exam 3 Flashcards
(141 cards)
1
Q
what are the 5 essential characteristics of hereditary material?
A
- localized in the nucleus and a component of chromosomes
- in stable form in cell
- sufficiently complex to contain the genetic information required to direct the structure, function,, development, and reproduction of organisms
- mutable, undergoing mutation at a low rate that introduces genetic variation and serves as a foundation for evolutionary change
2
Q
summarize the work of frederick griffith
A
A) injected mice with s-strain bacteria which produced death and injected mice with r-strain bacteria which did nothing as a control
B) denature s-strain does not produce death
C) injection of a mixture of denatured s-strain and r strain cause death and this proved that there was a transformation factor carrying genetic hereditary genetic information somewhere in the cells.
2
Q
describe DNA
A
DNA is composed of four nucleotide subunits joined together by phosphodiester bonds that link one nucleotide to another in nucleotide chains. the two polynucleotide chains come together to form a double helix, the nucleotides connect via complementary base pairing held together by hydrogen bonds.
3
Q
what are the 3 components of DNA nucleotides?
A
- a deoxyribose sugar
- one of four nitrogenous bases
- up to three phosphate groups
4
Q
what is deoxynucleotide monophosphate (dNMP)?
A
monophosphate forms of nucleotides
5
Q
what is deoxynucleotide triphosphate (dNTP)?
A
triphosphate forms of nucleotides which are identified as dATP, dGTP, dCTP, and dTTP
6
Q
DNA strand formation is catalyzed by the enzyme, ___ _________, catalyzing information between the 3 prime hydroxyl group of one nucleotide and the 5 prime triphosphate group of an adjacent nucleotide
A
DNA polymerase
7
Q
describe DNA strand elongation
A
complementary nucleotides form hydrogen bonds by the attraction of positive and negative charges. the nucleotide triphosphate complementary to the template strand nucleotide is recruited by DNA polymerase.
OR
DNA polymerase catalyzes the addition of the new nucleotide to the 3 prime end of the growing strand by removing two phosphates and forming a new phosphodiester bond.
8
Q
a __________ is the basic building block of nucleic acids
A
nucleotide
9
Q
5’ - ATCG - 3’ = …?
A
3’ TAGC - 5’
10
Q
antiparallel strand orientation is essential to the formation of stable __________ ______.
A
hydrogen bonds
11
Q
what is base stacking?
A
DNA base-pair interaction that rotates the base pairs around a central axis of symmetry and imparts twisting to the double helix.
12
Q
the major groove and minor groove are caused by ______ _____ __________, and these regions are what?
A
base pair stacking
these regions are where DNA-binding proteins can most easily make direct contact with nucleotides along one or both strand of the double helix
13
Q
where are the major and minor grooves located?
A
along the double helix
14
Q
what is B-form DNA
A
the most common form of DNA, has a right handed twisting of the sugar phosphate backbone
15
Q
what is A-form DNA?
A
also has a right hand twist but is more compact and larger than B-form DNA. Common among bacterophages
16
Q
what is Z-form DNA?
A
has a left handed twist and zizag sugar phosphate backbone, this form is common near the start site of genetic transcription.
17
Q
what are three attributes of DNA replication?
A
- each strand of the parental DNA molecule remains intact during replication
- each parental strand serves as a template directing the synthesis of a complementary antiparallel daughter strand
- completion of DNA replication results in the formation of two identical daughter duplexes, each composed of one parental strand and one daughter strand
18
Q
DNA replication proceeds in one direction or both directions?
A
it is bi-directional
19
Q
once replication has begun in bacteria, there is expansion around the origin of replication forming a __________ _______. There are two regions known as __________ _______ at either side of the ___________ _______.
A
replication bubble
replication forks
replication bubble
20
Q
bacteria have __ origin, while eukaryotes have ___.
