2 - GENETICS Flashcards
what’s heredity?
the genetic passing of traits from a parent to progeny
how genes can be inherited and expressed by your children
define gene and allele and locus
gene: sequence of nucleotides that code for a specific product/trait
allele: variation in genes. e.g. different eye colours
locus: where the gene is on the chromosome
note that the chromosomes you inherit from mom and dad generally have the same genes but different alleles
for every gene in the human body, you carry 2 sets of alleles
differentiate between somatic cells and germ cells and gametes
somatic cells
- any non-reproductive cell
- diploid
- mutations that occur in somatic cells are not passed down to offsprings
germ cells
- diploids
- mutation that occurs in germ cells would be passed down to offsprings
- located in testes (males) and in ovaries (females)
- undergoes meiosis to form gametes – NOTE: germ cells are not sperm and egg cells but what produces sperm and egg cells via meiosis
gametes
- haploids
- sex cells (sperm and egg)
- combine to form diploid zygotes
- mutation that occurs in germ cells would be passed down to offsprings
what is a genotype?
the individual organism’s unique set of all the genes
the result of 2 copies of genetic information. one from the mother, one from the father. combination of genes from the parents
what is a phenotype?
physically observable characteristics
expression of the genotype we actually see
differentiate between homozygous, heterozygous, and hemizygous
homozygous: same allele type from mother and father
heterozygous: different allele type from mother and father
hemizygous: only a single copy of the gene instead of two – usually only happens with genes located on the sex chromosomes of males bc they have two different sex chromosomes with two completely different sets of genes OR if one copy of the gene somehow got deleted
what are the (3) laws of inheritance?
law of segregation: how individual gametes are formed. the gametes we produce only contain one allele after multiple (2) disjunctions during the anaphases.
law of independent assortment: how homologous chromosomes are separated independently from one another — no coordination –> genetically diverse outcomes. mendel confirmed this using his dihybrid crosses
law of dominance: the expression of dominant alleles
differentiate between monohybrid and dihybrid crosses
monohybrid: used to examine the inheritance of one particular set of alleles when two heterozygotes are crossed together
dihybrid: to examine inheritance and relationship between two sets of alleles when heterozygotes are crossed together – are the traits dependent or independent of each other?
what’s a test cross?
when the genotype of an organism expressing the dominant phenotype is unknown, the unknown organism is crossed with a homozygous recessive
organism to determine if the unknown is homozygous dominant or heterozygous dominant
what are the (7) patterns of inheritance?
mendelian inheritance: one allele dominates over the other
incomplete dominance: more than one dominant allele, and neither is completely dominant over the other. the phenotype will be a blend of the two alleles
codominance: both inherited dominant alleles are completely expressed, simultaneously.
multiple alleles: more than two possible alleles for a gene. e.g. eye colour
epistasis: one’s gene expression affects the phenotypic expression of another. e.g. having a gene that determines hair colour but also having a gene for baldness which affects the phenotypic expression of your hair
pleiotropy: a single gene affects multiple phenotypic traits - e.g. some diseases caused by lack of production of certain substances
polygenic inheritance: interaction of many genes shapes one phenotype e.g. height and skin colour
why are most sex-linked genes present on the x-chromosome?
because the y-chromosome is small, thus can only carry a few genes
what are sex-influenced genes?
sex-influenced genes don’t have to be located on a sex chromosome. sex-influenced genes are genes affected by the sex of the individual carrying that trait
i.e. being male or female can affect how the gene is expressed
what’s genomic imprinting?
allele expression (activation or deactivation) affected by which parent it came from
affects autosomal chromosomes
– not random
MOST GENES DO NOT UNDERGO GENOMIC IMPRINTING
what is penetrance in regards to phenotypic expression?
probability that an organism with a specific genotype will express the corresponding phenotype
complete penetrance = 100% of the people with the affected genotype will display the corresponding phenotype
incomplete penetrance = not all individuals with the affected genotype will display the corresponding phenotype
what is expressivity in regards to phenotypic expression?
describes the variation of a phenotype for a specific genotype - variety in the level of expression
what’s X-inactivation?
occurs in females
only one of the X-chromosomes needs to be expressed so methyl groups are added to the other X-chromosome, causing it to condense into a tiny structure called a barr body
process is random in determining which X-chromosome gets “turned off” – note that the chromosome is not completely shut off (THIS DOESN’T CAUSE TURNERS SYNDROME WHICH IS THE ABSENCE OF THE X-CHROMOSOME) females need both X-chromosomes for healthy function
—– this is why calico cats have multiple patches of fur
occurs during embryonic development
what’s the heterozygote advantage? explain the sickle cell example
for sickle cell
homo recessive - sickle cell disease & resistant to malaria
homo dominant - no sickle cell disease & susceptible to malaria
heterozygous - no sickle cell disease & resistant to malaria: these ppl have a mixture of normal and sickle blood cells. majority normal blood cells but enough sickle blood cells to be resistant to malaria
what are linked genes?
when two or more genes reside physically close to one another and are inherited together– due to crossing over
the closer the genes are to each other, the less likely they are to be separated
we can quantify how close genes are with another via recombination frequency, a percentage likelihood that two genes will be separated by crossing over – note that the highest recombination frequency for genes on the same chromosome is 50% due to the possibility of multiple swapping overs
consanguinity increases the possibility of what reoccurring in the pedigree chart?
