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MOLECULAR BIO > Lecture 1: Intro to Nucleic Acids > Flashcards

Lecture 1: Intro to Nucleic Acids Flashcards

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1
Q

_______ - a polymer of deoxyribonucleotides
* double stranded molecule that is twisted into a
helix

A

DNA

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2
Q

where is DNA found?

A

chromosomes, mitochondria/chloroplasts, plasmids

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3
Q

what does DNA do?

A

carry genetic information

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4
Q

what does each strand of DNA consist of?

A

sugar-phosphate backbone
bases attached in pairs (adenine, cytosine, thymine, guanine)

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5
Q

the primary structure of DNA is…

A

the sequence!

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6
Q

DNA is written in the ____ direction

A

5’ - 3’

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7
Q

what is the secondary structure of DNA?

A

double helix!

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8
Q

______ structure:
Two anti-parallel polynucleotide
chains wound around the same axis.
* Sugar-phosphate chains wrap around
the periphery.
* Bases (A, T, C and G) occupy the
core, forming complementary A · T
and G · C Watson-Crick base pairs

A

double helix

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9
Q

DNA binding proteins
bind to _______ groove, why?

A

major

we can actually see the base-pairs, easier access and more information (some proteins are specifically designed to work in the major groove)

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10
Q

what kinds of proteins interact with the major groove (2 examples)

A

helix-turn-helix configuration
zinc-fingers (both minor and major)

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11
Q

Most of the DNA is in the classic Watson-Crick model
simply called as ________

A

B-DNA or B-form DNA

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12
Q

In certain conditions, different forms of DNAs are found… what are the two kinds and why?

A

A-DNA upon dehydration or protein binding (viral packaging, biochemical assays).

Z-DNA is “reverse” helix found in very salty condition
(4M NaCl), or to relieve supercoiling strain – disease
association, seen in Alzheimers and Lupus (SLE)

these are both found when we change the ionic concentration of the environment

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13
Q

A-DNA has a ______ helix, what does it look like?

A

right-handed helix

LARGE major groove, almost no minor groove

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14
Q

Z-DNA has a ______ helix, what does it look like?

A

left-handed helix

flips backwards from supercoiling, symmetrical (no LARGE distinction between major and minor grooves)

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15
Q

what is the tertiary structure of DNA?

A

DNA packaging inside the cell

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16
Q

_______→reduces the space
and allows for DNA to be
packaged into cell (bacterial
DNA is ~500 x length of cells)

A

Supercoiling

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17
Q

what kind of supercoils do prokaryotes have?

A

plectonemic
supercoils→ negative twist in
DNA, coils back onto itself

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18
Q

what kind of supercoils do eukaryotes have?

A

Solenoidal, with
proteins (higher compaction
needed!)
since there’s so much more DNA!

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19
Q

can prokaryotes have proteins similar to histones for DNA organization and compacting?

A

yes, there can be proteins that provide a bit more structure but they’re not nearly as organized or developed as those found in eukaryotes

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20
Q

In Eukaryotic cell: DNA is folded into ______

A

Chromatin

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21
Q

explain how DNA double-helical structure form chromosomes, which structures are intermediate?

A

double helix
wound on histones to create nucleosomes (euchromatin)
chromatin fiber (heterochromatin)
chromosomes

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22
Q

why does DNA unwind from chromosomes to 10-30 nm fibers?

A

very hard to transcribe, need better access to the DNA so when not actively dividing we unwind!

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23
Q

if we all have the same genes- why are we different?

A

epigenetics!

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24
Q

epigenetic mechanisms are affected by what kinds of things?

