biol1121chapter16
termination
1.the ribsosome comes to a stop codon on the mRNA. a release factor binds to the site 2. the release factor hydrolyzes the bond between the last tRNA at the P site and the polypeptide, releasing them. The ribosomal subunits dissociate
Where does the energy needed to add nucleotides come from?
2 phosphates being removed from the free nucleotides (exergonic)
Total codons
64
different mRNA codons
64 of them. 61 code for specific amino acids, 3 are stop codons
inducer
A compound that induces protein synthesis
inducer
A specific small molecule that inactivates the repressor in an operon
Fill in the blank," tRNA transfers_______ to the ribosomes.," using the given terms: nitrogen bases, polypeptides, amino acids, or proteins.
Amino Acids
Central Dogma
DNA -> RNA -> Protein; dubbed by Francis Crick
Crick "central dogma"
DNA to RNA to Protein
one
For each gene, are both strands of DNA or just one of strand used to transcribe DNA?
development and methylation
Need to be demthylated before development: need all genes to be turned on Other areas: turned off by methylating bc you don't need them
What is a ribozyme?
a biological catalyst made of RNA
B-galactosidase
an enzyme that hydrolyses lactose
mutation
an error in the genetic code
exit tunnel
are on the large ribosomal subunit where the polypeptide leaves the ribosome
exons
are the 5' and 3' UTRs parts of exons or introns?
yes (alternative RNA splicing)
can a single gene encode more than one kind of polypeptide?
How does a repressor protein work?
can turn on/off an operon. binds to operator & blocks attachment of RNA pol to promoter
What are oncogenes?
cancer-causing genes that arise from a genetic change, leading to increase of proto-oncogene's protein product or in the activity of these molecules.
disadvantage of adult stem cells
cant diff into all cells
example of unipotent cells
cardiomyocytes - cant replicate themselves, unipotent in heart to replace old/damaged
Translation
decoding of a mRNA message into a polypeptide chain
A site
holds the tRNA that carries the next amino acid to be added to the chain (amino-acyl tRNA)
polyadenylation signal
in eukaryotes, the _______________ ___________ tells the transcription to stop and terminate
when and why do not all mutations result in a change to the encoded amino acid
in gene mutations that only change one triplet code -> degenerate nature of genetic code
small ribosomal subunit, tRNA, Met
in the first step of the initiation stage of translation, a ______ ___________ __________ recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon and binds to mRNA; then an initiator ________ carrying the amino acid ________ base pairs with the start codon
bar body
inactive X chromosome
___________, non coding sequences, are removed from pre-mRNA.
introns
ribosomal RNA (rRNA)
makes up part of the ribosome produced in the nucleolus
A given gene may have _________ enhancers that are associated with ________________.
multiple enhancers that are associated with that gene and no other.
causes of mutations 2
mutagens such as environmental influences, radiation, uv, chemicals.
oncogenes
mutated proto-oncogenes
spontaneous mutations
mutations that are errors during DNA replication or repair
gene rearrangement
mutations that move an entire gene to a new location
advantages of adult stem cells
no ethical issue, valid consent, can diff into many
Is an entire DNA strand made into RNA in transcription?
no, just genes
release factor protein
recognizes the stop codon at the A site and binds to the A site
5' cap
reversed guanine containing nucleotide added to the 5' end of the pre-mRNA strand, the site where the ribosome attaches to the mRNA
RNA contains the sugar____instead of deoxyribose.
ribose
Where does translation take place?
ribosome
rRNA, proteins
ribosomes are made of _________ and __________
minor groove
shallow
tumour suppressor genes
slow down cell division
origins of replication
specific sites where DNA replication begins
AUG
start codon
What does the start codon do?
starts translation
What does the stop codon do?
stops translation
Polyribosome
string of ribosomes simultaneously translating regions of the same mRNA strand during protein synthesis
Accurate translation = 2 instance of molecular recognition
tRNA must be carrying correct amino acid and pairing tRNA to correct mRNA
Step 2 Elongation
tRNA's keeps coming in & has the anticodon and codon's match & adds in the next amino acid.
3'
the amino acid is attached to the tRNA molecule at the _______ end
ribosomal RNA (rRNA)
type of RNA that makes up ribosomes
Ribosomal RNA (rRNA)
type of RNA that makes up the major part of ribosomes
messenger RNA (mRNA)
type of RNA, synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein
introns
the noncoding regions in the mRNA removed before the mRNA leaves the nucleus
During translation, the ribosome moves in the ______ to _____ direction.
5' to 3'
The direction of synthesis of an RNA transcript is _____.
5' —> 3'
A particular triplet of bases in the template strand of DNA is 5-AGT-3. What would be the corresponding codon for the mRNA that is transcribed?
3-UCA-5
double helix
DNA's structure like a twisted ladder
Central Dogma of Biology
DNA- RNA- Protein- Phenotype
Find a connecting between metabolic disorder and inheritance.
Garrod was the first person to
DNA does not store the information to synthesize which of the following?
Organelles
Fill in the blank,"If the original DNA sequence is TGCGCA, which of the following represents point mutation?," using the given sequences: TGCCCA,ACGGCA, CCCGGG, or TGCGCA.
TGCCCA
Splicing
One type of eukaryotic mRNA processing in which introns are removed from the primary transcript and exons are ligated together. Accomplished by a spliceosome
Bacteria RNA polymerases
Only one type
Guanine
The base that pairs with Cytosine in DNA
change in gene expression of prokaryotes
allow bacterial cells to respond to environmental changes
Which of the following statements is true about protein synthesis in prokaryotes?
Translation can begin while transcription is still in progress. Submit
major and minor grooves
alternate
An RNA polymerase only adds a nucleotide to the 3' end of the polymer being constructed. A) True B) False
a
pre-mRNA
another name for the primary transcript of a protein-coding eukaryotic gene
How are positional information provided?
cytoplasmic determinates and inductive signals
5' > 3'
direction in which RNA polymerases can assemble a polynucleotide
no
does a gene build a protein directly?
nucleosome
histome with DNA wrapped around it can fold into itself and form chromatin structure
mutagenic agents
ionising radiation (x-ray, UV), chemicals (nitrogen dioxide, tobacco smoke)
After post-transcriptional modifications are complete, what does the mature mRNA do next?
leaves through nuclear pore to the cytoplasm
A site- P site- E site
locations on the large subunit of the ribosome each tRNA moves from A to P to E as they drop off their amino acid
pre-transcriptional regulation
regulation of gene expression that occurs before transcription most common
when do gene mutations occur
spontaneously
metastasis
spread of cancer cells beyond their original site
mechanisms transcription factors use for the regulation of gene expression
stabilize or block the binding of RNA polymerase to DNA catalyze the acetylation or deacetylation of histone proteins -Tcan either do this directly or recruit other proteins with this catalytic activity recruit coactivator or corepressor proteins to the transcription factor DNA complex
translation
stage of protein synthesis where there is a change in chemical language
translation
stage where the sequence of codons along an mRNA molecule is decoded into a sequence of amino acids
proto - oncogenes
stimulate cell division by producing proteins that make cells divide
Explain how the lac operon is under dual control:
stimulated by CAP, blocked by lac repressor. CAP controls rate, lac repressor controls if translation occurs at all.
Does the environment "change" your DNA and can this be inherited?
yes Environment can cause epigenetic changes which can be inherited
stop codons:
UGA, UAA, UAG UGA = U Go Away UAA = U Are Away UAG = U Are Gone
advantage of embryonic stem cells
diff into all, save lives, improve QoL
disadvantage of iPS
higher chance of cancer
15q11
region in genome that shows differential methylation between sperm and egg
transcription unit
region of DNA that is transcribed into an RNA molecule
In ________--, the product is single stranded mRNA
transcription
what's the most cost effective way to regulate gene expression?
transcription
What is added to the 5' end of the pre-MRNA strand?
5' cap
What is natural selection?
"survival of the fittest genotype"
Transcription phases:
1. Initiation 2. Elongation 3. Termination
start codon (initiator codon)
AUG; that is the first codon recognized during translation and specifies for the amino acid methionine
drugs and histones
Drugs acting as histone deacetylase inhibitors may be useful to treat the cancer
Ligase
Connects the fragments (like a glue).
TATA box
DNA sequence promoter
DNA sequencing
Determining the exact order of the base pairs in a segment of DNA.
Apoptosis
Programmed cell death
Other RNA polymerases
Protein synthesis
absence of lactose
Repressor is bound- transcription doesn't happen
Match the function with the type of RNA out of the following Messenger RNA (mRNA), ribosomal RNA (rRNA), or transfer RNA (tRNA): Is a structural component of the organelle responsible for protein synthesis
Ribosomal RNA (rRNA)
A nucleotide is built from how many subunits?
Three
(T)
Thymine -- a pyrimidine single ring
What is the role played by noncoding RNAs?
To regulate gene expression. Regulation by noncoding RNAs occurs at mRNA translation & chromatin configuration.
To initiate transcription, RNA pol II needs assistance of _______________.
Trancription factor proteins.
What is the process called that converts the genetic information stored in DNA to an RNA copy?
Transcription
________________ is the process in which a gene is used as a template to make RNA.
Transcription
Prokaryotes can couple what process together since they both happen in the cytoplasm?
Transcription & translation
With the repressor out of the operator site, RNA polyermase can ________ the genes of operon. Example? (inducible operon)
access, lac operon
major groove
deep
T
helicase is not needed in transcription (T/F)
transfer RNA (tRNA)
helps the ribosome translate mRNA by decoding codons
nucleotide
monomer of DNA has a five-carbon sugar called deoxyribose has a phosphate group has a nitrogenous base
circular chromosome
prokaryotes have one ____ ____
Avery, MacLeod, and McCarty
proved that DNA was the hereditary material
splicing
removal of introns from pre-mRNA
inversion mutation
sequence of bases is reversed
terminator
signals to end the transcription of a gene (the stop codon)
Transcription
synthesis of an RNA molecule from a DNA template
Make up of ribosomes
⅓ protein, 3(B) or 4(E) strands of rRNA
transfer RNA
* transports amino acids to the ribosomes * single stranded *correlates a specific nucleotide sequence with a specific amino acid *amino acid binds to one end, the opposite end has an anticodon *the order of mRNA codons determins the order in which tRNA brings in amino acids
ribosomal RNA
*ribosome has a binding site for mRNA and for 2 tRNAs *facilitate complementary base pairing *ribosome moves along mRNA and new tRNAs come in and line up in order *this brings amino acids in line in a specific order to form a polypeptide *several ribosomes may move along the same mRNA
Arguments FOR and AGAINST using stem cells from embryos
- *Stem cell controversy:* = Destruction of human blastocyst = no chance for fertilised egg to grow into adult human - *Chimeras:* - Org with both human & animal cells - Human cells inserted into animals (e.g. mice) - Some people object this - *Beginning of life:* - fertilised egg deserves same status as adult human = OR deserves status after development of organs
Structure and location of stem cells in humans
- 2 types = Adult & Embryonic - *Adult stem cells* found in Bone marrow + brain + skin = " " described as being able to: - divide unlimitedly = generate a range of cell types = regen entire organs - Multipotent - *Embryonic stem cells:* - Embryo blastocyst phase of development, = in uterus, or removed and found in IVF clinics - " " described as being: - Blastocysts (found in) = Inner cell mass (aka embryoblast) = cells that will differentiate into structures of Adult = totipotent cells = Outer cell mass (trophoblast) = becomes part of placenta
Give an example of where the turning 'OFF' of a gene is beneficial
- Agouti gene = produces protein that makes mice overweight + prone to cancer & diabetes = therefore better to not express gene
Regulation of the cell cycle (to prevent cancer from arising)
- Cell cycle involves G1 (& G0), S, G2 (interphase) & mitosis - Growth factor protein controls change of cell stage from G0 to G1 (but can lead to problems) - Checkpoint 1 = located at G1 stage, checks for if cells are: = Healthy? = DNA damaged? = sufficient substrate? (enough substances to aid reactions? - Checkpoint 2 = located at G2 stage, checks for: = Was DNA replicated correctly? - Checkpoint 3 = located at mitosis stage, checks for: = Chromosome distribution? (have chromosomes been placed in correct nuclei for cell div) - IF NO FOR ANY POINTS = APOPTOSIS (tumour suppressor genes & proto-oncogenes = transcribed / not = arises problems) - +ve & -ve regulators (switching on cell cycle / causing apoptosis / causing stop signal) (dont need to know names)
Epigenome
- Chemical tags that cover DNA + histones = respond to environmental changes (remember DNA & genes are fixed) = cause DNA coiling to tighten or loosen (either allowing transcription to occur, or not) - Determines the shape of DNA-histone complex
What is one way that stem cells in the future can be useful?
- Create replacement organs for patients - Wouldn't have to wait on waiting list
What are some common ways we use DNA
- DNA can serve as an individual identifier - Paternity tests - ID unknown bodies - Dog DNA tests
Epigenetics
- Environmental factors can cause heritable changes in gene expression = (not changing structure of gene, but gene expression) - without changing base seq of DNA
What is the relationship between gene expression and cancer?
- Gene expression causes cancer = as inactivation of normally active genes + activation of normally inactive genes can cause cancer - e.g. inactivation of tumour suppressor gene = altered gene expression
What is an example of a gene that is expressed?
- HBB gene codes for beta globin = protein associates alpha globin to form the common form of haemoglobin HbA
DNA replication ENZYMES:
- Helicase unwinds our double helix into two strands - DNA Polymerase adds nucleotides to an existing strand - Ligase brings together Okazaki fragments - Topoisomerase cuts and rejoins the helix - RNA primase catalyzes the synthesis of RNA primers
How are TF activated?
- Hormones bind to enzyme receptor in TF = causes TF to move into nucleus - some hormones are lipid soluble (passive diffusion) & others are proteins (active diffusion) = (enter into cell from outside cell)
Hypermethylation
- Increased methylation = can inactivate tumour suppressor genes = leading to formation of tumour / cancer
What are the keyword associations with acetylation & methylation?
- Increased methylation (DNA) = deacetylation - deacetylation (histones) = heterochromatin - Decreased methylation (DNA) = increased acetylation - increased acetylation (histones) = euchromatin
iPS cells
- Induced pluripotent stem cells - Produced from adult somatic cells - can divide to make LIMITLESS supplies - Use protein transcription factors to overcome ethical issues (genetic reprogramming) = culture in lab = test with dif conditions = trigger differentiation for each condition
Totipotency in plants
- Mature = many totipotent cells = can develop in another cell in right conditions = e.g. cutting root of cauliflower and placing in agar (suppling nutrients) will form a new cauliflower over a few weeks
What happens after fertilisation?
- Mitosis of cells - early cell = embryonic stem cells = totipotent = most cells later differentiate = specialised for specific function WHEN CERTAIN GENES ARE EXPRESSED = only part of cell DNA is translated into proteins = when cell specialised = only produces proteins req = no longer totipotent
What is an example of a hormone that is used to activate TF?
- Oestrogen-steroid hormone (aka as an external factor) = lipid soluble = passive diffusion into cell - is complementary to specific TF = forms an oestrogen-receptor (OR) complex with enzyme receptor on TF = ER releases inhibitor + activates TF to translocate into nucleus & binds to promoter region = TF can either be an ACTIVATOR or REPRESSOR - oestrogen doesn't choose the TF to bind to = RNA polymerase can either bind to the promoter region easier, or is blocked = Transcription either does or doesn't occur = if it sees a TF (that is complementary) it binds to it (OR complex)
Why do embryonic cells lose totipotency?
- Once animal cell specialised = irreversible (most cases - No longer develops into other cells - Only few totipotent cells exist in mature animals
If an error is made in replicating the DNA what mechanisms are in place to correct that?
- Proofreading by DNA polymerase (it reaches behind itself & if it feels a bump then it goes & puts in the right base.
What are protooncogenes and tumour suppressor genes?
- Proto-oncogenes enhance cell growth - Tumour Suppressor genes = Slow cell growth
How do you obtain stem cells?
- Spare embryos created during IVF = remove stem cells = embryo can still develop normally = cell can be cultured to produce stem cells
Pluripotent
- Stem cells found in blastocyst (3-5days after fertilisation) = can differentiate into ALMOST any type of cell
Totipotent
- Stem cells found in the early embryo (blastocyst) - can differentiate into any type of cell
Unipotent
- Stem cells that can only differentiate into a single type of cell - E.g. Muscle cells making more muscle cells
Embyonic stem cells
- Stem cells that come from embryos that are 3-5days old (blastocyst) = can differentiate into any type of cell
What environment factors can effect the epigenome?
- Stress - Diet - Exercise
Give an example of where the turning 'OFF' of a gene is harmful
- Tumour suppressor gene = Produces proteins that control cell division = No gene expression = cancer can result
Sources of stem cells
- Up to 16 days of embryos - umbilical cord
What is the promoter region on DNA?
- Where RNA polymerase binds during transcription
Acetylation
- acetyl groups transferred to histones - more = looser coiling of DNA
Histone tag
- acetylation occurs - acetyl groups = chemical tags - if there are many acetyl groups attached to histone (increased acetylation) = less charge = less attraction of DNA phosphate groups = looser coiling of DNA = more likely allows for polypeptides to be made as promoter region is more likely exposed (Euchromatin) - Fewer acetyl groups = more +ve charge = attracts more DNA phosphate groups = tighter coiling = Promoter region of DNA is less exposed (less/stops TF binding + transcription from happening) (heterochromatin) - Environmental factors like being overweight + stress + anxiety = can change no. of chemical tags
what are the features of malignant tumours?
- can grow to large size - cells don't produce adhesion molecules = spread to other regions of body (metastasis) = forming secondary tumours - arent surrounded by capsule = can grow finger-like projections into surrounding tissue - more likely to be life-threatening as abnormal tumour tissue replaces normal tissue - Removal involves radio/chemotherapy + surgery
what are the features of Benign tumours?
- can grow to large size - cells produce adhesion molecules = make them stick together = remain within original tissue from where they arise - surrounded by capsule of dense tissue = remain as compact structure - much less likely to be life threatening (but can disrupt function of vital organ) - usually removed by surgery alone
If someone experiences a lot of stress, how can it affect the epigenome?
- can increase methylation of DNA = decreases acetylation of Histones + makes histones more +ve = condenses DNA-histone complex tightly (heterochromatin
What are malignant tumours?
- cancerous tumours - spread all around the body as secondary tissue (in process of metastasis)
Cell differentiation
- cell develops into specialised structure - suited to the role that it will carry out = e.g. nerve, muscle, skin cells
DNA tag
- methylation occurs - High methylation = induces deacetylation (less acetyl groups binding to histones) = condensing DNA / histone (heterochromatin) - Low methylation = acetylation of histones = association is much weaker = not as condensed (euchromatin)
What are benign tumours?
- non-cancerous tumours - remains in single position (less likely to be life threatening)
What actually is gene expression?
- produces a protein that there is a gene for - Genes can be turned 'ON' or 'OFF' (gene regulation) = if gene is on it doesn't always mean a good thing = can be an inhibitor and stop a certain polypeptide being made - if gene is off, it doesn't always mean a bad thing = can be activator, = which could be responsible for cancer
Transcriptional factors (TF)
- proteins that move from cytoplasm into nucleus = cause transcription to begin - Come in 2 types: Activator & Repressor - Activators allow RNA polymerase to bind to the promoter region = switches gene 'ON' - Repressors stop RNA polymerase from binding to the promoter region = switches gene 'OFF' = (can be useful as it would be a waste of energy making polypeptides that the body doesn't need) = Both of the TF, need to be activated in order to move into nucleus thru nuclear pores - If TF is repressor = polypeptide can still be made (THIS MAY BE WRONG, you may have thought that repressor aren't bad?) (opposite for TF activated)
What is siRNA and what does it do?
- small pieces of double stranded RNA - It interferes with mRNA that has been formed from gene that no longer wants to be expressed = (like shutting stable doors after a horse has bolted) = therefore changing gene expression to a gene that codes for RNA instead of proteins (siRNA) = pathway that destroys original mRNA stopping original polypeptides from being made
What is cancer? How does it form?
- uncontrolled cell growth - incorrect activation of a normally inactive gene linked with cancer (proto-oncogenes?) - Incorrect inactivation of a normally active gene linked with cancer (tumour suppressor genes?) - *Check with teacher about this* - proto-oncogenes can MUTATE forming oncogenes = become permanently activated = uncontrolled cell growth - inactivation of ts genes = cell grow out of control + development of tumours
each end of a pre-mRNA molecule is modified in a specific way
-5' end receives a modified nucleotide called a 5' cap -3' end gets a poly(A) tail
components of the lac operon
-A promoter that binds RNA polymerase to initiate transcription -An operator that binds a repressor protein, which blocks transcription
Mechanism of miRNA
-DNA transcribes to RNA -RNA has specific sequences that allows it to fold up into a loop structure -What DNA is transcribed from (the gene it regulates) is usually in close proximity to where it is produces -1 micro RNA can regulate many different genes: just needs to hybridize to mRNA sequence -Complex (RISC and miRNA) blocks translation: ribosomes and tRNA can't bind, fall off -Specificity comes from the 22 bp sequence
What happens in the intitiation phase of transcription?
-RNA polymerase (& proteins) recognize a promoter and bind to a gene - Double helix is unwound once RNA polymerase recognizes correct promoter
What happens in termination of transcription?
-RNAP stops adding bases and leaves once it recognizes the termination sequence of bases
how do genes encode proteins
-a gene is a linear sequence of nucleotides -genes are transcribed into RNA -RNA is a linear sequence of nucleotides -mRNAs are translated into a protein -a protein is a linear sequence of amino acids
process of iPS
-adult cells injected w/ specially modified virus -virus has genes that code for particular transcription factors -when infected - DNA passed on
effect of substitution mutation
-formation of stop codon -formation of codon for diff amino acid -formation of codon for same amino acid
cancer: a failure of genetic control
...
causes of mutations 3
...
diagnosis of cancer
...
p53 tumor suppressor
...
prevention of cancer
...
proto-oncogenes
...
proto-oncogenes and tumor suppressor genes
...
transposon
...
treatment of cancer
...
tumor suppressor genes
...
The simplest type of mutation is called a point mutation (aka base pair substitution). _______ nucleotide(s) are changed.
1
1 codon codes for how many amino acids?
1 amino acid
What are the 3 sites on the ribosome involved in translation?
1. A site 2. P site 3. E site
Explain how enhancers and activators interact with transcription factors to affect gene expression:
1. Activator proteins bind to distal control elements grouped as an enhancer in the DNA, upstream of the gene. 2. A DNA bending protein brings the bound activators closer to the promoter. GTF, mediator proteins, and RNA pol are nearby. 3. The activators bind to certain mediator proteins and GTF's, helping them form an active transcription initiation complex on the promoter.
levels of gene control in eukaryotes
1. Chromatin Structure, 2. Transcription Control, 3. PostTranscription Control, 4. Translation Control, 5. PostTranslation Control
What are two important features of DNA?
1. DNA contains instructions on how to create a body and control its growth & development 2. Instructions are passed down from parent to offspring
summary of gene expression
1. DNA in nucleus serves as a template for mRNA 2. mRNA is processed before leaving the nucleus 3. mRNA moves into the cytoplasm and becomes associated with ribosomes 4. tRNAs with anticodons carry amino acids to mRNA 5. Anticodon-codon complementary base pairing occurs. 6. polypeptide synthesis takes place one amino acid at a time.
One of the noncoding RNAs that regulate gene expression is microRNA. Explain two modes of action of microRNAs (miRNAs):
1. Enzyme cuts each hairpin from the primary RNA transcript. 2. Second enzyme, the Dicer, trims the loop at the single stranded ends of the hairpin. 3. One strand of the double stranded RNA is degraded. The other strand then forms a complex with one or more proteins. 4. The miRnA can bind to any target mRNA that contains at least 6 bases of complementary sequence. 5. If miRna & mRNA bases are complementary all along their lenth, mRnA is degraded. If match is less complete, translation is blocked.
What are the 3 steps of translation?