likelihood of appearing recessive genetic conditions
what’s a point mutation? what are the (3) types of point mutations?
a mutation at the level of a single nucleotide
substitution
insertion
deletion
what’s a frame shift mutation?
caused by insertion and deletion mutations
shifts the template used (by the RNA transcript) to code for proteins – resulting in completely different amino acids being translated
differentiate between transition and transversion mutations
both are substitution mutations
transition: purine to purine; pyrimidine to pyrimidine
transversion: purine to pyrimidine, vice versa
differentiate between forward and backward mutations
forward: going from the (normal) wild type allele to a mutant allele
backward: going from a mutant allele back to the (normal) wild type allele
what’s non-disjunction?
when homologous chromosomes or sister chromatids do not separate during anaphase in mitosis/meiosis – resulting in too many genetic material in some cells and too little in others
if non-disjunction occurred at anaphase (mitosis), then the resulting cells would be labeled 2n+1 and 2n-1
if non-disjunction occurred at anaphase I or II (meiosis), then the resulting cells would be labeled n+1 (trisomy) and n-1 (monosomy)
what’s mosaicism?
occurs during embryonic development
when a multi-cellular organism has cells that are genetically different from one another - some cells will be abnormal some will be normal
can be caused from cells undergo mitotic non-disjunction during embryonic development
if from non-disjunction, fractions of body cells have extra or missing chromosomes
mosaicism can also result from point mutations and not just non-disjunction
what’s trisomy 21?
aka down syndrome
results from having an extra copy of the 21 chromosome due to non-disjunction
what’s aneuploidy?
occurrence of one or more extra or missing chromosomes in a cell or organism
– from non-disjunction
when it’s not 2n or n
what are chromosomal aberrations? what are the (5) types?
changes that occur to segments of DNA
- translocations
- duplications
- inversions
- substitutions
- deletions
describe the chromosomal aberration: translocations
when two different chromosomes swap segments
between non-homologous chromosomes
Robertsonian translocation: (one chromosome from a homologous pair becomes attached to another chromosome from a different pair).
For example, an extra chromosome 21 attached to chromosome 14 can cause
Down syndrome as well, due to the tripled 21 chromosome segment.
describe the chromosomal aberration: duplications
a segment of the chromosome gets duplicated – repeated segment
chromosome is longer than it initially was
describe the chromosomal aberration: inversions
a segment of the chromosome gets rearranged in the reverse orientation
chromosome has the same length it initially had
describe the chromosomal aberration: substitutions
only one chromosome segment gets moved to another chromosome
a one way donation, not a two way exchange like in translocation
describe the chromosomal aberration: deletions
a segment of the chromosome gets deleted
chromosome is shorter than it used to be
what’s a chromosomal breakage?
what comes before most chromosomal aberrations
a physical break forms in the chromosome that allows segments to detach
spontaneous or induced breakage of a chromosomal segment via mutagenic agents or X-rays
what are proto-oncogenes? what happens when a proto-oncogene becomes mutated?
they stimulate normal cell growth - tells the cell to multiply
after mutation: becomes hyperactive and starts overstimulating cell division– the now called oncogene can lead to cancer
e.g. RAS gene
what’s an oncogene?
a mutated proto-oncogene
it’s more hyperactive and overstimulates cell division in comparison to a regular proto-oncogene
can result in cancer
what are tumor supressing genes? what happens when a tumor supressing gene becomes mutated?
supresses excess cell growth - prevents cell from replicating too quickly/excessively
after mutation that decreases its function, cancer can potentially develop.
e.g. p53
how do viruses cause cancer?
viruses attach to cells and inject their genetic information
(in some viruses, the genetic info is used to make new copies of the virus which will eventually take over the cell and destroy it —– not cancer but….)
in other viruses, the genetic info gets integrated in the host genome. if the viral genome is inserted in the middle of genes that are critical for normal cell growth (like proto-oncogenes and tumor supressing genes) – then the function of the gene will be disrupted and cancer can develop
what are some commonly known autosomal dominant conditions? describe them
huntington’s disease: nervous system degeneration due to a protein accumulation in the brain
achondroplasia: causes dwarfism by limiting limb growth
hypercholesterolemia: excess cholesterol in the blood that progresses to heart disease
what are some commonly known autosomal recessive conditions? describe them
phenylketonuria (PKU): inability to produce the proper enzyme for the breakdown of the amino acid phenylalanine, leading to the degradation product, phenyl pyruvic acid accumulation which leads to health issues
cystic fibrosis: results in fluid buildup in the respiratory tract due to disrupted transport of salt and water across cell membranes
tay-sachs: defect in lysosomes so cells can’t break down lipids properly, affecting brain function
sickle-cell anemia: results in defective hemoglobin proteins that leads to misshaped blood cells that can’t carry oxygen properly
galactosemia: inability to break down the sugar galactose which can lead to organ damage
what are some commonly known sex-linked recessive conditions? describe them
hemophilia: abnormal blood clotting which leads to excess blood clotting from wounds
colour-blindness: inability to distinguish between red and green. primarily seen in males
duchenne’s muscular dystrophy: skeletal muscle mass is progressively lost
how can X-inactivation lead to one developing hemophilia?
