Nucleic Acids: Structure & Function Flashcards Preview

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Flashcards in Nucleic Acids: Structure & Function Deck (88):
1

plasma membrane

single phospholipid bilayer
- contains proteins embedded into its bilayers

2

nuclear membrane

continuous double phospholipid bilayer (inner & outer)
- contains proteins embedded into its bilayers

3

nucleolus

responsible for ribosomal RNA processing and assembling ribosomal subunits
- site of ribosome assembly

4

gene

a sequence of DNA—located at a specific locus—with a specific job or function

- made up of proteins

5

metabolic pathway

a linked series of biochemical reactions that build up or break down a particular molecule
- product of one reaction is the substrate of the next reaction

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locus

location on a chromosome

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allele

gene sequence variability, which leads to variations in the gene function

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nuclear localization signal (NLS)

a short amino acid sequence that marks a protein for delivery to nucleus

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components of a nucleic acid

(1) phosphate group

(2) 5 carbon sugar

(3) nitrogenous base

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antiparallel

opposing orientation of nucleic acid strands that are hydrogen bonded to one another
- one strand = 5’ -> 3’
- another strand = 3’ -> 5’

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complementary base pairs

pair of bases that only bond to one another
- A + T or A + U = 2 H-bonds
- G + C = 3 H-bonds

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ribozyme

RNA enzyme that act as a catalyst by speeding up a chemical reaction
- contains uracil instead of thymine

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genotype

alleles of a gene
- determined by sequence of bases in its DNA

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phenotype

physical traits expressed according to a genotype
- product of proteins it produces

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central dogma

scheme for information flow in the cell: DNA S RNA S protein

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types of transportation through nuclear pores

(1) nuclear export signal (mRNA)

(2) nuclear localization signal (lamin)

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nucleotide structure

1' - base

2' - R (DNA or RNA) = OH or H

3' - OH (polymer)

4' - connect to 5'

5' - phosphate

(1B 2R 3OH 45 5P)

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purine

class of small, nitrogen-containing, double-ringed bases found in nucleotides
- bases: adenine & guanine

*linked juntos by 9 atoms

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pyrimidine

class of small, nitrogen-containing, single-ringed bases found in nucleotides
- bases: cytosine, thymine OR uracil

*linked juntos by 6 atoms

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polymer properties

(1) condensation reaction

(2) phosphodiester bond

(3) sugar-phosphate backbone

(4) 5' & 3' ends

(5) primary structure depends on order of nucleotides

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primary structure

depends on order of nucleotides

- consists of sugar-phosphate backbone (phosphodiester linkages + sequence of 4 types of bases)
- RNA < stable than DNA
- supports catalytic activity in molecule

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secondary structure

depends on H-bonds

- result of complementary base pairing btwn purine & pyrimidine bases
- section where fold occurs =unpaired bases + stem-&-loop configuration

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nucleic acid functions in DNA

make up genetic material

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nucleic acid functions in RNA

(1) gene expression (mRNA, tRNA, rRNA, siRNA)

(2) ribozymes

(3) ATP & GTP

(4) genetic material in some viruses

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Watson & Crick

credited for discovery of DNA structure
- used Rosalind Franklin's collected data but she was not credited
- basically trial & error

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DNA structure

(1) double-stranded = secondary structure

(2) antiparallel

(3) self-perpetuating - can only be replicated/connected in 1 way

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types of RNA

(1) messenger RNA, mRNA

(2) transfer RNA, tRNA

(3) siRNA

(4) rRNA

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messenger RNA (mRNA)

complimentary to DNA
- carry info required to manufacture proteins

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ribosomal RNA (rRNA)

forms part of ribosome
- manufactured in nucleolus
- bind to proteins -> ribosomes
- machinery

*most RNA

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transfer RNA (tRNA)

interacts w/ amino acids & RNA

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siRNA

gets rid of mRNA
- regulates translation

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central dogma

scheme for info flow in cell

(1) DNA - info storage

TRANSCRIPTION

(2) mRNA - info carrier

TRANSLATION

(3) proteins - active cell machinery

[DNA -> RNA -> protein]

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reverse transcription

RNA becomes DNA

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translation

nonreversiable

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types of proteins

(1) cytosolic proteins

(2) lumenal proteins

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genetic code property

must be triplet code
- triplet code allows for more amino acids

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reading frame

3 combo letters stand for specific amino acid
- always start w/ AUG (start codon)
- 3 stop codons

