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mar bio 106 > Final Exam > Flashcards

Final Exam Flashcards

Things from Unit 4

1
Q

nucleic acids

A

a polymer of nucleotides

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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
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3
Q

RNA

A
  • ribonucleic acid (RNA)
  • has an OH sugar group
  • single stranded
  • carries protein encoding info, helps to make proteins
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4
Q

nucleotide

A
  • monomer of nucleic acid
    contain
  • one phosphate group
  • one sugar group
  • one nitrogenous base
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5
Q

how are nucleic acids formed and broken down?

A

formed through dehydration synthesis
broken down through hydrolysis

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6
Q

nitrogenous bases

A

adenine (A), thymine (T), cytosine (C), guanine (G), uracil (U)
U ~ RNA only
T ~ DNA only

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7
Q

gregor mendel (1822 - 1884)

A
  • patterns of inheritance experiments
  • Law of segregation
  • Law of independent assortment
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8
Q

law of segregation

A

2 separated factors (separated during development of gametes) recombine into one during fertilization

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9
Q

law of independent assortment

A

factors separate randomly when sperm and eggs form

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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)

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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

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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

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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
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14
Q

DNA studies determined…

A

Accumulatively determined that DNA was the inherited material, carrying traits of organisms

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15
Q

purines

A

adenine (2 bond) and guanine (3 bond)
2 ring!

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16
Q

pyrimidines

A

thymine (2 bond) and cytosine (3 bond)
1 ring!

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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
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18
Q

Rosalind Franklin and Maurice Wilkins

A

X-Ray diffraction experiment
- provided mathematical measurement of spacing between base pairs

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19
Q

Watson and Crick Model

A
  • nucleotides in DNA are arranged in a double helix
  • strands are antiparallel, and oriented in opposite directions
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20
Q

Semiconservative replication

A

half of the DNA is replicated, half is conserved

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21
Q

DNA helicase

A

unwinding DNA
unzipping

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22
Q

DNA primase

A

attaches RNA primer

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23
Q

DNA polymerase

A

complementary base pairing

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24
Q

DNA ligase

A

joining base pairs
gluing

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25
Q

starting DNA replication

A
  • DNA pol only binds in 5’ to 3’ direction
  • ## needs a primer to start complementary base pairing
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26
Q

replication fork

A

site of DNA rep on a chromosome

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27
Q

leading strand

A

side of DNA that allows synthesis in 5’ to 3’ direction continuously

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28
Q

lagging strand

A

opposite side of DNA, requires synthesis in segments which are eventually connected by DNA ligase
–> segments known as okazaki fragments

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29
Q

okazaki fragments

A

segments of DNA formed from lagging strand

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30
Q

prokaryotes and DNA replication

A

division can occur in two directions at once because DNA is circular

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31
Q

eukaryotes and DNA replication

A

replication occurs at numerous “bubbles” creating forks. The forks move away until they eventually meet

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32
Q

SSB

A

single stranded binding proteins - keep single stranded DNA stable

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33
Q

transcription

A
  • DNA –> RNA
  • uses mRNA
  • occurs in nucleus
  • writing actual recipe (the template)
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34
Q

translation

A
  • 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
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35
Q

mRNA

A

messenger RNA, used during transcription and translation as middle man for genetic code between DNA and protein, encodes amino acid sequence

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36
Q

tRNA

A

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)
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37
Q

rRNA

A

ribosomal RNA, used in translation, site of protein assembly composed of protein and RNA

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38
Q

transcription - initiation

A

RNA pol attaches promoter sequence to indicate start of transcription

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39
Q

transcription - elongation

A

RNA pol joins complementary nucleotides together in 5 to 3 direction to form new RNA

40
Q

transcription - termination

A

RNA pol encounters a gene stop sequence, copied RNA molecule is released and called an mRNA transcript (is single stranded)

41
Q

pre mRNA

A

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
Q

translation - initiation

A

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
Q

genetic code is…

A

universal to all organisms

44
Q

codon

A

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
Q

translation - elongation

A

peptide (protein) build 1 aa at a time, peptide bonds build together, creating a polypeptide (full protein)
- translocation occurs here

46
Q

translocation

A

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
Q

translation - termination

A

occurs at the stop codon
- release factor cleaves polypeptide
- ribosome dissociates into subunits
- mRNA and new protein are released

48
Q

gene expression in prokaryotes

A

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
Q

prokaryote characteristics

A

no nucleus, capsule, cell wall, DNA ribosomes, plasma membrane, cytoplasm

50
Q

operon

A

a group of regulatory or structural genes that function as a single unit and are found together on a bacterial chromosome

51
Q

transcription factors

A

proteins that bind to DNA to turn an operon “on” or “off”
- Activator “on”
- Repressor “off”

52
Q

promotor

A

short DNA sequence in operon where RNA polymerase attaches to begin transcription of grouped genes

53
Q

operator

A

short portion of DNA located before grouped genes but after the promotor. This is where repression binding occurs.

