three dimensional
shape after it is synthesized along DNA
Conformation
A sequence of three mRNA bases that form a genetic “code
word” for a specific amino acid
Codon
- Carries information that codes a specific
protein. - Differentiated cells produce certain mRNA
molecules called transcripts. - Information in the transcripts is used
to manufacture the encoded proteins. - Encodes AA sequence
mRNA (Messenger RNA)
- Associates with certain proteins to form a
ribosome - Provide structural support.
- Some are catalysts (ribozymes)
and others help align the ribosome and mRNA. - Associate with proteins to form ribosomes.
- Ribosomes – an organelle
consisting of RNA and protein
that is a scaffold and catalyst
for protein synthesis.
rRNA (Ribosomal RNA)
- Binds mRNA to an amino acid.
- Translation Transports specific amino acids to the
ribosome for protein synthesis.
tRNA (Transfer RNA)
an organelle
consisting of RNA and protein
that is a scaffold and catalyst
for protein synthesis.
Ribosomes
An rRNA catalyst
Ribozymes
Differentiated cells produce certain mRNA
molecules called
Transcripts
Information in the transcripts is used
to manufacture
encoded proteins
500 to 4,500+ Nucleotides involved in Transcription
mRNA (messenger RNA)
1000 to 3,000 Nucleotides involved in Translation
rRNA (Ribosomal RNA)
75 to 80 Nucleotides involved in Translation
tRNA (Transfer RNA)
A ribosome from a eukaryotic cell has two subunits; together, they consist of __ proteins and _ rRNA molecules.
79 proteins and 4 rRNA molecules
states that the pattern of information that
occurs most frequently in our cells is:
o From existing DNA to make new DNA (DNA replication)
o From DNA to make new RNA (transcription)
o From RNA to make new proteins (translation)
Central Dogma
- The transfer of information from RNA to make new DNA, this occurs in the case of retroviruses, such as HIV.
- It is the process by which the genetic information from RNA is assembled into new DNA.
Reverse Transcription
- Form an apparatus that binds DNA at certain sequences and initiates transcription at specific sites.
- Respond to extracellular signals to form a pocket for RNA polymerase and signal it to start building an RNA chain.
- Include DNA binding domains which guide them to the genes they control.
Transcription Factors
It is a mutation in the Transcription Factors
Rett syndrome
Transcription Factors and RNA polymerase in the stage of initiation bind to a
Promoter
It is the first Transcription Factor
TATA binding protein
TATA binding protein is attracted to what is called a
TATA box
RNA PROCESSING
the mechanism of combination of exons of a gene in different ways to form different versions of one protein product
Alternate splicing
assembles a protein using the information in the mRNA
sequence. Particular mRNA codons correspond to particular amino acids:
Translation
is transcribed from a locally unwound portion of DNA.
In translation
mRNA (Messenger RNA)
matches mRNA codons with amino acids.
tRNA (Transfer RNA)
UAA, UGA, and UAG are examples of what codon?
Stop Codon
The first two letters of this codon is always G
Glycine
The first two letters of this codon is always C
Proline
TRUE OR FALSE
Translation begins as the
initiation complex forms.
TRUE
ARRANGE THE SEQUENCE IN BUILDING A POLYPEPTIDE
Second Amino acid joins the initiation complex
Amino acid chain extends
Termination if reaching a stop codon
First peptide bond forms as new amino acid arrives
THE SEQUENCE IS AS FOLLOWS
Second Amino acid joins the initiation complex
First peptide bond forms as new amino acid arrives
Amino acid chain extends
Termination if reaching a stop codon
Due to the chemical forces bonding the molecules, proteins fold into:
Three-dimensional shapes or conformations
Mutations in the primary structure can happen if the change is
nonsynonymous
The 4 structures of a protein
PRIMARY
SECONDARY
TERTIARY
QUATERNARY
Protein structure with an amino acid sequence
PRIMARY
Folds dues to the chemical attraction of adjacent amino acids in the primary structure
SECONDARY
Winding of the protein due to chemical attraction of farther
amino acids and water molecules
TERTIARY
Protein that consists of more than one polypeptide
QUATERNARY
stabilize partially folded regions of a protein into
its correct form.