A
one
multiple
21
Q
what are the 7 steps of DNA replication in BACTERIA
A
- helicase breaks hydrogen bonds, topoisomerase relaxes the super coiling
- single-stranded binding (SSB) protein prevents reannealing
- primase synthesizes RNA primers
- DNA polymerase III synthesizes daughter strand
- DNA polymerase III elongates the leading strand continuously and the lagging strand discontinuously
- DNA polymerase I removes and replaces nucleotides of the RNA primer
- DNA ligase joins okazaki fragments
22
Q
the short segments of replicated DNA are ________ _________, they are the result of discontinuous synthesis on the lagging strand
A
okazaki fragments
23
Q
what is DNA proofreading
A
essential to accurate copying of DNA. This occurs as mismatches are detected in DNA replication
24
copying DNA causes over coiling to build up and stress the bonds of the DNA backbone. ____ _____________ relieve this stress.
DNA topiosomerases
25
replication of circular chromosomes generates what?
two complete copies of the original parental chromosme
26
linear chromosomes are unable to replicate fully and completely all the way to their ends.
TRUE OR FALSE
TRUE
linear chromosome replication falls a little short of reaching the chromosomes ends, thus these chromosomes get shorter with every replication cycle
27
what are telomeres?
they insert chromosomal ends that protect chromosomes, these ends consist of short repeating sequences.
28
what do telomeres protect DNA from?
- being chewed
- improper fusing with other DNA
- enables replication of ends of DNA
29
most human somatic cells experience telomere shortening with successive divisions
TRUE OR FALSE
TRUE
30
Telomerase expression allow chromosomes to do what?
maintain their ends
31
what are the steps of telomere lengthening?
1. attachment of telomerase
2. DNA elongation
3. translocation of telomerase
4. DNA elongation
5. telomere completion by DNA polymerase
6. Telomere and T loop structure form
32
what are the three steps of translation? (in bacteria)
1. initiation
2. elongation
3. termination
33
describe initiation (in bacteria)
begins when they small ribosomal subunit binds near the 5' end of the mRNA and identifies the start codon
the initiator tRNA, carrying the first amino acid of the polypeptide, binds to the start codon at the future P site
34
what is a polyribosome?
mRNA's with several ribosomes attached and translating at once
35
a cistron is ...
the name of a gene
36
what are polycistrons?
the genes that are transcribed in a unit, also known as operons
37
operons are always found in __________ but only occasionally found in _____________.
bacteria
eukaryotes
38
what does the shine-dalgarno sequence do?
tells the ribosome where to translate
39
each cistron (gene) has its own shine-dalgarno sequence
TRUE OR FALSE
TRUE
40
mRNA is read __' to __'
5' to 3'
41
each three letters of a sequence makes what?
a codon
42
the spelling of a codon indicates the spelling of a particular amino acid
TRUE OR FALSE
TRUE
43
tRNAs display ________.
wobble
44
what is the wobble effect?
when the 5' position of the anticodon can pair with more than one nucleotide
45
what is iosine?
a modified nucleotide that pairs with either purines or pyrimidines
46
because genetic code is __________, bacteria can be used to produce important proteins from plants and animals
universal
47
how does tRNA find the correct amino acid?
aminoacyl-tRNA synthesis charge tRNA with the correct amino acid
48
post-translational modification alters the ______ made and is considered part of gene expression control
protien
49
why is gene regulation important?
for efficiency, to take on specialized functions, and to respond to the environment appropriately
50
genes come in two types, what are they?
constitutive genes: expressed continually for day to day survival
regulated or dynamically expressed genes (inducible): most genes are this kind, these differ in expression depending on time and place
51
how are genes in bacteria regulated?
- mostly transcriptional regulation
- control results from interactions between DNA-binding proteins and regulatory sequences of DNA
- post transcriptional mechanisms are also important
52
there are two gene types in operon regulation, what are they?
1. regulatory genes which regulate expression of other genes
2. structural genes which encode proteins made by operons
53
what do regulatory elements do?
affect the expression of sequences to which they are phyisically linked
54
operons are regulated in either _________control or _______ control.
negative or positive
55
in negative operon control the protein ....
is a repressor, binds to the regulatory DNA sequence, and prevents transcription of a gene or operon
56
in positive operon control the protein....
is an activator, binds to regulatory DNA sequence, and initiates gene transcription.
