final Flashcards
histones/ chromatin
Histones are involved with bundling of eukaryotic cells’ DNA at various levels. Histones are positively charged essential proteins that can connect with DNA due to their positive charge, and the negative charge of DNA. Both histones and DNA work collaboratively in the chromosomes of eukaryotes, where histones assist in gathering the DNA into chromatin. There are five different types of histones: H1, H2A, H2B,H3, and H4. Since the amino acid sequence is comparative to that of eukaryotes, it is assumed they playout similar capacities. Histones are designed to pack DNA particles into the cell nucleus and to control and regulate DNA movement. DNA wraps around histone proteins in a coil in order to fit into a chromosome. Chromatin is the material that makes up the content of the nucleus in eukaryotes, comprised of proteins and DNA. Chromatin is directly affected by histones since DNA and histones proteins make up chromatin. Chromatin takes two structures. The primary shape is called euchromatin, which is less dense and can be transcribed. In contrast, the second is heterochromatin, which is exceedingly consolidated and can not be transcribed. Chromatin takes a similar appearance to beads on a string, the. beads representing the nucleosomes. The nucleosomes are made out of DNA which is wrapped into 30 nm spirals called solenoid, and extra histones proteins bolster chromatin structures. The main function of chromatin is to bundle DNA, so it will fit in the core of a nucleus, and ensure the DNA arrangement and structure. By DNA being bundled into chromatin, mitosis and meiosis can happen, quality
linkage/independent assortment
Both linkage and independent assortment are associated with genetics and how genes are orchestrated.
Greg Mendel ran tests in order to observe gene function and behaviour, and concluded that qenes grouped
autonomously. Chromosomes act independently during the process of meiosis, genes on every
chromosome are also sorted independently in the gamete development. It was discovered that genes part
of the same chromosome were NOT assorted independently, confirming that the chromosome was
actually single during meiosis. These ‘‘linked genes’’ are referred to as linkage. Linkage was tried occurs
in on fruit flies (Drosophilia), and revealed that genes sitting more distant from one another were more likely to separate from each other in comparison to independent assortment. This confirmed that genes
that are either on another chromosome or are further apart from each other have a recombination
frequency of fifty percent. Mendel’s Law of independent assortment expresses that alleles of two distinct
genes will be arranged to gametes freely of one another (independently). In spite of the fact that, if the
genes did not follow Mendel’s law of independent assortment, the qenes would dependably be a pair.
phosphodiester linkage/ double helix
The phosphodiester bond is the connection of the DNA nucleotides to form poly-nucleotide chains together.
The poly-nucleotide chains consist of deoxyribose sugars linked to phosphate groups, following the sugarphosphate-
sugar phosphate pattern that forms the backbone of the sugar-phosphate. The phosphates form the
bridge between one sugar’s 3’ carbon and the next sugar’s 5’ carbon. The phosphodiester bond is a two-ester
bond phosphorus. The DNA strands within the double helix consist of nucleotides connecting to in a chain,
which is connected by a phosphodiester linkage. The double helix has an exterior sugar- phosphate backbone
held together by strong covalent bonds. The interior hydrogen-bonded pairs have a much weaker hydrogen
bond. The double helix stands are composed of two twisted polynucleotide chains(visisually similar to that of a
double spiral staircase). The hydrogen bonds between the base pairs support the backbones and hold them
together. The double helix is made up of 10 base pairs per turn of the helix, and antiparalell polynucleotide
chains, which are 3.4nm per full twist. There is .34nm between the two base pairs, which is A and T, and C
and G. The phosphodiester bond, double helixes, and DNA all work closley and alongside one another for
maximum function. H bonds
join the chains; the phosphodiester bonds
join individual nucleotides in a chain
adenine/thymine
Thymine and Adenine C5H5N5 is one of four nitrogenous bases found in DNA.
Additionally, Adenine is found in RNA. Adenine assists in stabilizing the nucleic acid of both atoms and
molecules. Adenine is a purine base, featuring a double ring form, which is
structurally different than thymine which not only has a pyrimidine base, but a single ring form. Adenine
and thymine work alongside DNA and will meet up to form AT. Thymine is solely found in DNA and
acts as the principle stabilizer. It will only bind with adenine followed by two hydrogen bonds - to
stabilize that portion of the DNA. Adenine is found in ATP; when the adenine base associates with a ribose and chain of three phosphates, ATP is framed. Since thymine is absent in RNA adenine sets with
uracil.
exons/ pre-mrna
Exons are nucleotide sequences found in finished mRNA, that follows pre-mRNA. mRNA splicing in the
spliceosome (unit formed between pre-mRNA and snRNPs) involves joining two exons with such fragility
and accuracy that not even a single exon base is removed. In some circumstances, exons may be joined to form
alternate combinations that produce different mRNAs from a DNA sequence gene. Smooth muscles have
exons 2 and 12, whereas striated muscles have exons 3, 10, and 11.