a genetic disease that can result from
X-inactivation is hemophilia, a sex-linked recessive condition which results in an inability to form blood clots. XHXh is a normal carrier, but if XH (the normal, functional copy) is inactivated, then only Xh is expressed, leading to disease onset
what are some commonly known chromosomal (aneuploidy) disorders? describe them
down’s syndrome: 3 copies of chromosome 21. causes intellectual disability and health issues
turner’s syndrome: missing an x chromosome or part of it. they are sterile and have physical abnormalities
klinefelter’s syndrome: in males who have an extra x chromosome. they are sterile
cri du chat: individual is missing part of chromosome 5. results in intellectual disability
what does mitochondria with genetic defects result in?
reduced ATP production
what are maternal effect genes?
genes that when mutated in the mother, results in a mutant phenotype in the offspring (the mother has a normal phenotype)
maternal effect genes are like the genes that are responsible for producing critical materials for the eggs. if these gene products like egg proteins are defective in some way then the eggs will end up being defective as well.
what’s polyploidy?
when all chromosomes undergo meiotic nondisjunction and produce gametes with twice the number of chromosomes
is common in plants
how is colchicine a mutagenic agent?
colchicine functions by inhibiting spindle formation, which can cause polyploidy
how can a fetus be tested for genetic
disorders?
amniocentesis or chorionic villus sampling (CVS)
what does it mean when DNA replication is said to be a semi-conservative process?
each strand of DNA separately serves as a template, creating a new complimentary strand (for each)
so, every new DNA consists of one original strand and a new one
nucleotides on the same DNA strand are connected by what?
the DNA phosphodiester backbone
phosphodiester bonds between the sugar group of one nucleotide and the phosphate group of another
what holds together nucleotides on different strands of the DNA?
hydrogen bonds between the nucleobases
in what direction is DNA synthesized?
5’ to 3’
how are the two strands of DNA synthesized differently? why’s it done differently?
leading strand: top strand; synthesized continuously
lagging strand: synthesized as “okazaki fragments” that are later stitched together
the lagging strand is synthesized as fragments because it has to wait for the replication fork to unwound further before DNA polymerase can synthesize more fragments
describe the process of DNA replication
FORMATION OF REPLICATION FORK
- DNA separated into separate strands by an enzyme called DNA helicase, forming a y-shaped replication fork
- single-stranded binding proteins latch onto the separated strands to keep them separated and prevents them from coiling back together – this is done until the replication process is completed
- as we’re unwinding our DNA and separating the two strands, it can cause supercoiling and knots to build up in the DNA. to make sure the DNA structure remains nice and stable as we unwind, topoisomerase cuts and rejoins the DNA double helix just ahead of the replication fork, to prevent the knots and coils.
BINDING OF THE PRIMER
- primase lays out an RNA primer (a segment of RNA nucleotides) that allows the DNA polymerase to latch onto it
ELONGATION (LEADING AND LAGGING)
- in the leading strand, DNA polymerase III synthesizes DNA continuously in the 5’ to 3’ direction as the replication fork unzips
- at the same time, the lagging strand gets synthesized in fragments as it waits for the replication fork to unwind further (both strands are synthesized left to write and in the 5’ to 3’ direction at the same time!!)
- in the lagging strand as well, the DNA polymerase requires RNA primers to start synthesizing DNA. each okazaki fragment starts from a primer
TERMINATION
- DNA polymerase I removes the RNA primers and replaces them with DNA via a 5’ to 3’ exonuclease function
- DNA ligase fills in the gaps in the phosphodiester backbone between the fragments
- polymerase I and III also have a proofreading function that allows them to remove incorrect nucleotides and replace them
note that there are thousands of these replication bubbles open up, speeding up the process
what (3) enzymes are involved in the formation of the replication fork during DNA replication? describe what they do
DNA separated into separate strands by an enzyme called DNA helicase, forming a y-shaped replication fork
single-stranded binding proteins latch onto each of the separated strands to keep them separated and prevents them from coiling back together behind the helicase – this is done until the replication process is completed
as we’re unwinding our DNA and separating the two strands, it can cause supercoiling and knots to build up in the DNA. to make sure the DNA structure remains nice and stable as we unwind, topoisomerase cuts and rejoins the DNA double helix just ahead of the replication fork, to prevent the knots and coils.
what role does DNA polymerase III play in DNA replication?
synthesizes new DNA strands in the 5’ to 3’ direction
has a proofreading function where it can go back and remove incorrect nucleotides and replace them with the correct ones (a 3’ to 5’ exonuclease function)
mainly does replication
what role does DNA polymerase I play in DNA replication?
removes the RNA primers and replaces them with DNA nucleotides (a 5’ to 3’ exonuclease function) and can proofreads during this
has a proofreading function where it can go back and remove incorrect nucleotides and replace them with the correct ones (a 3’ to 5’ exonuclease function)
what does the central dogma of biology state?