1. Initiation 2. Elongation 3. Termination
What are the 3 steps of transcription?
1. Initiation 2.Elogation 3. Termination
3 steps of translation
1. Initiation (requires energy) 2. Elongation (requires energy) 3. Termination
movement of the DNA in the genome is a problem and will cause a proto-oncogene to become an oncogene because...
1. It could have a new promoter that caused excess production. 2. It could be transcribed over and over to make multiple copies.
What are 3 important landmarks on the mRNA molecule?
1. Leader sequence 2. start codon 3. stop codon
Name the 3 types of RNA molecules.
1. Messenger RNA (mRNA) 2. Ribosomal RNA (rRNA) 3. Transfer RNA (tRNA)
How does RNA differ from DNA?
1. RNA is SINGLE-stranded, not double-stranded 2. The five-carbon sugar in RNA is RIBOSE instead of deoxyribose 3. The RNA nitrogenous bases are adenine, guanine, cytosine, and a different base called URACIL. Uracil replaces thymine as adenine's partner.
What are the 4 classes of mutations?
1. Silent 2.Missense 3. Nonsense 4. Franshift
elongation
1. a tRNA amino acid approaches the ribosome and attaches to the A site 2. 2 tRNAs can be at a ribosome at the one time. The anticodons are paired to the codons. 3. peptide bond formation attaches the peptide chain to newly arrived amino acid 4. The ribosome moves forward, the empty tRNA exits from the E site. the next tRNA amino acid complex is
How much of human genes actually code for protein?
1.5%
Triplet code
3 bases of DNA that code for a single amino acid, so basically the DNA 's version of a codon
A site, P site, E site
3 binding sites of ribosomes
help mRNA leave nucleus, protect mRNA from degradation, help ribosomes attach to 5' end of mRNA in cytoplasm
3 functions of a 5' cap and a poly-A tail
codon
3 letter word
triplet code
3 nucleotides codes for one amino acid
Aminoacyl, Peptidyl, Exit
3 sites on a ribosome:
what part of codon can be changed and still code for same amino acid
3rd base
The Spliced RNA needs to be protected so what is added?
A 5' cap & 3' tail are added to prevent degrading.
replication fork
A Y-shaped region on a replicating DNA molecule where new strands are growing.
Nucleotide substitution?
A base was swapped out for another one. Could cause the amino acid to be changed or it could be silent & get the same amino acid.
gene mutation
A change in the base sequence of DNA
Mutagens
A chemical or physical agent that interacts with DNA and causes a mutation.
aminoacyl-tRNA synthetase
A family of enzymes that correctly match up tRNA and amino acids, active site only sits a spect tRNA and amino acid, 20 different for 20 different amino acids, uses one ATP
Deoxyribose
A five-carbon sugar that is a component of DNA nucleotides
operon
A gene cluster with a single promoter Share a promoter because involved in the same process
DNA ligase
A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.
Distinguish between a point mutation and a frame shift mutation.
A point mutation occurs when one DNA nucleotide is changed. A frame shift mutation occurs when a nucleotide is inserted or deleted.
Release factor
A protein shaped like an aminoacyl tRNA that binds to the stop codon in the A site and hydrolyzes the bond between the polypeptide and the tRNA in the P site.
Gene
A segment of DNA on a chromosome that codes for a specific trait
Operon
A segment of DNA that contains a cluster of genes that all have a related function, and can be regulated at the same time.
Codon
A sequence of three adjacent nucleotides in mRNA that codes for one amino acid
a ribosome has three binding sites for tRNA
A site P site E site
Transcription begins at a promoter. What is a promoter?
A site in DNA that recruits the RNA Polymerase
Plasmid
A small ring of DNA that carries accessory genes separate from those of the bacterial chromosome
inducer
A specific small molecule that inactivates the repressor in an operon.
enveloped virus
A virus enclosed within a phospholipid membrane derived from its host cell.
At which site do new aminoacyl tRNAs enter the ribosome during elongation?
A-site
start codon
AUG = methionine (met) translation always begins with this amino acid
Initiation Codon
AUG, codes for Met
Insertion
Addition of nucleotide pairs in a gene
(A)
Adenine -- a purine double ring
action of mutagenic agents - altering bases
Alkylating agents add alkyl group to G so it now pairs with T
Codons universal
All codons code for the same amino acids no matter the organism
Fill in the blank," Mutation rates are typically due to _____________________________________," using the given responses: Proof reading by DNA polymerase, DNA repair enzymes, Silent mutation, None of these are correct, or All of these are correct
All of these are correct(Proof reading by DNA polymerase, DNA repair enzymes,or Silent mutation)
Proteome
All the proteins produced by the genome
Proteome
All the proteins produced in a given type of cell (cellular proteome) or organism (complete proteome) at a given time under specific conditions
polycistronic transcript
An mRNA transcript that encodes multiple genes and is translated into multiple proteins in bacterial cells
host
An organism on which a virus lives.
Mutagenic agent
An outside factor that increases the number of mutations
Fill in the blank,"An operon is a short sequence of DNA___________________________________," using the given terms: That prevents RNA polymerase from binding to the promoter, That prevents transcription from occurring, And the sequences that control its transcription, That codes for the repressor protein, or That functions to prevent the repressor from binding to the operator
And the sequences that control its transcription
Human diseases associated with Genomic Imprinting
Angelman Syndrome and Prader-Willi Syndrome Both can be produced by the same genetic mutation on chromosome 15 (region 15q11). There is a partial deletion of this DNA region Even though you get same DNA- results are different because of which genes are activated/aren't because of methylation
Mutation
Any change to the quantity or the structure of the DNA of an organism.
homeotic genes
Any of the genes that control the overall body plan of animals by controlling the developmental fate of groups of cells.
Eukaryotic RNA polymerases
At least 3 types
Bound ribosomes
Attached to cytosolic side of the endoplasmic reticulum (ER) or nuclear envelope, make proteins for endomembrane system (nuclear envelope, ER, golgi apparatus, lysosomes, vacuoles, plasma membrane) or for export
Hydrogen bonds in DNA
Bonds that form between the nitrogenous bases that form the "rungs" of the DNA ladder
Initiation in Translation
Brings mRNA and tRNA with first amino acid and subunits of ribosome together using one GTP(energy)
Exons
Coding regions of nucleic acid that are spread through the sequencing of amino acids (exception UTRs but both Exit the nucleus)
Exons
Coding segments of eukaryotic DNA.
Steps of elongation
Codon recognition, peptide bond formation and translocation
Transcription factors
Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.
Just because something has more genes doesn't make it more what?
Complex; plants have more genes than humans, but humans are way more complicated.
Archibald Garrod
Concluded that missing enzyme cause genetic disease
Which of the following enzymes "unzips" DNA during DNA replication?," using the given terms: DNA polymerase, RNA polymerase, DNA helicase, or DNA ligase.
DNA helicase
Review of difference between DNA & RNA?
DNA is double bonded with CGAT and is missing an oxygen on the sugar molecule. RNA is single bonded with CGAU.
T
DNA needs a primer TF?
At the end of the strand the RNA gets replaced with what?
DNA polymerase
Recombinant DNA
DNA produced by combining DNA from different sources
Decreased methylation
DNA-histone complex less condensed, transcriptional factors can bind, euchromatin, gene is active
How can alternative RNA splicing result in different proteins derived from the same initial RNA transcript?
Different mRNA are produced from the same primary transcript, depending on what is treated as exons and what is treated as introns.
ways gene expression is controlled
Downregulate transcription Hydrolyze mRNA Prevent translation Hydrolyze protein after made Inhibit protein function
If lactose is predominant and glucose is low in E. coli
E. coli synthesizes all three enzymes genes turned on
high glucose and high lactose
E. coli wants to use glucose CRP no longer binds to promoter RNA polymerase isn't associated with promoter region
double helix
Each DNA molecule consists of two strands that wrap around each other to form a long, twisted ladder called a double helix
semi conservative replication
Each half of an original DNA molecule serves as a template for a new strand, and the two new DNA molecules each have one old and one new strand.
Termination in Translation
Elongation continues until stop codon of mRNA reaches A site (UAG, UAA, UGA) where release factore attaches disconnecting the peptide chain and all the component taken apart using 2 GTP
DNA polymerase
Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule; can add these nucleotides only to the 3' end of an existing strand
RNA polymerase
Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription (only to the 3' end). DOESN'T need a primer
restriction enzyme
Enzyme that cuts DNA at a specific sequence of nucleotides
RNA processing
Enzymes in nucleus modify both ends and some interior spots of the pre-mRNA to make mRNA ready for the cytoplasm
Where does transcription/translation occur?
Eukaryotes: transcription: nucleus of eukaryotes (where the DNA is kept) translation: cytoplasm of eukaryotes Prokaryotes: both occur in the cytoplasm at the same time
We only use the what in our DNA to construct proteins?
Exons (Introns are cut out of the product)
Purpose of RNA processing
Facilitate export of mature mRNA from nucleus, protect mRNA from damage, help ribosomes attach to 5' end
alternative RNA splicing
Genes giving rise to two or more different polypeptides depending upon which segments are treated as exons.
In ____, a frameshift mutation disables the receptor and makes a person immune to what disease?
HIV
The lagging strand?
Has to make it backwards so it is made in okazaki fragments. First a RNA primace lays down a RNA primer, then DNA polymerase 3 lays down new DNA. DNA polymerace 1 replaces the RNA primer's with DNA. Finally the ligase links okazaki fragments
structural motifs of proteins that bind to DNA
Helix-turn-helix Leucine zipper Zinc finger Helix-loop-helix
Chaperone protein
Helps polypeptide fold correctly after being released from ribosome
hnRNA
Heterogeneous nuclear RNA; the primary transcript made in eukaryotes before splicing. Contains both coding regions and noncoding regions.
Define potency
How many cells a stem cell can make
how do we know environment can change genes?
Identical Twin studies show that the environment can produce different epigenetic modifications, and thus differences in gene regulation in genetically identical individuals. If a germ line cell that forms gametes is changed in its methylation pattern, changes can be passed on
Angelman Syndrome
If deletion is found in the egg/maternal 15q11 then only the male methylation pattern is inherited characterized by epilepsy and tremors
Prader-Willi Syndrome
If deletion is found in the sperm/paternal 15q11 then only the female methylation pattern is inherited characterized by muscle weakness and obesity
T, U
In DNA replication you add _ and I transcription you add _ complementary to the A's
____________ of translation always happens at the start codon of the mRNA.
Initiation
Alternative splicing?
It enables us to have little coded DNA but have many different proteins in our body.
Compare and contrast the lac operon and the trp operon:
Lac operon: catabolic, inducible. Operon codes for enzymes to metabolize lactose, so it's inactive without lactose. Inducer inactivates repressor so genes can be transcribed. Trp Operon: Anabolic, repressible. Operon codes for enzymes to make trp, so its active without trp: repressible. repressor molecule activates repressor protein so genes can function.
This whole process works great for what strand?
Leading strand
Chromosome?
Linear or circular strand of DNA; makes up the genome - 23 types of chromosomes and humans have a total of 46 chromosomes
How ribosomes are made
Made in nucleolus, rRNA genes transcribed, proteins taken from cytoplasm(subuntues only attach when translating)
RNA polymerase ll
Makes mRNA
ribosomal RNA(rRNA)
Makes up ribosomes along with protein
inactive X chromosome in mammals
Males (XY) and females (XX) contain different numbers of X-linked genes, yet for most genes transcription rates are similar
Polyribosome
Many ribosomes on one mRNA another one binding as soon as the first is far enough past start codon
Stop codon
Mark the end of the polypeptide chain, and therefore is where transcription ends.
Match the function with the type of RNA out of the following Messenger RNA (mRNA), Ribosomal RNA (rRNA), or transfer RNA (tRNA): Carries information from genes to the translation machinery
Messenger RNA (mRNA)
Three classes of RNA
Messenger RNA (mRNA) -takes a message from DNA to ribosomes, ribosomal RNA (rRNA) - components of ribosomes (and proteins), and transfer RNA (tRNA) -transfers amino acids to ribosomes.
Fill in the blank,"During protein synthesis, an anticodon of a transfer RNA pairs with__________________," using the given terms: Ribosomal RNA nucelotide bases, Messenger RNA nucleotide bases, Amino Acids in the polypeptide, DNA nucleoide bases, or other tRNA nucleotide bases
Messenger RNA nucleotide bases
Fill in the blank," Which of these is not a possible cause of cancer?," using the given terms: Radiation, Metastiasis, Genes, Oncogenes, or Viruses
Metastiasis
Effects of DNA methylation
Methylated DNA attracts proteins that are involved in repression of transcription and can inactivate DNA Important in development—early demethylation in the egg and sperm DNA allows many genes to become active In cancer, misregulation of methylation can occur in oncogenes and tumor suppressor genes
miRNA
MicroRNA - endogenous single stranded RNA (often from non-coding DNA)
If the proof reading doesn't catch it then?
Mismatch repair enzymes: they detect the wrong base and cut it out (by nuclease action) & incorporate the correct one.
poly-A tail
Modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides.
Ribosomes
Molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains
The average length of a transcription unit along a eukaryotic DNA molecule is about 27,000 nucleotide pairs, whereas an averaged-sized protein is about 400 amino acids long. What is the best explanation for this fact?
Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that are not translated.
Every genetic feature in every organism is initially the result of what?
Mutation
Why does the chance of cancer increase greatly with age?
Mutations accumulate throughout life, and more than one somatic mutation is needed to produce all the changes of a full-on cancer cell.
Oncogenes
Mutations of proto-oncogenes
Stop codons signal the end of translation. Do they specify for an amino acid??
NO
Two types of regulatory proteins that can bind to promoters
Negative regulation Positive regulation
Not all mutations are what?
Negative, but they are essential to evolution when looking at mutations in a whole species.
Does all DNA contain instructions for making proteins?
No
Are chromosomes always present
No; they form around the time cells divide, when the 2 copies of cell's DNA needs to be separated.
Introns (intervening sequences)
Non Coding segments of nucleic acid that lie in between coding regions
Introns
Noncoding segments
Coding strand
Nontemplate strand of DNA, not actually used
Telomerase?
Not present in prokaryotes & is present in eukaryotes
Anticodon
Nucleotide triplet that base pairs to a specific mRNA codon
Fill in the blank,"DNA is a polymer of _________.," using the given terms : amino acids, nucleic acids, nucleotides, or proteins.
Nucleotides
Mutation occurs in the _____ of a gene, but the disease is caused by translation of a ______________?
Occurs in DNA & caused by translation of non-functional protein.
Some mutations may make what no longer viable?
Offspring.
Untranslated regions (UTRs)
On 5' and 3', an example is the polyadenylation, does not code for amino acids= other functions ex) ribosomal binding
Point mutations?
One base pair is changed. This can cause a frameshift mutation: the reading frame is altered
Operon Example (Real Life and Molecular)
One switch may turn on several lights in order to light a single room. The lac operon consists of three enzymes in E. coli that are needed to metabolize lactose.
x chromosome
Only active on one X chromosome Transcribes to make RNA, binds to same chromosome, interferes with transcription DNA becomes highly methylated- inactivates the X chromosome
gene expression in bacteria
Operon: a cluster of structural and regulatory genes that act as a unit. Usually codes for production of specific proteins. Sequences contain: Promoter: A sequence of DNA where transcription begins. Operator: A sequence of DNA where repressor protein binds
The two strands of DNA run in ?
Opposite directions
Phosphate
PO4 3-
Next the nucleosomes are ?
Packaged into a thread and the end result is a fiber known as chromatin. The fiber is looped & coiled again.
Examples of environmental stimuli affecting gene expression
Plants will adjust chlorophyll production based on the amount of light available. The decrease in the amount of daylight during winter causes a change in gene expression, resulting in arctic foxes having a white coat in the winter but a darker coat in the summer. - The same hydrangea can be a different color depending on the pH of the soil it is planted in. - Increased exposure to UV light can cause an animal to increase the production of melanin - In yeast, when the opposite mating type is nearby, pheromone production will increase. When the number of herbivores increases plants can increase the number and density of plant hairs. - Adding lactose to a Lac+ bacterial culture can stimulate growth and reproduction.
What is the difference between a poly peptide & a protein?
Polypeptide is the chain of amino acids & Protein is when the polypeptide is released and folds up into the 3 dimensional shape
What process ensures that all the tissues and organs of an organism are in their characteristic places? Where do the molecular cues that control this process arise?
Positional information controls pattern formation, development of front, back, top, bottom, and sides of embryo. Positional info is provided by cytoplasmic determinants and inductive signals. Tells the cell its relation to other cells & the body axes. Determines how the cell & its progeny will respond to future molecular signals.
Eukaryotic RNA processing?
Primary RNA transcript has Exon's & introns. When processed the Introns are spliced out so the final RNA piece only has the Exons smashed together.
processing of mRNA
Primary mRNA becomes mature mRNA. Enzymes add a 5' cap and a poly A tail. Contains bases completely to both intron and exon segments of DNA. *Introns are non-coding segments, intervening. *exons are the portion of a gene that is expressed. Introns are removed and ribozyme splices exons together
gel electrophoresis
Procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel
Translation
Process by which mRNA is decoded and a protein is produced
RNA Splicing
Process by which the introns are removed from RNA transcripts and the remaining exons are joined together.
exon shuffling
Process, important in the evolution of eukaryotic genes, by which exons of different genes are exchanged and mixed into new combinations, creating new genes
DNA replication in prokaryotes vs. eukaryotes?
Prokaryote has single origin of replication whereas eukaryotes have many. - Eukaryotes have more DNA than a prokaryote does.
Signal-recognition particle (SRP)
Protein RNA complex, recipe signal peptide as it comes out of ribose, brings ribosomes to repress in ER membrane
All stages of translation require
Protein factors to help the process
Release factor
Protein shaped like tRNA, binds to stop codon at A site, adds water instead of amino acid beachin the bond between the tRNA at Psite and the chain which is then released through the exit tunnel
Initiation factors
Protein that bind gall the compend for the translation initiation complex together
Elongation factors
Proteins involved in the elongation phase of translation, assisting ribosomes in the synthesis of the growing peptide chain.
Signal peptide
Proteins made for membrane system or out of cell have this, a series of 20 amino acids at or near leeding (N-terminus) end of polypeptide
Elongation factors
Proteins that help attach amino acids to the chain
RNAi
RNA interference
Which of the following processes occurs during transcription?
RNA is synthesized
Ribozymes
RNA molecules that function as enzymes
ribozymes
RNA molecules that function as enzymes
ribozymes
RNA molecules that function as enzymes (ex acting as a spliceosome, introns do it to themselves)
What enzyme is used in transcription?
RNA polymerase
nucleus, cytoplasm
RNA polymerase II transcribes both introns and exons from DNA to make the primary transcript from a gene, which is found in the __________, but the mRNA molecule that enters the ________ is an abridged version
Initiation Transcription
RNA polymerase and transcription factors bind to the promoter
transcription / the assembly of mRNA
RNA polymerase binds to a promoter (special DNA sequence), DNA helix is opened so complementary base pairing can occur. RNA polymerase joins new RNA nucleotides in a sequence complementary to that on the DNA segment. Terminator sequence ends transcription
Termination Transcription (Eukaryotic)
RNA polymerase ll pus on a polyadenylation signal (AAUAAA) and 10-55 nucleotide down from the signal a protein cuts the pre-mRNA
RNA polymerase?
Recognizes the start of a gene on DNA strand & builds a complementary mRNA copy.
Gene
Region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule
What are the two main ways of controlling metabolism in bacterial cells?
Regulation of Enzyme activity: feedback inhibition Regulation of enzyme production: repress expression of the genes that code for the enzymes in this pathway.
Just one base pair change causes what?
Sickle cell anemia.
SNPs
Single nucleotide polymorphisms
sticky ends
Single stranded ends of DNA left after cutting with enzymes
What does siRNA stand for?
Small interfering RNA
Order of binding in translation in eukaryotic cells
Small subunit binds with mRNA(finds starts codon) -> tRNA -> large subunit of ribosomes
Non- coding gene, Coding gene
Some gene do not code for protein but code for different forms of RNA. They are called ____ The ones that code for protein are called____
Repressor protein-mediated suppression of translation
Some mRNAs can form secondary structure -Can get base pairing between some mRNA: H bonds -Upstream of translation site -Ribosome can break H bonds and unfold the secondary structure If secondary structure is stabilized by a protein bound to it, ribosome can't break it
types of regulatory sequences
Some regulatory sequences are common to promoters of many genes, such as the TATA box. Some sequences are specific to a few genes and are recognized by transcription factors found only in certain tissues
Umbilical cord blood
Source of stem cells
Placental
Stem cells that are found in the placenta and develop into specific types of cells
Translation broken down into the 3 steps?
Step 1: recognize & initiate protein building Step 2: elongate Step 3: Terminate
Proto-oncogenes
Stimulate a cell to divide when growth factors attach to a protein receptor on its cell-surface membrane, this activated the genes that cause DNA to replicate and the cell to divide
3 codons that do not code for amino acids
Stop codons/termination codons which end translation
sense/coding strand
Strand of DNA that is not used during transcription (5'-3')
Nonsense mutation
Substitutions that change codons for amino acid to a stop codon, almost all proteins affected by this do not work
Free ribosomes
Suspend in cytosol, make proteins that stay in cytomoles and function there
Transpiration
Synthesis of RNA using information in the DNA
Translation
Synthesis of polypeptide using the information from mRNA
Explain what occurs in morphogenesis:
Th physical processes that give an organism its shape. Literally meaning, "creation of form." Changes in shape, motility, and other characteristics of the cells that make up sections of the embryo.
Promoter
The DNA sequence where RNA polymerase attaches and initiates transcription, shows where to start and which strand is the template (several dozen nucleotides upstream of start point)
Summarize the different levels of gene regulation in eukaryotes.
The Pre-transcriptional control, Transcriptional control and Post-transcriptional control all occur in the nucleus. The Translational and the Post-translational occur in the cytoplasm.
DNA methylation
The addition of methyl groups to DNA, which causes DNA to be more tightly packed, reducing gene expression
Cytosine
The base that pairs with Guanine with DNA
Adenine
The base that pairs with Thymine in DNA
Explain why gene expression would not be the same in all cells of an organism.
The control of gene expression in eukaryotes involves 5 levels: Pre-transcriptional, Transcriptional, Post-transcriptional, Translational, and Post-translational. Each level of control results in variation between one cell and another.
Triplet code
The genetic instruction for polypeptide chain are within DNA as a series of nonoverlapping 3 nucleotide words
Primary transcript
The initial mRNA transcript that is transcribed from a protein coding gene. Also called pre-mRNA.
Primary translation
The initial mRNA transport from any gene in a eukaryotic cell before being altered
Euchromatin
The less condensed form of eukaryotic chromatin that is available for transcription.
What is the difference between DNA and RNA?
The main difference between DNA and RNA is the sugar present in the molecules. While the sugar present in an RNA molecule is ribose, the sugar present in a molecule of DNA is deoxyribose.One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). A fifth pyrimidine base, called uracil (U), usually takes the place of thymine in RNA
RNA processing
The modification of mRNA before it leaves the nucleus that is unique to eukaryotes.
Positional Information
The molecular cues that control pattern formation
leading strand
The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.
Start point
The nucleotide where RNA synthesis actually begins
anticodon
The particular nucleotide triplet that base pairs to a specific mRNA codon usually 3' to 5' (OPPOSITE of usual)
Gene expression
The process by which DNA directs the synthesis of proteins
Morphogenesis
The process by which an organism takes shape and the differentiated cells occupy their appropriate locations.
Which of the following statements best describes the promoter of a protein-coding gene?
The promoter is a nontranscribed region of a gene.
Translocation
The ribosome move tRNA at A site to Site while tRNA at P site (now empty) goes to A site where it is released, mRNA moves with tRNA with nest codon now at A site, used GTP
Transcription unite
The stretch of DNA that transcribed into an RNA molecule
Some mutation can be ______ especially if they occur in the what base?