Pre-mRNA is solely found in eukaryotes since the eukaryotes process differs from prokaryotes. Pre-mRNA
formed during transcription represents the entire length of DNA from which it was transcribed, therefore
containing all of the non-coding elements. Eukaryotes have to transcribe and process mRNA in the nucleus
before it is then moved to the cytoplasm to be transcribed. The eukaryote RNA polymerase synthesizes a premRNA
molecule with extra segments later to be removed by the RNA in order to produce the translatable
mRNA. Eukaryotic DNA features many non-coding regions, also known as introns. Exons and pre-mRNA
come together with the help of spliceosomes that removes the introns and joins the exons adding a 5’ cap and
poly (A) tail to create mature mRNA. To obtain the final mRNA without the regions transcribed from the
introns, splicing removes these segments and rejoins the remaining exon products.
Chromosomes of eukaryotes consist of
proteins and their dna
If meiosis did not occur in sexually reproducing organisms, then
chromosome number would double in each generation
Barr body in a female mammalian is
an inactivated condensed X chromosome
After the S phase of mitosis, a replicated chromosome consists of
two sister chromatids
What causes the unwinding of the DNA double helix?
DNA helicase
he presence of detectable variation in the genomes of different individuals of a population is termed
polymorphism
the lactose repressor blocks transcription of the lactose operon by
binding to the operator
Autosomal aneuploidies arise by
nondisjunction
autosome
a chromosome that is not a sex chromosome
Y chromosome
Y chromosome, occurs in males but not in females. The Y chromosome has a short region of homology with the X chromosome that allows them to pair during meiosis - sex chromosome
phosphodiester linkage
the connection between adjacent deoxyribose sugars is a phosphodiester bond
Each phosphate group is a “bridge” between the 3 carbon of one sugar and the 5 carbon of the next sugar; the entire linkage, including the bridging phosphate group, is called a phosphodiester bond.
double helix
Watson and crick discovered that: DNA molecule consists of two polynucleotide chains twisted around each other into a right-handed double helix. Each nucleotide of the chains consists of deoxyribose, a phosphate group, and either adenine, thymine, guanine, or cytosine. The deoxyribose sugars are linked by phosphate groups to form an alternating sugar– phosphate backbone. The two strands are held together by adenine–thymine and guanine–cytosine base pairs
four nitrogenous bases
adenine, thymine, guanine, cytosine
exons
the amino acid–coding sequences that are retained in finished mRNAs are called exons.
pre-mRNA
When an RNA transcript is first made in a eukaryotic cell, it is considered a pre-mRNA and must be processed into a messenger RNA (mRNA).
lysogenic cycle
- phage inserts linear viral DNA into a bacterium
- viral DNA forms a circle
- viral DNA is integrated into host chromosome
- during cell division, bacterial DNA with the integrated viral DNA is replicated
- following cell division, each daughter cell has viral DNA incorporated
- at some point, viral DNA may be exised from the bacterial chromosome (perhaps as a result of UV induced DNA damage). it becomes active, the prophage activates several genes, releases itself from the chromosome by a recombination event, and proceeds to manufacturer new page
- new phages are released as cell bursts as a result of lytic growth
lytic cycle
- phage inserts linear viral DNA into a bacterium
- viral DNA forms a circle
- viral enzymes break down the bacterial chromosome and host cell machinery to produce viral proteins and linear copies of viral DNA
- viral particles are assembled with DNA packed inside
- viral-encoded enzyme breaks down the host cell wall, releasing infective viral particles
postranscriptional regulation
- variations in pre-mRNA processing
- removal of masking proteins
- variations in rate of mRNA breakdown
- RNA interference
=Determines types and availability of mRNAs to ribosomes
translational regulation
-variations in rate of initiation of protein synthesis
=Determines rate at which proteins are made
tRNA
'’transfer rNA’’
The RNA that brings amino acids to the ribosome for addition to the polypeptide chain
rRNA
'’ribosomal rna’’
The RNA component of ribosomes.
RNA primer
laid down as the first series of nucleotides in a new DNA strand. RNA primers are removed and replaced with DNA later in replication
-allows DNA polymerase to copy lagging strand (which is in the 3’->5’ end)
DNA polymerase
- major enzyme of DNA replication
- Assemble DNA chains on primers; replace primers while simultaneously replacing primer nucleotides with DNA nucleotides
- can only copy stands in 5 prime to 3 prime direction (lagging strand is opposite)
- DNA polymerase can proofread - and gets it wrong about once every 1000 or 10000 nucleotides assembled
operator
- a short segment to which a regulatory protein binds.