the flow of information goes:
DNA -> can also replicate
- storage of genes
(transcription)
RNA
- intermediate for expression of genes
(translation)
proteins
- functional component of genes
note that DNA is simply a storage medium. to have our DNA become function, it must first be converted to an RNA intermediate and then, proteins. RNA can be said to serve as the bridge between the genotype and phenotype.
define gene expression
process by which DNA results in the synthesis of RNA and proteins, leading to expressible changes
gene expression = transcription + translation
note that DNA is simply a storage medium. to have our DNA become function, it must first be converted to an RNA intermediate and then, proteins. RNA can be said to serve as the bridge between the genotype and phenotype.
differentiate between RNA and DNA
RNA: ribonucleic acid
DNA: deoxyribonucleic acid
DNA contains deoxyribose sugar while RNA has ribose sugar. the key difference between these is that RNA has one more hydroxyl group
DNA is double stranded while RNA is single stranded
DNA has thymine while RNA has uracil as a nitrogenous base
where does the transcription of DNA take place?
in eukaryotes: nucleus
in prokaryotes: cytoplasm
what are the two strands of DNA called in transcription?
coding (aka sense) strand
template (aka anti-sense) strand: used by RNA polymerase to create mRNA
the mRNA will look very similar to the coding strand (but the mRNA will have uracil instead of thymine)
describe the process of transcription
RNA polymerase binds to a region in front of the region it’s going to transcribe, called the promoter (TATA box aka -10 element). the RNA polymerase is particularly attracted to the TATA box.
INTITATION
- transcription factors help the RNA polymerase bind to the promoter of the specific region we’re interested in expressing
- RNA polymerase unwinds the DNA
ELONGATION
- RNA polymerase continues to unwind the DNA as it synthesizes a strand of mRNA in the 5’ to 3’ direction using the template/anti-sense strand
TERMINATION
- RNA polymerase encounters a special sequence on the that causes the RNA polymerase to disassemble (usually a sequence of adenine nucleotides “AAAAAA”)
in what direction does transcription occur?
transcription is occurring in the 3’
to 5’ direction of the DNA template strand (but synthesis of the RNA strand is, as always, 5’ to 3’)
Rin the process of transcription, where does the RNA polymerase bind onto?
RNA polymerase binds to a region in front of the region it’s going to transcribe, called the promoter (TATA box aka -10 element). the RNA polymerase is particularly attracted to the TATA box.
the most common sequence of
nucleotides at the promoter region is
called the consensus sequence -
variations from it cause less tight RNA
polymerase binding, and therefore a
lower transcription rate
promoter region is upstream of the transcription start site
for transcription, how does your body decide which specific genes to express?
transcription factors
what are post-transcriptional modifications? what are the (3) types?
when mRNA gets made, it first has to be processed before it’s translated into a protein
this process only occurs in eukaryotes
includes the 5’ cap and poly-A tail and snRNPs
what’s the 5’ cap? its purpose?
5’ GTP cap (Guanine-Triphosphate) (“GPPP”)
added to the 5’ end of the mRNA
stabilizes the mRNA & acts as an attachment point for ribosomes so that it can be more easily translated
what’s the poly-A tail? its purpose?
addition of many (approx 200) adenine nucleotides (poly-A) to the end of the mRNA
helps stabilizes the mRNA and prevents it from being degraded and controls movement of mRNA across the nuclear envelope
what’s snRNPs (small nuclear ribonucleoprotein particles)? what role do they play in RNA splicing?
snRNA and proteins form a snRNP which combines with other snRNPs to form a complex called a spliceosome which helps remove introns from the mRNA sequence
the snRNPs assemble (spliceosome) around the intron and lift it out of the mRNA sequence so that all we’re left with are the relevant exons. the snRNPs/spliceosome combine the exons together
note: prokaryotes have no introns
differentiate between introns and exons
introns: noncoding sections of an RNA transcript that are spliced out before the RNA molecule is translated into a protein.
exons: sections of DNA (or RNA) that code for proteins
what does RNA splicing do?
gives us the opportunity create multiple different mRNA as well as different functional proteins from a single RNA transcript (alternative splicing).
alternative splicing lets you combine exons in different ways to create unique proteins
how’s transcription regulated through activator and repressor proteins?
remember!!: transcription factors help the RNA polymerase bind to the promoter of the specific region we’re interested in expressing
ACTIVATE
activator proteins: they sit on or near the promotor sequence and help transcription factors assemble. once assembled, RNA polymerase can more easily bind
INHIBIT
repressor proteins: bind to the promoter, preventing transcription factors from assembling. RNA polymerase will struggle to bind, blocking transcription
what’s the most effective way to prevent gene expression?
to completely delete the promoter region! (repressor proteins only slow down transcription)
by deleting the promoter region, RNA polymerase can’t bind
how’s transcription regulated through microRNA (miRNA) and small-interfering RNA (siRNA)?
remember!!: transcription factors help the RNA polymerase bind to the promoter of the specific region we’re interested in expressing
microRNA (miRNA) and small-interfering RNA (siRNA): causes RNA interference which will lead to gene silencing. even tho RNA is being transcribed it won’t be able to be successfully translated into a protein
siRNA (double stranded RNA) will have sequences that matches those in the mRNA that the body wants silenced. it will bind to the target mRNA, chopping it up into small, ineffective pieces (bc it binds perfectly) - which now can’t be translated
miRNA (single stranded RNA) will also have sequences that match the mRNA that the body wants to be silenced. it will bind to the target mRNA, as a block, preventing it from being translated into functional proteins. can also chop up/degrade if a perfect match.
why is the genetic code considered redundant and unambiguous?