They can be silent, especially if they occur in wobble base. (doesn't cause anything to happen)
If a mistake still slips through then?
This causes a mutation. A permanent change in the DNA sequence.
When does DNA Replication happen
This happens anytime a cell is dividing. You need DNA in the new cell so you have to make a copy
One, Genes, Polymerases, Single Uracil- thymine.
Transcription (DNA to RNA) - similar to DNA replication except: - only ____1_____ DNA strand is used as a template -Only transcribes the _______2_____ - RNA _____ used - RNA are ____3____ strands (single/ double) - _______ replaces ______
Fill in the blank,"Determine the sequence of amino acids that would be produced following transcription and translation of the following DNA template strand: TACGTTCCAACT:________," using the given terms: Tyrosine-Valine-Proline-Threonine, Methionine-Glutamic Acid-Glycine, Isoleucine-Valine-Proline, or Methionine-Glutamic Acid-Glycine-Threonine
Tyrosine-Valine-Proline-Threonine
Fill in the blank," The structure of DNA was determined by_____________," using the given terms :Watson and Crick, Erwin Chargaff, Rosalind Franklin, or Hershey and Chase.
Watson and Crick
Transcription?
We are making a piece of messenger RNA based off of a template strand of DNA.
Post-translational modification
When a protein is altered after translation before it is ready for cellular functions (ex add macromolecules, remove some amino acids, cut in half, 2 or more join to form quaternary structure)
What is DNA methylation? How does it affect gene expression?
When methyl groups are added to certain bases, that section of DNA becomes inactive. Removal of the methyl can allow transcription to occur: there are proteins that bind to methylated DNA & recruit enzymes to demethylate them.
Frame shift
Whenever the number of nucleotides interred or delayed is note a multiple of three, causes incorrect groupings and excessive misssnese and a protein that is too long or short
What is genomic imprinting, and how is it maintained?
Where methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development. (X chromosome methylation)
Wobble base?
Where several codons code for the same amino acid.
Transcription initiation complex
Whole complex of transcription factors and RNA polymerase II bound to the promoter
WGS
Whole-genome shotgun
Spontaneous mutations
Wrong codon matched up during DNA replication
Do purines & pyrimidines always pair together?
Yes
Ex of how they can be good?
You get a mutation that makes 10% of pop resistant to a disease, but if you get the disease then you can fight it off so your good.
eukaryotes
________________________ must perform mRNA processing in between transcription and translation (whereas prokaryotes do not have to do this)
Which of the following is confined to the nucleus in eukaryotes? A) DNA B) RNA C) proteins
a
B-galactoside permease
a carrier protein that moves sugar into the cell
spliceosome
a complex made up of small ribonucleoprotein particles and pre-mRNA
primary structure
a gene determines _____ _______ of a protein which in turn determines protein shape
functional
a gene is fully expressed when the protein that it makes is fully ________________
transcription factors
a group of proteins that can either encourage or inhibit RNA polymerase from binding to a promoter
polyribosomes (polysomes)
a group of several ribosomes attached to, and translating, the same messenger RNA molecule
frameshift mutation
a mutation in which a base-pair insertion or deletion alters the READING FRAME after the point of mutation
silent mutation
a mutation that changes a sense codon to a different sense codon that codes for the SAME amino acid
Vector
a plasmid is predesigned to have some special helpful genes in it, and together, these are called a vector. Plasmid vectors often contain genes for antibiotic resistance and restriction sites
Activator
a protein that helps the enhancers bind to the promoter completing the transcription initiation complex (enhancers contain activtors)
signal recognition particle (SRP)
a protein-RNA complex that recognizes a signal peptide as it emerges from a ribosome; helps direct the ribosome to the ER by binding to a receptor protein on the ER
gene
a segment of DNA on a chromosome that codes for a specific trait
genes
a segment of DNA that specifies the amino acid sequence of a polypeptide, DNA does not directly control protein synthesis instead its information is transcribed into RNA then translated into proteins
operator
a short stretch of DNA between the promoter and the structural genes activators or repressors bind to promote/inhibit transcription
simultaneously
a single gene can be transcribed _________ by several molecules of RNA polymerase following each other like trucks in a convoy
What is a promoter?
a site where RNA pol can bind to DNA to begin transcription
plasmid
a small ring of DNA that carries accessory genes separate from those of the bacterial chromosome
hydrogen bonds
a tRNA molecule adds its amino acid cargo to a growing polypeptide chain when the anticodon _______ ______ to the complementary codon on the mRNA
RNA pol requires
a template DNA molecule and nucleotides and only adds nucleotides to a 3' OH **does not require a primer
duplications
a type of gene rearrangement mutation that can result in a copy of genes usually caused by unequal crossing-over during meiosis or chromosome rearrangements may result in new traits because one copy of the gene can maintain the original function and the other copy may evolve a new function
inversions
a type of gene rearrangement mutation that can result when changes occur in the orientation of chromosomal regions may cause harmful effects if the inversion involves a gene or an important regulatory sequence
bacteriophage
a virus that infects bacteria
Increased acetylation
acetyl group added to histone ->. DNA = less tightly condensed therefore transcription factors can access DNA
Deacetylation
acetyl groups removed from histones
Histone acetylation
aceytl groups are added to amino acids of histone proteins, thus making the chromatin less tightly packed and encouraging transcription
action of mutagenic agents
acting as a base, altering bases, changing DNA structure
What does the p53 tumor suppressor gene do?
activated p53 promotes transcription of the gene for a protein that inhibits the cell cycle, ensuring that damaged DNA cells aren't replicated. Or, it just blocks the cells cycle until the damage can be repaired. When DNA damage is irreparable, p53 activates genes whose products cause apoptosis.
Sigma-70 factor
active most of the time and binds to consensus sequences of housekeeping genes (genes normally expressed in actively growing cells) Others Sigma factors are activated only under specific conditions
types of gene mutations
addition, deletion, substitution, inversion, duplication, translocation of bases
post translational modifications
additional steps after translation that may be required before a protein can begin doing its particular job in the cell
consensus sequences
all promoters have them allow them to be recognized by RNA polymerase located before the start codon
Histomes
allow DNA to wind around them so it can't be transcribed Eukaryotic cells need to unwind DNA from histomes
wobble pairing
allows less stringent pairing between the 3' base of the codon and the 5' base of the anticodon
wobble pairing
allows less stringent pairing between the 3' base of the codon and the 5' base of the anticodon usually in the third nucleotide of the tRNA anticodon\ things that don't usually bind together, like guanine and uracil, can pair up
T
aminoacylation requires ATP (T/F)
spliceosome
an RNA-protein complex that cuts out introns and joins together eons during pre-mRNA processing
polycistronic transcript
an mRNA transcript that encodes multiple genes and is translated into multiple proteins in bacterial cells
no
are the 5' cap and poly A tail translated into proteins?
The ribosome acts as the __________ _______________ during translation.
assembly center
Where can you find a stop codon?
at the end of the coding sequence
when is lactose regulated
at the transcriptional level goes up/down in the presence/absence of lactose mRNA level goes up, so does protein Remove lactose, mRNA levels go down
one, three
bacteria have _______ type of RNA polymerase while eukaryotes have at least _______ types of RNA polymerase
Gene
base sequence of DNA on chromosome that codes for a polypeptide
Explain why CAP binding and stimulation of gene expression is positive regulation:
because CAP binds directly to the promoter so it directly stimulates gene expression
single stranded
because RNA is _________ _______, a region of an RNA molecule may base pair with a complementary region elsewhere in the same molecule, giving RNA a specific 3D structure
Corepressor (Repressible Operon)
binds to the inactive repressor protein and thus activates it, causing it to bind to the operator site, shutting down the operon
binding site for the inducer in the lac operon
binds to the lactose. Binding changes shape of repressor protein and prevents it from binding to the operator
Repressor
binds to the operator and blocks RNA polymerase from attaching
In some mRNAs, the initiation of translation can be ______ by regulatory proteins that bind to specific sequences or structures within the untranslated region at the 3' or 3', _________ the attachment of ribosomes
blocked, preventing
A cell biologist found that two different proteins with largely different structures were translated from two different mRNAs. These mRNAs, however, were transcribed from the same template within the cell nucleus. Which mechanism below could best account for this? () a. Different systems of DNA unpacking could result in two different mRNAs. b, A point mutation might have altered the gene. c. Exons from the same gene could be spliced in different ways to make different mRNAs. d. Different transcription factors were involved in the transcription of the two mRNAs. e. The two proteins have different functions in the cell.
c
A piece of mRNA directs the sequence of amino acids in a polypeptide during _____. A) replication B) transcription C) translation
c
Amino acids are carried to the ribosomes by _____. A) mRNA B) rRNA C) tRNA
c
During the transcription of a given portion of a DNA molecule _____. () a. mRNA is synthesized on both chains of the DNA molecule at once b. mRNA is synthesized on both chains of the DNA molecule, but first on one side and then the other c. mRNA is synthesized on only one of the chains d. half of the mRNA is synthesized on half of one chain; then the other half of the mRNA is made on the other half of the DNA e. Any of the listed patterns may be found.
c
Each codon is made up of _____ base(s). A) one B) two C) three D) four
c
Ribosomes have _____ binding site(s) for tRNA molecules. A) one B) two C) three D) four
c
The _____ causes RNA polymerase to stop transcribing the DNA. A) promoter B) anticodon C) terminator D) operator
c
The first amino acid inserted into a new polypeptide chain in eukaryotic cells is usually _____. () a. glycine b. serine c. methionine d. adenosine monophosphate e. alanine
c
The nucleolus of a nucleus is the location of synthesis of _____. A) mRNA B) proteins C) rRNA D) RER
c
The three-nucleotide codon system can be arranged into ______________ combinations. A) 16 B) 20 C) 64 D) 128
c
There is/are _____ class(es) of RNA. A) one B) two C) three D) four
c
Transfer RNA transfers __________ to the ribosomes. A) chromosomes B) phosphates C) amino acids D) all of the above
c
What is a key difference in gene expression between eukaryotic and prokaryotic cells? () a. In prokaryotes, proteins are assembled directly from DNA. b. RNA polymerases are involved only in initiation in eukaryotes. c. In prokaryotic cells, the mRNA transcript is immediately available as mRNA without processing. d. In eukaryotic cells, transcribed RNA sequences function as termination signals. e. Prokaryotes do not contain ribosomes.
c
When RNA is being made, the RNA base _____ always pairs with the base _____ in DNA. () a.U ... T b.T ... G c.U ... A d.A ... U e. T ... A
c
Which of the following is not found in RNA? A) cytosine B) guanine C) thymine D) adenine
c
Amino acids are added to the ____ terminus of the poly peptide chain
c-terminus
heterochromatin
called this when the genetic material is fully condensed into coils genes are generally inactive
euchromatin
called this when the genetic material is in a loose form in the nucleus genes are active and ready for transcription
methylation
catalyzed by DNA methyltransferase, methylate on both strands -methylation is in juxtaposition of each other -why it's associated with the GC islands Usually occurs in combination of GC ("GC islands" often sites of methylation)
During embryonic development, a zygote gives rise to cells of many different types, each with a different structure and function. This remarkable transformation results from three interrelated processes; __________, ___________, __________
cell division, cell differentiation, and morphogenesis
What are the three processes that lead to the transformation of a zygote into an organism?
cell division, cell differentiation, and morphogenesis.
organizers
cells that release signals that let each cell know how they should develop
DNA > RNA > protein
central dogma (the directional flow of genetic information)
DNA Structure characteristics
chain of nucleotides, double-helix
What is evolution?
change in a population over time, caused by natural selection
mutation
change in quantity or base sequence of DNA
Nonsense mutation
changes a normal codon into a stop codon
What happens in a nonsense mutation?
changes a regular codon into a stop codon
What happens in a frameshift mutation?
changes codon squ. downstream from mutation
DNA ligase
checks for proper bonds and repairs any breaks in the sugar-phosphate backbone
Examples of epigenetic inheritance
chromatin modifications (DNA methylation)
tRNA
clover-leaf shaped RNAs that bring specific amino acids to the ribosome; contain an anticodon
Transcription Initiation Complex
cluster of proteins on the promoter that greatly enhances the initiation of transciption
CBP
co-activator in muring TNF alpha stabilizes transcription factors, unwinding of DNA, RNA polymerase binding
structural genes
code for enzymes needed in a chemical reaction they will be transcribed at the same time to produce particular enzymes
structural genes
code for enzymes needed in a chemical reaction. These genes will be transcribed at the same time to produce particular enzymes. In the lac operon, three enzymes (beta-galactosidase) galactose permease, and thiogalactoside transacetylase) involved in digesting lactose are coded for.
Structural genes
code for proteins which do the "work" of the cell. Contrast with regulatory genes
regulatory gene
codes for a specific regulatory protein called the repressor, which is capable of attaching to the operator and blocking transcription if the repressor binds to the operator, then transcription will not occur, but if the repressor does not bind to the operator, then transcription will occur
regulatory gene
codes for a specific regulatory protein called the repressor. The repressor is capable of attaching to the operator and blocking transcription. If the repressor binds to the operator, transcription will not occur. On the other hand, if the repressor does not bind to the operator, RNA polymerase moves right along the operator and transcription occurs. In the lac operon, the inducer, lactose, binds to the repressor, causing it to fall of the operator, and turns on transcription
exons (expressed sequences)
coding segments of nucleic acid that are eventually expressed, usually by being translated into amino acid sequences
In a silent mutation, the nucleotide of one ________ is changed
codon
What happens in a missense mutation?
codon now encodes a different amino acid
elongation (translation)
codon recognition, peptide bond formation, translocation
transcription factors
collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription
At the end of determination a cell is _____ to its fate
committed (once a cell becomes a muscle cell it can't become a brain cell)
Which of the following terms best describes the relationship between the newly synthesized RNA molecule and the DNA template strand?
complementary
nucleotide
complex of three subunits: phosphoric acid (phosphates), a pentose 5C sugar (deoxyribose), nitrogen containing base
Hershey-Chase
concluded that the genetic material of the bacteriophage was DNA, not a protein
Heterochromatin
condensed, dark-staining, contains genes not transcribed
Hershey-Chase Experiment
confirmed that DNA is the genetic material because only radiolabeled DNA could be found in bacteriophage-infected bacteria
spliceosomes
consist of a variety of proteins and several small ncRNA's that recognize sequences at the splice sites and catalyze removal of the introns *remove introns
What would occur if the repressor of an inducible operon were mutated so that it couldn't bind to the operon?
continuous transcription of the operon's genes
sequencing methods
continuously updated, become automated
promoter
control sequence that initiates transcription; found upstream of transcriptional unit
Operator
controls the access of RNA polymerase to the genes
A lack of this nonprotein molecule would result in the inability of the cell to 'turn off' genes:
corepressor (nonprotein molecule)
TATA box
crucial promoter DNA sequence in forming the initiation complex at a eukaryotic promoter
whats the effect of siRNA
cut mRNA ->. fragments so mRNA can't be translated to form complete protein
The mRNA codons 5′-CAA-3′ or 5′-CAG-3′ are translated as the amino acid glutamine by _____. () a. the tRNA with an anticodon 5′-GUU-3′ and glutamine at its other end b. by tRNA molecules that have been charged with glutamine by two different aminoacyl-tRNA synthetases c. separate tRNA molecules with anticodons 3′-GUU-5′ and 3′-GUC-5′, respectively d. the same tRNA with the anticodon 3′-GUU-5′ e.the small and large ribosomal units
d
Transcription takes place _____ of eukaryotic cells. A) on the plasma membrane B) at the ribosome C) in the golgi complex D) in the nucleus
d
Mutation that _____ the normal activity of these tumor-suppressor genes may contribute to ______
decrease, cancer
Avery-MacLeod-McCarty experiment
demonstrated that DNA is the genetic material because degradation of DNA led to a cessation of bacterial transformation
DNA is
deoxyribonucleic acid
DNA sequencing
determining the exact order of the base pairs in a segment of DNA
MicroRNAs play an important role in the ________ of organisms and the ______ of cellular functions
development, control
what can affect chemical tags
diet, stress
what can mutations result in
diff amino acid sequence in encoded polypeptide
Differential gene expression
difference between cell types are not due to different genes but are due to different genes being expressed. (Gene expression can be turned "on" or "off"
How do different sets of activators come to be present in two cells? just name the two ways:
distribution of cytoplasmic determinants, and different inductive signals.
no
does bacterial RNA transcript require further modification before translation after the terminator sequence signals RNA polymerase to release it?
yes
does eukaryotic pre-mRNA require further modification before translation after it is released from the RNA transcript?
hydrolysis of ATP
drives the covalent attachment of the amino acid to its tRNA
transcription factors, RNA polymerase
during initiation of transcription, once the appropriate ________ ________ are firmly attached to the promoter DNA and the ______ __________ is bound to them in the correct orientation on the DNA, the enzyme unwinds the two DNA strands and beings transcribing the template strand at the start point
unwinds DNA, elongates RNA transcript in 5' to 3' direction
during the elongation stage of transcription, what happens as the RNA polymerase moves downstream alonf the DNA?
5'
during the elongation stage of translation, which end of the mRNA first moves through the ribosome?
One strand of a DNA molecule has the following sequence: 3′-AGTACAAACTATCCACCGTC-5′. In order for transcription to occur in that strand, there would have to be a specific recognition sequence, called a(n) _____, to the left of the DNA sequence indicated. () a.centromere b.intron c.exon d.AUG codon e.promoter
e
Using the metabolic needs of e. coli, explain why all genes aren't on all of the time:
e. coli living in the stomach of a human have to adapt to whatever the person eats, and they also need tryptophan for their own fuel. E. coli activate their own metabolic pathway to make trp in absence, but if the person eats it the presence inhibits enzyme 1 by feedback inhibition.
semi-conservative replication
each daughter DNA molecule consists of one new chain of nucleotides and one from the parent DNA molecule
In prokaryotes, functionally related genes are usually clustered in a single operon. What has been found to be the case in eukaryotes?
each gene in a cluster of functionally related genes has its own promoter and is individually transcribed. Can be on the same chromosome or on different chromosomes.
chromosome
each separate chunk of DNA in a genome
Mutant bicoid (anterior) gene in drosophila mother=
embryo with posterior structures at both ends and no front half.
where are stem cells found
embryo, adult tissue
T
energy is required during initiation of translation (T/F)
what happens when lactose (inducer) is present
enters nucleus, binds to repressor, causes conformational change -change leads to removal of repressor from DNA and can allow RNA polymerase and transcription to happen Necessary but not sufficient to get the process moving
In DNA replication, the ______ DNA is copied
entire
How can proteins be degraded and example (with nucleases):
enzymatic shortening of Poly-A tail & removal of 5' cap = nucleases chew up the mRNA. ex: cyclins that regulate the cell cycle need to be short lived for the cell to function properly. Marked by ubiquitin for destruction, this is recognized by proteasomes that degrade them.
RNA polymerase
enzyme similar to DNA polymerase that builds RNA and adds nucleotides to the 3' side of the mRNA molecule binds to the 3' end of the template strand
RNA primase
enzyme that adds a short strand of RNA nucleotides to start off replication
Methylase
enzyme that can methylate the second strand after transcription Now have both strands methylated, retained through cell division
What does RNA polymerase do?
enzyme that copies DNA into RNA
Poly A polymerase
enzyme that creates the poly-A tail
Aminoacyl-tRNA synthetase
enzyme that joins each amino acid to the appropriate tRNA
DNA polymerase
enzyme that performs the actual addition of nucleotides to the freshly built strand can only add nucleotides to the 3' end of an existing strand
Genomic Imprinting
epigenetic phenomenon by which certain genes are expressed in a parent-of-origin-specific manner passing on changes from mother/father to offspring -atypical pattern of inheritance
causes of mutations 1
errors in replication
small RNAs in spliceosome
example of RNA molecules that function as ribozymes during pre-mRNA splicing
how can a mutation in a growth factor (proto-oncogen) cause cancer
excessive amounts of growth factor produced causing lots of division
Mutation that knocks out the p53 gene can lead to _______ cell growth and ______
excessive, cancer
E site
exit site -uncharged tRNAs leave the ribosome
Coding sequences, also called _______________, are spliced together to form one continuous message.
exons
The RNA segments joined to one another by spliceosomes are _____.
exons
exons
expressed sequence of DNA; codes for a protein
What happens when double-stranded RNA molecules are injected into a cell?
expression of a gene with the same sequence as the injected RNA is turned off. This is called RNA interference (RNAi) due to siRNAs.
Cell differentiation results from the ______ of genes for __________________
expression, tissue-specific proteins
Differentiation in development is due to ______ and ____ cues that trigger gene regulation by ________ that bind to DNA
external, internal, proteins
addition mutation
extra bases inserted
Ribosomes
facilitates the specimen coupling of tRNA's anticodon with mRNA's codon during protein synthesis, made of one large and one small subunit
True or false. A tRNA with an anticodon complementary to the stop codon catalyzes the reaction by which translation is terminated.
false
amount of promoters and other regulatory sequences in prokaryotes
few
yes
for any given gene, is the same strand used as the template every time the gene is transcribed?
Transfer RNA (tRNA)
form of RNA that brings amino acids to ribosomes during protein synthesis by reading the message carried by the mRNA
How are miRNAs formed?
formed from RNA precursors that fold back on themselves, forming short hairpin structures held together by Hbonds.