Chaperone proteins
tags misfolded proteins which are sent to the cytoplasm for
proper refolding.
Ubiquitin
Degrade misfolded proteins with more than one tag in order
to be able to recycle the amino acids used.
Proteasomes
TRUE OR FALSE
Changes in gene expression occur over time at the molecular and organ levels
o Changes to DNA alter gene expression, but do not change the DNA sequence.
o Changes to the chemical groups that associate with DNA that are transmitted to daughter cells after cell division.
Epigenetics
has four globular polypeptide chains:
Adult Hemoglobin
The Two alpha (α) chains of Hemoglobin are encoded on what chromosome number?
Chromosome 11
The Two beta (β) chains of Hemoglobin are encoded on what chromosome number?
Chromosome 16
No of amino acids in Two alpha (α) chains of polypeptide in Hemoglobin
141
No of amino acids in Two beta (β) chains of polypeptide in Hemoglobin
146
surrounds an iron-containing heme group
Globin
Hemoglobin subunits change in response to
Oxygen levels
TRUE OR FALSE
Subunit makeup in Hemoglobin varies over a specific period.
FALSE, it varies over a lifetime
The Globin Chains are Two epsilon (ε) + two zeta (ζ) in this Hemoglobin
Gower – 1
The Globin Chains are Two alpha (α) + two epsilon (ε) in this Hemoglobin
Gower - 2
The Globin Chains are Two zeta (ζ) + two gamma (γ) in this Hemoglobin
Portland
The Globin Chains are Two Alpha (ζ) + two gamma (γ) in this Hemoglobin
F
THESE ARE OBSERVED IN THIS STAGE
Begins in early embryogenesis; peaks during third trimester and begins to decline just before birth
Early embryogenesis
(product of yolk sac erythroblasts)
INTRAUTERINE STAGE
THESE ARE OBSERVED IN THIS STAGE
Two gamma (γ) + two alpha (α)
F (60% to 90%)
Two beta (β) + two alpha (α)
A (10% to 40%)
BIRTH STAGE
THESE ARE OBSERVED IN THIS STAGE
Two gamma (γ) + two alpha (α)
F (1% to 2%)
Two alpha (α) + two delta (d)
A2 (<3.5%)
Two beta (β) + two alpha (α)
A (>95%)
2YRS - ADULTHOOD STAGE
This plasma contains about 40,000 different types of proteins.
Blood Plasma
MODIFIED TRUE OR FALSE
Changing conditions DO NOT cause a change in the protein profile of the plasma.
FALSE, DO
sheds light on how genes are turned on and off.
Stem Cell Biology
The 2 glands in a Pancreas
Exocrine and Endocrine
Releases digestive enzymes into ducts.
Exocrine glands
Secretes polypeptide hormones directly into
the bloodstream.
sabi sa histo they are ductless
Endocrine glands
produces either endocrine or exocrine cells.
Differential gene expression
- Belong to a class of molecules called noncoding RNAs
- 21–22 bases long:
miRNA (Micro RNA)
When a microRNA binds to a target mRNA, it prevents a certain process
what does it prevent?