REDUNDANT
multiple codons can be used to create the same amino acids
helpful if there’s an error in the nucleotides, likely we can still produce the same amino acids
UNAMBIGUOUS
codons can not be used for multiple amino acids
what’s the start codon? what does this mean?
AUG, which encodes for methionine
all sequences start with methionine
what are the (3) stop codons?
UAA
UAG
UGA
how many possible codons are there? how many encode for amino acids?
64 codons
61 codons for amino acids
3 stop codons
what is the reading frame?
the way we divide sequences of nucleotides, 3 at a time, into consecutive sets of codons
what’s tRNA? what role does it play and how does it work with ribosomes?
clover shaped molecule responsible for transporting nucleotide triplets called anti-codons (complementary to the codon sequence of mRNA) and their associated amino acids
the C-C-A-3’ end of tRNA attaches to the amino acid being transported
this is how is able to convert the mRNA nucleotides into amino acids
each tRNA molecule is designed to carry a specific amino acid
ribosomes allow tRNA anticodons to bind to mRNA codons. ribosomes is the place where we connect mRNA with tRNA to create the amino acid chain. the ribosomes have 3 binding sites for the tRNA molecules called A, P, and E as well as an additional binding site for the mRNA molecule
where can ribosomes be found?
cytosol
they can be free-floating directly in the cytosol or attached to the ER as the rough endoplasmic reticulum (where they are known as bound ribosomes)
differentiate between ribosomes in prokaryotes and eukaryotes
prokaryotes have smaller ribosomes: small subunit = 30S
large subunit = 50S
eukaryotes have larger ribosomes
small subunit = 40S
large subunit = 60S
what happens at the (3) ribosome binding sites for tRNA? what purpose does each site serve?
A (aminoacyl): where the tRNA molecule will bound to deliver the (next) amino acid
P (peptidyl): the site that carries the tRNA molecule that’s bound to the elongating peptide chain
E (exit): where the tRNA molecule will detach from the ribosome after the tRNA contributed to the process of translation
describe the process of translation
INITIATION
- the small ribsomal subunit attaches to the 5’ end of the mRNA
- the tRNA anticodon (with methionine) that’s complementary to the start codon of AUG will attach to the start sequence
- the large ribosomal subunit will be able to assemble - the first tRNA molecule will be in the P site (there’s room for another tRNA molecule to join during elongation in the A site)
ELONGATION
- the next amino acid is brought into the empty A site via another tRNA
- a peptide bond between the growing chain in the P site and the new amino acid in the A site is formed
- ribosomes will move in the 5’ to 3’ direction
- translocation is when a tRNA moves from the A site to the P site
TERMINATION
- occurs when the stop codon enters the A site
- proteins called release factors attach to the stop codon in the A site. the tRNA and the polypeptide will detach (release factors break down the bond between them). the release factors will then unbind from the mRNA and the ribosomal subunits will completely disassemble
what happens following translation of amino acids?
translation begins on a free floating ribosome
a signal peptide at the beginning of the translated polypeptide may direct the ribosome to attach to the endoplasmic reticulum, in which case the polypeptide is injected into the ER lumen. if injected, the polypeptide may be secreted from the cell via the Golgi apparatus.
post-translational modifications (addition of sugars, lipids, phosphate groups to the
amino acids) may occur. however, the
protein may be subsequently processed by the Golgi before it is truly functional
how much ATP is used in the process of translation?
initiation = 1 ATP
elongation = 2 ATP per linkage
termination =
the folding process of the amino acid sequence that happens while the polypeptide is being translated requires 1 GTP and chaperone proteins
what’s the one exception to the central dogma of genetics?
reverse transcription
a process that some viruses can perform to turn RNA back into DNA
an exception because it is performed by a non-living thing
what is the RNA world hypothesis?
suggests that RNA was the first form of genetic material to exist (long before DNA and proteins)
implicates that the earliest precursor to life was self-replicating RNA molecules. this is possible because RNA is able to store/carry genetic information like DNA and catalyze reactions like proteins
DNA formed due to the instability and reactivity (good for catalyzing reactions) of RNA caused by it’s extra hydroxyl group – not good as a carrier of genetic information.
what is the purpose of telomeres?
they are short, repeating sequences of nucleotides
extra segments of DNA at the end of chromosomes that prevents important genetic information from being lost with successive round of DNA replication
they don’t code for anything important and get shortened instead.
added by telomerase
why do chromosomes get shorter with each round of replication
DNA polymerase can’t lay down new DNA from scratch so an RNA primer is placed
normally, after elongation, DNA polymerase I would then remove the primer and replace it with nucleotides. but for primers on the end, since there is no DNA sequence to latch onto the segments can’t be filled. so the ends of DNA get deleted with each round of replication
how are telomeres added to DNA?
