Untitled Flashcards Set
Molecular Biology
Exam 1
Lecture 2: DNA
Chargaff- purines= pyrimidines (T=A, G= C)
Rosalind Franklin- helical structural and distance between nitrogenous bases
DNA strands are held together by what type of bonds?
Hydrogen bonding
Which bases pair together and how many bonds are formed between them?
Guanine and cytosine- 3 bonds
Adenine and Thymine- 2 bonds
AT2 GC3
Which macromolecule is used to package DNA in eukaryotes?
Euchromatin- more loosely packaged heterochromatin
Heterochromatin
What does DNA look like in interphase versus during cell division?
DNA serves what role in cells?
Genetic material
What are nucleosomes and how does DNA get packaged in them?
DNA+histones
DNA is wrapped around a protein core of eight histone molecules
How does DNA replicate?
Semi conservatively
Half of it and replicate it (5’ to 3’)
What are replication origins?
Where the DNA will begin to replicate
These are called replication forks
What are replication forks and what do they look like?
The two sides surrounding the origin of replication
Y-shaped junctions
What molecule primes the replication of DNA?
DNA polymerase
What role does telomerase play?
adds a little primer to basically copy more of the strand
Allows the Okazaki fragments to be completely filled in
What are telomeres?
Replicated DNA sequence
Which enzyme replicates DNA?
DNA Polymerase
How does DNA fix mistakes?
DNA Polymerase
Homologous recombination
What proteins are involved in DNA replication and what roles do they play?
DNA Polymerase- replication and fix mistakes
DNA ligase- seals the gaps between Okazaki fragments
DNA Helicase- breaks the bonds and ‘unzips’ the DNA
DNA Topoisomerases- release the stress for the DNA in front of a replication fork
Telomerase- adds a little primer to basically copy more of the strand
Prevent linear eukaryotic chromosomes from shortening with each cell division
What are Okazaki fragments and what role do they play in DNA replication?
Short little fragments of DNA that is added 5’ to 3’
Added as the replication fork opens up
Label this figure(slide 26)
Lecture 3: RNA
What are the major differences between RNA and DNA?
Sugar difference
DNA uses deoxyribose
2nd carbon-H
RNA uses ribose
2nd carbon- OH
Base difference
DNA- thymine
RNA- uracil (binds with adenine- 2 Hydrogen bonds)
RNA is single stranded
DNA is double stranded
RNA in cells differs from DNA in that
Single stranded and can fold into a variety of structures
RNA can make secondary structures, why is this critical?
Hydrogen bonding
Change shape you can change the function
What are some examples of functional RNAs and what do they do?
Messenger RNAs (mRNAs)- code for proteins
Ribosomal RNAs (rRNAs)- form the core of the ribosome’s structure and catalyze protein synthesis
microRNAs (miRNAs)- regulate gene expression
Transfer RNAs (tRNAs)- serve as adaptors between mRNA and amino acids during protein synthesis
Other noncoding RNAs- used in RNA splicing, gene regulation, telomere maintenance, and many other processes
Which enzyme generates RNA from DNA?
RNA Polymerase
RNA polymerase 1- transcribes most rRNA genes
RNA polymerase 2- transcribes all protein-coding genes, miRNA genes, and genes for other noncoding RNAs (those of the spliceosome)
RNA polymerase 3- transcribes tRNA genes, 5S rRNA gene, genes for many other small RNAs
How is transcription regulated at the DNA level?
Promoters
Terminators
What is a promoter?
Immediately before the start site of transcription that tells the enzymes needed to begin to assemble here
What is a terminator?
Site that says stop transcribing
How does transcription begin in prokaryotes?
Specific nucleotide sequences that are recognized by RNA polymerase
How does transcription begin in eukaryotes?
RNA polymerase 2 requires a set of general transcription factors
TATA box
What is a transcription factor?
They bind to the TATA box and they they are able to allow for transcription to begin
Basically they control which genes are transcribed and which are not
Transcription in bacteria differs from transcription in a eukaryotic cell because
RNA polymerase (along with its sigma subunit) can initiate transcription on its own
Where does transcription take place in eukaryotes?
Nucleus
What structures do eukaryotic mRNA have at the 5’ and the 3’ ends?
5’ - cap structure
Modified guanosine which has a triphosphate bridge
3’- poly A tail
This is a noncoding sequence
How are the introns spliced out of eukaryotic RNA?
Signals from the secondary OH group
Allows for alternative splicing
Done by snRNPs
What are the differences in transcription between eukaryotes and prokaryotes?