5' cap, poly A tail
forms of pre-mRNA modification that involve the alteration of mRNA ends
the role of oncogenes in the development of tumours
gene = overactive ->. stimulate cell to divide uncontrollably
frame shift
gene mutation that change nature of all base triplets downstream from the mutation
_________ and __________ allow cell division, differentiation, morphogenesis
gene regulation and expression
transposons
gene segments that can cut and paste themselves throughout the genome the presence of one can interrupt a gene and cause errors in gene expression
Transposons
gene segments that can cut/paste themselves throughout the genome
Oncogene
gene that is involved in triggering molecular events that can lead to cancer
Tumor-suppressor genes
gene whose protein product inhibits cell division, thereby preventing the uncontrolled cell growth that contributes to cancer
recombinant DNA
generated by combining DNA from multiple sources to create a unique DNA molecule that is not found in nature common application: the introduction of a eukaryotic gene of interest (insulin) into a bacterium for production to make more insulin
messenger RNA
genes program protein synthesis via genetic messages in the form of what?
operons
genes that coordinate the regulation of gene expression
what have sequencing projects read
genomes of wide range of organisms e.g. humans
gene expression
going from the instructions to the finished product. going from DNA to proteins. Requires 2 steps transcription and translation
Anticodon
group of three bases on a tRNA molecule that are complementary to an mRNA codon
nucleosome
groups of histones bunched together
replication of DNA is for
growing and healing
Proto-oncogene normally code fro proteins that stimulate normal cell _______ and _______
growth, division
(G)
guanine --a purine double ring
repressor protein of lac operon
has two binding sites: One for the operator One for the inducer
Epigenetics
heritable change in gene function, without change to base sequence of DNA
what levels of oestrogen are linked with breast cancer
high
how does high energy ultraviolet light mutate DNA
high energy causes disruption to the molecule
after menopause
higher chance of breast cancer -> exposed to higher oe -> fat cells produce more oe
two hydrogen bonds
hold adenine and thymine together
A site
holds the tRNA carrying the next amino acid to be added to the chain
P site
holds the tRNA that carries the growing polypeptide chain (peptidyl tRNA)
Hox genes are a group of ___________ genes that are associated with controlling the development of the body
homeotic
HRT
hormone replacement therapy
61
how many sense codons are there?
the role of abnormal methylation of tumour suppressor genes in the development of tumours
hypermethylated - genes not transcribed
the role of abnormal methylation of oncogenes in the development of tumours
hypomethylated - increase production of proteins that stimulate cell division
one gene - one enzyme hypothesis
hypothesis that states that there is a direct relationship between genes and enzymes
DNA daughter molecules
identical to parent molecule
what are some applications fo determining of the proteins of a proteome
identification of potential antigens for use in vaccine production
complementary
if you know the sequence of bases in one DNA strand, you use the ___ base pairs to find the sequence of bases in the other strand
complementary
if you know the sequence of bases in one strand, you'll know the sequence of bases in the other strand (ex: base sequence in one DNA strand is A-T-C = base sequence in the complementary strand will be T-A-G)
introns, exons
in RNA splicing, the ______ are cut out from the molecule and the _______ are joined together, forming an mRNA molecule with a continuous coding sequence
directly
in prokaryotes RNA polymerase binds _____________ to DNA
The repressor protein produced by the regulatory gene is _____ (for repressible operon)
inactive
highly methylated DNA
inactive DNA- won't be transcribed
example of Heterochromatin
inactive X chromosome in mammals
Two types of operons
inducible system repressible system
Epigenetic inheritance
inheritance of traits that are transmitted to offspring without directly involving the nucleotide sequence
Harmful mutations can cause dysfunction, _________, & _______________.
inherited disease cancer
epigenetics on treatment of cancer
inhibit methylation by physically blocking enzymes
what is the effect of RNAi in eukaryotes and some prokaryotes
inhibit translation of mRNA produced from target genes
three stages of translation
initiation elongation termination
genotype of an organism
is its specific genetic makeup *the particular alleles of each gene that it carries
Fill in the blank," RNA , unlike DNA____________," using the given terms: is single stranded, is longer, contains only three different nitrogen bases, or contains five nitrogen bases.
is single stranded
no
is the linear polypeptide product of translation functional as is?
what happens if the gene inherited from the father is imprinted
it is thereby silenced, and only the gene from the mother is expressed
amino acid structure
know how to draw it bby
What are the 2 subunits of ribosomes?
large and small subunits
spliceosome
large complex made of proteins and small RNAs that removes introns and carries out pre-mRNA splicing
epigenome
layer made oF chemical tags - determines shape of DNA histone complex and whether gene is active/inactive
telomeres
less important or repeated sequences of DNA placed at the end of chromosomes to enable DNA polymerase to have more space to replicate needed DNA sequences they get shorter and shorter over time
hydrogen bonds
link DNA strands together by the base pairs
why can oestrogen diffuse thorough phospholipid bilayer
lipid soluble
introns
long non-protein coding stretches of nucleotides interspersed between protein-coding regions *intervening sequences
mRNA
long strand of RNA arranged as single helix - base sequence determined by base sequence of DNA
deletion mutation
loss of nucleotides
RNA processing converts the RNA transcript into _____.
mRNA
tRNA recognises ______ codon for amino acids
mRNA
Post-transcriptional control includes regulation of mRNA degradation. Explain how this affects translation:
mRNA are degraded in cytoplasm a few minutes after synthesis in bacteria (hours/days/weeks in euk), allowing patterns of protein synthesis to change quickly in response to stimuli.
pre-mRNA (precursor-mRNA)
mRNA before it is processed is known as _______________
amount of promoters and other regulatory sequences in eukaryotes
many
alternative RNA splicing
many eukaryotic genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing
benign tumour
mass of uncontrolled cell growth, stays in one place, most are differentiated
malignant tumour
mass of unspecialised, uncontrollable cell division, metastasis occurs
Cytoplasmic determinates
maternal substances (RNA and proteins) in the egg that influence the course of early development (early mitotic divisions distribute the zygote's cytoplasm unevenly which results in different effects)
Genes for proteins with related functions
may be at different locations in the genome, but share consensus sequences and can be recognized by the same sigma factors
mRNA
messenger RNA; type of RNA that carries instructions from DNA to ribosome
P site (peptidyl site)
met-tRNA is the only type of tRNA to go straight to the __ _________ and skips the A site
Alkaptonuria
metabolic disorder in which urine turns black that Garrod studied and connected to inheritance
inducible system
metabolic substrate (inducer) interacts with a regulatory protein (repressor) repressor doesn't bind and allows transcription control catabolic pathways—turned on when substrate is available
How do malignant tumors spread?
metastasis though bld vessels/ lymphatic system
Sickle cell anemia is caused by a point mutation that leads to a _____________ mutation, which changes hydrophobic glutamic acid to hydrophobic valine.
missense
RNA processing
modification of RNA primary transcripts to produce an mRNA molecule ready for translation
During RNA processing a(n) _____ is added to the 5' end of the RNA.
modified guanine nucleotide
product of the Bicoid gene=
morphogen that determines the anterior end of a fly.
rRNA
most abundant type of cellular RNA
redundancy
most amino acids are specified by several different codons and this is called __________________
What are three mechanisms for converting a proto-oncogene to an oncogene?
movement of DNA within the genome, amplification of a proto-oncogene, and point mutations in a control element of the proto-oncogene itself. All result from broken and incorrectly rejoined chromosomes.
what stem cells are found in mature mammals and can form limited number of diff cell types
multipotent, unipotent
E. coli
must adapt quickly to food supply changes Needs to cleave lactose to use as an energy source
how is the mutation rate increased
mutagenic agents
frameshift mutation
mutation that occurs whenever the number of nucleotides inserted or deleted is not a multiple of three; causes a shift in the reading of codons
frameshift mutation
mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide
Frameshift mutation
mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide that is not a multiple of three
missense mutation
mutation where one amino acid substitutes for another; may have a range of effects depending on the location within the protein and the identity of the new amino acid
mutations are rare
mutations are rare because DNA ligase cleaves out errors
induced mutations
mutations in which physical, chemical, and biological agents (mutagens) generate mutations
spontaneous mutations
mutations that occur under normal conditions (in the absence of a mutagen)
Silent mutations have ______ effect on the product
no
What are the effects of a silent mutation?
no change in amino acid, just in DNA sequence
introns
non protein coding sequences in pre-mRNA; must be removed before translation
What is the leader sequence of mRNA?
non-coding seq. on 5' end -recognition site for ribosomes to bind
However, recent research has shown that the DNA is transcribed into _________________. It is believed that these RNA molecules help ________ gene expression.
non-protein coding RNAs, control
Introns
noncoding regions of mRNA that must be removed before the mRNA leaves the nucleus
introns (intervening sequences)
noncoding segments of nucleic acid that lie between coding sequences
viruses
nonliving agents capable of infecting cells
coding strand
nontemplate strand of DNA which has the same sequence as the mRNA except it has thymine (T) instead of uracil (U)
Proto-oncogenes
normal cellular gene that has the potential to become an oncogene
What are proto-oncogenes:
normal versions of oncogenes. They encode for proteins that stimulate normal cell growth & division.
During epigenetic inheritance the DNA sequence is _____ _______, just its expression
not changed
In a missense mutation, the _______ of one codon is changed
nucleotide
In a nonsense mutation, a __________ in one codon is different.
nucleotide
During transcription, the DNA molecule unwinds and separates, exposing the nitrogenous bases. Free RNA____ pair with the exposed bases.
nucleotides
Where does transcription occur?
nucleus
from the DNA in the_____to the ribosomes.
nucleus
amount of RNA polymerase in prokaryotes
one
substitution mutation
one or more bases swapped for another
duplication mutation
one/more bases are repeated
In transcription we end up with:
only a tiny specific section copied into an mRNA
unipotent cells
only differentiate into one type
Fill in the blank,"A cluster of genes usually coding for proteins related to a particular metabolic pathway is called a (an)___________," using the given terms: repressor, regulator, operon, or linkage.
operon
Repressible operon
operon that is normally on but can be inhibited by the regressor protein
In bacteria, genes are often clustered into units called ______
operons
untranslated region (UTR)
parts of the mRNAs at the 5' and 3' ends that will not be translated into protein; have other functions such as ribosome binding
epigenetic changes
pass from one cell generation to the next but do not alter the DNA sequence.
What is controlled by homeotic genes?
pattern formation in late embryo, larva, and adult. Regulatory genes that cause placement of structures.
how can a mutation in a receptor that responds to growth (proto-oncogen) cause cancer
permanently activated - even in absence of growth factor - so more division
transcription
process in which a nucleotide sequence in DNA is copied into a complementary sequence in an mRNA strand
translation
process in which mRNA molecule specifies amino acid sequence in polypeptides
Induction (Embryonic induction in developments results in the ________ timing of events)
process in which one group of embryonic cells influence the development of another, usually causing changes in gene expression (correct)
Transformation
process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria
untranslated
prokaryotes and eukaryotes each have coding regions which are flanked (surrounded) by 5' to 3' _________________ regions and eukaryotes also have non coding elements within the coding region that don't code for anything whereas prokaryotes do NOT have introns
RNA Polymerase II
prokaryotes use ________ ________________ ____ for ALL transcription
all genes have a
promoter, transcribed region and terminator
Proteasomnes
protein complexes that can recognize and degrade proteins
Transcriptional factors
protein molecule that moves from cytoplasm ->. nucleus & binds to DNA to stimulate/inhibit transcription
Histones
protein molecules around which DNA is tightly coiled in chromatin; bunched together in groups called a nucleosome
release factor
protein shaped like an aminoacyl tRNA that binds directly to the stop codon in the A site during termination of translation; causes the addition of a water molecule instead of an amino acid to the polypeptide chain
sorting signals
proteins are distributed within cells by _____________ ____________; which are coded in DNA
DNA
provides a template for making a new complementary sequence of RNA nucleotides
hydrolysis of GTP
provides the energy for some steps of initiation and elongation in protein synthesis
Non-coding genes
rRNA is made by transcribing ______________ _________
Recognition sequence
recognized by RNA polymerase
antiparallel
referring to the arrangement of the sugar-phosphate backbones in a DNA double helix (they run in opposite 5' -3' directions).
operator
region that controls whether transcription will occur; this is where the repressor binds
Promoters
regions of DNA that have specific base sequences
non-coding regions
regions of the genome that do not code for expressed proteins but instead code for rRNA and tRNA
Murine TNF-alpha promoter
regulate TNF-alpha expression Bind some sites: turns on a little Bind more: turns it on more Bind all: turn it on a lot
In addition to affecting mRNAs, siRNAs can cause......
remodeling of the chromatin structure. siRNAs form heterochromatin at centromeres. They bind to a certain protein complex and bring it to the centromere, where they recruit enzymes to make that area highly condensed heterchromatin.
Histone deacetylase
remodels chromatin by removing the acetyl groups from the histones, repressing transcription
one gene one polypeptide hypothesis
restated the one gene one enzyme hypothesis to say that each gene codes for a polypeptide; not entirely accurate
base substitution mutation
results when a single nucleotide base is substituted for another (point mutation) three types: nonsense, missense, and silent
rRNA
ribosomal RNA; type of RNA that makes up part of the ribosome. Primarily responsible for the ribosomes structure and function
Fill in the blank," Once formed mRNA carries genetic information from DNA to the ____________," using the given terms: endoplasmic reticulum, ribosomes, Golgi apparatus, or secretory vesicles.
ribosomes
during translation, cells read messenger RNAs using
ribosomes and transfer RNAs to make a specific protein based on the specific sequence of an mRNA
Where does translation take place?
ribosomes in the cytoplasm
Gene regulation system that go wrong during cancer turns out to be the very ________ systems that play important roles in embryonic development, the immune response, and many other biological process
same
elongation
second stage of translation where amino acids are added to the growing polypeptide
sense strand (coding strand)
segment of DNA running from 5'-3' that is complementary to the antisense strand of DNA
Enhancer. Enhancers also contain proteins called _______
segment of DNA that is far upstream from the promoter, which helps initiate and regulate transcription. (Activators)
RNA polymerase
separates the DNA strands near the start of a gene and covalently links together RNA nucleotides
With a missense mutation, there will be changes in _____________ and __________.
seq. of DNA phenotype
What is a promoter?
sequence in DNA that RNAP recognizes and binds to
poly A tail
sequence of 50-250 adenine (A) nucleotides added to the 3' end of pre-mRNA
transfer RNA (tRNA)
shuttles amino acids to ribosomes responsible for bringing the appropriate amino acids into place at the appropriate time by reading the message carried by the mRNA
difference between miRNA and siRNA
siRNA used as a mechanism to fight off viral infections -Viral RNA within cytoplasm is spliced by dicer -Viral RNA + protein: RISC complex (little piece of viral RNA) -Little piece of viral RNA binds to large piece of viral RNA to inhibit
missense
sickle cell disease is caused by a single ____________ mutation; GAG--> GUG = glutamine --> valine
stop codons (termination codons)
signal the end of a polypeptide- encoded in mRNA sequence; UAA, UAG,UGA... signals to stop translation
Low glucose but lactose present
signaling molecule (cyclic AMP) is present in higher concentrations -transported to nucleus -binds to activator protein -binds to promoter region and stabilizes RNA polymerase transcription occurs
start codon (AUG)
signifies the start of the protein-encoding sequence in mRNA
Bacteria
single-celled organisms that lack a nucleus; prokaryotes. divide by fission
pyrimidine
single-ringed nitrogenous base (ex. cytosine and thymine)
Promoter? What to think promoter as?
site at which the RNA poymerase attaches to the gene on-off switch
the role of tumour suppressor genes
slow down cell division by producing proteins that stop cells dividing/apoptosis
Regulation of protein synthesis
slower but conserves energy and resources. Protein synthesis requires a lot of energy
microRNAs (miRNAs) and small interfering RNAs (siRNAs)
small RNA molecule that binds to the complementary sequence in mRNA molecules and then degrades the mRNA molecule or blocks translation
posttranslational control
some proteins must be activated after synthesis. many proteins function only for a short time before they are degraded or destroyed by the cell.
Histone code hypothesis:
specific combinations of modifications, rather than the overall level of histone acetylation, help determine the chromatin configuration, influencing transcription.
the information contained in genes contains instruction for making
specific proteins and non-coding RNA molecules
promoters
specific region of a gene where RNA polymerase can bind and begin transcription
promoter
specific region of a gene where RNA polymerase can bind and begin transcription - stimulated/blocked by transcriptional factors
oestrogen and its effect
steroid hormone, initiates transcription
ribosomes
structure made of proteins and ribosomal RNA which is also a type of ncRNA -sites of protein synthesis in cells -consist of large and small subunits, which are separate until they are used to translate an mRNA
Morphogens
substances in which the concentration of them helps establish an embryo's axes and other features of its form
Genetic transplantation experiments _____ the link between gene expression and normal development
support (DNA transplanted to damaged cell, cell develops properly because has healthy DNA
transcription
synthesis of RNA under direction of DNA. Segments of DNA provide a template for assembling RNA nucleotides. RNA molecule is a transcript of protein building instructions of that gene
translation
synthesis of polypeptides. translation of RNA language to amino acid language. occurs at ribosomes. tRNA is the interpreter. The genetic code
P site (peptidyl tRNA binding site)
tRNA binding site on a ribosome that holds the tRNA carrying the growing polypeptide chain
A site (aminoacyl tRNA binding site)
tRNA binding site on a ribosome that holds the tRNA carrying the next amino acid to be added to the chain
E site (exit site)
tRNA binding site where the discharged tRNAs leave the ribosome from
transcription continues through a gene until it reaches a
terminator *DNA sequences that indicate where transcription stops
tRNA binds to an mRNA codon specifying a particular amino acid, pairing of the tRNA anticodon with the appropriate mRNA codon
the 2 instances of molecular recognition that allow for the accurate translation of a genetic message
large subunit, small subunit
the 2 parts of a ribosome
genetic engineering
the branch of technology that produces new organisms or products by transferring genes between cells
RNA
the bridge between DNA and protein synthesis
post-transcriptional regulation
the control of gene expression at the RNA level, therefore between the transcription and the translation of the gene.
The lactose operon is likely to be transcribed when
the cyclic amp and lactose levels are both high in the cell.
peptidyl transferase
the enzyme that catalyzes formation of the first peptide bond and cleaves tRNA that is in the P site from it's amino acid
RNA polymerase III
the enzyme used to transcribe non-coding regions for tRNA and 1 rRNA
RNA Polymerase I
the enzyme used to transcribe non-coding regions that make 3 rRNA
amino-acyl tRNA synthetases
the enzymes that add amino acids to tRNAs
wobble
the flexible base pairing at the 3rd codon position; explains why the synonymous codons for a given amino acid most often differ in their third nucleotide base
heterogeneous nuclear RNA (hnRNA)
the freshly transcribed RNA contains both coding regions and noncoding regions
universal
the genetic code is considered _____________________ because same codons specify the same amino acids in all species and organisms which tells us that the genetic code evolved long ago
triplet code
the genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words
start point
the nucleotide where RNA polymerase actually begins synthesis of the mRNA
Within a cell, the amount of protein made using a given mRNA molecule depends partly on
the number of introns present in the mRNA.
start site
the official starting point of transcription
lac operon
the operon that encodes for the lactose enzymes
anticodon
the opposite of a codon that is found at the bottom of tRNA molecules that pairs and identifies the codon
not translated into protein
the other RNA polymerase molecules in a eukaryotic cell (besides RNA polymerase II which synthesizes pre-mRNA) synthesize RNA molecules that are what?
anticodon
the particular nucleotide triplet that base-pairs to a specific mRNA codon; located on one end of a tRNA molecule
morphogenesis
the process of a cell changing shape and organization many times by going through a succession of stages
tRNA charging
the process of adding amino acids to specific tRNAs
Aminoacylation
the process of adding amino acids to tRNA molecules
where does gene expression begin?
the promoter
SRP receptor
the receptor that SRP binds to... located on the ER membrane near channels in the membrane in order to push the new polypeptide that will be built into the ER lumen
promoter gene
the region where the RNA polymerase binds to begin transcription
Exons
the regions that express the code that will be turned into protein
exons
the regions that express the code that will be turned into protein
ribosomes
the sites of translation; molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains
promoter
the spot where RNA polymerase binds to on the gene is called the _________________
antisense strand/non-coding/template strand
the strand of DNA that runs 3' to 5' and is complementary to the sense strand. It acts as a template strand during transcription.
antisense strand (non-coding strand) (minus-strand) (template strand)
the strand of DNA that serves as the template for transcription
transcription
the synthesis of RNA using information in the DNA
translation
the synthesis of a polypeptide using the information in the mRNA
What is an anticodon?
the tRNA complement to the mRNA codon
the genetic code
the table which shows which codons go with which amino acids
Transduction
the transfer of DNA between bacterial cells using a lysogenic virus
transduction
the transfer of DNA between bacterial cells using a lysogenic virus
transfer RNA (tRNA)
the translators that transfer the required amino acids from the cytoplasm to a growing polypeptide in a ribosome
transcription and translation
the two stages for the expression of genes that code for proteins
phosphodiester bond
the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide
translation initiation complex
the union of mRNA, initiator tRNA, a small ribosomal subunit, and a large ribosomal subunit
stop codons
there are three codons that serve as stop codons don't always code for an amino acid results in termination once one is reached
zinc finger motif
these proteins are steroid hormone receptors
termination
third stage of translation where elongation stops and the polypeptide is released
one gene - one polypeptide hypothesis
this is the hypothesis that states that functional proteins contain more than one polypeptide sometimes and different genes encode each polypeptide; fixed the previous hypothesis also because not all proteins are enzymes
Chromosomes
threadlike structures made of DNA molecules that contain the genes
amount of RNA polymerase in eukaryotes
three I transcribes rRNA II transcribes mRNA III transcribes tRNA and small RNAs
A codon consists of _____ bases and specifies which _____ will be inserted into the polypeptide chain.
three ... amino acid
Watson, Crick, and Franklin
three scientists who deduced the structure of DNA in 1953
There is no___ in RNA. _____ pairs with adenine (A) instead.
thymine (T), uracil (U)
where does RNA pol bind
to a specific DNA sequence near the start of a gene called a promoter
where do transcription factors bind?
to either enhancer or promoter regions of DNA adjacent to the genes that they regulate
During development
totipotent cells translate only part on DNA resulting in cell specialisation
The combination of _______ _______ binding to the regulatory regions at any one time determines how much, if any, of the gene product will be produced
transciption factors
RNA polymerase II
transcribes mRNA
In ________, only ceratin regions (genes), are transcribed
transcription
In _____________, the enzyme used in RNA polymerase
transcription
The process of producing mRNA from instructions in the DNA is called______.
transcription
What name is given to the process in which a strand of DNA is used as a template for the manufacture of a strand of pre-mRNA?
transcription
Explain repressible operons and describe one example
transcription is usually on but can be inhibited when small molecule binds to regulatory protein. Repressor molecule activates the repressor protein. Ex: the trp operon
The functioning of enhancers is an example of
transcriptional control of gene expression
What is tRNA?
transfer RNA, physically brings in correct amino acid
tRNA
transfer RNA; type of RNA that carries amino acids to the ribosome
Beginning within the nucleus, the first step leading to the synthesis of a polypeptide is _____.
transferring of information from DNA to messenger RNA
B-galactoside transacetylase
transfers acetyl groups to certain B-galactosides
The process, performed by the ribosome, of reading mRNA and synthesizing a protein is called __________.
translation
What name is given to the process in which the information encoded in a strand of mRNA is used to construct a protein?
translation
stops
translation _________ temporarily after the signal peptide has been translated in order to move the rest of the polypeptide to the rough ER
ribosomes
translation occurs on __________________
fertilization
triggers the zygote to go through a series of cell divisions that further differentiate the embryo
Fertilization
triggers the zygote to go through a series of cell divisions. As these occur, the embryo becomes increasingly differentiated, or specialized
p53 gene
tumor suppressor gene that codes for a specific transcription factor that promotes the synthesis of proteins that inhibit the cell cylce
pre-transcriptional gene regulation
turns transcription of genes on/off or up/down based on the needs of the cell
single nucleotide pair substitutions, nucleotide pair insertions/deletions
two general categories of small scale mutations within a gene
make multiple mRNAs from the same gene, make multiple polypeptides from the same mRNA
two ways in which cells increase the number of copies of a polypeptide
mRNA
type of RNA molecule that carries a genetic message from the DNA to the protein-synthesizing machinery of the cell
RNA polymerase II
type of RNA polymerase that is used for pre-mRNA synthesis in eukaryotic cells
point mutations
type of mutation that involves changes in a single nucleotide pair of a gene
stem cells
unspecialised cells that can differentiate into specialised cells
Enzyme DNA helicase
unwinds and unzips the double stranded DNA
retroviruses
viruses that use an reverse transcriptase to convert their RNA genomes into DNA so that they can be inserted into a host genome
enveloped viruses
viruses with a lipid envelope
ribosome
what assembles the amino acid sequence for the mRNA strand (process of translation)
Alkaptonuria
what did Garrod study?
stop codon
when a ribosome reaches a _______ _______ during the termination stage of translation, the A site of the ribosome accepts a release factor
coordinate control:
when a single on/off switch can control a group of genes with the same function (transcription unit)
Zygote
when an egg is fertilized by a sperm, it forms a diploid cell called a zygote
exon shuffling
when different proteins are generated due to the rearrangement of the order of the exons; allows for quick evolution
alternative splicing
when different versions of mRNA produced based on the various ways splicing can occur (some exons used and some exons not used);
after polyadenylation signal (AAUAAA) is transcribed
when is pre-mRNA cut and released during transcription
Maternal effect genes=
when mutant in mother, mutant phenotype in offspring even if offspring genotype is normal. mRNA protein products of maternal effect genes are put in egg when it's still in the ovary.
cytoplasm
where does translation occur?
Multipotent
- Stem cells found in adults - differentiate into limited no. of specialised cells
2 types of mutations
...
For transcription & translation we are only doing that with what?
1 gene (3,000 base pairs)
specific structure, bases contain functional groups that participate in catalysis, ability to hydrogen bond with other nucleic acid molecules adds specificity
3 properties of RNA that enable some RNA molecules to function as enzymes
initiation, elongation, termination
3 stages of translation:
removal of an amino acid or two, addition of organic groups, folding guided by chaperones
3 things done in polypeptide processing:
Transcription uses what strand as a template?
3' to 5'
triplets
3-letter codes in DNA are considered ____________
codons
3-letter codes in mRNA/ RNA are considered ________________
Transcription happens in what direction?
5' to 3'
As the amino acids get kicked of, it forms what?