57
repressor proteins block what?
RNA polymerase, effectively blocking transcription
58
summarize the work of avery, macleod, and mcCarty were able to use in vitro transformation for show that DNA is the hereditary molecule
Beginning with s-type bacteria, this was heavily filtered to separate cell from excess material. They took a few samples of this, and in one sample added Rnase that was the plated and allowed to grow bacteria. This bacteria grew both target strains, 2r and 3S bacteria. This told them that RNA was not the hereditary molecule. Next, they did the same experiment with protease with the same results. However. Dnase resulted in growth of only 2r bacteria, which confirmed this was the hereditary molecule.
59
provide 4 similarities of DNA replication and transcription
1. both have 3 major steps in their processes
2. heavily moderated by different types of RNA's
3. both are bi-directional
4. both are concerned with making copies of a parental unit
59
what are some differences between DNA replication and transcription
They have difference purposes: replication is concerned with parental genetic code and passing that on to the next generation. transcription is concerned with encoding genetic information into a different language (RNA)
only one strand is needed for transcription and two strands are needed for replication
59
describe basic structure of a ribosome
all ribosomes have a large subunit and a small one, which has an A, P, and E sites.
60
what are the 3 ways humans diseases can be caused?
1. a mutated gene
2. any one of multiple genes (that likely work together in one process) can be mutated to cause disease
3. both environmental or developmental factors and genes contribute to onset of disease
60
what is a mendelian condition?
single gene mutation
60
what is molecular analysis?
molecular analysis of DNA or RNA is a specific way to test for suspected conditions
61
what is chromosomal analysis?
chromosomal analysis is used for diagnosis of a newborn, individuals with unexplained symptoms, and in cases of long term infertility
62
what is huntington's disease
a tri-nucleotide repeat disorder where abnormal hunting protein is expressed in brain and other cells, it causes aggregations that kill neurons leading to progressive loss of motor control and chorea movements
62
in PCR, what happens to DNA?
it is amplified and then separated by gel electrophoresis
62
what is maternal serum screening?
measures the levels of 3 or 4 proteins in the pregnant womans blood
62
what is fetal cell sorting?
this involves identifying and isolating fetal cells in maternal blood circulation
62
what is preimplantation genetic screening?
paired with IVF to select egg with normal number of chromosomes or without a known genetic condition
63
the DNA -binding domain does what ?
locates and binds operator DNA sequence or other target regulatory DNA sequences
63
DNA and RNA are both grown by using a single strand of ____ as a template in the process of transcription
DNA
63
what does the allosteric domain do?
binds to molecule or protein, which causes a change in conformation of the DNA-binding domain; this property is called allostery
63
Both DNA and RNA are nucleic acids. they are composed of ___________ that are joined together by phosphosiester bonds to form polynucleotide strands
nucleotides
63
list three differenes between RNA and DNA
- RNA is single stranded, DNA is double stranded
- RNA will adopt folded secondary structures by complementary base pairing, which DNA does not do
- RNA contains uracil, in place of thymine.
63
activator proteins do what
bind to activator binding sites on the DNA and assiste RNA polymerase in binding
63
63
RNA molecules are transcribed from genes and are of several types
TRUE OR FALSE
TRUE
63
what does mRNA do
used to encode the sequence of amino acids that become a protein
63
what does telomerase RNA do
is part of the telomerase ribonucleoprotein complexes and acts as a template for telomere maintainace and elongation.
63
what does miRNA and siRNA do
play key roles in post-transcriptional gene regulation by pairing with mRNAs and altering their stability and translation
63
what does rRNA do
works with many proteins to build ribosomes
63
describe transcription initiation in bacteria
RNA polymerase binds to the promoter and opens the DNA to create an open promoter complex. the polymerase travels downstream to the template strand to initiate transcription. because promoter regions vary with the roles of genes, RNA polymerase is aided in recognizing promoters by distinct sigma subunits
63
what does tRNA do
carries amino acids to ribosomes
63
what does SnRNA do
involved in the splicing of precursor mRNA in the eukaryotic nucleus
63
describe bacterial transcription
the promoter is a region just upstream of the gene that is used at the 5' start of transcription. The promoter is recgonized by RNA polymerase to direct the production of the RNA transcript. The template for production of the RNA is the "template strand" and the RNA transcript that is made matches the coding strand (nontemplate strand) of DNA. after the coding region, is termination. this rgion regulates the end of transcription and is downstream of the gene.