- operator was named because it controls the operation of the genes adjacent to it
- If repressor is bound to operator, blocks RNA polymerase and it cannot move forward in making RNA
Southern blot analysis
In this technique, genomic DNA is digested with a restriction enzyme, and the DNA fragments are separated using agarose gel electrophoresis. The fragments are then transferred—blotted—to a filter paper, and a labelled probe is used to identify a DNA sequence of interest from among the many thousands of fragments on the filter paper.
RFLPs
.
pleiotropy
- single genes affect more than one character of an organism
- ex sickle cell disease is caused by a recessive allele of a single gene that affects hemoglobin structure and function
- however, altered hemoglobin, the primary phenotypic change of the sickle cell mutation, leads to blood vessel blockage, which can damage many tissues and organs in the body and affect many body functions, producing such wide-ranging symptoms as fatigue, abdominal pain, heart failure, paralysis, and pneumonia
polygenic inheritance
- several to many different genes contribute to the same character
- can be detected by defining classes of a variation (ex, human body height of 180cmn in one class and 182cm in the next, etc, plotted on a graph, if the plot produces a bell shaped curve, it is a good indication it is a quantitative trait)
- often modified by the environment (ex- human height is not modified by the environment alone, poor nutrition during infancy and childhood can lead to limited growth and expected height)
gene
A unit containing the code for a protein molecule or one of its parts, or for functioning RNA molecules such as tRNA and rRNA
chiasmata
-regions in which non-sister chromatids cross one another
interchangeable with ‘‘crossover’’: site of recombination during meiosis
nondisjunction
- when chromosome segregation fails at either meiosis I or II
- failure of homologous pairs to separate during first meiotic division or of chromatids to separate during the second meiotic division
- most zygotes of nondisjunction do not survive: exception being down syndrome - which is a nondisjunction on chromosome 21 (they have 3 instead of 2)
topoisomerase
-An enzyme which relieves overtwisting and strain of DNA ahead of replication fork (in circular DNA)
leading strand
the new DNA strand assembled in the direction of DNA unwinding
lagging strand
the strand assembled discontinuously in the opposite direction
okazaki fragments
- during DNA replication, for the lagging strand, DNA polymerases copy the strand in short lengths, which are then linked into a continuously polynucleotide chain.
- the short lengths are Okazaki fragments
RNA interference
The phenomenon of silencing a gene posttranscriptionally by a small, single-stranded RNA that is complementary to part of an mRNA is termed RNA interference (RNAi)
miRNA
a micro RNA
- discovery of micro RNA revolutionized understanding of gene control
- small, single stranded RNAs found in diverse organisms
- each miRNA is coded with a non-protein-coding gene
- transcription of the gene produces a RNA that is the precursor to the miRNA
- precursor RNA folds and base pairs with itself (stem loop structure)
- dicer (enzyme) cuts stem-loop to produce a double stranded RNA
- protein complex binds to the RNA and degreased one of the strands, leaving a small single stranded RNA, the miRNA.
- miRNA binds to any mRNA that has a complementary sequence, and gene expression is then silenced by either
1) proteins in the complex cleave the mRNA where the miRNA is blinded
2) double stranded segment formed between the miRNA and mRNA blocks ribosomes from translating the mRNA
inducible operon
Operon whose expression is increased by an inducer molecule
Lac operon is an inducible operon
repressor
when active, prevents the genes of the operon from being expressed.
cleavage furrow
.
cell plate
.
Golgi complex
- The Golgi complex receives proteins made in the ER and transported to the Golgi complex in vesicles.
- Within the Golgi complex, further chemical modifications of the proteins occur.
- The modified proteins are then sorted into other vesicles that pinch off from the margins of Golgi sacs on the side of the complex that faces the plasma membrane.
- The Golgi complex regulates the movement of several types of proteins. Some are secreted from the cell, others become embedded in the plasma membrane, and yet others are placed in lysosomes. For example, proteins secreted from the cell are transported to the plasma membrane by secretory vesicles, which release their contents to the exterior by exocytosis.
- Vesicles may also form by the reverse process, called endocytosis, which brings molecules into the cell from the exterior.
CAM pathway
.
c4 pathway
.
glycolysis
- first step of cellular respiration
- enzymes break down a molecule of glucose to 2 molecules of pyruvate
- does not require o2
fermentation
Following glycolysis, cellular respiration can continue along one of two distinct pathways depending on whether or not oxygen is present
- When oxygen is plentiful, the pyruvate and two NADH produced by glycolysis are transported into the mitochondrion, where they are oxidized using the citric acid cycle and electron transport chain.
- If, instead, oxygen is absent or in short supply, the pyruvate remains in the cytosol, where it is reduced, consuming the NADH generated by glycolysis by a series of reactions that are called fermentation.