A

development
envirpnmental chemicals
drugs
aging
diet

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25
what are the two modifications we can make to DNA to control epigenetics?
DNA methylation histone modification
26
________ components: 1.Genes = [mostly] ORF = open reading frame (ATG-Stop) regulatory regions: 2a. Promoters = RNApol binding sites 2b. Operators = protein binding sites in DNA to regulate transcription; Others – translational regulation (for example)
Bacterial genomes
27
promoter sequences are ______ elements, why?
CIS-acting they must physically be in the area they're acting upon
28
regulatory factors are ______ elements, why?
trans-acting they're movable!
29
what are some main examples of regulatory factors?
proteins and RNA molecules metabolites that use allosteric interactions
30
what is gene finding?
identifying regions of DNA that encode genes—particularly protein-coding genes—within a genome and figuring out their function!
31
what are the key elements of gene finding? (i.e. what are we looking for?)
ORFs start/stop codons promoters and regulatory sequences splice sites (eukaryotes only)
32
what are the advantages and disadvantages of prokaryote genomes?
Advantages  Simple gene structure  Small genomes (0.5 to 10 million bp)  No introns  High coding density (>90%)  Disadvantages  Some genes overlap (nested)  Some genes are quite short (<60 bp)
33
_____: Complex gene structure  Exons and Introns  Large genomes (0.1 to >100 billion bases)  Low coding density (<30%)  3% in humans, 25% in Fugu, 60% in yeast  Alternate splicing (40-60% of all genes)  Considerable number of pseudogenes
eukaryote genome
34
what is an open reading frame?
a continuous stretch of DNA or RNA that could potentially encode a protein. It starts with a start codon and ends with a stop codon, without any stop codons in between.
35
An open reading frame is defined within ___________
one specific reading frame
36
T/F: Since codons are three nucleotides long, any sequence of DNA has three possible reading frames on a single strand (and six total if you count the reverse complement).
true!
37
T/F: there are six possible reading frames for each DNA strand (3 for each strand), but only one open reading frame
true!! our ORF needs to start with the start codon, so the six different frames helps us find the exact 3-base codon we need to start the ORF
38
what are the four ORF/gene finding approaches?
rule-based (start/stop) feature-based (recognizable elements) content based (GC/codon ratio) similarity based (orthologs)
39
________: Look for putative start codon (ATG)  Staying in same frame, scan in groups of three until a stop codon is found  If # of codons >=50, assume it’s a gene (>150 bps)  If # of codons <50, go back to last start codon, increment by 1 & start again  At end of chromosome, repeat process for reverse complement
rule-based gene finding
40
T/F: the number of codons in rule-based gene finding is somewhat arbitrary
true!! the statistics of something being really true or just being chance after 50 codons significantly decreases... why we picked 50!
41
what is fasta format?
>NAME sequence
42
do bacteria have alternate start codons?
yes!! they don't always use ATG for their ORF, allows them to be more flexible!! there are some Class I and Class II Class I: ATG, GTG, TTG Class II: CTG, ATT, ATA, ACG
43
T/F: When applied to whole genomes, simple ORF finding programs tend to overlook small genes and tend to over predict the number of long genes
true!! we either have to prioritize one or the other
44
what do we look for when using feature-based gene finding?
Cis-acting regulatory features (transcription or translation initiation or termination signals) * RNA polymerase binding (promoter) site * Shine-Dalgarno sequence (Ribosome binding site-RBS) * Transcriptional terminators
45
the ______ consists of two short sequences at -10 and - 35 positions upstream from the transcription start site.
promoter
46
The sequence at -10 is called the ________, or the -10 element, and usually consists of the six nucleotides TATAAT
Pribnow or TATA box - where we first pull apart DNA sequence because of the weaker bonds
47
what is the shine-dalgarno motif?
ribosome bindign site located 13 bases upstream of AUG start codon (sequence: 5'- AGGAGGU-3' almost always there!! ribosome has similar sequence to match- the motif recruits the ribosome to the right place- ensuring accurate translation
48
what kind of structures are stem-loop terminators?
cis-acting elements
49
______: Mechanism utilized to terminate transcription via release and dissociation of RNA polymerase
stem-loop terminators rho-independent!!
50
T/F: rho-dependant termination is nearly impossible to predict
true!!
51
T/F: An organism may have changes in relative proportion of A/T to G/C bases in coding regions
true!
52
do organisms have codon preference?
yes!! based on tRNA availability and ratios
53
_______: Take all known genes from a related genome and compare them to the query genome via BLAST
similarity-based gene finding
54
what are the disadvantages to similarity-based gene finding?
Orthologs/paralogs sometimes lose function and become pseudogenes. * Not all genes will always be known in the comparison genome * The best species for comparison isn’t always obvious
55
how has tech improved to mitigate the issues with similarity-based gene finding?
more sophisticated data allows us to pck out likely pseudogenes, many unidentified genes appear repeatedly in different species, can now compare large databases covering many different species at once!
56
______: Modern genomics typically uses a combination of homology, content/feature and rule based methods to identify genes in new genomes
gene annotation
57
T/F: homology replaces experimental characterization
FALSE!!! homology is not infalliable and we still need experimental testing to confirm results
58
why do eukaryote genes have low coding density? what does that mean?
most are not useful and meaningless... lots of junk there's also lots of pseudogenes present... basically glorified fossils from evolution
59
what are the five ways we find eukaryotic genes?
rule-based content-based feature-based similarity-based methods pattern-based
60
why don't we use rule-based gene finding for eukaryotes as much?
not as applicable- too many false positives
61
________: CpG islands, GC content, hexamer repeats,, codon frequencies in eukaryotic genomes
content-based gene finding
62
_______: donor sites, acceptor sites, promoter sites, start/stop codons, polyA signals in eukaryotic genomes
feature-based methods
63
what program do we use to perform sequence homology in similarity-based gene finding
BLAST
64
_______: uses HMMs, Artificial Neural Networks (“AI”)
pattern-based gene finding
65
what is the best way to perform gene finding on eukaryotes?
a combination of all five gene finding methods! eventually have to go to the lab and find out experimentally (physically sequence if no homology)
66
can we use AI to sequence genes?
yes! becoming increasingly popular! lots of different programs available to combine many different search methods

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