A chain called peptide chain that grows longer & longer as more amino acids are added to it.
Carcinogen
A chemical, a form of radiation, or another agent that causes cancer
Genes ("sentence") might range from? Genome would be what?
A few to many thousands. The manual on how to make you, you.
DNA?
A molecule that all living organisms carry in every cell in their body.
mutagens
A number of physical and chemical agents interact twitch DNA in easy that cause mutations
Which of the following processes occurs when termination of translation takes place?
A stop codon is reached.
Mutation?
Alteration of sequence of bases in DNA.
Mutagen
Any agent that induces a mutation
Fill in the blank," A purine is always bonded to a pyrimadine. This called___________" using the given terms : a polynucleotide strand, helical replication, complimentary base pairing, or diffraction.
Complimentary Base Pairing
Fill in the blank,"In contrast to DNA, RNA_____________" using the given responses: is a helix, is double-stranded, Contains uracil, or Contains deoxyribose sugar
Contains uracil
The process starts when?
DNA is wrapped around special proteins molecules called histones. The combined loop of DNA & protein is called a nucleosome
Fill in the blank," To complete replication, the enzyme_______ seals any breaks in the sugar-phosphate backbone" using the given terms: DNA polymerase, DNA ligase, DNA helicase, or transcriptase
DNA ligase
DNA is made out of _______ which has what 3 components?
DNA made out of nucleotide. The 3 components of nucleotide are Phosphate group, Nitrogenous base (ATGC), and a Sugag
Fill in the blank," The process of copying one DNA double helix into two identical double helices is called_______," using the given terms: DNA profiling, DNA base pairing, DNA transcription, or DNA replication.
DNA replication
In ________, the enzyme used is DNA polymerase
DNA replication
In _________, the product is double stranded DNA
DNA replication
Promoter
DNA sequence where RNA polymerase attaches and initiates transcription
promoter
DNA sequence where RNA polymerase attaches and initiates transcription
1) 3' to 5' 2) 5' to 3'
DNA strand read ______1______ during transcription and mRNA is build __________2________
Heterochromatin
DNA that is densely packed around histones. The genes in heterochromatin are generally inaccessible to enzymes and are turned off.
DNA replication
DNA unzips into two parts and splits with the cell. In it's new home each side of the DNA strand attack to matching nucleotides to create 2 exact copies. It is important in puberty and other times of growth as it is the reproducing of your cells.
Be able to replicate the diagram ?
DNA w/replication > transcription to RNA > and translation into a polypeptide or protein
DNA would up in histomes
DNA won't be transcribed
Central Dogma of Biology
DNA->transcription->RNA->translation->Protein. (the flow of information in this order).
Beadle and Tatum
Diabled gene by gene looking for the effect on phenotype in bread mold though mutation in an x-ray, 1 gene-one protein(polypeptide)
Marshall Nirenberg
Figured out which codons code for which amino acids
Three criteria for DNA recognition by a protein motif
Fits into major or minor groove Has amino acids that can project into interior of double helix Has amino acids that can bond with interior bases
Wobble
Flexibility in the base-pairing rules in which the nucleotide at the 5' end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position of a codon.
Two types of ribosomes
Free ribosomes and bound ribosomes (are same chemical make up just different locations and can alternate)
What happens with the lagging strands?
It has to make DNA basically backwards, causing it to only make little fragments of DNA (called okazaki fragments). The primace part gets removed & the correct DNA gets incorporated.
What happens to RNA polymerase II after it has completed transcription of a gene?
It is free to bind to another promoter and begin transcription.
What happens when a repressor is bound to the operator?
It switches off the operons if in active form (negative control)
DNA is single or double stranded and does what kind of pairing?
Its double bonded and does complementary base pairing meaning AT & GC
What name is given to the process in which pre-mRNA is edited into mRNA?
RNA processing
Messenger RNA (mRNA)
RNA produced during Transcription, that brings the DNA message out of the cell to instruct protein creation, complementary and antiparallel to DNA template strand,
What is translation?
RNA to protein
Reading frame
Reading in correct groupings/ nonoverlapping 3 letter words
Terminator
Sequence that signals the end of transcription in bacteria
Adult
Stem cells that are found in the body of the fetus through to the adult, they're specific to a particular tissue or organ within which they produce the cells to maintain and repair tissues throughout an organisms life
what are the environmental factors which lead to epigenetic changes (change methylation pattern)?
Stress—certain genes become more methylated Environmental chemicals and drugs Diet Aging Addiction or psychosis may produce different methylation or acetylation patterns
Template strand
The DNA strand that provides the template
the lac operon
The lac operon is a set of control and structural genes in E. coli that allow the digestion of lactose., prevents lactose-utilizing enzymes from being expressed when lactose is absent from the environment
Bacterial transcription translation
Translation can start before transcription is done
STOP codons (messenger RNA codons)
UAA UGA UAG
stop codons
UAA, UAG, UGA ends synthesis of the polypeptide
action of mutagenic agents - changing DNA structure
UV radiation can cause adjacent T bases to pair up together
15 Open Hint for Question 15 in a new window Which of the following catalyzes the linkage between ribonucleotides to form RNA during gene expression? () a.RNA polymerase b.RNA ligase c.a ribozyme d.reverse transcriptase e. tRNA
a
A virus infects a cell and randomly inserts many short segments of DNA containing a stop codon throughout an organism's chromosomes. This will probably cause _____. () a. manufactured proteins to be short and defective b. the DNA to break up into thousands of short segments c. incorrect pairing between mRNA codons and amino acids d. no bad effects, as long as the stop codons are not also inserted into tRNA e. All of the listed responses are correct
a
Completion of the polypeptide synthesis occurs at a(n) _____. A) stop codon B) terminator C) intron D) stop anticodon
a
During transcription DNA serves as a template for ______ synthesis. A) mRNA B) rRNA C) tRNA
a
Each triplet codon has only one meaning. A) True B) False
a
In eukaryotes, which of the following mechanisms of gene regulation operates after transcription, but before translation of mRNA into protein? () a. RNA splicing b. DNA packaging into nucleosomes c. action of repressors and activators d.protein degradation e.All of the listed responses are correct.
a
Information is taken from DNA in the nucleus to the ribosomes in the cytoplasm by the _____. A) mRNA B) rRNA C) tRNA
a
RNA is single stranded and does not form a double helix like DNA's. A) True B) False
a
Some tRNA molecules can pair with more than one codon. A) True B) False
a
Which one of the following is not a type of RNA? . A) nRNA (nuclear RNA) B) mRNA (messenger RNA) C) rRNA (ribosomal RNA) D) tRNA (transfer RNA)
a Feedback: Answer d is incorrect because transfer RNA is a type of RNA. tRNA is the molecule that binds to and transfers amino acids to the mRNA-rRNA complex to synthesize proteins.
anticodon
a group of three bases on a tRNA molecule that can complementarily base pair with the codon in the mRNA these are a bit flexible when they bind with a codon on an mRNA, especially the third nucleotide in an anticodon
During RNA processing a(n) _____ is added to the 3' end of the RNA.
a long string of adenine nucleotides
repressible system
a metabolic product (co-repressor) binds to regulatory protein, which then binds to the operator and blocks transcription (e.g trp operon) control anabolic pathways—turned on until product concentration becomes excessive
5' cap
a modified form of guanine (G) nucleotide added onto the 5' end of pre-mRNA after transcription of the first 20-40 nucleotides
Spontaneous mutation
a random change in the DNA arising from errors in replication that occur randomly
Mutation
a random error in gene replication that leads to a change
Fill in the blank,"A promoter is _____________________," using the given sentences: a region of DNA that contains a special sequence of nucleotides that beings transcription, a region of DNA that contains a special sequence of nucleotides that begins translation, or a region of DNA that contain a special sequence of nucleotides that begins replication, or region of DNA that contains a special sequence of nucleotides that begins synthesizing primary mRNA.
a region of DNA that contains a special sequence of nucleotides that begins transcription.
deletions
a type of gene rearrangement mutation that results in the removal of as little as a single base or much larger sequences of DNA results in a frameshift of the sequence
lytic cycle
a viral replication cycle in which the virus starts using the host cell's machinery to replicate the genetic material and create more capsid proteins. These spontaneously assemble into mature viruses and cause the cell to lyse, or break open, releasing new viruses into the environment.
lytic cycle
a viral reproductive cycle in which copies of a virus are made within a host cell, which then bursts open, releasing new viruses
lysogenic cycle
a viral reproductive cycle in which the viral DNA is added to the host cell's DNA and is copied along with the host cell's DNA the viral DNA lies dormant until it is triggered to switch into the lytic cycle
lysogenic cycle
a viral reproductive cycle in which the virus incorporates itself into the host genome and remains dormant until it is triggered to switch into the lytic cycle.
replication fork
a y-shaped point that results when a double helix of DNA operates so that the DNA molecule can replicate
The repressor protein produced by the regulatory gene is _____ (for inducible operon)
active
insertions and deletions
additions or loses of nucleotide pairs in a gene
Insertions and deletions
additions or losses of nucleotide pairs in a gene
insertions and deletions
additions or losses of nucleotide pairs in a gene
What is the poly A tail made of?
adenine
four nitrogenous bases
adenine guanine cytosine thymine
Environmental stimuli can ________ gene expression in a mature cell
affect
genome
all of the DNA for a species
What happens at the A site?
amino acids on tRNA enter here
What enzyme catalyzes the attachment of an amino acid to tRNA?
aminoacyl-tRNA synthetase
Amino acids are attached to tRNA by enzymes called _________ ___________
aminoacyl-tRNA synthetase.
positive regulation
an activator protein stimulates transcription
5-bromouracil
an analogue (means similar to) of thymine but contains a bromine instead of a methyl group; can be a mutagen
reverse transcriptase
an enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis
DNA topoisomerase
an enzyme that alleviates DNA supercoiling during DNA replication
Inducible operon
an operon that is normally off but can be activated by disabling the repressor protein
action of mutagenic agents - acting as a base
analogs (chemicals) can substitute for base during replication
tRNA has a _________codon
anticodon
The most common form of gene expression regulation in both bacteria and eukaryotes is A) translational control B) transcriptional control C) post-transcriptional control D) post-translational control E) control of passage from the nucleus
b
The nucleotide sequences on DNA that actually have information encoding a sequence of amino acids are A) introns. B) exons. C) UAA. D) UGA.
b
The only difference between DNA and RNA is the type of sugar. A) True B) False
b
tRNA molecules transport any amino acid they encounter. A) True B) False
b
_______________ mutations provide genetic diversity to overcome environmental changes in the environment.
beneficial
What are adaptations?
beneficial mutations
initiation of transcription in prokaryotes
binding of RNA polymerase to promoter
initiation of transcription in eukaryotes
binding of many protein, including RNA polymerase
Accuracy in the translation of mRNA into the primary structure of a polypeptide depends on specificity in the _____.
binding of the anticodon to the codon and the attachment of amino acids to tRNAs
promoter
binding site for RNA polymerase and other transcription factors bind and orient RNA polymerase so that the correct DNA strand is transcribed
Open Hint for Question 14 in a new window At one point, as a cell carried out its day-to-day activities, the nucleotides GAT were paired with the nucleotides CUA. This pairing occurred _____. () a. in a double-stranded DNA molecule b. during translation c. during transcription d. when an mRNA codon paired with a tRNA anticodon e. It is impossible to say, given this information.
c
Polysomes may be defined as _____. () a. microfilaments and microtubules b. groups of lysosomes c. groups of ribosomes d. groups of chromosomes e. groups of peroxisomes
c
RNA nucleotides are joined together by _____. A) DNA polymerase B) DNA ligase C) RNA polymerase D) helicase
c
Ribosomes are located _____. A) in the cytosol B) on the endoplasmic reticulum C) both A and B
c
Which of the following accurately describes the usual process of transcription for eukaryotic genes? () a. Exons are not transcribed. b. Introns are not transcribed. c. Exons are transcribed, but the RNA transcribed from introns does not leave the nucleus. d. Both introns and exons are transcribed, but the RNA transcribed from them does not leave the nucleus. e. Exons and introns are transcribed, and the RNA transcribed from them leaves the nucleus.
c
Which of the following must be done in order to make a protein? A) transcription B) translaton C) both A and B
c
multipotent cells
can differentiate into few kinds of cell - e.g. bld cells in bone marrow express genes for haemoglobin and removing nucleus
totipotent cells
can divide and produce any type of body cell - including placenta -only occur for limited time in early mammalian embryos
pluripotent cells
can divide in unlimited numbers and any cell (not placenta), used to treat human disorders
post-transitional regulation
can occur if a cell has already made a protein, but does not yet need to use it. Common regulation for enzymes because when the cell needs them , it needs them ASAP
Explain what occurs in cell differentiation:
cells become specialized in structure and function, and these are organized into tissues and organs. Activities of a cell depend on the genes it expresses and the proteins it produces. Specific activators turn on the collection of genes whose products are needed in the cell. Materials placed into the cell by the mother set up a sequential program of gene regulation that's carried out as cells divide.
What are mutations?
changes in DNA sequence
what are the heritable changes in gene function of epigenetics caused by
changes in enviro, that inhibit transcription by increased methylation of DNA or decreased acetylation of associated histones
Mutations
changes in genetic material
chromosome mutation
changes in structure/number of a whole chromosome
epigenetics
changes in the expression of a gene or set of genes, without a change in the DNA sequence
mutations
changes in the genetic material; responsible for the huge diversity of genes found among organisms
Post-translational modification
changes made to polypeptides following translation
polypeptide processing
changes made to the linear polypeptide after translation in order to make it fully functional
base substitution
changes the base of a single DNA nucleotide
each codon specifies the amino acid to be placed at the
corresponding position along a polypeptide
A nonsense mutation in the CFTR gene replaces glycine with a stop codon. What disease does this describe?
cystic fibrosis
During translation, amino acid chain elongation occurs until _____. () a. no further amino acids are needed by the cell b. all tRNAs are empty c. the polypeptide is long enough d. the ribosome encounters a "stop" codon e. the ribosome runs off the end of the mRNA strand
d
Each amino acid in a protein is specified by A) several genes. B) a promoter. C) an mRNA molecule. D) a codon.
d
Protein synthesis involves __________. A) initiation B) elongation C) termination D) all of the above
d
Which of the following summaries of protein synthesis is correct? () a. DNA transposons leave the nucleus, are transported to a ribosome, and catalyze the polymerization of amino acids in a protein. b. DNA exchanges its thymine units with uracil in polymerase. This activates polymerase, and it starts joining amino acids together. c. Transfer RNAs line up on a ribosome, and amino acids bind to them with hydrogen bonds. d. Messenger RNA is made on a DNA template, and then amino-acid-bearing transfer RNAs bind to it through codon-anticodon pairing. e. DNA strands separate in the nucleus to form mRNA. mRNA leaves the nucleus and is transcribed into tRNA on ribosomes.
d
A geneticist found that a particular mutation had no effect on the polypeptide encoded by the gene. This mutation probably involved _____. () a. the deletion of one nucleotide b. a missense mutation c. the insertion of one nucleotide d. a nonsense mutation e. a silent or neutral mutation
e
Open Hint for Question 12 in a new window In a eukaryotic cell, transcription takes place _____. () a. on the cell membrane b. in the rough endoplasmic reticulum c.in the cytoplasm d. on free ribosomes e. in the nucleus
e
The bonds that hold tRNA molecules in the correct three-dimensional shape are _____. () a. peptide linkages b. hydrophobic interactions c. covalent bonds d. ionic bonds e. hydrogen bonds
e
Transcription factors are found in _____. () a. archaea b. bacteria and eukaryotes c. bacteria and archaea d. eukaryotes e. archaea and eukaryotes
e
When genes are expressed, they produce _____. () a. enzymes b. RNA molecules c. phenotypic traits d. polypeptides e. The second and fourth responses are correct.
e
Which of the following statements is true? () a.Each DNA base codes for three amino acids. b.Each gene codes for three proteins. c.It takes three genes to code for one protein. d.Each triplet has many different meanings. e.Each amino acid in a protein is coded for by three bases in the DNA.
e
triplets
each 3-nucleotide unit is called a codon
Genes of the operon? What to think genes of the operon as?
entire stretch of DNA (cluster of genes) required for all the enzymes produced by the operons Lights that get "turned on"
topoisomerase
enzyme that cuts and rejoins the helix to prevent tangling as the DNA helix twists and rotates during DNA replication
RNA polymerase
enzyme that joins together nucleotides to form messenger RNA during transcriptase
DNA ligase
enzyme that links together Okazaki fragments to produce a continuous strand of DNA
RNA polymerase
enzyme that pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide
signal peptidase
enzyme that removes sorting signal sequence once we no longer need it
helicase
enzyme that unwinds the double helix by breaking the hydrogen bonds
enzymes in the eukaryotic nucleus modify ____________ before they are transported to the ____________ as mature mRNA's in a process called ___________ _____________
enzymes in the eukaryotic nucleus modify PRE-MRNA'S before they are transported to the CYTOPLASM as mature mRNA's in a process called PRE-MRNA PROCESSING
Where is the operator found?
found within the promoter site or after the promoter
effect of deletion mutation
frameshift - if # deleted not multiple of 3
effect of addition mutation
frameshift - if number of bases added not multiple of 3
The flow of information in a cell proceeds in what sequence?
from DNA to RNA to protein
How are siRNAs formed?
from much longer double stranded RNAs, which give rise to many siRNAs.
20
how many different amino acids are there?
20 (one for each amino acid)
how many different synthetases are there?
why cant the knowledge of the genome be easily translated into the proteome
in complex organisms - presence of non-coding DNA and regulatory genes
does not
in eukaryotes RNA polymerase ___________ (does/does not) bind directly to DNA
stops
in initiation of translation, complex of initiator tRNA and small subunit temporarily _________ when it finds the AUG codon to allow the large subunit to bind
Explain the distribution of cytoplasmic determinants for how different sets of activators come to be present in two cells:
maternal substances in the egg that influence early development. They're unevenly distributed in the cytoplasm of the egg, so different cells end up with different amounts of molecules as the cells divide.
location of genes that are regulated simultaneously
may be far apart or even on different chromosomes
How do cancer-causing viruses work?
may donate an oncogene to the cell, disrupt a tumor-suppressor gene, or convert a proto-oncogene to an oncogene. Some viruses also produce proteins that inactivate p53 and other tumor-suppressor proteins, making the cell more prone to cancer.
patterns of DNA methylation
may include large regions or whole chromosomes
duplications
may result in an extra copy of genes and are usually caused by unequal crossing-over during meiosis and chromosome rearrangements
20
number of amino acids
64
number of codons
translocations
occur when two different chromosomes (or a single chromosome in two different places) break and rejoin in a way that causes the DNA sequence or gene to be lost, repeated, or interrupted
post-transcriptional regulation
occurs when the cell creates an RNA, but then decides that it should not be translated into a protein RNAi molecules can bind to an RNA via complementary base pairing, creating a double-stranded RNA, which signals to some special destruction machinery that the RNA should be destroyed, preventing it from being translated
reading frame
on an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis
Where does histone acetylation occur. ________ gene expression (reduces or increases)
on histones, increases
ER lumen
once on the rough ER membrane.... the ribosome will translate the mRNA strand and push the new polypeptide into the ____ __________
what happens if the gene inherited from the mother is imprinted
only the gene from the father is expressed
Regulatory genes
regulate the structural genes
Very ____ Hox genes have been find in fruit flies, vertebrates, invertebrates, plants and even yeast. (Suggests that this DNA sequence evolved very ______ in the history of life
similar, early
prokaryotes
simultaneous transcription and translation can only occur in ____________________ since they don't have to process mRNA before translation and both processes happen in the same spot
Is mRNA single stranded or double stranded?
single
The mRNA molecule is a____strand unlike DNA.
single
is tRNA single or double stranded?
single
Spliceosomes are composed of _____.
small RNAs and proteins
Okazaki fragments
small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a completed strand
The RNA that has an amino acid attached to it, and that binds to the codon on the mRNA, is called a ______
tRNA
Which type of RNA can fold back on itself and also physically carries polypeptides?
tRNA
What happens in the E-site of the ribosome?
tRNA exits
anticodon, amino acid
tRNA molecules have a specific ___________ on one end and a corresponding _______ _______ on the other
aminoacyl tRNA
tRNA molecules that have an amino acid attached at the 3' end
Translation initiation complex
tRNA, mRNA, and the small and large ribosomal subunit bound together
recycled
tRNAs can be _________________
A site
termination in translation begins when the ___ ______ reaches stop codon
transcription factors
transcription factors: proteins which help RNA polymerase bind to a promoter
Explain inducible operons and describe one example
transcription is sually off but can be induced when a small molecule binds to regulatory protein. Inducer inactivates the repressor. Ex: the lac operon
signal peptide
translated at the beginning of a polypeptide chain... tells the cell where the polypeptide will go
alternative RNA splicing
type of eukaryotic gene regulation at the RNA processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns
N terminus (amino end) to C terminus (carboxyl end)
what direction is a polypeptide always synthesized in?
Start site
where RNA polymerase initiates transcription
phosphodiester bonds
bonds between the sugars and the phosphate group in DNA makes the sugar-phosphate backbone of DNA possible
The mRNA molecule is completed by the formation of____between the RNA____and it then separates from the DNA.
bonds, nucleotides
small
the 3 sites are found on the ___________ (small/large) subunit of the ribosome
epigenetic changes
changes to the packaging of DNA that alter the ability of the transcription machinery to access a gene usually occur through a modification to a histone protein that is involved in winding up the DNA (a tighter wrap around a histone makes the DNA more difficult to access, whereas a looser wrap makes it easier to access)
nucleotide pair substitution
type of small scale mutation that involves the replacement of one nucleotide and its partner with another pair of nucleotides
codons are read in what direction
5' to 3' direction
Transcription begins when RNA polymerase attaches to a promoter. A) True B) False
a
What RNA nucleotide is paired with the DNA nucleotide T during transcription? A) adenine B) guanine C) cytosine D) uracil
a
What are ribsomes made of?
-rRNA -proteins
2 possible leads to cancer
...
nitrogenous base
A molecule found in DNA and RNA that encodes genetic information in cells.
A typical operon consists of
A promoter Two or more structural genes An operator
Upstream
Against the direction of translation
Bacteriophage
A virus that infects bacteria
Eukaryotic transcription and translation
Before mRNA leaves the nucleus it must be altered
Large mutation
Chromosomal rearrangements that affect long strand of DNA
What would occur if the repressor of an inducible operon were mutated so it could not bind to the operator?
Continuous transcription of the operon's genes
What is the 5' cap made of?
Guanosine triphosphate
Three main types of RNA
Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA) - all three types are key players in the synthesis of proteins
A DNA molecule can directly control protein synthesis. A) True B) False
b
The _____ are removed during an mRNA processing event called mRNA splicing. A) exons B) introns C) promoters D) poly-A tails
b
RNA nucleotides contain _____. A) a phosphate group B) the sugar ribose C) the base uracil D) all of the above
d
disadvantage embryonic stem cells
ethical issues, higher chance of cancer
Where do gene mutations occur?
interphase/S phase of DNA replication
inducible proteins
proteins that can be induced lactose proteins
6 Simple steps of colorectal cancer development:
1. loss of tumor suppressor gene in normal colon epitherial cells 2. small benign growth (polyp) occurs 3. Activation of ras oncogene 3. loss of DCC tumor suppressor gene 4. Larger benign growth occurs (adenoma) 5. loss of TSG p53 5. more mutations 6. malignant tumor forms (carcineroma)
What 3 things are needed for translation to take place?
1. mRNA 2. tRNA 3. ribisomes
What can cause mutations?
1. mistakes in DNA replication/transcription 2. carcinogens/mutagens 3. radiation
What is a good example to remember epigenetics?