2 types:
1) Lactate fermentation: pyruvate is converted into lactate
2) alcohol fermentation: pyruvate is reduced in two successive reactions to a molecule of co2. can occur in the environment
NADPH
.
ATP
.
photosystem I
.
photosystem II
.
endoplasmic reticulum
.
flourescence
.
microtubule
.
microfilament
.
pinocytosis
.
exocytosis
.
NADH
.
aerobic respiration
.
photo respiration
.
allosteric inhibition
.
peripheral membrane proteins
.
integral membrane proteins
.
ribozymes
.
light dependent reactions
.
light independent reactions
.
rhodopsin
.
intermediate filament
.
9+2 structure
.
vesicles
.
ribosomes
.
reducing atmosphere
.
oxydizing atmosphere
.
chemotroph
.
autotroph
.
phototroph
.
Coriolis effect
.
spontaneous reactions
.
energy coupling
.
allosteric regulation
.
co-factor
.
phagocytosis
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facilitated diffusion
.
pinocytosis
.
channel proteins
.
phospholipids
.
proton pump
.
redox reaction
An oxidation-reduction reaction
-partially or completely transfer electrons from donor to acceptor atoms; donor is oxidized as it releases electrons, acceptor is reduced (OILRIG)
oxidative phosphorylation
.
strict anaerobes
-A number of prokaryotes and a few fungi are classified as strict anaerobes because they require an oxygen-free environment to survive. –Strict anaerobes gain ATP either from fermentation or anaerobic respiration. Among these organisms are the bacteria that cause botulism, tetanus, and some other serious diseases
pyruvate oxidation
In pyruvate oxidation, which occurs inside mitochondria, one pyruvate (three carbons) is oxidized to one acetyl group (two carbons) and one CO2. Electrons removed in the oxidation are accepted by 1 NAD to produce one NADH. The acetyl group is transferred to coenzyme A, which carries it to the citric acid cycle.
citric acid cycle
In the citric acid cycle, acetyl groups are oxidized completely to CO2. Electrons removed in the oxidation are accepted by NAD or FAD, and substrate-level phosphorylation produces ATP. For each acetyl group oxidized by the cycle, two CO2, one ATP, three NADH, and one FADH2 are produced.
uncoupling
.
ATP synthase
.
chemiosmosis
.
inductive resonance
.
antenna complex
.
dark reactions (Calvin cycle)
.
PEP carboxylase
.
photorespiration
.
thylakoid
.
rubisco
.
telomeres
- repetitive DNA sequences that are added to the ends of chromosomes by the enzyme telomerase
- since DNA replication machinery is unable to replicate the entire ends of linear chromosomes, telomere sequence is lost at each round of replication
- once telomeres diminish to a certain minimum length = cells stop dividing (senesce) and may die
karyotype
- the complete collection of metaphase chromosomes, arranged according to size and shape, forms the karyotype of a given species. In many cases, the karyotype is so distinctive that a species can be identified from this characteristic alone.
centrosome
- site near the nucleus which microtubules radiate outward in all directions
- main MTOC of the cell
- anchors the microtubule cytoskeleton during interphase and positions cytoplasmic organelles
- contrains centrioles
MTOC
An anchoring point near the centre of a eukaryotic cell from which most microtubules extend outward
ORI
Origin of Replication
- in prokaryotes
- found in the middle of the cell where the enzymes for DNA replication are located
provirus
-the inserted viral DNA when a retrovirus infects a host cell
gametophytes
(in the life cycle of plants with alternating generations) the gamete-producing and usually haploid phase, producing the zygote from which the sporophyte arises.
temperate
- phage Lambda is a temperate bacteriophage : when it first infects a new host, it determines whether the host is likely to be a good one (starving? suffering from DNA damage?)
- if yes, lambda chromosome lines up with a small region of homology on bacterial chromosome and results in a recombination event
synapsis
early in meiosis I, homologous chromosomes find their partners and pair lengthwise, gene for gene, in a process called synapsis. During this intimate pairing, recombination occurs, and chromosomal segments are exchanged.
virulent
virulent bacteriophages: kill their host cells during each cycle of infection
reverse transcriptase
An enzyme that uses RNA as a template to make a DNA copy of the retrotransposon. Reverse transcriptase is used to make DNA copies of RNA in test tube reactions
crossing-over
The recombination process in meiosis (prophase 1), in which chromatids exchange segments
locus
the particular site on a chromosome at which a gene is located
epistasis
Interaction of genes, with one or more alleles of a gene at one locus inhibiting or masking the effects of one or more alleles of a gene at a different locus.
monohybrid cross
a cross between two individuals that are each heterozygous for the same pair of alleles (Pp x Pp)
wild-type
-normal, any variation is a mutant
sex-linked gene
they are inherited differently in males and females.