Prokaryotes- just transcripted
Eukaryotes- exons get transcribed and introns do not
Genes in eukaryotic cells often have intronic sequences coded within the DNA. These sequences are ultimately not translated into proteins. Why?
Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus
How many proteins are made from a single prokaryotic mRNA?
many
From a eukaryotic mRNA?
One
Transcription- in the nucleus
Translation- in the cytoplasm
RNA splicing- nucleus
Polyadenylation- nucleus
RNA capping- nucleus
Lecture 4: Proteins
How many amino acids are commonly used in life?
20
Shape determines function
What are the levels of protein structure?
Primary- sequence of amino acid
Secondary- hydrogen bonds on the peptide backbone
Tertiary- bonds between side chains
Quaternary- multiple protein subunits
How does the primary sequence of amino acids influence protein function?
Amino acid residues/side chains- polar or nonpolar, or hydrophobic or hydrophilic etc
What role does shape have in protein function?
Determines it
What type of bond results in alpha helices and beta sheets?
Hydrogen bonding
What molecules are involved in this bond?
NOF
What happens when proteins are misfolded?
They lose their function
Tertiary bonds in proteins include
Ionic bonds,
Van der waal attraction,
Hydrogen bonds,
Disulfide bonds
Why does denaturing proteins tend to make them non-functional?
Changes the 3d shape (tertiary function) so it can not do its function
How does covalent modification of proteins alter function?
Makes it so the enzyme can not function anymore
How does phosphorylation work in regulating proteins?
Adding a phosphate group
What are chaperones and what are some examples of the different types?
Chaperones help guide proteins to fold into the correct shape
They also can act as an isolation chamber that can help the polypeptide fold
What role(s) do tRNAs play in translation?
Molecular adaptors- link amino acids to codon
What are the active sites in the ribosomes?
A, P, and E site
tRNA move from A to P to E
Which of the following is TRUE?
Ribosomes are large RNA structures composed solely of rRNA
Ribosomes are synthesized entirely in the cytoplasm
****rRNA contains the catalytic activity that joins amino acids together
A ribosome binds one tRNA at a time
What are ribosomes composed of?
Four rRNAs and more than 80 small proteins
Also has abiding site for mRNA
Three binding sites for tRNAs
Which macromolecules catalyzes the peptide bond formation?
Free floating ribosomes
Rough Endoplasmic Reticulum
Lecture 5: Gene Expression
What stages of gene expression does the cell regulate expression and how?
Basically all steps
What is a transcription regulator?
Proteins that interact and can help determine if there will be transcription or not
Interact with the bases themselves
Bound as dimers
What is an operon? What type(s) of organisms are operons found in?
Clusters of genes that get transcribed
Bacteria or prokaryotes
(enzymes in biosynthetic pathway)
Operons: contain a cluster of genes transcribed as a single mRNA
What are repressor proteins?
If there is an excess of the end product acts as inhibitor of operon expression
So for example tryptophan repressor binds to the operon to stop transcription
How does the Lac operon work?
Alternative energy source for bacteria
How does gene activation work in eukaryotes?
It occurs at a distance
DNA loops to have genes accessible
Why does regulation of gene expression matter in eukaryotic cells?
Lots of genes
How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter?
By looping out the intervening DNA between their binding site and the promoter
How do the following functional RNAs regulate gene expression?
miRNA- host encoded gene that forms a double stranded RNA construct that gets exported to the cytoplasm
siRNA- RNA silencing
Produced from double stranded, foreign RNAs during the process of RNA interference
Long non-coding RNA
What is X inactivation?
Entire chromosomes can be “switched off” from expression
How does methylation of DNA regulate gene transcription?
Stops transcription
How do siRNAs and miRNAs function in gene regulation?
miRNA- increase how long it is available for translation
How does dsRNA trigger siRNA formation and what is the result?
What is the Histone Code Hypothesis?
Modifications of histone tails act as marks that can be read by other proteins to control the expression or replication of chromosomal regions
Coding in the histones may be heritable
What does the following histone modification mean for gene expression?
Methylation- gene silence
Acetylation- gene expression
What is heterochromatin and what is euchromatin?
Heterochromatin
Highly condensed in interphase
Transcriptionally inactive
Replicates late in S phase
Euchromatin
Organized in 30 nm fiber during interphase
Transcriptionally active
Replicates early in the S phase
What role does alternative splicing have in gene regulation?
Increases gene expression
Which of the following statements about RNAi is true?
RNAi is induced when double-stranded, foreign RNA is present in the cell
Lecture 6: Molecular Biology of the Cell Cycle
What are the phases of the cell cycle and what happens in each phase?
