Final Exam Flashcards
Things from Unit 4 (97 cards)
1
Q
nucleic acids
A
a polymer of nucleotides
2
Q
DNA
A
- deoxyribonucleic acid (DNA)
- Has an H sugar group
- double helix structure
- stores RNA and protein encoding info transfers into next generation of a cell
3
Q
RNA
A
- ribonucleic acid (RNA)
- has an OH sugar group
- single stranded
- carries protein encoding info, helps to make proteins
4
Q
nucleotide
A
- monomer of nucleic acid
contain - one phosphate group
- one sugar group
- one nitrogenous base
5
Q
how are nucleic acids formed and broken down?
A
formed through dehydration synthesis
broken down through hydrolysis
6
Q
nitrogenous bases
A
adenine (A), thymine (T), cytosine (C), guanine (G), uracil (U)
U ~ RNA only
T ~ DNA only
7
Q
gregor mendel (1822 - 1884)
A
- patterns of inheritance experiments
- Law of segregation
- Law of independent assortment
8
Q
law of segregation
A
2 separated factors (separated during development of gametes) recombine into one during fertilization
9
Q
law of independent assortment
A
factors separate randomly when sperm and eggs form
10
Q
knowledge about genetic material (during Gregor Mendel time, 1822-1884)
or rather, what are the requirements of genetic material?
A
1) Had to store info related to structure and function of cells
2) stable enough to replicate repeatedly
3) able to have small changes that don’t hurt organism but maintain variability in population (mutations)
11
Q
chromosome theory (1902 /1908)
A
Walter Sutton and Theodor Boveri independently conclude that chromosomes are involved in matter of genetics through staining cells undergoing meiosis and mitosis
12
Q
Avery et al (1944)
A
comparing disease causing vs non disease causing bacteria
- Evidence for DNA
1) DNA not proteins from S strain cause R strain bacteria to be “transformed” and become virulent
2) DNase (enzyme that breaks down DNA) stops R strain from becoming virulent
3) addition of enzymes to degrade proteins or addition of RNase did not stop R strain from becoming virulent
13
Q
Hershey-Chase Experiment (1952)
A
- T bacteriophage composed of radioactively labeled DNA or capsid proteins
- radioactive tracers on DNA were transmitted to bacterial cells but not radioactive proteins
14
Q
DNA studies determined…
A
Accumulatively determined that DNA was the inherited material, carrying traits of organisms
15
Q
purines
A
adenine (2 bond) and guanine (3 bond)
2 ring!
16
Q
pyrimidines
A
thymine (2 bond) and cytosine (3 bond)
1 ring!
17
Q
Chargaff’s experiment
A
- % of each nucleotide differs from species to species
- % is same for A & T
- % is the same for C & G
18
Q
Rosalind Franklin and Maurice Wilkins
A
X-Ray diffraction experiment
- provided mathematical measurement of spacing between base pairs
19
Q
Watson and Crick Model
A
- nucleotides in DNA are arranged in a double helix
- strands are antiparallel, and oriented in opposite directions
20
Q
Semiconservative replication
A
half of the DNA is replicated, half is conserved
21
Q
DNA helicase
A
unwinding DNA
unzipping
22
Q
DNA primase
A
attaches RNA primer
23
Q
DNA polymerase
A
complementary base pairing
24
Q
DNA ligase
A
joining base pairs
gluing
25
starting DNA replication
- DNA pol only binds in 5' to 3' direction
- needs a primer to start complementary base pairing
-
26
replication fork
site of DNA rep on a chromosome
27
leading strand
side of DNA that allows synthesis in 5' to 3' direction continuously
28
lagging strand
opposite side of DNA, requires synthesis in segments which are eventually connected by DNA ligase
--> segments known as okazaki fragments
29
okazaki fragments
segments of DNA formed from lagging strand
30
prokaryotes and DNA replication
division can occur in two directions at once because DNA is circular
31
eukaryotes and DNA replication
replication occurs at numerous "bubbles" creating forks. The forks move away until they eventually meet
32
SSB
single stranded binding proteins - keep single stranded DNA stable
33
transcription
- DNA --> RNA
- uses mRNA
- occurs in nucleus
- writing actual recipe (the template)
34
translation
- RNA --> protein
- uses mRNA, tRNA, and rRNA
- occurs in cytoplasm by ribosomes
- reading recipe to make baked good (product)
- involves a set of rules that cells use to assemble correct sequences of amino acids
35
mRNA