telomerase will carry the RNA template that allows lengthening of the opposite strand
the telomerase will bind to the 3’ DNA overhang of the strand and then the RNA template is used to synthesize a new strand and then telomerase will shift over to allow more lengthening of the strand of DNA. later, polymerase will elongate the other strand from a primer added at the finished end of the strand lengthened by telomerase
what’s the hayflick limit?
number of times a cell can replicate before cell division stops due to loss of important genetic information
the limit is dependent on the length of the telomeres
– the shortening of telomeres over time
prokaryotes do not have this issue since their DNA is circular and doesn’t have telomeres
what’s a silent mutation?
when there’s no change to the desired amino acid following a nucleotide mutation
due to the redundancy of the genetic code
what’s a neutral mutation?
cause a change in amino acid that doesn’t change affect protein function
what’s a missense mutation?
when there’s a change from the desired amino acid following a nucleotide mutation
what’s a nonsense mutation?
when the desired amino acid has been converted to a stop codon following a nucleotide mutation
this terminates the process of protein translation prematurely, resulting in a much shorter protein
describe the bond between histones and DNA
ionic bond
DNA is negatively charged. histones are positively charged
what are the (2) types of chromatin? describe them
euchromatin
- loosely packed
- allows for RNA polymerase to transcribe
heterochromatin
- tightly packed
- prevents RNA polymerase from transcribing
- “inhibited gene transcription” - no expression of these genes
- contains lots of satellite DNA (large
tandem repeats of noncoding DNA concentrated at centromeres and ends of chromosomes)
- appears darker
define genome
your complete set of DNA
ALL THE DNA YOU HAVE!!
define genomics
the study of genomes, their structure, their function, their evolution, and how to map them
define transcriptome
entire set of EXPRESSED mRNA that can be produced (so only exons not introns)
all the possible mRNA you can make
define proteome
entire set of proteins you can produce
what is something to note about the genome/transcriptome/proteome?
you can make more proteins than mRNA AND more mRNA than DNA
this is because of processes like alternative splicing and post-translational modifications
define bioinformatics
application of computer science to analyze biological data
what is the human genome project?
an attempt to sequence the human genome
produced the human reference genome which is an example of a full genetic human sequence
what are the (2) types of methods for genome sequencing?
sanger sequencing
whole genome shot gun sequencing
what is sanger sequencing?
a method of genome sequencing
involves splitting a strand of DNA into two separate strands. then we synthesize new strands using fluorescent nucleotides that allow us to determine the order of the genetic sequence
what is whole genome shot gun sequencing?
a method of genome sequencing
DNA is cloned and cut apart into fragments of various sizes. based on how these fragments overlap, computer software is able place the overall sequence in order
what is metagenomics?
sequencing the DNA of entire communities of species
helpful in sequencing of microorganism and microbial population
helps determine genome size, gene number, and gene density
differentiate between genome size and gene number
genome size
- total number of nucleotides that an organism has regardless of it contributes to coding of proteins
(NOTE: genome size is not correlated to complexity of an organism)
gene number
- number of genes an organism has
- the nucleotide sequences that actually codes for a protein product
gene number and genome size are not correlated BUT eukaryotes tend to have, overall, a larger genome size and gene number
what is gene density? how does it differ between prokaryotes and eukaryotes?
ratio of the number of genes to the number of nucleotides
eukaryotes have lower gene density than prokaryotes because eukaryotes have a lot of introns while prokaryotes have very little non-coding sequences
what are the components of the human genome?
exons (what actually results in proteins) = 1.5%
regulatory sequences (controls the expression of genes by serving as a binding site for regulatory proteins)
introns (non-coding sequences in between other gene sequences)
non-coding
repetitive (DNA sequences repeated thru out the length of the genome)
- can be long or short; short ones called short tandem repeats
- includes telomeres
transposable elements (stretches of DNA that can move from one region of the genome to another) - found in both eukaryotes and prokaryotes
what are the (2) types of eukaryotic transposable elements?
transposons
- seen in larger genome sizes
retrotransposons
- seen in smaller genome sizes
how do transposons move their genetic sequences? describe the (2) methods?
cut and paste
- DNA gets completely cut out from one location and relocated to another
copy and paste
- sequence of DNA is copied. the copy is inserted into the new location
how do retrotransposons move their genetic sequences?
the retrotransposon DNA sequence first gets transcribed to create an RNA intermediate
the RNA intermediate gets converted to DNA via reverse transcriptase. the newly formed DNA is inserted into the target location
similar to copy and paste method of transposons but uses an RNA intermediate
what are the consequences of transposable elements?
** rmbr: transposable elements insert themselves into new regions of the genome, potentially disrupting the gene sequence
could create a non-functional version of the protein OR could enhance the protein and improve it, providing an evolutionary advantage
differentiate between identical multigenes and non-identical multigenes
identical
- multiple copies of identical genes
- grouped adjacent to each other so we can produce many copies of a certain gene product
e.g. ribosomal RNA genes are close together to allow for simultaneous production of many ribosomal subunits
non-identical
- multiple copies of related families of genes
e.g. genes that code for different globin subunits for hemoglobin
how do we compare genomes for distantly-related species, closely-related species, and organisms in the same species?
distantly-related species
- observing genes that have remained the same
- gene sequences that have remained the same are called “highly conserved sequences” - nucleotides haven’t really mutated or been altered over the course of time
closely-related species
- comparison of small genetic differences
organisms in the same species
- look at small variations in SNPs (single base pair difference) and CNVs
what are SNPs and CNVs?