translocation
occurs if a broken segment is attached to a different, nonhomologous chromosome.
turner syndrome
XO combination of chromosomes:
females with underdeveloped ovaries, sterile, intelligence and external genitalia are normal, short in stature with underdeveloped breast
prenatal diagnosis
Techniques in which cells derived from a developing embryo or its surrounding tissues or fluids are tested for the presence of mutant alleles or chromosomal alterations
cytoplasmic inheritance
pattern of inheritance follows that of the genes in the cytoplasmic organelles, mitochondria, or chloroplasts
DNA methylation
process in which a methyl group (-CH3) is added enzymatically to cytosine bases in the DNA
- DNA methylation in some cases silences blocks of genes or even chromosomes
- DNA methylation underlies genomic imprinting
deletion
occurs if a broken segment is lost from a chromosome.
inversion
occurs if a broken segment reattaches to the same chromosome from which it was lost, but in reversed orientation, so that the order of genes is reversed
aneuploids
individuals who have an extra or are missing a chromosome
-in animals,
klinefelter syndrome
XXY combination of chromosomes
male external genitalia with very small underdeveloped testes, sterile, normal intelligence, sparse body hair and some development of the breasts
similar characteristics in XXXY and XXXXY
amniocentesis
Technique of prenatal diagnosis
-cells are obtained from the amniotic fluid
triploids
-triploids have 3 copies of each chromosome instead of 2
haemophilia
Haemophilia is a disease in which normal blood clotting is inhibited because the suf- ferer lacks one of the proteins important in the pathway leading to the formation of clots. It is a sex-linked genetic disease associated with the X chromosome
-People with haemophilia lack either factor VIII or factor IX of the blood-clotting proteins
trisomy 21
Down syndrome
genetic counselling
allows prospective parents to assess the possibility that they might have an affected child (of a genetic disorder)
- ex: parents may seek counselling they, a close relative, or one of their existing children has a genetic disorder
- begins with identification of parental genotypes through family pedigrees or direct testing for an altered protein or DNA sequence, allowing counsellors to predict the chances of having a child with the trait in question
genetic screening
biochemical or molecular tests for identifying inherited disorders after a child is born
genomic imprinting
the expression of an allele of a particular nuclear gene is based on whether an individual inherits the allele from the male or female. parent
autosomal recessive inheritance
ex: sickle cell anemia and cystic fibrosis
- individuals who are homozygous for the dominant allele are free of symptoms and are not carriers; heterozygotes are usually symptom free but are carriers. People who are homozygous for the recessive allele show the trait.
map unit
Theunitofalinkagemap,equivalenttoarecom- bination frequency of 1%. Also referred to as a centimorgan.
complementary base pairing
wherever an A occurs in one strand, a T must be opposite it in the other strand; wherever a G occurs in one strand, a C must be opposite it. This feature of DNA is called comple- mentary base pairing, and one strand is said to be complementary to the other. The base pairs, which fit together like pieces of a jigsaw puzzle, are stabilized by hydrogen bonds—two between A and T and three between G and C
semiconservative replication
model of replication termed by Watson and Crick
mismatch repair
-mismatch repair mechanisms increase accuracy of DNA replication
-A-T AND G-C base pairs fit lie a jigsaw puzzle, and their dimensions separate the sugar-phosphate backbone chains by a constant distant
-mispaired bases are too large/small to maintain correct separation and cannot form the hydrogen bonds like normal base pairs, and they distort the structure of the double helix
-these distortions provide recognition sites for the enzymes catalyzing mismatch repair
-if they encounter a distortion:
they remove a portion of the new chain including mismatched nucleotides (step 1), gap left by removal (step 2) is filled by a DNA polymerase using the template strand as a guide (step 3), and repair is completed by DNA ligase, which seals it (step 4)
-same mechanisms detect and correct alterations in DNA by damaging effects of chemicals and radiation
heterochromatin
densely packed regions of chromatin fibres (in interphase nuclei)
-several experiments indicate heterochromatin represents large blocks of genes that have been turned off and placed in compact storage form (Barr body- which is when one of the two X chromosomes becomes inactive in cells early in development, it packs down into a block of heterochromatin, large enough to see under a microscope)
single-stranded binding proteins
Protein that coats single- stranded segments of DNA, stabilizing the DNA for the replication process
discontinuous replication
Replication in which a DNA strand is formed in short lengths that are synthesized in the direction opposite of DNA unwinding.
replication fork
DNA unwinding produces a Y-shaped structure called a replication fork, which consists of the two unwound template strands transitioning to double-helical DNA
purines
adenine and guanine (2 of the nitrogenous bases)
built from a pair of fused rings of carbon and nitrogen atoms
nucleiod
The central region of a prokaryotic cell with no boundary membrane separating it from the cytoplasm, where DNA replication and RNA transcription occur.