63
what are the three parts of the transcription unit on the gene?
1. promoter
2. template
3. terminator
64
what are bacterial promoters?
double stranded regulatory DNA sequences that bind transcription proteins such as RNA polymerase and direct the RNA polymerase to the nearby start of transcription
64
describe transcription elongation in bacteria
once polymerase has added 8-10 nucleotides the sigma subunit disassociates, DNA about 18p ahead of polymerase is unwound
65
describe transcription termination in bacteria
the end point of transcription is after the last stop codon in the RNA transcript. two transcription termination mechanisms occur in bacteria; A) intrinsic termination which involves a stem-loop structure or B) Rho-dependent termination, which involves a rho protein binding to a specific termination sequence.
66
what makes eukaryotic transcription more diverse and complex?
they have 3 distinct polymerases, RNA pol I,RNA pol II, and RNA pol III.
66
eukaryotes have 4 steps of transcription...
1. promoter recognition and identification
2. initiation and transcript synthesis
3. transcript elongation
4. transcript termination
66
what are some differences between bacteria and eukaryotes.
eukaryotic promoter and consensus sequences are more variable and transcription is more complex than that of bacteria
eukaryotic genes often contain introns
eukaryotic DNA is more complexed with proteins than that of bacteria
67
what are introns?
noncoding regions between the coding exons in a gene.
68
introns do not need to be removed before translation
TRUE OR FALSE
FALSE
they do need to be removed before translation
68
what does the TATA binding protein do?
determines the start site of transcription and binds the core promoter
68
pre mRNA is processed into mature RNA in the nucleus through three steps
1. 5'capping
2. 3' capping
3. intron splicing
68
do all introns need a spliceosome?
no
68
RNA editing is...
a post-transcriptional subsitiution of nucleotides in mRNA
69
____ different amino acids are the building blocks of nucleotides
20
69
what are the shares features of amino acids?
- central carbon molecule
- an amino NH3+ group
- a carboxyl COO- group
69
what is a distinctive portion of an amino acid?
its side chain, known as an R-group
69
polypeptides have four levels of organization...
1. primary
2. secondary
3. tertiary
4. quaternary
70
in all 3 domains ribosomes perform 3 tasks...
1. bind to messenger RNA and identify the start codon where translation begins
2. facilitate the complementary base pairing of mRNA codons and tRNA anticodons, that determines the amino order in the polypeptide
3. catalyze peptide bond formation between amino acids during polypeptide formation
70
3 major phases of translation are...
1. initiation
2. elongation
3. termination
70
polypeptide elongation occurs in 6 steps in bacteria...
1. a charged tRNA is bound by elongation factor
2. the charged tRNA enters the A site
3. te GTP is hydrolyzed to release EF-Tu-GDP
4. peptide transferase catalyzes the formation of a peptide bond between the chain at the P site to the new amino acid brought in by the tRNA at the A site
5. the spent tRNA exit the ribosome through the E site and translocation of the ribosome occurs toward the 3' end of the strand
6. (back to step 1)
70
when glucose is present, little transcription comes from the lac operon. why?
glucose blocks adenyl cyclase
70
the lac operon is maximally functional when ________ and __________ are both present.
glucose and lactose
70
what are structural gene mutations
they affect the structure of the enzymes but not the regulation of their synthesis
70
genes are regulated at many levels but _____________ regulation is one of the most important
transcriptional
70
what are the 8 general steps of eukaryotic gene regulation?
1. DNA unpacking
2. transcription
3. RNA processing
4. transport to cytoplasm
5. breakdown of mRNA
6. translation
7. cleavage/ modification / activation
8. breakdown of protein
70
what is the first kind of cis-element regulatory structure?
the core promote region which contains the TATA box and other sequences and bind RNA pol II and its associated general transcription factors (GTFs)
70
describe enhancers
located on either side of the gene, some distance from the gene, or even with the gene. These are important for reaching maximum levels of transcription.