M phase- entry into mitosis
G1- growth
S phase- DNA replication
G2- growth phase
Mitosis
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
Cytokinesis
(please pass me another taco chef)
What prevents the cell from proceeding to the next stage when something is wrong?
Lots of checks- this is known as the cell-cycle control system
Protein-protein interactions
What are the stages of the M phase?
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
What would be the most obvious outcome of repeated cell cycles consisting of S phase and M phase only?
S phase- DNA replicates
Mitotic spindle form in M so
It will get smaller and smaller because missing the G (growth phases)
M phase has two cytoskeletal elements
Actin and myosin separates the two cells
ORC + CDC= phosphorylate
Order these events:
4-Alignment of the chromosomes at the spindle equator
3- Attachment of spindle microtubules to chromosomes
2- Breakdown of the nuclear envelope
7-Pinching of cell in two
6-Separation of two centrosomes and initiation of mitotic spindle assembly
8-Re-formation of the nuclear envelope
1- Condensation of the chromosomes
5- Separation of sister chromatids
Plant cells create a cell wall to separate the daughter cells
The chromosomes condense during which phase of cell reproduction?
Prophase
How is DNA packaged into chromosomes?
DNA wraps around histone proteins to form tight loops called nucleosomes
These nucleosomes coil and stack together to create chromatin
What are loop domains?
Distant genomic regions brought together by protein complexes to form a loop-like structure
What proteins help duplicated chromosomes be configured for segregation?
Microtubules
What role does APC/C play in the separation of sibling chromatids and how does it work?
Promotes the destruction of cohesion
Cytokinesis in animal cells
Requires ATP
Lecture 7: Sexual reproduction
Organisms that reproduce sexually
Undergo a sexual reproductive cycle that involves an alternation of haploid cells with the generation of diploid cells
Germ line- reproductive
Somatic cells- maintain the organism
Ensure germ line function
What are the phases of meiosis?
Chromosome duplication
Meiosis 1
Duplicated homologous pairs line up on the metaphase spindle
Duplicated homologous pairs line up at anaphase of meiosis 1
Separation of homologs at anaphase of meiosis 1
Meiosis 2
What are the similarities between mitosis and meiosis?
Follow basically all the same steps
Except there is crossing over in meiosis
What are the differences between mitosis and meiosis?
Mitosis- 2 identical diploid
Meiosis- 4 non identical haploid
Meiosis 1 and Meiosis 2
Two cell divisions- divide twice
Meiosis 1- crossing over
The duplicated lines up in the middle
Non sister chromatids in each bivalent swap segments of DNA
Allows for crossing over
Meiosis 2- basically divide
Each sister chromatid is pulled apart
Very random- independent assortment
What happens when chromosomes don’t properly separate during meiosis?
Gametes with incorrect numbers of chromosomes
Extra chromosome- down syndrome
Lots when they don’t properly separate are fatal
Which of the following statements most correctly describes meiosis?
Meiosis involves a single round of DNA replication followed by two successive cell divisions
What are Mendel’s Laws?
Alleles for the different traits segregated independently
Genes are on the same chromosome- can segregate independently but only through crossing over
So the closer they are on the same chromosome, the less likely they are to be inherited independently
Dominant and recessive alleles
How can we determine inheritance of genetic traits?
Recessive vs dominant
Dihybrid cross shows that alleles can segregate independently
Explains Mendel’s laws of segregation and independent assortment
Which of the following about Mendel’s experiments is FALSE?
The pea plants could undergo both cross-fertilization and self-fertilization
The true breeding strains were homozygous for the traits that Mendel examined
The egg can carry either the allele from the maternal or the paternal chromosome
***All the traits that Mendel studied were recessive
Lecture 8: Mutations and Cancer
What are the types of mutations that can occur in the cell?
Mutations can exist in protein-coding genes
Loss function:
Point mutation
Truncation- premature stop function
Deletion
Gain of function mutation
Improves the function
Increases the ability
Silent mutation- change in the nucleotide leading to a change in the amino acid sequence
Nonsense mutation- change in the nucleotide leading to a premature stop codon
UAA
UAG
UGA
Nucleotide additions and deletions- change the reading frame of the amino acid sequence
Base changes
Transitions- one base type to the same base type
Purine-purine
Pyrimidine-pyrimidine
Transversion- changing one base type to another
Purine-pyrimidine or vise versa
Bases can also be deleted
Nucleotide substitution
Nucleotide insertion
Nucleotide deletion
Insertion of multiple nucleotides
Deletion of multiple nucleotides
Which type of mutation causes a premature stop codon in an open reading frame?
nonsense
How do cells repair mutations?