primer
A short nucleotide chain made of RNA that is laid down as the first series of nucleotides in a new DNA strand or made of DNA for use in the polymerase chain reaction (PCR)
one gene-one polypeptide hypothesis
Beadle and Tatum’s one gene-one enzyme hypothesis was later restated as the one gene–one polypeptide hypothesis ; because it would not explain proteins like hemoglobin (4 polypeptides- two each of an a subunit and 2 each of a B unit, which gives it its functional property of transporting oxygen rather than catalyzing a reaction) - 2 different genes to encode the hemoglobin protein - one for the a polypeptide and one for the b polypeptide, so their hypothesis was restated as one gene-one polypeptide hypothesis
codon
Each three-letter word (triplet) of the genetic code.
promoter
- to initiate transcription, RNA polymerase binds to the promoter, unwinds the DNA in that region, and stays synthesizing an RNA molecule at the transcription start point
- promoter specifies where on the DNA transcription begins
transcription factors
Proteins that recognize and bind to the TATA box and then recruit the polymerase
A site
'’aminoacyl site’’ of a ribosome
-can bind to an aminoacyl-tRNA
termination/release factor
A protein that recognizes stop codons in the A site of a ribosome translating an mRNA and terminates translation.
initiator-tRNA
The aminoacyl–tRNA used for initiation, with an anticodon to the methionine-specifying AUG start codon
nonsense mutation
- mutation changes a sense codon to a nonsense codon in the mRNA
- translation of an mRNA containing a nonsense mutation results in a premature ‘‘stop’’ and a shorter than normal polypeptide which will be partially functional at best
P site
'’peptidyl site’’ of ribosome
-with one exception(initiator tRNA, which is recognized by the site as peptidyl-tRNA even though it carries methionine) can bind to peptidyl-tRNA
terminators
-trigger the end of transcription
in PROKARYOTES, there are two types of DNA sequences (terminators) that signal the end of transcription of the gene, both act after they are transcribed.
1) terminator sequence on the mRNA base-pairs with itself to form a ‘‘hairpin’’
2) protein binds to the terminator sequence on the mRNA
-in EUKARYOTES, there are no equivalent ‘‘transcription terminators’’: instead, at the 3’ end of the gene is a sequence that is transcribed into pre-mRNA (polydenylation signal) and cleave the pre-mRNA at that point- singling RNA polymerase to stop transcription
redundancy (of code)
- the feature of the genetic code in which, with 2 exceptions, more than one codon represents each amino acid
- Only two amino acids, methionine and tryptophan, are specified by a single codon. All the rest are represented by at least two, some by as many as six. In other words, there are many synonyms in the nucleic acid code, a feature known as degen- eracy (or redundancy). For example, UGU and UGC both specify cysteine, whereas CCU, CCC, CCA, and CCG all specify proline.
uracil
- found in RNA but not DNA, is replaced by thymine in DNA
- reason for this is common mutation in DNA: conversion of cytosine into oracle
- by utilizing thymine in DNA, any uracil is recognized as damaged cytosine and can be repaired
stop codon
- also known as nonsense or termination codons
- act as ‘‘periods’’ indicating the end of a polypeptide-encoding sentence
- The three nonsense codons are UAG, UAA, and UGA
TATA box
- A regulatory DNA sequence found in the promoters of many eukaryotic genes transcribed by RNA polymerase II
- important in transcription initiation. RNA polymerase II itself cannot recognize the promoter sequence. Instead, proteins called transcription factors recognize and bind to the TATA box and then recruit the polymerase.
introns
an intron is a non–protein-coding sequence that interrupts the protein-coding sequence in a eukaryotic gene. Introns are removed by splicing in the processing of pre-mRNA to mRNA.
alternative splicing
- removal of introns from a gene is not absolute
- exons may be joined in different combinations to produce different mRNAs from a single DNA gene sequence
- alternative splicing greatly increases the number and variety of proteins encoded in the cell without increasing the size of the genome
- current data says three quarters of human pre-mRNAs are subject to alternative splicing
anticodon
At the tip of one of the double-helical segments
-anti codon is the three-nucleotide segment in tRNAs that pairs with a codon in the mRNAs
E site
'’exit site’’ of a ribosome:
where tRNA is released
base pair substitution mutation
involve a change of one particular base to another in the genetic material. This will change a base in a codon.
wobble hypothesis
Francis and Cricks hypothesis stating that the complete set of 61 sense codons can be read by fewer than 61 distinct tRNAs because of particular pairing properties of the bases in the anticodons.
poly (A) tail
The string of A nucleotides added posttranscriptionally to the 3 ́ end of a pre-mRNA molecule and retained in the mRNA produced from it that enables the mRNA to be translated efficiently and protects it from attack by RNA-digesting enzymes in the cytoplasm.
operon
- a cluster of prokaryotic genes and the DNA sequences involved in their regulation
- some operons controlled by a regulatory protein like a repressor or an activator
- each operon is transcribed as a unit from the promoter int a single mRNA, and as a result, the mRNA encodes for several proteins
- many operons are controlled by more than one regulatory mechanism, and a number of the repressors or activators control more than one operon. The result is a complex network of superimposed controls that provides regulation of transcription, allowing almost instantaneous responses to changing environmental conditions.