messenger RNA, used during transcription and translation as middle man for genetic code between DNA and protein, encodes amino acid sequence
36
tRNA
transfer RNA, used in translation, transfers amino acids to ribosome for protein formation, physically links message in mRNA to an amino acid with an anticodon, carries amino acid to correct placement on mRNA
- ACCEPTOR END - that holds animo acid (aminoacyl-tRNA synthases are responsible for attachment of aa to tRNA)
- ANTICODON END - 3 bases that are complementary and antiparallel to a specific mRNA codon (at least one for each of the 20 aa's)
37
rRNA
ribosomal RNA, used in translation, site of protein assembly composed of protein and RNA
38
transcription - initiation
RNA pol attaches promoter sequence to indicate start of transcription
39
transcription - elongation
RNA pol joins complementary nucleotides together in 5 to 3 direction to form new RNA
40
transcription - termination
RNA pol encounters a gene stop sequence, copied RNA molecule is released and called an mRNA transcript (is single stranded)
41
pre mRNA
exons - protein coding regions (are expressed)
introns - non protein coding regions ("in the way")
- cap and poly A tail are added
- spliceosomes cut intron RNA
42
translation - initiation
large ribosomal unit has 3 tRNA binding sites
--> E: EXIT
--> P: PEPTIDE SITE
--> A: AMINO ACID SITE
- small ribosomal unit binds to mRNA, initiation tRNA pairs with mRNA start codon AUG
- ribosomal subunit completes ribosome, initiator tRNA occupies P site, A site is ready for next tRNA
43
genetic code is...
universal to all organisms
44
codon
3 base sequence of nucleotides, codes for a specific amino acid
- translator of RNA language into protein language
- all 20 amino acids make up genetic code
- start codon: AUG --> methionine
- stop codons: UAA, UAG, UGA
45
translation - elongation
peptide (protein) build 1 aa at a time, peptide bonds build together, creating a polypeptide (full protein)
- translocation occurs here
46
translocation
occurs as ribosome moves forward on mRNA as a whole during translation
- spent tRNA is in in E site
- peptide bearing tRNA is in P site
47
translation - termination
occurs at the stop codon
- release factor cleaves polypeptide
- ribosome dissociates into subunits
- mRNA and new protein are released
48
gene expression in prokaryotes
expression occurs when product (protein or RNA) is made and operating in cell
- has transcription factors, that bind DNA to turn an operon "on" or "off"
49
prokaryote characteristics
no nucleus, capsule, cell wall, DNA ribosomes, plasma membrane, cytoplasm
50
operon
a group of regulatory or structural genes that function as a single unit and are found together on a bacterial chromosome
51
transcription factors
proteins that bind to DNA to turn an operon "on" or "off"
- Activator "on"
- Repressor "off"
52
promotor
short DNA sequence in operon where RNA polymerase attaches to begin transcription of grouped genes
53
operator
short portion of DNA located before grouped genes but after the promotor. This is where repression binding occurs.
54
regulator gene
gene outside the operon that codes for a repressor
55
bacterial trp operon
- tryptophan is one of the 20 amino acids
- bacteria need tryptophan to create proteins during translation
- trp operon is default "on" because tryptophan is regularly needed
- repressor is always made but cannot bind to operator unless trp is present
- IF trp is present, bacteria turn the trp operon "off"
- trp is a corepressor
56
bacterial lac operon
- lactose is a type of carb (sugar) molecule that can be broken down to create energy (ATP)
- lac operon is default "off" because lactose is not always available
- repressor is always made and is actively bound to operator to PREVENT transcription of the operon
- if there is a lactose available, bacteria turn lac operon "on" so enzymes that break it down are produced
- lactose is an inducer
57
inducible operon
catabolic (breakdown) -- lac operon
58
repressible operon
anabolic (build up) -- trp operon
59
Glucose and lactose relationship
if there is both glucose and lactose available, bacteria slow the lac operon, and break glucose down first
- cAMP (cyclic adenosine monophosphate) is the activator
60
CAP
catabolic activator protein
61
eukaryotic gene expression
| what are the defining characteristics? different from prokaryotes?