54
Q

regulator gene

A

gene outside the operon that codes for a repressor

55
Q

bacterial trp operon

A
  • 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
Q

bacterial lac operon

A
  • 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
Q

inducible operon

A

catabolic (breakdown) – lac operon

58
Q

repressible operon

A

anabolic (build up) – trp operon

59
Q

Glucose and lactose relationship

A

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
Q

CAP

A

catabolic activator protein

61
Q

eukaryotic gene expression

what are the defining characteristics? different from prokaryotes?

A
  • 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
Q

mutation

A

any change in a DNA sequence

63
Q

subsitution

A

replacement of one DNA base with another, may or may not change aa sequence

64
Q

insertion

A

adds a nucleotide to a gene

65
Q

deletion

A

removes a nucleotide from a gene

66
Q

frameshift

A

nucleotides are added or deleted by a # other than a multiple of 3
- deletion and insertion can apply

67
Q

cause of mutation

A

spontaneous
- DNA replication error
- meiotic error duplication or deletion
induced
- mutagen is responsible
- UV radiation, x rays, radioactive fallout, pollution, pesticides

68
Q

mutagen

A

an external agent that induces mutations

69
Q

somatic mutations

A

occur in somatic cells
- all cells derived from mutated cell have mutation
- not passed to offspring

70
Q

germline mutations

A

occur in germ cells
- heritable (passed on to every gamete)

71
Q

DNA technology

A

used to manipulate genes for a practical purpose
- research
- medicine
- agriculture
- criminal justice

72
Q

DNA tech use in marine env

A
  • 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
Q

restriction enzymes

A

aka endonucleases
- create sticky ends
- if DNA is cut by same restriction enzymes, different DNA sources can be combined

74
Q

recombinant DNA technology

A

contains DNA from 2 or more sources
- requires a vector (carrier)
- restriction enzyme (cutter)
- DNA ligase (gluer)

75
Q

traditional lab workflow of DNA analysis

A

1) DNA extraction
2) PCR
3) Gel electrophoresis
4) gel extraction
5) sequencing
6) sequence analysis

76
Q

nucleic acid extraction

A

purification of DNA from a sample, involving the breakdown of the membrane in cell (through chemical or physical distruption)

77
Q

PCR

A

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
Q

functions and uses of PCR

A

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
Q

pcr steps

A
  • denaturation (96 C) – splits double strand
  • annealing of primers (50 C)
  • taq pol synthesizes DNA (60 C)

x21 cycles

80
Q

gel electrophoresis

A
  • 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
Q

DNA fingerprinting

A

pcr copies certain regions of DNA, gel electrophoresis separates

82
Q

genetic sequencing

A

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
Q

types of sequencing

A

sanger sequencing, illumina 1 (next generation sequencing), pyrosequencing

84
Q

bioinformatics / sequence analysis

A

running DNA through a program that matches sequence with DNA in database
BLAST (NIH), protein data bank, RDP

85
Q

DNA probes

A

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
Q

oligonucleotide

A

short sequence of DNA, <20 bp long

87
Q

16s RNA

A

mitochondrial DNA that is very conserved, so it evolves very slowly

88
Q

DNA microarrays

A

pieces of DNA for certain genes that are attached to a small glass and if mRNA are present, they bind

89
Q

stem cells

A

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
Q

totipotent stem cells

A

embryonic stem cells, develop into every cell type in the body

91
Q

pluripotent stem cells

A

adult stem cells, develop into a subset of cell types

92
Q

CRISPR

A

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
Q

gene drive

A

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
Q

genomics

A

coding genes, non coding genes

95
Q

transcriptomics

A

mRNAs, small noncoding RNAs long noncoding RNAs

96
Q

proteomics

A

structural proteins, non structural proteins, enzymes, functional proteins

97
Q

metabolomics

A

lipids, amino acids, carbs, nucleotides

mar bio 106 (4 decks)

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