- typically, the proteins coded by an operon catalyze steps in the same function, such as enzymes acting in sequence in a biological pathway
activator
when active, stimulates the expression of genes
negative gene regulation
.
gene silencing
.
tumour-suppressor genes
.
tumour
.
coactivator
a large multiprotein complex, forms a bridge between the activators at the enhancer and the proteins at the promoter and promoter proximal region and causes the DNA to loop around on itself. The interactions between the coactivator, the proteins at the promoter, and the RNA polymerase stimulate transcription to its maximal rate
repressible operon
an operon whose expression is prevented by a repressor molecule
dedifferentiation
cells lose their normal regulatory controls and revert partially or completely to an embryonic developmental state, in a process called dedifferentiation
proto-oncogenes
one of the two main types of genes that commonly show altered activities as cells become cancerous
- proto-ocogenes: genes in normal cells that encode various kinds of proteins that stimulate cell division
- in cancer cells, the porto-oncogenes are altered to become oncogenes (stimulate the cell to progress to the cancerous state)
combinatorial gene regulation
.
transcription unit
The cluster of genes transcribed into a single mRNA
malignant
If the cells of a tumour invade and disrupt surrounding tissues, the tumour is said to be malignant and is called a cancer
-cells from malignant tumours may break off and move through blood/lymphatic system forming new tumours
spreading tumours =metastasis
restriction fragments
.
germ-line gene therapy
.
genomic library
.
whole genome-shotgun method
.
DNA chips
.
recombinant DNA
.
sticky ends
.
complementary DNA
.
gel electrophoresis
.
plant pharming
.
structural genomics
.
comparative genomics
.
proteomics
.
restriction endonucleases
.
DNA hybridization
.
cDNA library
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restriction fragment length polymorphisms (RFLPs)
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short tandem repeat
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somatic gene therapy
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genetically modified organisms (GMOs)
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functionalists genomics
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DNA microrrays
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transgenic
Organisms that have undergone a gene transfer are called transgenic, meaning that they have been modified to contain genetic information—the transgene—from an external source
where does transcription take place
nucleus
where does translation take place
cytoplasm
one gene-one enzyme hypothesis
Proposed in 1941 by beadle and tatum, was the idea that each gene codes for an individual enzyme and thus impacts a specific step in a metabolic pathway. -beadle and tatum exposed spores of wild type Neurospora to x-rays (which are a mutagen), and found some of the treated spores would not germinate and grow unless the minimal medium was supplemented with nutrients. By testing to see if each mutant strain would grow on MM supplemented with a given nutrient, Beadle and Tatum discovered which specific nutrient each mutant needed to grow and, therefore, which gene defect it had. Ex: arginine auxotrophs (arg mutants) had a defect in the gene for an enzyme involved in the synthesis of arginine. The synthesis of arginine is a multi step process with an enzyme catalyzing each step, and they included in their hypothesis that that each step wascontrolled by a gene that encoded the enzyme for the step – in the end, they had shown the direct relationship between genes and enzymes.
transcription
the mechanism by which the information encoded in DNA is made into a complementary RNA copy.
translation
the use of the information ended in the RNA to assemble amino acids into a polypeptide. Called translation because the information in a nucleic acid, in orm of nucleotides, is converted into a different kind of molecule—amino acids. In 1956, Francis Crick gave the name central dogma to the flow of information from DNA to RNA to protein
template strand
-template strand for the leading strand (template for lagging strand is called lagging strand template)
the sequence of DNA that is copied during the synthesis of mRNA.
For each of the several thousand genes that will be appropriate to express in a given cell, one DNA strand or the other is the template strand and is read by the RNA polymerase.
genetic code
The nucleotide information that specifies the amino acid sequence of a polypeptide is called the genetic code .
mRNA splicing
-removes introns from pre-mRNAs and joins exons together
-how?: occurs in a spliceosome, snRNPs bind in a particular order to an intron
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spliceosome
complex formed between the pre-mRNA and the snRNPs.