Endonucleases
Cleave the phosphodiester bond between nucleotides and cut it
Can be nonspecific
Restrictive one- cut a specific sequence
Exclusively in molecule biology
Methylation of the DNA prevents the cutting
Base Excision repair
Removes single bases
How?
Glycosylase removes the base from the phosphate backbone
AP endonucleases removes the phosphate backbone
DNA polymerase adds the correct base
DNA ligase seals the gap in the phosphate backbone
Nucleotide excision repair
Multiple bases are removed at once
How?
Damage is detected by UVr proteins
Endonucleases cleave out a stretch of DNA with damage in a single ‘chunk’
DNA polymerase fills in the bases
DNA ligase seals any gaps
Mismatch repair
Detects mismatches missed by DNA polymerases
Can differentiated between old and newly synthesized DNA strands (based on nicks from the lagging strand)
How?
Mut proteins recognizes the mismatch
An endonuclease cuts out the nucleotide(base-sugar-phosphate backbone)
DNA polymerase replaces the correct base
DNA ligase closes the phosphate backbone
Non-homologous and end joining repair
Can repair double-strand breaks
How?
Double-strand break is detected
The ends are processes by removing a few nucleotides
DNA polymerase uses an adjacent DNA molecule with short homologies to extend and copy the nucleotides
DNA ligase seals the gaps in the phosphate background
Disadvantage: DNA can not be replicated completely
Types of mutations:
Spontaneous
Random
May be due to error in replication that isn’t corrected
Tautomerism- reposition of a hydrogen to change the base
Depurination- loss of A or G base
Deamination-
Hydrolysis to change C> U or A>
Hypoxanthine C> T (rarer as the C must be methylated)
Slipped strand mispairing-slippage of the strand during replication
Replication slippage
Chemical Mutagen
Chemical compound to induces mutations by damaging bases
Base analogs- cause changes during replication
Alkylating agents- causes transitions, transversions, or deletions
DNA intercalating agents- get between DNA strands
DNA crosslinkers- causes bases to have hydrogen bonds
Oxidative damage- alters functional groups
Nitrous acid- converts A and C to diazo groups (changes hydrogen bonding)
Radiation
Non-ionizing radiation
UV light
Pyrimidine dimers (CC and TT)
Uncorrected- inhibit polymerases
Fixed through nucleotide excision repair
Causes melanomas if uncorrected
Ionizing radiation
Ionizing atoms and/or molecules
Gamma rays
X-rays
Higher energy UV rays
Can break chemical bonds, leading to damage
Errors in DNA repair
NHEJ can repair double-strand breaks
But it requires the removal of a few nucleotides from the ends
Causes deletions from the sequence
Can alter the frame of a gene
What is a mutagen?
Any compound or factor that causes damage to the DNA
Results go to loss of function, gain of function, and cancer
Results of Mutations
Loss of function mutation
Change shape which change function
Knockout genetics
Alanie is the most common amino acid used for this
Gain of function mutations
Some can improve the function
Could change in shape may allow for better binding to ligands
Hard to predict
What do mutations lead to in somatic cells?
Not passed to offspring- can cause cancer
What do mutations lead to in germ line cells?
Passed down to offspring- can cause genetic diseases
What is cancer?
Uncontrollable cell growth and division
What types of mutations lead to cancer?
Not causes by a single mutation
Proto Oncogenes- genes when mutated cause cancer
Tumor suppressor genes- suppressor genes- suppress tumor formation
Both mutations to cause oncogenes and loss of function of the tumor suppressor genes
Apoptosis- pre programmed cell death
Cancer cells this system is damaged in nonfunctional
How is cancer treated?
Chemotherapy
Different chemicals to inhibit mitosis, induce backway pathways apoptosis in actively growing cells
Different compounds for different types of cancer
Radiation
Target application of ionizing radiation to certain cancer cells that are radiation sensitive
Triggers a separate apoptosis pathway than chemotherapy
Low dose treatments have low side effects, but higher doses can have acute side effects
Newer techniques
Cancer immunotherapy
Seek to stimulate the immune system to cancer cells
Dendritic cell therapy-causes dendritic cells to present tumor antigens
CAR-T cell therapy- modifies T-cells to recognize cancer cells
T-cell receptor T-cell therapy- targets the MHC recognition system
Antibody therapy- antibodies produced for different cancer cells
Why are treatments like radiation and chemotherapy used even though the side effects can be debilitating
These treatments trigger backup pathway for apoptosis
Hope it kills the cancer cells before other cells
Lecture 9: Genomes
What are the mechanisms that cause genomes to evolve?