Translation
A practical application of microRNAs is best exemplified with this disease
Cancer
Technology wherein small synthetic, double-stranded RNA molecules are introduced into selected cells to block gene expression
RNAi (RNA Interference)
Mechanisms that maximize Genetic Information
Alternate Splicing
An intron encoding one isoform is
an exon in another
An intron on one DNA strand is an
exon on the other
Adding sugars to form glycoproteins
or lipids to form lipoproteins
Precursor protein is cut to yield two
proteins
MECHANISMS THAT MAXIMIZE GENETIC INFORMATION
An example of Alternate Splicing mechanism
Cell surface and secreted forms of
antibodies
MECHANISMS THAT MAXIMIZE GENETIC INFORMATION
An example wherein an intron encoding one isoform is an exon in another
Prostate specific antigen (PSA) and
PSA-linked molecule (PSA-LM)
MECHANISMS THAT MAXIMIZE GENETIC INFORMATION
An example wherein an intron on one DNA strand is an
exon on the other
Neurofibromin and three other
genes
MECHANISMS THAT MAXIMIZE GENETIC INFORMATION
An example wherein adding sugars form glycoproteins
or lipids to form lipoproteins
Cell surface molecules important in
cell-cell recognition
MECHANISMS THAT MAXIMIZE GENETIC INFORMATION
An example wherein Precursor protein is cut to yield two
proteins
Dentinogenesis imperfecta
MECHANISMS THAT MAXIMIZE GENETIC INFORMATION
o Caused by a deficiency in the two proteins DPP and DSP
o Both are cut from the same DSPP protein
Dentinogenesis imperfecta
TRUE OR FALSE
Most human genomes do not encode protein
TRUE
- Only 1.5% of human DNA encodes protein
- Rest of genome includes:
o Viral DNA
o Noncoding RNAs
o Introns
o Promoters and other control sequences
o Repeated sequences
copies DNA from RNA, enabling viruses to insert
their genetic material into human chromosomes
Reverse transcriptase
These RNA control gene expression.
Long noncoding RNAs
About 8% of our genome is derived from RNA viruses called
Retroviruses
Genetic material
in the human chromosomes
Human endogenous retroviruses, or HERVs:
TRUE OR FALSE
Viral DNA helps in evidence of past infection
TRUE
Nearly all of the human genome can be transcribed, and much of it is in the form of
noncoding RNAs (ncRNAs).
noncoding RNA’s are transcribed from
pseudogenes
Genes that are not translated into proteins
DNA sequences very similar to known
genes, but again are not translated
pseudogenes
Connect mRNA codons to amino acids
tRNA genes
Parts of ribosomes
rRNA genes
Keeps transposons out of germline cells
Piwi-interacting RNA (piRNA)
noncoding RNA between genes
Large intergenic noncoding RNAs
Process rRNAs in nucleolus
Small nucleolar RNAs (snoRNAs)
Parts of spliceosomes
Small nuclear RNAs (snRNAs)
Adds bases to chromosome tips
Telomerase RNA
Inactivates one X chromosome in cells
of females
Xist RNA
Parts of genes that are cut out of mRNA
Introns
Guide enzymes that carry out DNA
replication, transcription, or translation
Promoters and other control
sequences
Noncoding RNA that controls translation
Small interfering RNAs (siRNAs)
Noncoding RNA that controls translation of many genes
MicroRNAs (miRNAs)
Repeats that move around the genome
Transposons
Protects chromosome tips
Telomeres
Largest constrictions in
chromosomes, providing attachment
points for spindle fibers
Centromeres
Exome is the DNA that encodes proteins. Parental strand provides a template for DNA polymerase to bind complementary bases (A with T and G with C).
Both statements are true.
The first statement is true, and the second statement is false
.
Both statements are false.
The first statement is false, and the second statement is true.
The first statement is false, and the second statement is true.
What identifies all the mRNA molecules made in a specific cell under specific circumstances?
Transcriptome
What is the Genetic code for Arginine?
CGA
What is the accepted hypothesis for DNA replication?
Semi-conservative
DNA polymerase adds RNA polymerase chain to the RNA primer. RNA polymerases checks the bases and replaces incorrect ones.
Both statements are true.
The first statement is true, and the second statement is false
.
Both statements are false.
The first statement is false, and the second statement is true.
BOTH STATEMENTS ARE FALSE
What enables a retrovirus to copy its RNA into DNA?
Reverse transcriptase
Which chromosome encodes the two beta chain in adult hemoglobin?
Chromosome 16
Two epsilon (ε) + two zeta (ζ), are seen in an?
Embryo
Which of the following is composed of pentose sugar and nitrogenous base?
Nucleoside
Nucleophosphate
Nucleotide
Nucleic acid
Nucleoside