DNA ligase
Seals nicks left after RNA primers replaced with DNA
major enzymes of DNA replication
- helicase
- single stranded binding proteins (stabilize DNA in single chain form)
- primase (ssembles RNA primers)
- DNA polymerases
- DNA ligase
- topoisomerases
pyrimidines
thymine and cytosine (2 of the nitrogenous bases)
-built from a single carbon ring
proofreading mechanism
The correct base pairs allow the fully stabilizing hydrogen bonds to form (step 1), if a newly added nucleotide is mismatched (step 2), DNA polymerase reverses it, using a built in deoxyribonuclease to remove the added incorrect nucleotide (step 3), the enzyme resumes working forward, inserting the correct nucleotide (step 4)
Why is a proofreading mechanism important for DNA replication?
Very few replication errors remain in DNA after proofreading and DNA repair.
- The errors that persist, although extremely rare, are a primary source of mutations
- When a mutation occurs in a gene, it can alter the property of the protein encoded by the gene, which, in turn, may alter how the organism functions. Hence, mutations are highly important to the evolutionary process because they are the ultimate source of the variability in off- spring acted on by natural selection
histones that DNA winds around
H2A, H2B, H3, H4
euchromatin
loosely packed regions of chromatin fibres (in interphase nuclei)
nonhistone proteins
- loosely defined as all the proteins associated with DNA that are NOT histones
- vary in structure, most are negatively charged or neutral, but some as positively
- range in size from polypeptides smaller than histones, to some of the largest cellular proteins
- many help control the expression of individual genes (ex: if gene is packed into heterochromatin it is not available for activation, but is more accessible as euchromatin, nonhistones affect gene accessibility by modifying histones/how they associate with DNA in chromatin, either loosening or tightening the association), others are regulatory proteins that activate or repress expression of a gene
Whats the role of histone h1 in eukaryotic chromosome structure?
One H1 molecule binds both to the nucleosome at the point where the DNA enters and leaves the core particle and to the linker DNA. This binding causes the nucleosomes to package into a coiled structure 30 nm in diameter, called the 30 nm chromatin fibre or solenoid, with about six nucleosomes per turn
missense mutation
- If a mutation alters the codon to specify a different amino acid, then the resulting protein will have a different amino acid sequence, called a missense mutation because although an amino acid is placed in the polypeptide, it is the wrong one
- Whether the polypeptide’s function is altered significantly or not depends on which amino acid is changed and what it is changed to. A missense mutation in the gene for one of the two hemoglobin polypeptides results in the genetic disease sickle cell anemia .
silent mutation
A base-pair substitution mutation in a protein-coding gene that does not alter the amino acid specified by the gene.
frameshift mutation
Mutation in a protein-coding gene that causes the reading frame of an mRNA transcribed from the gene to be altered, resulting in the production of a different, and nonfunctional, amino acid sequence in the polypeptide.
transcriptional regulation
- regulation of gene expression
- chromatin remodelling to make genes accessible for transcription
- regulation of transcription imitation
=Determines which genes are translated
posttranslational regulation
- variations in rate of protein processing
- removal of masking segments
- variations in rate of protein breakdown
=determines availability of finished proteins
differences in gene regulation (transcription and translation) in eukaryotes vs prokaryotes
- more complicated in eukaryotes bc eukaryotes are more complex, nuclear DNA is organized with histones into chromatin, and multicellular eukaryotes produce large numbers and different types of cells
- eukaryotic envelope separates process of transcription and translation, whereas in prokaryotes, translation can start on an mRNA that is still being made
- in eukaryotes, gene expression is regulated in levels (transcriptional, post transcriptional, translational, post translational)
linkage
The phenomenon explained by the inheritance behaviour of genes located on the same chromosome
how is the map unit distance between 2 genes calculated?
The number of recombinants over the total number of progeny multiplied by 100
XYY syndrome
XXY sex chromosome combination; apparently normal males but often taller than average
Triple-X syndrome
apparently normal female with normal or slightly retarded mental function
duplication
occurs if a segment is broken from one chromosome and inserted into its homologue. In the receiving homologue, the alleles in the inserted fragment are added to the ones already there
facultative anaerobes
can switch between fermentation and full oxidative pathways, depending on the oxygen supply.
ex: e coli
strict aerobes
have an absolute requirement for oxygen to survive and are unable to live solely by fermentation. Vertebrate brain cells are key examples of strictly aerobic cells that need a constant supply of oxygen to function.
3 stages of cellular respiration
1) in glycolysis, glucose is converted to two molecules of pyruvate through a serious of enzyme-catalyzed reactions
2) in pyruvate oxidation and the citric acid cycle, pyruvate is converted to n acetyl compound that is oxidized completely to co2
3) in the electron transfer system and oxidative phosphorylation, high energy electrons produced from the first 2 stages pass through the transfer system, with much of their energy being used to establish an H+ gradient across the membrane that drives the synthesis of ATP