- initiation of transcription: efficient binding = increased speed
- exon splicing: (introns are cut, exons are kept)
- passage through nuclear membrane: (mRNA receptors control message)
- destruction of mRNA
- translation control (outside nucleus, the availability of aa's)
62
mutation
any change in a DNA sequence
63
subsitution
replacement of one DNA base with another, may or may not change aa sequence
64
insertion
adds a nucleotide to a gene
65
deletion
removes a nucleotide from a gene
66
frameshift
nucleotides are added or deleted by a # other than a multiple of 3
- deletion and insertion can apply
67
cause of mutation
spontaneous
- DNA replication error
- meiotic error duplication or deletion
induced
- mutagen is responsible
- UV radiation, x rays, radioactive fallout, pollution, pesticides
68
mutagen
an external agent that induces mutations
69
somatic mutations
occur in somatic cells
- all cells derived from mutated cell have mutation
- not passed to offspring
70
germline mutations
occur in germ cells
- heritable (passed on to every gamete)
71
DNA technology
used to manipulate genes for a practical purpose
- research
- medicine
- agriculture
- criminal justice
72
DNA tech use in marine env
- fisheries forensics (enforcing fishing laws, IUU fishing, ID'ing fish on market)
- environmental DNA (eDNA) to ID whales
- octopus genome and evolution of neural and morphological novelties
- striped bass eDNA in the Saco River
73
restriction enzymes
aka endonucleases
- create sticky ends
- if DNA is cut by same restriction enzymes, different DNA sources can be combined
74
recombinant DNA technology
contains DNA from 2 or more sources
- requires a vector (carrier)
- restriction enzyme (cutter)
- DNA ligase (gluer)
75
traditional lab workflow of DNA analysis
1) DNA extraction
2) PCR
3) Gel electrophoresis
4) gel extraction
5) sequencing
6) sequence analysis
76
nucleic acid extraction
purification of DNA from a sample, involving the breakdown of the membrane in cell (through chemical or physical distruption)
77
PCR
rapid amplification of DNA, next step needs a lot of DNA, so this process makes a little bit of DNA into many many copies (A lot of DNA)
78
functions and uses of PCR
use
- familial relationship
- id disease causing agents
- env sci
- criminal justice
- evolutionary id
function
- mimics processes of DNA replication in cell
- amplifies only a target gene if a specific primer is used
79
pcr steps
- denaturation (96 C) -- splits double strand
- annealing of primers (50 C)
- taq pol synthesizes DNA (60 C)
x21 cycles
80
gel electrophoresis
- separation of DNA by length
- DNA is negatively charged, so it moves towards positive charge
- smaller the piece, the further it moves
- ladders are used to determine distance DNA fragments travel
81
DNA fingerprinting
pcr copies certain regions of DNA, gel electrophoresis separates
82
genetic sequencing
understanding exact order of DNA strand
needs
- DNA
- replication enzymes
- primers
- normal nucleotides
- labeled nucleotides (terminators)
steps
- replication occurs, labelling base pairs with terminators
- capillary gel electrophoresis sorts by size and scans fluorescent tags
- computer generates readout of sequence through color coding
83
types of sequencing
sanger sequencing, illumina 1 (next generation sequencing), pyrosequencing
84
bioinformatics / sequence analysis
running DNA through a program that matches sequence with DNA in database
BLAST (NIH), protein data bank, RDP
85
DNA probes
single stranded sequence of nucleotides that is used to detect a complementary sequence
- allows targetted isolation of certain genes
- labelled with radioactive isotopes or fluorescent tags
IF BINDING OCCURS
- target allele is detected
IF BINDING DOES NOT OCCUR
- target allele is not detected
86
oligonucleotide
short sequence of DNA, <20 bp long
87
16s RNA
mitochondrial DNA that is very conserved, so it evolves very slowly
88
DNA microarrays
pieces of DNA for certain genes that are attached to a small glass and if mRNA are present, they bind
89
stem cells
any undifferentiated cell that can give rise to any cell type
- when divided, one remains a stem cell while the other is differentiated
--> as development occurs, more cells are permentantly differentiated
--> lot of ethical concern about use of stem cell technology especially when harvested from embryos
90
totipotent stem cells
embryonic stem cells, develop into every cell type in the body
91
pluripotent stem cells
adult stem cells, develop into a subset of cell types
92
CRISPR
clustered regularly interspaced short palindromic repeats
- used to edit genes by replacing specific nucleotides
- can install more transcription factors
- installing transcription inhibitors
- fluorescently labelling CRISPR to ID where action is happening...
93
gene drive
copies mutation made by CRISPR on one chromosome into its partner chromosome, ensuring that all offspring will inherit (to stop the expression of a certain phenotype....) ecological effects?
94
genomics
coding genes, non coding genes
95
transcriptomics
mRNAs, small noncoding RNAs long noncoding RNAs
96
proteomics
structural proteins, non structural proteins, enzymes, functional proteins
97
metabolomics
lipids, amino acids, carbs, nucleotides