70
describe silencers
repress the level of transcription initiation
71
what is chromatin remodeling?
the repositioning or removal of nucleosomes to make chromosomes accessible to transcription machinery. Chromatin remodelers are specifically targeted to certain DNA sequences by transcriptional activators
71
chromatin does not change structure throughout the cell cycle
TRUE OR FALSE
FALSE
chromatin does change structure throughout the cell cycle
72
no cell expresses all genes
TRUE OR FALSE
TRUE
only a few thousand are expressed in each cell
73
what are some differences between eukaryotic and bacterial cells
the genomes of eukaryotic organisms are larger than bacterial and archeal organisms
the processes that regulate expression in eukaryotic cells are more varied and multifaceted than those governing expression in bacterial genomes
eukaryotes also localize chromosomes in the nucleus, unlike bacteria or archaea
74
what do cis-acting regulatory sequences do?
they bind trans-acting regulatory proteins to control eukaryotic transcription.
75
trans-acting proteins are ________ proteins
activator
76
what do repressor proteins do?
bind to other regulatory sequences to hinder transcription
77
bacteria gene regulation can be identified as ___________ or __________
housekeeping or inducible
78
do eukaryotes have housekeeping and inducible genes?
yes, plus multiple other kinds
79
define inducible gene
gene that activation is in response to a change in environmental conditions
80
define housekeeping gene
they are required for basic cellular function
81
bacterial genes have ______ regulation but eukaryotic genes have ______ regulation
leaky
tight
82
enhancer sequences do what?
they are a group of regulatory sequences that increase the level of transcription
83
what does the enhanceosome do?
direct the bending of DNA into loops that bring the enhanceosome into contact with the RNA polymerase and transcription factors bound at the core promoter
84
what do insulator sequences do?
these are cis-acting sequences that prevent enhancers from acting on the wrong gene
85
euchromatin is loosely packed and available for what?
transcription
86
what do euchromatin modifiers do?
they enzymatically modify histones by adding or removing methyl or acetyl groups
87
for eukaryotes, describe promoter regions and their effects on eukaryotic gene expression
The TATA box, the CAAT box, and the GC-rich box play roles in the binding of transcription factors and regulate expression levels
88
if a promoter was mutated in a eukaryotic gene, what would happen?
a total loss of gene expression due to inability to initiate transcription
89
what is an enhancer region made of and what is its role?
enhancer sequences attract activator proteins to recruit RNA pol II for transcription. They are made of a specific nucleotide DNA sequence with transcription factor binding sites
90
what is a silencer region and what is its role?
silencer repress the level of transcription initiation and are made of a nucleotide sequence that contains binding sites for repressors
91
describe and give an example of an enhanceosome
enhanceosomes direct DNA bending into loops that bring the enhanceosome into contact with RNA pol I and transcription factors found at the core promoter
in the GAL gene system, Gal4 is an activating protein and when it binds to UASg it leads to the formation of a mediator which is an enhanceosome. this induces the formation of a DNA loop and makes contact with general transcription operons
92
describe chromatin remodeling
involves the enzymatically caused changed in the composition / distribution of nucleosomes. these enzymes are called to sites in the chromatin by trans-acting factors that bind to specific DNA sequences
93
what is the general role of acetylation of histone protein amino acids in transcription of eukaryotic genes?
promotes transcription by making DNA more accessible for transcription factors
94
compare regulation of eukaryotic gene expression to prokaryotic gene expression. what additional levels of regulation is seen in eukaryotes?
eukaryotic gene expression is far more complex than prokaryotic gene control and includes things that prokaryotes do not such as chromatin remodeling, organization of genes which are mostly individually regulated, post-transcriptional modifications as well. Prokaryotes do not have a defined nucleus and their DNA is more accessible for transcription.
95
what is the central dogma of biology?
DNA is replicated --> transcribed --> into RNA --> which is translated --> into protein