Mutation in genome
Mutation in regulatory DNA
Gene duplication and divergence
Exon shuffling (shuffling the order of exons)
Transposition
Horizontal transfer
What is the difference between a mutation in a germ line cell and a somatic cell?
Somatic- maintain the body
Leads to cancer
Germ line- dividing into different cell types or gametes
Will be passed to the next generation
Which of the following statements is FALSE?
****A mutation that arises in a mother’s somatic cell often causes disease in her daughter
All mutations in an asexually reproducing single-celled organism are passed on to the progeny
In an evolutionary sense, somatic cells only to help propagate germ-line cells
A mutation is passed onto offspring only if it is present in the germ line
What role does recombination play in genome evolution and how does it work?
Crossing over
Rather than swapping you can get additional sequences on one chromosome than other
Rare: repeated rounds of duplication
What is Exon shuffling?
The exons are being moved about by different things
Through transposon or retrotransposon, unequal crossing over event, changing what domains (motifs- something that gives the protein function) are being included
Are the positions of introns conserved among vertebrates?
Yes
What is whole genome duplication and which group of eukaryotes is this common in?
plants
What role do mobile elements play in the evolution of genomes?
Can move exons from one gene to another
Can change the body plan of an organism
In bacteria there are cut and paste transposition and replicative transposition
Which of the following statements about gene families is FALSE?
*****Because gene duplication can occur when crossover events occur, genes are always duplicated onto homologous chromosomes
Not all duplicated genes will become functional members of gene families
Whole-genome duplication can contribute to the formation of gene families
Duplicated genes can diverge in both their regulatory regions and their coding regions
Which of the following statements is TRUE?
****The position of introns in most genes is conserved among vertebrates
The more nucleotides there are in an organism’s genome, the more genes there will be in its genome
Because the fly Drosophila melanogaster and humans diverged from a common ancestor so long ago, any two fly genes will show more similarity to each other than it will to a human gene
Two closely related organisms are more likely to have a genome of the same size than a more evolutionary diverged animal
Lecture 10: Junk DNA
Why is most of the human genome called “junk” DNA in popular media?
98% of DNA is noncoding
Large numbers of repeats
Individuals 99.9% identical (1 difference/1000 bp)
The majority is repetitive nucleotide sequences and other noncoding DNA
Genes are sparsely distributed in the human genome
Why is this wrong?
Non-coding sequences have a variety of roles- absolutely needed
Non Coding functional RNA
Cis and trans regulatory elements
Introns
Pseudogenes
Repeat sequences
Transposons
Viral elements
Telomeres
May have an impact such as the development of cancer
Regulatory elements
Control the transcription of a gene
Elements located in the 5’ to 3’ untranslated region of the genes
Cis-regulatory elements control the gene they are located near
Trans-regulatory elements control distant genes
Introns
Non Coding sections of genes
Transcribed in the precursor messenger RNA
Removed via RNA splicing to form the mature mRNA
May be from mobile genetic elements
Pseudogenes
Related to known genes but have lost protein coding or expression
Loss of regulatory elements
Aside from retrotransposition or genomic duplication of functional genes
Are genomic fossils as they are nonfunctional
Repeat sequences
Highlightly repetitive- tandem repeats
Middle repetitive- dispersed through the genome, transcribed
Single Copy- structural genes
Telomeres
Repeated sequences
End of chromosomes
Protect linear chromosomes from deterioration as a result of DNA replication
What is Junk DNA?
A misrepresentation of what non-coding DNA is
What are the transposons?
Mobile DNA elements that can be transcribed
Barbara McClintock 1948 discovered
Classify strategy used and the sequence
The genes responsible for kernel color could be disrupted
Inserting and disrupting the color in the kernels
Two classes- DNA intermediate and those that use a RNA intermediate
What are retrotransposons?
Transcribed as RNA and then reverse Transcriptase goes back to DNA and integrates into the genome as DNA
Viral in origin (lost the capsid protein and the ability to infect new host cells)
LTR retrotransposons- long repetitive DNA at the end
Endogenous retroviruses- still have many viral genes but can not cause disease
What role do the intergenic regions play in the genome?
Regulate the expression of nearby genes
What role might integrated viruses play in the genome and the evolution of humans?
ENV: retroviral envelope protein
Placental formation for live birth
HERV: human endogenous retrovirus
HERV-K- active during development
Provides protection against other viruses
HERV-H helps keep early embryonic cells pluripotent
Sycynthins: retroviral envelope proteins that are responsible for regulating muscle formation through myoblast fusion
Arc: a viral capsid protein that transports mRNA between neural cells
Which of the following are viral genes that were repurposed by eukaryotes?
Arc, Env, and Syncythins