SNPs (single nucleotide polymorphism)
- single base pair difference in the genome
CNVs (copy number variants)
- region where one or more gene copies is present
- arise from irregular genome duplications/deletions
both contribute to diversity within species
what’s evolutionary developmental biology?
study of developmental changes in different organisms
what are homeotic genes?
involved in the structural development of body formation
what’s the homeobox?
a specific DNA sequence found in homeotic genes
encodes for homeodomain proteins: transcription factors that control the expression of many other developmental genes
the homeobox is highly conserved. nucleotides don’t change across different members of the species
what are hox genes?
an example of a homeotic gene
ensure body parts are being located in the correct anatomic sequence
describe the DNA backbone
consists of 5’ to 3’ phosphodiester bonds to form a sugar-phosphate backbone
describe the shapes of the different types of RNA
mRNA is linear
tRNA is in a clover shape
rRNA is globular
why is DNA replication faster in prokaryotes than in eukaryotes?
DNA replication is almost 20x faster in prokaryotes than in eukaryotes, primarily because eukaryotes have more complex genomes
in prokaryotes, what happens to DNA strands that have been replicated without any error? why?
the strands without any errors is methylated after it has been successfully replicated, so it doesn’t become accidentally repaired as proofreading is done
what provides the energy for DNA polymerase during elongation in DNA replication?
provided by two additional phosphates that are attached to each new nucleotide
when the bonds holding the two extra phosphates are broken, the breakage provides chemical energy for the process, which is the same for DNA
in general, an amino acid
attaches to the 3’ end of a tRNA (termed an aminoacyl-tRNA) and one 1 ATP is converted to AMP per amino acid added the polypeptide chain.
which type of RNA is the least abundant? which type is the most abundant
mRNA is the least abundant due to mRNA’s high turnover rate (amount being translated into proteins)
rRNA is the most abundant
M for meager!
R for rich!
what is the wobble hypothesis?
suggests that the pairing between the third base of the codon and the first base of the anticodon is more flexible than the other two positions
instead of requiring a unique tRNA for each codon, the wobble allows 45 different tRNA molecules to efficiently recognize and pair with the 61 codons that specify amino acids
out of the RNA molecules, which type is the smallest?
tRNA
what holds together tRNA’s clover shape?
hydrogen bonds
how are ribosomes (to be used in translation) made?
the nucleolus is an assemblage of DNA actively being transcribed into rRNA, which come together to form ribosomes.
the ribosome is assembled in
nucleolus but the large and small
subunits are exported separately to
the cytoplasm.
describe proofreading in transcription (RNA synthesis)
RNA polymerase doesn’t have
proofreading ability, therefore RNA synthesis has a much greater error level than that of DNA synthesis
why is translation faster in prokaryotes?
translation can occur simultaneously
with transcription in prokaryotes, but not in eukaryotes
multiple ribosomes may, however, simultaneously translate 1 mRNA
what are the (3) types of repair mechanism? describe them
proofreading: DNA polymerase checks base pairs
mismatch repair: enzymes repair the errors DNA polymerase missed — mismatch repair deals with correcting mismatches between normal bases
excision repair: enzymes remove nucleotides damaged by mutagens
what are the (2) types of excision repair mechanisms? describe them
nucleotide excision repair: can be used to repair issues like thymine dimers
base excision repair: similar in function to nucleotide excision repair, but uses different enzymes.
the main difference is that nucleotide excision repair will chunk out an entire segment around the faulty base by nicking the entire surrounding
phosphodiester backbone, not just the faulty base.
base excision repair first chunks out just the faulty base, then the phosphodiester backbone around the base is cut out, then polymerase I does some 5’ to 3’
exonuclease cutting and fills in the gaps
what are pseudogenes?
pseudogenes are former genes that
have accumulated mutations over a
long time and no longer produce a
functional protein
they are nonfunctional segments of DNA that resemble functional genes (don’t produce functional proteins)
what are the (4) components of a virus? describe them
nucleic acid: RNA or DNA that can be double or single stranded
capsid: a protein coat that encloses the nucleic acid
capsomeres: assemble to form the capsid
viral envelope: surrounds capsid of
some viruses and incorporates phospholipids and proteins obtained from the cell membrane of the host
what’s a bacteriophage?
a virus that only attacks bacteria, is usually specific to a type of cell via viral surface proteins binding to specific receptors on the host cell of the species
define host range
host range is a term used to define the range of organisms or species a virus can attack
what are the (2) cycles a virus can take when it needs to replicate?
lytic cycle
lysogenic cycle
briefly describe the lytic cycle
when the virus penetrates the host cell membrane and uses host machinery to produce nucleic acids and viral proteins that are then assembled to make new viruses
these viruses then burst out of the cell (the cell lyses) and infect other cells
briefly describe the lysogenic cycle
when viral DNA is incorporated into the DNA of the host cell; there are two phases to the lysogenic cycle
- dormant stage: the virus is referred to as a provirus (prophage if a bacteriophage) and remains inactive until an external stimuli triggers the virus. the prophage DNA can remain dormant even when the cell undergoes division
- when triggered, the virus enters the lytic cycle, and follows the same steps as mentioned in the previous bullet
what are prions?