- DNA sequence is like a paragraph = "I like to play on my xbox. Having fun while playing rocket league and eating pizza." - Epigenetics is the alteration of the paragraph (i.e. affects how cells read genes) = i likE to. PlAy on my xBox having Fun. While PlaYing Rocket. League aNd eating pizza." = DNA seq doesn't change
Increased acetylation
- DNA-histone complex LESS condensed - transcriptional factors can bind - euchromatin - gene is active
Decreased acetylation
- DNA-histone complex MORE condensed - transcription factors cannot bind - heterochromatin - gene is inactive
How do stem cells have the potential to treat sick people?
- Extracted embryonic stem cells are: - *Totipotent* = can regen damaged tissue under right conditions = Organ & tissue regen = Kidney & liver failure = New skins for burned victims (under skin = multipotent) = Brain disease treatments = Parkinson's = Alzheimer's = Treatments promising with replenishing dmg brain tissue = Cell deficiency therapy = Heart disease = Type 1 diabetes = Replacing insulin-producing cells lost to imm sys with pancreatic cells
How does dsRNA have a complementary strand to mRNA that was produced unnecessarily produced from a gene?
- Gene 2 (a dif gene to gene 1 that is producing polypeptide unnecessarily) = control gene for gene 1 = therefore it has complementary nucleotide sequence to mRNA from gene 1
What is the process of siRNA in destroying mRNA produced from another gene?
- Gene is changed (lets say from gene 1 to 2) (gene 1 being gene that wants to be changed, need to stop mRNA of this gene being made) - Gene 2 transcribes into very long strand of RNA = double backs on itself = forming dsRNA = as RNA dependent RNA polymerase replicates RNA from RNA template (originally from transcription of gene) - DICER enzyme = hydrolysis of dsRNA into siRNA (breaking RNA strands) - 1/2 (strand) of siRNA fragments joins to an enzyme-containing molecule (RISC) (other half is degraded) = RISC uses siRNA as a template for recognising complementary mRNA from gene 1 (after mRNA leaves nucleus) - Breaks up mRNA before transcription = no polypeptide made = Gene is turned off (gene 1) = no longer expressed - an e.g. for gene 1 could be adrenaline from a fight or flight protein = as it lasts for a short period of time
What is therapeutic cloning?
- Nucleus of ovum removed & replaced with nucleus of a cell from a patient = small electric shock = starts division of cell = once reaches blastocyst stage = stem cells can be removed & cultured to produce genetically identical tissues for patient = allowed by gov but all embryos must be destroyed after 14 days to avoid = to avoid human cloning
Take home message for step 2 translation?
- Occurs in cytoplasm - mRNA code is translated - Ingredients in cytoplasm build a protein
Take home message about transcription?
- Occurs in the nucleus - A single copy of 1 specific gene in DNA is made (mRNA)
stages of transcriptional factors (using oestrogen or Oe)
- Oe diffuses through phospholipid bilayer -oe binds to receptor of transcription factor -changes shape of DNA binding site on TF -TF enters nucleus -transcription factor binds to promoter & stimulates transcription of gene
Oestrogen can cause breast cancer in women after menopausal stage. How does this happen?
- Oestrogen is goes thru CSM by passive diffusion - Molecule can activate an activator TF for the transcription of proto-oncogenes - Normal situations = should be transcribed in controlled conditions (and in relation to oestrogen) = if there is a higher conc of oestrogen than there should be (so in women after menopause) = more transcription of proto-oncogenes when there shouldn't be = cell division occurs when there shouldn't be (gene is considered as oncogene) = cancer - Despite tumour suppressor genes being activated, the oncogenes can still unbalance the cell cycle
consensus sequence in prokaryotes
-35 region, -10 region
transcriptional control
1. most important level of control. 2. enhancers and promoters = sequences on DNA that are involved. 3. transcription factors and activators = proteins which regulate these sites
What 4 parts make up the initiation complex?
1. ribosome 2. mRNA 3. initiation tRNA (binds to start codon) 4. initiation factors
Nucleotide insertion & deletion?
Add in an extra base pair or deletion of a base pair. It alters all the amino acids after that spot b/c it changed the reading frame.
What happens in elongation of translation?
-amino acids added to c-terminus end of polypeptide -ribosomes move along mRNA from 5' to 3' -polypeptide chain grows
the role of increased oestrogen concentrations in the development of tumours or some breast cancers
-can stimulate certain breast cells to divide - more division = higher chance of mutations -if cells become cancerous - oe would further enhance rapid replication -research suggest oe can introduce mutation directly ->. breast cell
tRNA molecules are NOT identical
-each carries a specific amino acid on one end -each has an anticodon on the other end, complementary and antiparallel to a specific codon; the anticodon base-pairs with a complementary codon on mRNA
stages of siRNA
-enzyme cuts double stranded RNA ->. siRNA -in cytoplasm - double stranded siRNA unwinds -one of single strands degraded, one selected -selected binds to enzyme then both bind to target mRNA -protein associated w/ siRNA cut mRNA ->. fragments
epigenetics on development of cancer
-increased methylation of tumour suppressor genes ->. turn off genes - cell able to divide uncontrollably and form tumour
translation initiation
-mRNA binds to small subunit along with an initiator tRNA, a tRNA with methionine, that recognizes the AUG start codon -large ribosomal subunit binds to complete the complex -initiator tRNA is at the P site of the ribosome
Increased DNA methylation
-methyl group attached to DNA at CpG ->. DNA histone complex = tightly packed - TF can't access gene therefore gene = inactive
ways to regulate mRNA translation
-microRNAs can inhibit translation -Repressor proteins can block translation directly -GTP cap on 5′ end of mRNA is usually modified—if cap is unmodified mRNA is not translated
What happens in the elongation phase of transcription?
-nucleotides are added to DNA's 3' end - 2 phosphates are removed from a free nucleotide
polypeptides
-polymers of amino acids -covalently linked by peptide bonds -polypeptides range in length from a few AAs to more than a thousand monomers
What happens in termination of translation?
-process ends when stop codon is read - release factors release components
stages of miRNA
-processed ->. double stranded DNA, then 2 single strands (one degraded) -one strand associates w/ protein then binds to target mRNA (blocks translation) -mRNA moved to processing body where its stored or degraded
function of the modifications
-protect mRNA from degradation -translation -export to cytoplasm
all three stages of translation require
-protein factors that aid in the translation process -energy in the form of GTP hydrolysis at several steps -basic mechanism of translation is the same in eukaryotes and prokaryotes although a few details are different
What happens in initiation of translation?
-translation starts -intiation complex formed
Causes of mutations?
1) Spontaneous mutations 2) Radiation induced mutations 3) Chemical induced mutations.
Repressor specific transcription factors (STF) work in two ways:
1. turning off transcription even when activators are bound, by binding between the general transcription factors (GTF's) and the enhancer. 2. Not allowing binding of activators, by blocking that site.
Genome sequencing has revealed that protein-coding (exons) DNA accounts for ______% of the human genome. It was originally thought that the remaining DNA was ________
1.5, untranscribed.
Summarize the sequences of events that occur during DNA replication.
1) The sequence of DNA replications are the enzyme DNA helicase unwinds and unzips the double stranded DNA by breaking the weak hydrogen bonds between the paired bases. 2) New complementary DNA nucleotides, always present in the nucleus, fit into place by the process of complementary base pairing. These are positions and joined by the enzyme DNA polymerase. 3) Because the strands of DNA are oriented in an antiparallel configuration, DNA polymerase may add new nucleotides only to one end of the chain, DNA synthesis occurs in opposite directions. The leading strand follows the helicase enzyme while synthesis on the lagging strand results in the formation of short segments of DNA called okazaki fragments. 4) To complete replication, the enzyme DNA ligase connects the okazaki fragments and seals any breaks in the sugar phosphate backbone. 5) The two double helix molecules are identical to each other and to the original DNA molecule.
two basic definitions of a gene
1) a unit of heredity 2) a DNA segment that can be transcribed and encodes a protein or a non-coding RNA molecule
stages of transcription
1) initiation 2) elongation 3) termination
2 broad classes of RNA's in cells
1) messenger RNA's: encode proteins 2) non-coding RNA's: do NOT encode proteins
3 kinds of point mutations?
1) nucleotide substitution 2) nucleotide insertion 3) Nucleotide deletion
Properties of a ribozyme
1)Contains one strandt but is completely formsing a 3D shape 2)Bases contain functional groups=interact 3)Hydrogen bond with DNA or RNA
SRP steps
1)synthesis begins in cytoplasm 2)SRP binds and stops synthesis 3)SRP binds to ER pore 4)SRP leaves and synthesis resumes 5)Signal cleaving enzyme cuts off signal peptide 6)Peptide is in ER and forms shape as ribosome leaves
What are the stop codons?
1. UAA 2. UGA 3. UAG
What do release factors do?
1. break apart large & small ribosomal subunits 2. free mRNA and polypeptides
chromatin structure-- pretranscriptional control
1. chromatin packing is used to keep genes turned off. 2. hereochromatin: inactive genes located within darkly staining portions of chromatin. 3. euchromatin: loosely packed areas of active genes
Steps of the cell stimulating pathway:
1. growth factor binds to receptor in plasma membrane. 2. Signal is related to a G protein called Ras that needs GTP bound to it to relay signal. Hyperactive Ras protein (product of oncogene) issues signals on its own. 3. The last kinase that the signal is relayed to activates a transcription activator that turns on one or more genes for proteins that stimulate the cell cycle.
control of gene expression
1. if all somatic cells have all the genes (full set of dna) of an organism, how do cells differ? 2. Gene expression = genes can be turned on or off according to what the cells needs are 3. gene expression occurs in many steps
Before replication begins
2 strands of the parent molecule are hydrogen-bonded together
With humans only _______ of DNA is coding for proteins?
2%
histome tails
20 amino acids in length, highly charged (lycine residues, highly positive charged) DNA is negatively charged interaction between tails and DNA- keep it wound around the histomes
What percentage of the genes of a typical human cell are expressed at any give time?
20%
Upstream
3'-5' on mRNA strand
mutagen
5 bromouracil is a ____________ since it can cause an induced mutation
When we read DNA, we read it in the direction of what?
5 prime to 3 prime. Starts on the right side goes down and then goes up from the bottom on the left side.
RNA polymerase adds RNA nucleotides in
5' --> 3' direction
triple-H bond with guanine (this is rare)
5-bromouracil is only dangerous to our cells when it forms a:
It is believed that ____% of all human genes are regulated by miRNas
50
poly-A tail
50-250 adenine nucleotides added to the 3' end that protects mRNA from RNA-digesting enzymes
Codons that code for amino acids
61
There are 64 total codons, but only _____ code for amino acids.
61
sense codons
61 codons that specify for amino acids
Fidelity?
Adherence to fact or detail (accuracy; exactness) (DNA has a high fidelity)
Pattern formation
After cells have differentiated, the cells arrange themselves into organs and tissues in their characteristic places creating a multicellular organism
DNA polymerase
After the DNA has been unzipped, this enzyme creates more complimentary nucleotides on each half, which in turn makes one DNA strand into two full DNA strands.
missense mutation
A base-pair substitution that results in a codon that codes for a different amino acid.
Which of the following processes occurs in eukaryotic gene expression?
A cap is added to the 5 end of the mRNA.
Transcription factors
A collection of proteins mediate the binding of RNA polymerase and the initiation of transcription, these will bind to the promoter before RNA polymerase
Which of these is currently considered the best definition of a gene?
A gene codes for either a polypeptide or an RNA molecule.
gene of interest
A gene for a desired trait; the one being added to a plasmid.
What is a Gene and explain what a Genetic Code is?
A gene is the basic physical and functional unit of heredity. Genes, which are made up of DNA, act as instructions to make molecules called proteins. The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells.
Homeotic genes
A group of regulatory genes that control the placement and organization of body parts in the late embryo to adult stage of development
Sliceosome
A large complex made of proteins and small RNAs that removes introns and connects remaining exons
Spliceosome
A large complex made up of proteins and RNA molecules that splices RNA
spliceosome
A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.
5' cap
A modified from the guanine nucleotide (GTP) added to 5' end, added after first 20-40 nucleotides of pre-mRNA transcribed
Describe the potential effects of a mutation in a tumor suppressor gene versus an oncogene.
A mutation in a tumor suppressor gene means that its function as a break to cell division will be altered. A mutation in a proto oncogene that results in an active oncogene results in constantly stimulated cell division.
Translocation
A mutation in which a group of bases become separated from the DNA sequence on one chromosome and become inserted into the DNA sequence on a different chromosome
Inversion
A mutation in which a group of nucleotide bases become separated from the DNA sequence and rejoin at the same position but in the inverse order
Deletion
A mutation in which a nucleotide base from DNA sequence is lost
Substitution
A mutation in which a nucleotide in a section of DNA is replaced by another nucleotide that has a different base
Addition
A mutation in which an extra nucleotide base is inserted in the DNA sequence
Duplication
A mutation in which one or more nucleotide bases are repeated
Silent mutation
A mutation that changes a single nucleotide, but does not change the amino acid created.
silent mutation
A mutation that changes a single nucleotide, but does not change the amino acid created.
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting early termination of protein synthesis, which then leads to a shorter and usually nonfunctional protein.
Explain why DNA replication is said to be semiconservative.
A new double strand of DNA is composed of one old strands and one newly synthesized strand.
signal recognition particle (SRP)
A protein-RNA complex that recognizes a signal peptide as it emerges from a ribosome and helps direct the ribosome to the endoplasmic reticulum (ER) by binding to a receptor protein on the ER
Signal-recognition particle
A protein-RNA complex that recognizes a signal peptide as it emerges from the ribosome.
Gene
A region of DNA that can be expressed to process a final fictional product that is wither a polypeptide or RNA molecule
stress response element (SRE)
A regulatory sequence in plant genes encodes for proteins needed to cope with drought Turns on regulator protein, which binds to stress response element that's in front of many different promoters -even though the promoters may be VERY far apart from each other
start codon
AUG (codes for methionine) starts off translation complementary anticodon UAC is AUG's personal shuttle when AUG is read on the mRNA, it is delivered to the ribosome
What is the start codon for translation?
AUG (methionine)
Which one of the following structures, if missing, would usually prevent translation from starting?
AUG codon
Messanger RNA (mRNA)
A single strand of RNA that carries instructions from a gene to make a protein
Codon
A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid
Step 3 Terminate
A stop codon (3 different types) used to initiate release factor, so polypeptide comes loose & ribosome disassembles from the mRNA.
Signal peptide
A stretch of amino acids on a polypeptide that targets the protein to a specific destination in a eukaryotic cell.
Tumour
A swelling in an organism that is made up of cells that continue to divide in an abnormal way
polymerase chain reaction (PCR)
A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides.
Conjugation
A temporary union of two organisms (such as bacteria) for the purpose of DNA transfer.
Virus
A tiny, NONLIVING particle that invades and then reproduces inside a living cell. Consists of two main components: a protein capsid and genetic material made of DNA or RNA, depending on the virus
What occurs in histone acetylation? How does it affect gene expression?
Acetylation of histone tails promotes loose chromatin structure (beads on a string), permitting transcription. Acetyl groups are attached to lysines in histone tails, so their positive charges are neutralized and histone tails no longer bind to neighboring molecules.
Fill in the blank," According to Chargaff's rules in any DNA the amount of ____________," using the given terms: A=T and G=C, A=G and T=C, A=C and T=G, or A=T=C=G
A=T and G=C
Which of the following is (are) primary characteristics of cancer cells?, using the given terms: Cancer cells are genetically unstable, Cancer cells do not correctly regulate the cell cycle, Cancer cells escape the signals for cell death, or All of these are primary characteristics of cancer cells.
All of these, Cancer cells are genetically unstable, Cancer cells do not correctly regulate the cell cycle, or Cancer cells escape the signals for cell death, are primary characteristics of cancer cells.
two ways metabolic pathways can be regulated
Allosteric regulation of enzyme-catalyzed reactions Regulation of protein synthesis
Translation bound vs free
Always starts in cytoplasm
Elongation in Translation
Amino acids are added one by one to the previous amino acid at the C-terminus of the chain moving with the mRNA 5' to 3'
What are the 3 ingredients needed for translation?
Amino acids: building blocks of proteins Ribosomes: protein-production factories Transfer RNA (tRNA): Read & translate mRNA code into protein
Which of the following molecules is/are produced by translation? Include molecules that are subject to further modification after initial synthesis.
Aminoacyl-tRNA synthetase RNA polymerase
What determines which base is to be added to an RNA strand during transcription?
Base pairing between the DNA template strand and the RNA nucleotides
Retrovirus
An RNA virus that uses an enzyme called reverse transcriptase to convert their RNA genomes into DNA so that they can be inserted into a host genome
poly-A tail
An enzyme adds 50-250 adines on to 3' end after the polyadenylation signal
reverse transcriptase
An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.
RNA primase
An enzyme that creates a short RNA primer for initiation of DNA replication.
aminoacyl-tRNA Synthetases
An enzyme that joins each amino acid to the appropriate tRNA... catalyzes aminoacylation
RNA polymerase
An enzyme that separates the two strands of DNA and points together RNA nucleotide complementary to the DNA template strand elongates the RNA polynucleotide
Mutations
Changes in one or a few nucleotides that affects protein structure and function, responsible for diversity and exposing new genes
Gene mutation
Any change to one or more nucleotide bases, or any rearrangement of the bases, in DNA
proteins involved in the uptake and metabolism of lactose
B-galactoside permease B-galactosidase B-galactoside transacetylase
The basic genetic code ("letters") is the ________ for all organisms. Order of the code ("words") will what?
Basic genetic code is the same. Order of code will differ from species to species.
How is transcription directly controlled in eukaryotic cells?
By using transcription factors and activators
Cytosine & Thymine are ____________, while Guanine & adenine are ________?
C & T are pyrimidines and G & C are purines.
example of miRNAs
C. elegans, the lin-4 RNA is involved in negative regulation of development; it encodes not for a protein but for an miRNA The miRNA inhibits lin-14 translation by binding to its mRNA. The Lin-14 protein regulates one of the early development stages in C. elegans
The tRNA anticodon, GAC, is complementary to the mRNA codon with the sequence _____.
CUG
___________________ results from other embryonic cells in the vicinity, which causes cells to differentiate.
Cell-cell signaling
Expressed genes undergo the __________________ _______________.
Central Dogma
How can functionally related genes with different promoters and at different places in the chromosome be affected all at the same time?
Change in chromatin structure to make a whole group available or unavailable
Point mutations
Changes In a single nucleotide pair of a gene
epigenetic changes
Changes are sometimes heritable and stable, but are reversible 1) DNA methylation 2) chromosomal protein alterations
After they are looped and coiled again. It leads to what?
Chromosomes which can be seen in the nucleus of dividing cells.
Chromosome structure in pro and euk?
Circular in prokaryotes & linear in eukaryotes
transcription factors
Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.
How do you regulate protein expression?
Control mechanisms include: -processing of pre-mRNA -use of microRNAs -use of translation repressors -regulation of protein breakdown
How slicesome works
Cuts up introns and at each end, introns are released and degraded, RNAs in spliceosome catalyzes process of joining exons together
(C)
Cytosine -- a pyrimidine single ring
helix-turn-helix motif
DNA binding helix, turn, Dimer binding helix these proteins regulate genes involved in development
Elongation or extention?
DNA polymerase is going to move along & incorporate the complimentary nucleotide to the template strand. The template strand has all the different templates and things
template strand
DNA strand to which new nucleotides form hydrogen bonds during transcriptions from
Increased methylation
DNA-histone complex more condensed, transcription factors cannot bind, heterochromatin, gene is inactive
Comparison of DNA and RNA
DNA: double stranded, more stable, deoxyribose, has thymine, cannot functions as enzyme, helix. RNA: single stranded, unstable, Ribose, uracil, can function as enzyme, not a helix
Restriction Fragment Length Polymorphisms (RFLPs)
Differences in DNA sequence on homologous chromosomes that can result in different patterns of restriction fragment lengths (DNA segments resulting from treatment with restriction enzymes).
downstream
Direction of transcription
Downstream
Direction of transcription; 5'- 3' on mRNA strand
Chromosomal aberrations?
Either sections or an entire chromosome is missing or added.
Fill in the blank,"Active genes in eukaryotic cells are associated with more loosely packed chromatin, called____________," using the given terms: transcription activators, chromosomes, chromatid, or euchromatin.
Euchromatin
kinds of chromatin visible during interphase
Euchromatin Heterochromatin
Transcription
Formation of mRNA molecules from DNA that makes a particular gene
cell methylation at 3 years (twins)
Found they were very similar- inherited same epigenetic footprint from parents
Genome?
Full set of DNA present in an individual organisms (3 billion base pairs)
Fill in the blank," During transcription, a segment of the DNA called a _________ serves as template for the production of a RNA molecule.," using the given terms: codon, anticodon, promoter, or gene.
Gene
What are regulatory genes?
Genes that code for repressors or inducers for the operon that they control. Expressed continuously but at fluxuating levels
4
Genetic code: One nucleotide- only _ combinations
64
Genetic code: Three nucleotides- _ combinations
16
Genetic code: Two nucleotides- only _ combinations
How can proteins be activated and example:
Global control (of translation of all mRNAs) involves activation or inactivation of Transcription initiation factors. After fertilization, transcription of mRNA in eggs is triggered by activation of transcription initiation factors.
histones and cancers
In some cancers, genes that inhibit cell division are associated with histones which are excessively deacetylated
Describe how the LAC operon represents an on/off switch for gene expression.
In the absence of lactose a repressor is bound to the promoter/operator complex and no lactase is produced. Lactose will bind to the repressor and prevent it from binding to the operator. The gene for lactase can then be expressed.
Exit tunnel
In ribosome's large subunit, allows polypeptide to extend as it increases is then released though here
____________ use the product of a biosynthetic pathway to regulate gene expression
Inducible operons (biosynthetic= making something)
Explain epigenetic inheritance and give an example:
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence. (modifications to chromatin that can be reversed.) ex: one identical twin getting schizophrenia, a genetically based disease, while the other twin is fine.
3 stages of transcription and translation
Initiation, elongation and termination
Fill in the blank,"What are the three steps required in translation?," using the given sequences: Initiation--Elongation--Termination, Initiation--Replication--Termination, Initiation--Synthesis--Termination, or Initiation--Synthesis--Elongation.
Initiation--Elongation--Termination
Transfection
Insertion of recombinant DNA (plasmid) into a eukaryotic cell
What does the helicase molecule do in replication
It acts as a wedge to separate the 2 strands of DNA. At the start site helicase will come and pry it open so the machinery can come in & replicate DNA.
After the Helicase molecule does that, a primace molecule does what?
It lays down a little RNA primer. This happens because DNA polymerase cant bind single stranded DNA. The green primer helps the yellow polymerase bind.
Where does RNA polymerase begin transcribing a gene into mRNA?
It starts after a certain nucleotide sequence called a promoter.
Deletion
Loss of nucleotide pairs in a gene
The genetic code is redundant. What is meant by this statement?
More than one codon can specify the addition of the same amino acid.
Missense mutations
Most common type of mutation, a base pair mutation in which the new codon makes sense in that it still codes for an amino acid.
Eukaryotic gene expression
Must be regulated to ensure proper timing and location of protein production Regulation can occur at multiple points during transcription and translation
Alternative RNA splicing
One gene can produce different types of proteins based on what is treated as an exon, there are more types of proteins and different genes
The initiator tRNA attaches at the ribosome's _____ site.
P
gene mutations
Permanent change in the sequence of bases in genes. can lead to malfunctioning proteins in cells
Ubiquitin-mediated degradation of proteins through the proteasome
Posttranslational regulation: protein degradation 1. protein is targeted for breakdown 2. enzyme attaches ubiquidin to the protein 3. target protein is recognized by a proteasome 4. ubiquitin is released and recycled 5. proteasome hydrolyzes the target protein (breaks down)
Elongation Transcription
RNA polymerase moves along untwisting double helix and exposing 10 to 20 DNA to be paired with RNA nucleotides, added to 3' end, mRNA peels away and DNA reforms(can have multiple RNA polymerases transcribing mRNA)
transcription factors
RNA polymerase requires ______________ ____________ in order to bind to the DNA indirectly; these are small proteins that bind to genes to show the RNA polymerase where the gene is
During Elongation?
RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5' to 3' direction, & unwinds then rewinds the DNA as it is read.
cancers and methylation
Show too much/too little methylation Demethylate oncogenes that you don't want to express
Rate of replication in prokaryotes & eukaryotes?
Rate is much slower in eukaryotes b/c it has all those repair mechanisms, so its going slower to avoid having a lot of mistakes. Prokaryotes make more mistakes.
Reading frame
Reading mRNA nucleotides in the correct groupings.
Nucleotide excision?
Repairs thymine dimers. When exposed to UV, instead of the t's bonding with the A's, the t's bond to each other creating a thymine diner (mutation). The nucleotide excision molecules that come in and cuts out that bond to prevent the thymine diner from forming.
telomeres
Repeated DNA sequences at the ends of eukaryotic chromosomes.
Nucleotide-pair substitution
Replacement of one nucleotide and its partner with another pair of nucleotides
Step 1 Recognize & initiate protein building
Ribosome assembles & there is a start codon.
E site (exit site)
Ribosome bind site where discharged tRNA leave the ribosome from here
P site (peptidyl-tRNA binding site)
Ribosome bind site where it holds tRNA carrying growing polypeptide chain
A site (aminoacyl-tRNA)
Ribosome bind site where it holds the tRNA carrying the next amino acid to be added to the chain
What excises (removes) the introns and ligates (glues together) the exons?
SNERPS small nuclear ribonucleoprotein complexes
DNA is what when it's replicating?
Semiconservative: gray indicates the original DNA strands, and blue indicates newly synthesized DNA. (identical sequence of nucleotide bases)
Gene?
Sequence of bases that contain instructions for making a specific protein; section of a chromosome. - 22,000 genes roughly in a person - 3,000 bases long for 1 gene
Explain the different inductive signals for how different sets of activators come to be present in two cells:
Signals to the embryonic cell from other embryonic cells in the vicinity. ex: binding of growth factors secreted by neighbouring cells. These signals cause changes in the target cell (induction) and send the cell down a noticeably differentiated path.
SNPs
Single-base variations in the genome that are associated with disease and other disorders
origins of replication
Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.
Tumour suppressor genes
Slow down cell division, repair mistakes in DNA and tell cells when to die
Okazaki fragments
Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.
Domains
Structural and functional regions
Mutations typically change the _________ & ________ of the proteins produced b/c why?
Structure & function because it changes the amino acid that is incorporated.
Silent mutation
Subsitors with noabersble effect on the phenotype(can occur outside of genes too), codes for same amino acid= resuncey in codons
Missense munitions
Substitution that change one amino acid for another, little effect of most proteins but does cause sickle cell disease
DNA vs RNA
Sugar (deoxyribose, ribose), double vs single strand, bases (AT(U), GC)
Termination Transcription (Bacteria)
Terminator sequence in DNA which is a RNA sequence, mRNA detaches and is ready for translation
Codon recognition
The anticodon of tRNA and company codon of mRNA bind in A site, uses GTP, there are other tRNAs around but only the right one can bind
Fill in the blank," Because of Human Genome Project we now know______________________________," using the given sequences: The sequence of the base pairs of our DNA, The sequence of all genes along the human chromosomes, All of the above are correct, Only A and C are correct.
The sequence of the base pairs of our DNA
(bacteria)terminator
The sequence that signals the end of transcription
Wobble
The Third nucleotide in a codon of an mRNA is more relaxed when pairing with a anticodon of tRNA(because 45 tRNAs but 61 codons)
Phenotype
The characteristics of an organism, often visible, resulting from both its genotype and the effects of the environment
monocistronic
The coding pattern of eukaryotes in which one mRNA molecule codes for only one protein.
Genome
The complete map of all the genetic material in an organism
How is translation initiated?
The small ribosomal subunit binds to the mRNA. The tRNA bearing methionine binds to the start codon. The large ribosomal subunit binds to the small one. The start codon signals the start of translation.
Which of the following steps occurs last in the initiation phase of translation?
The large ribosomal subunit joins the complex.
Bioinformatics
The science of collecting and analysing complex biological data, such as genetic codes, it uses computers and algorithms to read, store, organise, analyse and interpret biological data
Gene expression
The process by which DNA directs the synthesis of proteins or, in some cases, just RNAs.
Determination
The progressive restriction of development potential in which the possible fate of each cell becomes more limited as an embryo develops.
What is meant by translocation?
The ribosome slides one codon down the mRNA.
x-inactivation
The second X chromosome in females in females condenses; occurs by chance/random
Template strand
The stand of DNA that is used to make mRNA (one gene be on one strand and another on the opposite side)
lagging strand
The strand in replication that is copied 3' to 5' as Okazaki fragments and then joined up.
Things to do: - If hypermethylation occurs in a promoter region of a tumour suppressor gene, what would happen? - How does oestrogen cause uncontrolled cell division? (KINDA DONE WITH MENOPAUSAL F.C) - look at page 258 summary Q5) How does histone deacetylase have an impact on histones, what happens to the DNA + gene expression? - finish describing and explaining about proto... and tumour suppressor genes + relation to higher oestrogen levels in breasts of menopausal women -'Predict what the effect of decreased & increased acetylation will have on tumour suppressor genes + protooncogenes' - What is cancer? (look in notepad 9/2/21) - relationship between protooncogenes + ts genes with in relation to cell division and uncontrolled cellgrowth (2 pages after 2/3/21) - potential use of human cells table on page 243
Things to do: - If hypermethylation occurs in a promoter region of a tumour suppressor gene, what would happen? - How does oestrogen cause uncontrolled cell division? - look at page 258 summary Q5) How does histone deacetylase have an impact on histones, what happens to the DNA + gene expression? - finish describing and explaining about proto... and tumour suppressor genes + relation to higher oestrogen levels in breasts of menopausal women -'Predict what the effect of decreased & increased acetylation will have on tumour suppressor genes + protooncogenes' - What is cancer? (look in notepad 9/2/21) -siRNA look in notepad (near 2/3/21) - relationship between protooncogenes + ts genes with in relation to cell division and uncontrolled cellgrowth (2 pages after 2/3/21) - potential use of human cells table on page 243
What are egg polarity genes?
This is a different name for maternal effect genes, since they also set up the axes of an embryo.
Transcription initiation complex
Transcription factors and RNA polymerase ii bound to the promoter (protein protein interactions), once in place transcription can start
Match the function with the type of RNA out of the following Messenger RNA (mRNA), ribosomal RNA (rRNA), or transfer RNA (tRNA): Carries amino acids to ribosomes
Transfer RNA(tRNA)
Transfer RNA(tRNA)
Transfers amino acids form the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome, translates a specific mRNA codon into a giving amino acid, one side holds amino acid and the other a anticodon, 1 strand of RNA, has 3D shape, transcribed by DNA, reusable
Fill in the blank,"The process of converting information contained in the nucleotide sequence of RNA in to a sequence of amino acids is called ________," using the given terms: Transcription, Translocation, Translation, or Replication.
Translation
Stem cells
Undifferentiated dividing cells
Fill in the blank," The nitrogen base________ occurs in RNA in place of thymine.", using the given terms: adenine, guanine, cytosine, or uracil.
Uracil
How to read a codon chart?
Use your codon (ex CGU) and see what amino acid it coordinates with
The function of tRNA during protein synthesis is to _____. () a. deliver amino acids to their proper site during protein synthesis b. guide ribosome subunits out of the nucleus through nuclear pores c. attach mRNA to the small subunit of the ribosome d. process mRNA e. transcribe mRNA
a
The genetic code is just about universally used by living things, suggesting that all living things are related. A) True B) False
a
The newly formed mRNA molecule, called the primary mRNA transcript, is modified before it leaves the eukaryotic nucleus. A) True B) False
a
The site where RNA polymerase attaches to the DNA molecule to start the formation of RNA is called a(n) A) promoter. B) exon. C) intron. D) GC hairpin.
a
The structures called snRNPs are _____. () a. part of a spliceosome b. involved in the removal of exons from DNA c. a type of specialized carbohydrate d. a critical component of the initiation complex e. All of the listed responses are correct.
a
The three bases on the tRNA molecule that are complementary to the triplet of mRNA are referred to as a _____ A) anticodon B) codon C) exon D) intron
a
Open Hint for Question 11 in a new window Bacteria can transcribe and translate human genes to produce functional human proteins because _____. () a.the genetic code is nearly universal b.bacterial ribosomes and eukaryotic ribosomes are identical c.eukaryotes do not really need a nucleus d.RNA has catalytic properties e. bacterial and eukaryotic RNA polymerases are identical
a
Question 23 23 Open Hint for Question 23 in a new window Which of the following statements correctly describes mRNA processing? () a. Introns are cut out of the primary transcript, and the resulting exons are spliced together. b. Exons are cut out of the primary transcript, and the introns are spliced together. c. Introns are cut out of the primary transcript and spliced together at the end of the transcript. d. Exons are cut out of the primary transcript and transported to the endoplasmic reticulum. e. Introns are cut out of the primary transcript and transported to the ribosomes.
a
Ribosomes are composed of two subunits that combine when translation begins. A) True B) False
a
Several ribosomes are often attached to and translating the same mRNA. A) True B) False
a
The TATA box in eukaryotes is a A) core promoter. B) - 35 sequence. C) - 10 sequence. D) 5' cap.
a
The thyroid gland and pituitary gland process the same primary mRNA transcript differently and therefore produce related but different hormones. A) True B) False
a
Which of the following is a post-translational modification of a polypeptide? () a. cleavage of a polypeptide into two or more chains b. removal of introns and splicing of exons c. formation of a polysome that allows simultaneous formation of many polypeptides from one mRNA transcript d. The growing polypeptide signals the ribosome to attach to the ER. e. complementary base pairing of mRNA and tRNA in the ribosome
a
the ____ facilitates the transport of the mRNA out of the nucleus and inhibits the degradation of mRNA by hydrolytic enzymes. A) poly-A tail B) promoter C) modified guanine nucleotide cap D) terminator
a
lagging strand
a discontinuously synthesized DNA strand that elongates by means of Okazaki fragments , each synthesized in a 5' to 3' direction away from the replication fork it can build only until it hits a previously built stretch once the helix unwinds a bit more, it can build another Okazaki fragment, and so on
operator
a region that controls whether transcription will occur this is where the repressor binds
negative regulation
a repressor protein prevents transcription
Regulatory Genes
a segment of DNA before the operon that produces a regressor protein (or RNA) that can bind to the operator site and turn the operon on or off
poly(A) tail
a sequence of 50-250 adenine nucleotides added onto the 3' end of a pre-mRNA molecule
what is the operator?
a sequence of DNA that controls access of RNA pol to a cluster of functionally related genes. Positioned within promoter or between promoter & genes
codon
a specific sequence of three adjacent bases on a strand of mRNA each one corresponds to a particular amino acid
messenger RNA (mRNA)
a temporary RNA version of a DNA recipe that gets sent to the ribosome
missense mutations
a type of base substitution mutation that causes the original codon to be altered and produce a different amino acid
nonsense mutations
a type of base substitution mutation that causes the original codon to become a stop codon, which results in early termination of protein synthesis
silent mutations
a type of base substitution mutation that happens when a codon that codes for the same amino acid is created and therefore does not change the corresponding protein sequence
translocations
a type of gene rearrangement mutation that occurs when two different chromosomes (or a single chromosome in two different places) break and rejoin in a way that causes the DNA sequence or gene to be lost, repeated, or interrupted
insertions
a type of gene rearrangement mutation that results in the addition of as little as a single base or much larger sequences of DNA results in a frameshift of the sequence
when attached to mRNA
after being exported to the cytoplasm, when do a large and small subunit join to form a functional ribosome?
when can RNA polymerase II bind to the promoter
after general transcription factors have assembled on the chromosome: TFIID binds to TATA box; then other factors bind to form an initiation complex
Where can you find the start codon?
after the leader sequence
double helix reforms
after transcription of a new RNA molecule, what happens to the DNA?
Allosteric regulation of enzyme-catalyzed reactions
allows rapid fine tuning enzymes are tuned on/produced, product is made, once you get enough of product, proteins turned off by allosteric mechanism end product comes back, in high enough concentrations it binds to one of enzymes, turns enzyme off/other's and stop functioning, too
the genetic code is redundant
almost all amino acids are encoded by more than one codon
how do you get genetic diversity of proteins?
alternative splicing Can make different (mature) mRNA from the same transcript (pre RNA)- from alternative splicing
diversity
alternative splicing and exon shuffling creates _____________ in a species which is good for evolution
exons
amino acid coding sequences in pre-mRNA; joined together sequentially in final mRNA
Polypeptides are assembled from _____.
amino acids
translation elongation
amino acids are added one by one to the C-terminus of the preceding amino acid each amino acid is added to the growing polypeptide in three steps: 1) codon recognition by new amino-acyl tRNA at A site 2) peptide bond formation (peptidyl tRNA at A site) 3) translocation along mRNA AND peptidyl tRNA shifted to P site
in between
amino acids are added to growing polypeptide ______ ____________ the subunits
DNA fingerprinting
analysis of sections of DNA that have little or no known function, but vary widely from one individual to another, in order to identify individuals
three structural genes for lactose transport and cleavage
are adjacent on the chromosome, share a promoter, and are transcribed together
rRNAs
are rRNAs or proteins primarily responsible for both the structure and function of the ribosome?
where can gene expression be controlled?
at three levels: transcription, translation, or post-translation (protein activation)
What is the common control point of gene expression for all organisms?
at transcription: regulation at this stage is often in response to signals coming from outside the cell (ex:hormones). For this reason, gene expression is often equated with transcription.
A base-pair substitution mutation in a germ cell line is likely to have no effect on phenotype if the substitution _____. () a. forms a new stop codon b. occurs in an intron c. changes a stop codon to a codon specifying an amino acid d. changes the structure of an enzyme e. prevents the initiation of transcription of the DNA sequence that codes for ATP synthase
b
A point mutation in which a single base pair is inserted or deleted from DNA is called a(n) _____. () a. nonsense mutation b. frame-shift mutation c. inversion mutation d. translocation mutation e. missense mutation
b
Both exons and introns are present in the mature mRNA transcript. A) True B) False
b
During _____ amino acids are added one at a time to the growing polypeptide. A) chain initiation B) chain elongation C) chain termination
b
Generally speaking, how many genetic codes are there? () a.20 b.one c.four d. one for each organism e.three
b
Only one copy of mRNA is made at any time. A) True B) False
b
Proteins and _____ make up the ribosomes where polypeptides are synthesized. A) mRNA B) rRNA C) tRNA
b
RNA is confined to the nucleus. A) True B) False
b
Segments of DNA which are expressed are called _____. A) introns B) exons
b
The P site of a ribosome does which of the following? () a. It holds the tRNA that is carrying the next amino acid to be added to the growing polypeptide chain. b. It holds the tRNA carrying the growing polypeptide chain. c. It helps "unzip" DNA during transcription. d. It catalyzes the addition of amino acids to the tRNAs. e. It recognizes the promoter during transcription initiation.
b
The bases of RNA are the same as those of DNA with the exception that RNA contains A) cysteine instead of cytosine. B) uracil instead of thymine. C) cytosine instead of guanine. D) uracil instead of adenine.
b
The initiator tRNA binds to the _____ of the ribosome. A) A site B) P site
b
The order of amino acids in a polypeptide is specified by _____. A) a random set of nucleotides B) an exact sequence of DNA nucleotides C) DNA polymerase D) RNA polymerase
b
What is the proper order of the following events in the expression of a eukaryotic gene? () 1. translation 2. RNA processing 3. transcription 4. modification of protein a. 1, 2, 3, 4 b. 3, 2, 1, 4 c. 4, 2, 3, 1 d. 2, 3, 4, 1 e. 1, 2, 4, 3
b
What mRNA codon would be made from the DNA triplet CGT? () a.ATU b.GCA c.TCU d.CTA e.UCG
b
When mRNA leaves the cell's nucleus, it next becomes associated with A) proteins. B) a ribosome. C) tRNA. D) RNA polymerase.
b
Which of the following statements is correct about prokaryotic gene expression? A) Prokaryotic mRNAs must have introns spliced out. B) Prokaryotic mRNAs are often translated before transcription is complete. C) Prokaryotic mRNAs contain the transcript of only one gene. D) All of these statements are correct.
b
Which of the following types of mutation is least likely to affect the function of the protein corresponding to the gene in which the mutation occurs? () a. addition of single bases b. base-pair substitution c. transposition d. deletion of single bases e.nonsense mutation
b
what regulates whether transcription occurs?
binding to enhancer and promoter regions
binding site for the operator in the lac operon
binds to the DNA
Inducer (Inducible operon)
binds to the active repressor protein and thus inactivates it
How can both repressible and inducible operons be negative regulators?
both need inducer/repressor proteins to bind to the regulatory protein in order to function.
During translation in a eukaryotic cell _____. () a. ribosomes move into the nucleus b. tRNA carries amino acid molecules to the nucleus, where they are added to a growing polypeptide chain c. polypeptides are synthesized at ribosomes, according to instructions carried by mRNA d. mRNA is synthesized by the bonding of free nucleotides to the bases on the template strand of DNA e. ribosomes move out of the nucleus
c
During translation in a eukaryotic cell _____. () a. ribosomes move into the nucleus b. tRNA carries amino acid molecules to the nucleus, where they are added to a growing polypeptide chain c. polypeptides are synthesized at ribosomes, according to instructions carried by mRNA d. mRNA is synthesized by the bonding of free nucleotides to the bases on the template strand of DNA e. ribosomes move out of the nucleus
c
Genetic information of eukaryotic cells is transferred from the nucleus to the cytoplasm in the form of _____. () a. proteins b. lipids c.RNA d.carbohydrates e.DNA
c
If an mRNA codon reads UAC, its complementary anticodon will be A) TUC. B) ATG. C) AUG. D) CAG.
c
If the template strand of DNA has the following sequence of nucleotides: AAGCGT, the sequence of nucleotides in the mRNA will be _____. A) TTCGCA B) TTCGCU C) UUCGCA D) UUCGCU
c
In order for a gene to be transcribed, RNA polymerase must have access to the DNA helix and be able to bind to the genes A) activator B) regulator C) promoter D) operator E) repressor
c
Which of the following are not matched correctly? A) exon splicing-occurs in nucleus B) post-translational modifications-phosphorylation C) snRNA-splice out exons from transcript D) activated enhancers-trigger transcription E) all are matched correctly
c
Describe the relationship between the glucose supply, cAMP, and CAP.
cAMP accumulates when glucose is scarce. When cAMP binds to CAP, CAP becomes active and binds to an upstream area of the lac promoter. This increases the affinity of RNA pol for the promoter. CAP facilitates RNA pol binding and increased rate of transcription. If glucose is in high concentration and cAMP is low, CAP detaches from the operon. Then RNA pol binds less efficiently and rate of transcription is decreased.
problems of epigenetics on treatment of cancer
can affect many cells - need to drugs as specific as possible
post-translational regulation
can also occur if a cell has already made a protein, but doesn't yet need to use it ex. enzymes aren't always needed, but when they are, they are needed immediately
relationship between genotype and phenotype in an individual
can be fairly simple or highly complex
Where can distal control elements be?
can be in an intron, can be grouped as enhancers or separate, and can be near or far from the promoter.
ehancer regions
can be thousands of base pairs away from promoter regions DNA can bend, protein can interact with transcription factors complex can be more stabilized and transcription can happen
inversions
can result when changes occur in the orientation of chromosomal regions
In response to chemical signals, prokaryotes can do what?
can turn off translation of their mRNA
What is tRNA's job?
carries amino acids that are added to the polypeptide chain
What is mRNA's job?
carries information (codons)to make proteins
What is CAP? how does CAP work?
catabolite activator protein is a regulatory protein that binds to DNA & stimulates transcription of a gene. Positive regulator.
morphogens stimulate _____ ______ and ______
cell differentiation, development
Translation occurs in the _____.
cytoplasm
A promoter defines ______. A) the start of a gene B) the direction of transcription C) the strand to be copied D) all of the above
d
In eukaryotic cells, a terminator in mRNA synthesis is _____. () a. an enzyme whose specific function is to stop synthesis b. a molecule of tRNA that recognizes a stop codon c. a specific nucleotide sequence in DNA that signals the RNA polymerase to stop d. a specific nucleotide sequence in mRNA that signals the RNA polymerase to stop and to release from the DNA e. None of the listed responses is correct.
d
In many cases, more than one codon codes for the same amino acid. Because of this, we say that the code is _____. () a.inaccurate b.incomplete c.not specific d.redundant e.tricky
d
Nuclei of eukaryotic cells contain spliceosomes that are made up of _____. () a. snRNA b. snRNA and tRNA c. snRNA and DNA d. snRNA and protein e. DNA and protein
d
Open Hint for Question 19 in a new window In transcription, _____. () a.the promoter region acts as an initial binding site for RNA polymerase b. only one of the DNA strands is used as the template c. the RNA nucleotides used are produced by the cell d.All of the listed responses are correct. e.None of the listed responses is correct.
d
Open Hint for Question 7 in a new window The number of nucleotide bases "read" together on the mRNA to designate each amino acid is _____; this unit is called a(n) _____. () a.two ... dipeptide b.three ... triose c.two ... anticodon d.three ... codon e. one ... amino acid
d
The amino acid alanine would be carried by a tRNA with the anticodon _____. A) CGC B) CGU C) CGA D) all of the above
d
The correct amino acid is attached to the correct tRNA molecule by _____. A) RNA polymerase B) DNA ligase C) spliceosomes D) tRNA synthetases
d
The genetic code _____. A) is degenerate B) unambiguous C) has only one start signal D) all of the above
d
Translation repressor proteins may shut down translation of processed mRNA transcripts by A) binding with the poly-A tail B) resetting the reading frame C) reinserting introns into the transcript D) excising a short sequence of nucleotides
d
Which of the following takes place in the nucleus? A) replication B) transcription C) translation D) both A and B
d
five carbon sugar
deoxyribose
restriction fragment length polymorphisms (RFLPs)
differences in DNA sequence on homologous chromosomes that can result in different patterns of restriction fragment lengths (DNA segments resulting from treatment with restriction enzymes)
translational control
differences in the poly-A tails and or guanine caps may determine how long mRNA is available for translation. specific hormones may also affect longevity of mRNA
domains
different exons code may code for different ________ in the protein
transcription factors
different types of _____________ ______________ are needed to bind to different promoter regions in eukaryotes
Euchromatin
diffuse and light-staining; contains DNA for mRNA transcription
5' > 3'
direction mRNA codons are read by the translation machinery
downstream
direction of transcription
Watson, Crick, and Franklin
discovered the structure of DNA in 1953
domains
discrete structural and functional regions of proteins
characteristics of benign tumours
doesn't cause cancer, doesn't invade other tissues causing damage -> cell adhesion molecules, don't spread easily/bits that break off don't start tumours elsewhere, easy to treat(surgery), cells often differentiated
purine
double-ringed nitrogenous base (ex. adenine and guanine)
DNA strands unwind, polymerase initiates RNA synthesis
during the initiation stage of transcription, what happens after RNA polymerase binds to the promoter?
peptide
during the second step of the elongation stage of translation, an rRNA molecule of the large ribosomal subunit will catalyze the formation of a ________ bond between the amino group of the amino acid in the A site and the carboxyl end of the growing polypeptide in the P site
dissociate to be reused
during the termination stage of translation, what happens to the two ribosomal subunits and the other components of polypeptide assembly after the polypeptide is released?
translocates
during the third step of the elongation stage of translation, the ribosome ________ the tRNA in the A site to the P site
antiparallel
during transcription, the RNA molecule is synthesized in an antiparallel direction to the template strand of DNA
nucleotides, amino acids
during translation, the cell must translate the ____________ sequence of an mRNA molecule into the ________ _______ sequence of a polypeptide (change in chemical language)
Which of the following statements is false?() a.In bacteria, proteins called transcription factors enhance the affinity of RNA polymerase to the promoter sites of genes. b.In bacteria, transcription of a gene is initiated when the RNA polymerase by itself recognizes and binds to the promoter of the gene. c. The initiation of gene transcription in eukaryotes requires the binding of proteins called transcription factors to the TATA box in the promoter region of a gene. d. A relaxation of chromatin packing in eukaryotic cells can facilitate the binding of transcription factors to a promoter of a gene. e. All of the listed responses are correct.
e
restriction enzyme
enzyme that cuts DNA as well as plasmids at very specific predetermined sequences
RNA polymerase II
enzyme that is used in the initiation stage of transcription; unwinds and then elongates
aminoacyl tRNA synthetases
enzymes that catalyze the attachment of the amino acid and tRNA
General transcription factors (GTF) are _____ for all protein coding sequences. what do they do?
essential. They bind to other proteins and only when the whole transcription initiation complex is complete will RNA pol II begin.
advantage of iPS
ethical, less chance of rejection
In _________cells, mRNA has to go through some extra processing in the nucleus.
eukaryotes
Post transcriptional modifications only happen in what type of cells?
eukaryotes
linear chromosomes
eukaryotes have ____ ____ to keep the DNA more organized
different, one
eukaryotes have ______________ promoters for each gene whereas prokaryotes only have _______ promoter region (therefore the same promoter region in prokaryotes)
T
eukaryotes perform transcription and translation in different places in the cell whereas prokaryotes perform them simultaneously sometimes and always in the same spot (T/F)
How can proteins be processed and example:
ex: cleavage of protein insulin = active insulin. Chemical modifications for functionality. Proteins for cell surface have sugars added to them
initiation
first stage of translation in which the translation initiation complex forms
protein coding region is read from
fixed starting point and continues reading in blocks of 3 nucleotides until the end point is reached (stop codon)
transcription
formation of mRNA molecules from DNA that makes up particular gene
hybrid RNA-DNA double helix
formed after elongation before termination occurs; combined helix of DNA and RNA before separation is called:
methylation at 50 years (twins)
found they were different environmental factors influence epigenetics/methylation patterns/histomes around DNA in individuals
operons
functioning units of DNA that contain genes that coordinate the regulation of gene expression ex. lac operon
RNA interference (RNAi) regulate _______ _____ at the level of mRNA transcription. RNAi is due to _____ and ______
gene expression, miRNAs, siRNAs
Point mutation
gene mutation in which a single base pair in DNA has been changed
Coordinately Controlled Genes
genes that are controlled by the same control elements even though they are on different chromosomes
three hydrogen bonds
hold cytosine and guanine together
P site
holds the tRNA carrying the growing polypeptide chain
3' to 5'
how are anticodons written?
don't need a primer
how do RNA polymerases differ from DNA polymerases?
ribose, uracil, single stranded
how does RNA differ from DNA?
translation of mRNA begins while transcription is still in progress
how does the lack of a nucleus in bacteria cause bacterial transcription and translation to differ from eukaryotic transcription and translation?
1
how many DNA strands are used as a template for the transcription of 1 mRNA?
3
how many nucleotides are necessary to code for a single amino acid?
how is gene expression coordinated
if genes have the same regulatory sequences that bind same transcription factors
mRNA, tRNA
in addition to a binding site for _________, each ribosome has three binding sites for _______
methionine (Met)
in addition to functioning as a start codon, AUG also codes for which amino acid?
detach from DNA and release transcript
in bacteria, the transcribed terminator sequence function as the termination signal, causing the polymerase to do what?
5' end
in initiation of translation, initiator tRNA (met-tRNA) forms complex with small subunit... complex binds to _________ of mRNA and scans to find the AUG start codon
ribozyme
in some organisms, the intron RNA functions as a _______ and catalyzes its own excision without the help of proteins or additional RNA molecules
Epigenetics and inheritance
in sperm/eggs - special mechanisms search genome to erase epigenetic tags -some escape and passed to offspring
release factor (termination factor)
in termination in translation, a ____________ ___________ binds to the A site and the polypeptide chain is then released from the P site
large ribosomal subunit, translation initiation complex
in the second step of the initiation stage of translation, a _________ __________ _________ attaches to the mRNA, tRNA carrying Met, and the small ribosomal subunit to form the __________ _________ ___________
phases of transcription/translation
initiation, elongation, and termination
What causes a frameshift mutation?
inserting/deleting one base in a gene
transfection
insertion of a plasmid or recombinant DNA into a eukaryote
RNAi (RNA interference)
introduction of double-stranded RNA into a cell to inhibit gene expression
Which of the following are removed during the processing of primary mRNA using the given terms:exons, RNA polymerase, introns, or both introns and exons.
introns
After an RNA molecule is transcribed from a eukaryotic gene, what are removed and what are spliced together to produce an mRNA molecule with a continuous coding sequence
introns ... exons
phenotype of an organism
is its physical characteristics or traits
The inactive mammalian X chromosome is heavily methylated. What is the result of this methylation?
it becomes inactive, and will stay this way not because it can't go back, but because the cell monitors is to stay untranscribable. This way different alleles of the same genes won't be expressed at the same time.
According to the central dogma, what is the intermediate molecule involved in the flow of information in a cell that should go in the blank?DNA → ________ → Proteins
mRNA
Which nucleic acid is translated to make a protein?
mRNA
Which of the following molecular structures contain codons?
mRNA
Translation
mRNA has the ribosome around it and has letter attached to it. The letters read in groups of 3 called codons. The tRNA has 2 sides; the anticodon side has the complimentary bases that go with the mRNA. The other side has corresponding amino acid. The tRNA comes in the ribosome & incorporates its amino acid, then gets kicked off, then next tRNA comes in & the cycle keeps happening.
initiation of translation
mRNA is attached to a subunit of the ribosome, the first codon is always AUG
codon
mRNA nucleotide triplet usually written 5' -> 3' code for amino acid (also used to describe nontemplate DNA strand which is identical to mRNA except for T for U)
Codons
mRNA nucleotide triplets
codons
mRNA nucleotide triplets
Fill in the blank," During protein synthesis an anticodon of a transfer RNA (tRNA) pairs with__________," using the given terms: Amino acids in a polypeptide, DNAnucleotide basis, rRNA(ribosomal RNA) nucleotide basis, mRNA( Messenger RNA) nucleotide basis, or other tRNA( Transfer RNA) nucleotide basis
mRNA( Messenger RNA) nucleotide basis
Which of the following molecules are required for the process of translation?
mRNA, tRNA, and rRNA
Thermocycler
machine that raises and lowers temp of DNA in precise intervals for PCR
thermocycler
machine that raises and lowers temp of DNA in precise intervals for PCR
Constitutive proteins
made at a constant rate
small ribonucleoprotein particles (snRNPs)
made up of small nuclear RNA (nRNA) and several other proteins... used in mRNA splicing; bind to introns, loop introns, clip the intron loop, join adjacent axons together
RNA polymerases
major enzyme in transcription that reads DNA strand and builds mRNA strand; separate the strand itself and then reads it
What are master regulatory genes, example, and what do they do?
master regulatory genes make proteins that will commit the cell to their destiny. ex: myoD protein stimulates expression of itself so the cell will stay this way.
semiconservative
method of replication that implies that each new strand of DNA is half original and half new
Methylation
methyl groups added to DNA cytosine nucleotides
demethylase
methylation is reversible, can be removed and demethylate -not permanemt change to DNA -enzyme
Difference between miRNAs and siRNAs
miRNA molecules are from single stranded RNA molecules, while siRNA molecules come from much longer, linear, double stranded RNA molecules
How can a proto-oncogene become an oncogene?
movement of DNA within the genome (translocation), amplification of a proto-oncogene, or point mutations in the control elements
Fill in the blank,"Environmental influences called__________ cause mutations in humans," using the given terms: antigens, mutagens, transposons, or nonfunctional proteins.
mutagens
the role of tumour suppressor genes in the development of tumours
mutation ->. inactivation ->. less proteins made therefore cause cell to divide uncontrollably
missense mutation
mutation that changes a sense codon to a different sense codon
nonsense mutation
mutation that changes a sense codon to a stop codon
nonsense mutation
mutation that changes an amino acid codon to a stop codon; causes translation to be terminated prematurely; effect depends on how close the new stop codon is to the beginning of the coding sequence
silent mutation
mutation that has no observable effect on the phenotype due to the redundancy of the genetic code
acquired mutation
mutation that occurs in individual cells after fertilisation
Where does DNA methylation occur? ________ gene expression (reduces or increases)
on DNA, reduces
gene rearrangements
mutations that involve DNA sequences that have deletions, duplications, inversions, and translocations
tRNAs (transfer) are a type of
ncRNA (non-coding)
In e. coli regulating trp synthesis, is it positive or negative inhibition?
negative because the rate decreases as concentration of product increases.
Do eukaryotes have operons?
no
RNA interference (RNAi)
occurs when a small segment of RNA matches and binds tot he mRNA interfering with the ability of tRNA to read the mRNA strand and build the protein (it can also degrade the mRNA)
termination of translation
occurs when a stop codon in the mRNA reaches the A site of the ribosome
Alternative RNA splicing
occurs when different mRNA molecules are produced form the same pre-mRNA molecule depending on which segments are treated as exons and introns
locations of functionally related genes in prokaryotes
often clustered in operons
locations of functionally related genes in eukaryotes
often distant from one another with separate promoters
Which of the following processes is an example of a post-translational modification?
phosphorylation
mutagens
physical and chemical agents that interact with DNA in ways that cause mutations
Morphogenesis
physical processes that give an organism its shape (distinct)
mutagens
physical, chemical, and biological agents that generate mutations
What is added to the 3' end of the pre-mRNA strand?
poly A tail
12
polysomes can build up to _____ copies at once
transcription unit
portion of the gene that is copied into RNA
What process happens to the pre-mRNA after termination?
post-transcriptional modifications
F
primers are needed to start building complementary copy of the mRNA strand in transcription (T/F)
base pairing
principle that bonds in DNA can form only between adenine and thymine and between guanine and cytosine
gel electrophoresis
procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel
Differentiation
process by which cells become specialized in structure and function (leads to all different cells types)
conjugation
process in which paramecia and some prokaryotes exchange genetic information helps to build genetic diversity among bacteria since they reproduce via binary fission
RNA splicing
process where large portions of the RNA molecules are removed and the remaining portions are reconnected
induced pluripotent stem cells - iPS cells
produced from adult somatic cells using appropriate protein transcription factors associated with pluripotent
regulatory gene
produces a protein, which regulates other gene expression Some DNA sequences—operators and promoters—do not encode for proteins but are binding sites for other proteins
F
prokaryotes have introns (T/F)
In ________ cells, there mRNA does not go through extra processing. In fact, _________ & ______________ happen at the same time in the cytoplasm.
prokaryotic transcription & translation
List the 3 components of an operon and explain the role of each one:
promoter: where RNA pol binds to begin transcription. Operator: on/off sequence in or after promoter Operon Genes: functionally related genes controlled by the same operator
messenger RNA carries the instructions to make a particular____
protein
Explain how proteins are degraded with proteasomes:
proteins are marked for destruction by ubiquitin molecules (requires ATP). Proteasome protein complexes then see this tag, unfold the protein, and put it in their central cavity. Enzymatic components of the proteasome then cut the protein into small peptides which can be further degraded by other enzymes in the cytosol.
histones
proteins around which DNA is wrapped to keep it organized
elongation factors
proteins involved in the elongation phase of translation, assisting ribosomes in the synthesis of the growing peptide chain
initiation factors
proteins required to bring all the components of a translation initiation complex together
Initiation factors
proteins that bring in the large subunit that completes the translation initiation complex
Tumor suppressor genes code for...
proteins that prevent uncontrolled cell growth. Some TS proteins (TSP) repair damaged DNA, or control adhesions of cells to each other or to the ecm, or are components of cell signaling pathways that inhibit the cell cycle. Any mutation that decreases the amount of TSP increases the chance of cancer.
transcription activators
proteins which speed up transcription 1. bind to an enhancer region on DNA 2. enhancer and promoter may be far apart and dna forms a loop to bring them close together
Peptide bond formation
rRNA (from large subunit) catalyzed peptide bond between amino groups (new amino acid in A site) and carboxyl group (polypeptide in P site), removes peptide chain form tRNA at P site and attach it to tRNA at A site
characteristics of malignant tumours
rapid growth, no cell adhesion molecules so grow finger like projections, spread easily, hard to treat(surgery, chemo/radiotherapy), cells often dedifferentiated
a proto-oncogen can code for:
receptor that responds to growth, growth factor
antiparallel
referring to the arrangement of the sugar-phosphate backbones in a DNA double helix (they run in opposite 5' - 3' directions)
where do transcription factors act?
regulatory proteins and bind to the eukaryotic promoter
sigma factors
regulatory proteins that recognize different classes of consensus sequences in prokaroytes bind to RNA polymerase and direct it to certain promoters
post transcriptional control
removal of introns and splicing of exons. different patterns of splicing can occur
RNA splicing
removal of large portions called introns from mRNA molecule that is initially synthesized and paste together the remaining ones called exons
pre-RNA slicing
removes introns and joins exons creating an mRNA molecule with a continuous protein coding sequence
Nucleosome
repeating subunit of chromatin fibers, consisting of DNA coiled around histones
Some transcription factors, instead of acting as activators may act as _____ and ________ expression.
repressors, decrease (Gene expression shut down)
what does the determining the genome of simpler organisms allow
sequences of proteins that derive from the genetic code/proteome of organism to be determined
exons
sequences that end up in mature mRNA's *expressed sequences
introns
sequence of DNA that is not involved in coding for a protein
signal peptide
sequence of about 20 amino acids at or near the N terminus of a polypeptide that targets the protein to the ER or other organelles in a eukaryotic cell
translocation of bases
sequence of bases moved from one location in genome to another - could be movement within same chromosome or to a diff chromosome
polyadenylation signal sequence (AAUAAA)
sequence on DNA which specifies a polyadenylation signal in the pre-mRNA; in eukaryotes, proteins cut the RNA transcript free from the polymerase and release the pre-mRNA downstream from this signal
Different sets of genes are _______ expressed in a _____ manner as new cells arise from mitosis
sequentially, regulated
Hox genes
series of genes that controls the differentiation of cells and tissues in an embryo
Hox genes
series of genes that controls the organs and tissues that develop in various parts of an embryo a subset of homeotic genes
Cell division
series of mitotic divisions that increase the number of cells (if that only occurred, would be ball of cells
What is a codon?
set of 3 nucleotides that specify an amino acid
Cancer
set of diseases in which cells escape from the control mechanisms that normally limit their growth
How do eukaryotes make specific products? These genes usually have the same _____. Example in real life?
several different enzymes located on different chromosomes may be involved. (activators) Mailman knows to check mailbox because certain ones have flags up.
Polysomes
several ribosomes that are attached to the same mRNA simultaneously are called _________________
siRNA
short interfering RNA - exogenous double stranded RNA taken by cells - generally viral RNA
mRNA degradation
short nucleotide sequences that can cause the newly made mRNA molecule to be quickly broken down
RNA primer
short segment of RNA used to initiate synthesis of a new strand of DNA during replication
RNA primer
short segment of RNA used to initiate synthesis of a new strand of DNA during replication degraded by enzymes and and replaced with DNA after replication so that the final strand contains only DNA
Mutations can either be ___________, ___________, or _____________.
silent harmful beneficial
Corepressor:
small molecule that cooperates with repressor protein to switch operon off
MicroRNAs (miRNAs)
small molecules of noncoding RNA—are important regulators of gene expression
initiation
small ribosomal subunit binds to mRNA and initiator tRNA with the anticodon UAC pairs with the mRNA start codon AUG. The large ribosomal unit completes the ribosome. Initiator tRNA occupies the P site. The A site is ready for the next tRNA.
interfering RNAs (RNAi)
small snippets of RNA that are naturally made in the body or intentionally created by humans can bind to specific sequences of RNA and mark them for destruction ex. siRNA or miRNA
ribozyme
snRNP acts as an enzyme and does the cutting so therefore it is considered a ________________
Explain what redundancy means.
some amino acids have more than one codon
in eukaryotes, how can target genes be stimulated/inhibited
specific transcriptional factors move from cytoplasm -> nucleus
What does mRNA do in translation?
specifies amino acid
Transcription has ________ & _________ signals that help it only to transcribe genes.
start and stop
when would a women have high levels of oestrogen/ be exposed to it for longer
started menstruation earlier , HRT
wobble hypothesis
states that 61 different sense codons do not require 61 different tRNAs.... first 2 codons of anticodon and codon must match up exactly, 3rd nucleotide has more flexibility
one gene one enzyme hypothesis
states that the function of a gene is to dictate the production of a specific enzyme; proposed by Beadle and Tatum; later revised
UAA, UAG, UGA
stop codons
What does rRNA's job?
structural component of ribosomes
ribosome
structure made of RNA and proteins that adds each amino acid brought to it by the tRNA to the growing end of a polypeptide chain
Garrod
studied alkaptonuria disease drew a correlation between metabolic disorders and inheritance
Beadle and Tatum
studied bread mould and it's ability to produce the amino acid arginine through a synthesis pathway... some mould was unable to synthesize the entire arginine pathway depending on where a gene was altered ... these alterations transformed the mould groups from PHOTOTROPHS TO AUXOTROPHS (using x-rays) (auxotrophs cannot grow on minimal media whereas phototrophs can) so we gave them help to make the arginine and saw that some needed more help than others depending on where the mutation was
5' GTP cap
substance that is added to newly synthesized mRNA in RNA processing to the 5' end
What are morphogens?
substances that establish an embryo's axes and features.
If lactose is removed in E. coli
synthesis stops genes turned off
polymerase chain reaction (PCR)
technique that allows molecular biologists to make many copies of a particular gene
___________ of translation happens when the ribosome hits a stop codon on the mRNA
termination
P site, A site, E site
the 3 binding sites for tRNA on a ribosome
5' cap, poly-A tail, splicing introns
the 3 modifications made to precursor-mRNA to make it into functional mRNA
initiation, elongation, termination
the 3 stages of polypeptide synthesis
initiation, elongation, termination
the 3 stages of transcription
initiation, elongation, termination
the 3 stages of transcription:
C-terminus (carboxyl terminus)
the 3' side of the polypeptide is considered to be the _______________
N-terminus (amino terminus)
the 5' side of a polypeptide is considered to be the _______________
protein, RNA
the DNA inherited by an organism leads to specific traits by dictating the synthesis of ________ and ______ molecules involved in protein synthesis
terminator
the DNA sequence that signals the end of transcription in bacteria
template strand
the DNA strand that provides the pattern, or template, for the sequence of nucleotides in an RNA transcript
RNA
the ______ part of the snRNP acts as an enzyme and does the cutting
mRNA splicing
the act of removing introns
elongation
the addition of monomers to make a longer RNA or protein during transcription or translation (nucleotides for transcription and amino acids for translation)
If a particular operon encodes enzymes for making an essential amino acid and is regulated like the trp operon, then
the amino acid acts as a corepressor.
monocistronic transcript
the coding pattern of eukaryotes in which one mRNA molecule codes for only one protein
DNA is an information containing molecule
the information in genes on a chromosome is in the form of a specific sequence of nucleotides
Genome
the complete instructions for making an organism, consisting of all the genetic material in that organism's chromosomes
homeotic genes
the early genes that turn certain cells in the early embryo into differentiated cells
What is meant by determination? Explain what this means within an embryonic cell:
the events that lead to the observable differentiation of the cell. Not reversible, even if the determined cell is placed elsewhere in the embryo. Cells have become noticeably different in structure and function. Cells express the genes they'll need in the tissue they're destined for (tissue specific proteins, ex: liver makes albumin).
E site
the exit site, where discharged tRNAs leave the ribosome
how is the lac operon an inducible system?
the expression of the proteins is induced upon exposure to some material
zygote
the fertilized egg resulting in an egg being fertilized by a sperm diploid
primary transcript
the initial RNA transcript from any gene, including those specifying RNA that is not translated into protein
tRNA
the key to translating a genetic message into a specific amino acid sequence is the fact that each ________ molecule enables translation of a given mRNA codon into a certain amino acid
inducer in lactose process
the lactose
proteins
the link between genotype and phenotype
coding, template
the mRNA synthesized during transcription has the same sequence of nucleotides (except U instead of T) as the ___________ strand of DNA and a complementary sequence of nucleotides to the _________ strand of DNA
leading strand
the new, continuous, complementary DNA strand synthesized along the template strand in the 5' to 3' direction nucleotides are steadily added one after the other by DNA polymerase
Thymine
the nucleotide that hydrogen bonds with the nucleotide adenine in DNA.
How does the primary transcript in the nucleus of a eukaryotic cell compare to the functional mRNA?
the primary transcript is larger than the mRNA
gene expression
the process by which DNA directs the synthesis of proteins (or in some cases just RNA)
gene expression
the process by which DNA is used to make RNA molecules and proteins *includes two major stages 1) transcription (RNA synthesis) 2) translation (protein synthesis)
transformation
the process of giving bacteria foreign DNA
transcription
the process of making RNA from DNA takes place in the nucleus of eukaryotic cells
DNA replication
the process of making a copy of DNA
translation
the process of making a protein from an RNA molecule takes place in the cytoplasm of eukaryotic cells
Mutagenesis
the process of mutagens causing mutations and changing our genetic sequence
splicing
the process of removing introns and reconnecting exons
TATA box
the promoter of eukaryotes contains the _______ ______ which identifies the sequence as the promoter region for the transcription factors
upstream
the promoter sequence of DNA is ________ from the terminator sequence
Nucleotide-pair substitution
the replacement of one nucleotide and its partner with another pair of nucleotides
reading frame
the start codon establishes the ______________ ___________
Transcription unit
the stretch of DNA downstream from the promoter that is transcribed into an RNA molecule
sticky ends
the uneven ends of a double-stranded DNA molecule that has been cut with a restriction enzyme when placed together, the gene is inserted into the plasmid creating recombinant DNA
leucine zipper motif
these proteins regulate cell division genes
helix-loop-helix motif
these proteins regulate immune system genes
Fill in the blank," The two DNA strands are antiparallel. This means that____________.," using the given responses : they run in opposite directions, they run parallel to each other, the daughter strand is longer than the parent strand, or the parent strand is longer than the daughter strand.
they run in opposite directions
what stem cells are found in embryo
totipotent, pluripotent
Which of the following processes occurs in prokaryotes but not in eukaryotes?
transcription and translation occur simultaneously
repressors
transcription factor that decreases rate of transcription
Activators
transcription factor that increases rate of transcription
stop signals
what do the three codons that do not designate amino acids function as?
cuts out intron, joins together the two exons
what does a spliceosome do during pre-mRNA splicing?
RNA transcript released, polymerase detaches from the DNA
what happens during the termination stage of translation?
return to cytoplasm to be reused
what happens to empty tRNAs after they leave the E site?
the lac operon in e.coli
when lactose is absent: a regulator gene codes for a repressor protein. the repressor protein binds to the operator. RNA polymerase cannot transcribe the three structural genes of the operon and the structural genes are not expressed. when lactose is present: lactose binds with the lac repressor. repressor is unable to bind to the operator. structural genes are transcribed and translated. enzymes are produced as needed.
CpG site
where C and G are next to one another
TATA box
where DNA begins to denature and expose the template strand
nuclear envelope, rough ER, cytosol
where are ribosomes found in the cell? (free or bound)
an intron
where does the spliceosome complex binds to several short nucleotide sequences along what?
nucleus
where does transcription take place?
nucleolus
where ribosomal subunits are made
What happens at the P site of the ribosome?
where the growing polypeptide is held -peptide bond formation
carboxyl
which end of a polypeptide is the new amino acid added to?
3'
which end of the growing RNA molecule does RNA polymerase add nucleotides to?
template strand (3' to 5')
which strand of DNA is read in order to copy the mRNA strand?
transcription initiation complex
whole complex of transcription factors and RNA polymerase II bound to the promoter