are not viruses or cells, but are
infectious, mis-folded versions of proteins in the brain that cause normal versions of proteins to also become mis-folded
prions are fatal, and are implicated in
diseases such as Mad Cow disease, kuru,
scrapie in sheep, and Creutzfeldt-Jakob
disease
what are viroids?
very small (even smaller than viruses!) circular RNA molecules that infect plants.
these do not encode for proteins, but replicate in host plant cells via host enzymes, and cause errors in the
regulatory systems of plant growth
how is DNA structured in prokaryotes?
generally single, circular, double stranded DNA molecule (that is tightly condensed and called a nucleoid), and have no histones or other associated proteins
what’s binary fission?
bacteria reproduce via this method in which the chromosome replicates, the cell divides into two cells, and each cell now holds the exact same copy of the original chromosome
note: because bacteria lack a nucleus,
they also lack microtubules, spindles, and centrioles
what are plasmids?
plasmids - short, circular DNA outside
of chromosomes that carry genes that
are beneficial, but not essential for
survival
episomes - plasmids that can
incorporate into bacterial
chromosomes
plasmids are what help bacteria gain
characteristics like antibiotic
resistance
what are the (3) ways that bacteria can exchange information with each other or their surroundings? (genetic exchange)
conjugation
transduction
transformation
how does conjugation, a type of genetic exchange bacteria can undergo, work?
donor bacteria produces a bridge (pilus) and connects to the recipient bacteria; this allows the donor to send a chromosome or plasmid to the recipient, thus allowing recombination to occur
An F plasmid allows a pilus to form, and a once the recipient receives the F plasmid, it is now F+ and can donate this plasmid
as well
Pili are also used for cell adhesion!
how does transduction, a type of genetic exchange bacteria can undergo, work?
DNA is introduced into a genome via virus.
when the virus is assembled during the lytic cycle, some bacterial DNA is incorporated in the place of viral DNA.
when the virus infects another host, the bacterial DNA part that it delivers can recombine with the resident DNA.
how does transformation, a type of genetic exchange bacteria can undergo, work?
bacteria take in DNA from surroundings and incorporate it into the genome
what are operons? what does it consist of?
generally found in prokaryotes
region of DNA that controls gene transcription
consists of:
- promoter: sequence of DNA where RNA polymerase attaches to begin transcription
- operator: region that can block action of RNA polymerase if occupied by repressor proteins
- structural genes: DNA sequences that code for related proteins
- regulatory genes: located outside of operon region, and produce repressor proteins. others produce activator proteins that assist the attachment of RNA polymerase to the promoter region
what’s the lac operon? where’s it found? what does it do?
found in E. coli
controls the breakdown of lactose; the regulatory gene produces an active repressor that binds to the operator and blocks RNA polymerase
what (3) components make up the lac operon? describe them
the lac operon consists of three lac genes (Z, Y, A), which code for the following:
- B-galactosidase that converts lactose → glucose and galactose
- Lactose permease that transports
lactose into the cell - Thiogalactoside transacetylase
how is the lac operon controlled/regulated? (2) describe them
when lactose is available, lactose binds to the repressor and inactivates it, therefore allowing RNA polymerase to transcribe the genes.
moreover, lactose induces the operon, and enzymes that the operon produces as a result are termed “inducible enzymes”
the important signaling molecule cAMP plays a regulatory role as well:
- when glucose is low, cAMP is high. this cAMP binds to a CAP binding site of the promoter, which enhances the binding and transcription via RNA polymerase,
allowing for lactose to be broken down - if lactose AND glucose are high, the
operon is shut off. this is because cAMP is low, and doesn’t bind to CAP. Bacteria
uses one sugar at a time, and prefers glucose.
what’s the Trp operon? where’s it found? what does it do?
found in E. coli
produces enzymes for tryptophan synthesis; regulator genes produce an inactive repressor, which allows RNA polymerase to produce enzymes.
when tryptophan is available, we no longer need to synthesize it internally: it binds to an inactive repressor and activates the repressor, which binds to the operator and blocks RNA polymerase.
tryptophan is a co-repressor here
how is nucleosome packaging regulated/controlled? (3) describe them
note this is regulation at the chromosome level
methylation of histones: results in tighter packing that prevents transcription
acetylation of histones: uncoils chromatin, encouraging transcription
direct DNA methylation: epigenetic control of DNA that can be inherited and usually leads to lower expression
note: while histone methylation usually prevents transcription, it can sometime activate it as well
how are eukaryotic genes regulated?
regulatory proteins: influence RNA polymerase attachment
nucleosome packaging
- methylation of histones
- acetylation of histones
- direct DNA methylation
RNA interference
- miRNA
- siRNA
what are the (2) types of microscopy?
optical microscopy: uses visible light and optical lenses to magnify and view samples
electron microscopy: uses a focused beam of electrons to magnify and view samples. has higher magnification!