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gene characteristics

(1) redundant

(2) unambiguous

(3) nearly universal

(4) conservative

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redundant gene

more than 1 codon

all amino acids (except methionine & tryptophan) are coded by more than 1 codon

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unambiguous gene

know codon, know amino acid

single codon never codes for more than 1 amino acid

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nearly universal gene

all codons specify the same amino acids in all orgs
- few minor exceptions

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conservative

several codons specify the same amino acid

1st 2 bases in those codons are almost always identical

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mutations

(1) single base change

(2) few bases change

(3) part of chromosome change

(4) whole chromosome changes

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karyotype

spread of all chromosome

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RNA world hypothesis

chemical evolution produced RNAs that could catalyze key reactions involved in their own replication & basic metabolism

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nucleic acid

macromolecule composed of nucleotide monomers

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nucleic acid properties

(1) polymer

(2) made up of nucleotides

(3) stores & processes info

(4) examples: DNA & RNA

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types of nucleotides in living cells

(1) ribonucleotide (RNA)

(2) deoxribonucleotide (DNA)

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ribonucleotides (RNA)

monomers of ribonucleic acid
- sugar: ribose

*more stable than DNA

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deoxyribonucleotide (DNA)

monomers of deoxyribonucleic acid
- sugar: deoxyribose
- carries info required for org's growth & reproduction

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phosphodiester linkage/bond

chemical linkage btwn adjacent nucleotide residues in DNA & RNA
- result of: condensation reaction

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nucleic acid directionality

(1) 5' end = phosphate

(2) 3' end = hydroxyl

(3) base sequence always written in 5'-3' direction

(4) bases only added at 3' end of growing molecule

(5) primary

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adenine triphosphate (ATP)

molecule consisting of adenine base, sugar & 3 phosphate groups that can be hydrolyzed to release energy
- universally used by cells to store & transfer energy

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DNA points to prove (Watson/Crick)

(1) sugar phosphate backbone

(2) Erwin Chargaff empirical rules (# purines = # pyrimidines)

(3) DNA = helical (Rosalind Franklin)

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complementary strand

new strand of RNA or DNA that has a base sequence complementary to template strand

5'-3'

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template strand

original DNA strand

3'-5'

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DNA double helix

(1) highly structured

(2) regular

(3) symmetric

(4) held together via H-bonds + hydrophobic interactions + phosphodiester bonds

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hairpin

a stable loop formed by H-bonds btwn purine & pyrimidine bases on same strand
- reduces entropy of RNA molecules
- secondary structure in RNA

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tertiary structure

3-D folding
- arises when secondary structures fold into more complex shapes

*not present in DNA

60

nucleus

info center of eukaryotic cells
- corporate headquarters
- design center
- library
- highly organized interior

61

nuclear lamina

lattice-like sheet of fibrous nuclear lamins
- type of intermediate filament
- lines inner membrane of nuclear envelope
- stiffens envelope
- organizes chromosomes
- defines organelle's overall shape & structure

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nuclear envelope

separates nucleus from rest of cell

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nuclear pore

opening in nuclear envelope
- connects inside of nucleus w/ cytoplasm
- molecules (mRNA & some proteins) pass through here

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nuclear pore complex

large complex of dozens of proteins lining a nuclear pore, defining its shape & regulating transport through pore

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zip code

molecular address tag
- marks them for transport through nuclear pore complex
- allows nuclear pore complex to open in some way that permits larger proteins & RNA molecule to pass through

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RNA polymerase

enzyme that catalyzes the synthesis RNA molecules from ribonucleotides according to info provided by sequence of bases using a DNA template

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exceptions to central dogma

(1) many genes code for RNA molecules that ≠ fcn as mRNAs -> translated into proteins

(2) info flows from RNA back to DNA

(3) reverse transcriptase

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reverse transcriptase

enzyme that can synthesize double-stranded DNA from a single-stranded RNA template
- RNA virus infecting cells use this mode of synthesis

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genetic code

set of all codons & their meanings
- rules that specify relationship btwn nucleotide sequence in DNA or RNA & amino acid sequence in proteins
- triplet code

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reading frame

series of non-overlapping, 3-base-long sequence (potential codons) in DNA or RNA

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start codon

AUG triplet in mRNA @ which protein synthesis begins
- codes for amino acid, methionine

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stop codon

any of 3 mRNA triplets (UAG, UGA, or UAA) that cause termination of protein synthesis
- signals protein = complete
- does not code for an amino acid
- ends translation

(aka) termination codon

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mutation

any permanent change in an org’s DNA
- create new alleles
- modification in cell’s info archive
- alter DNA sequences that range in size from a single base pair in DNA to whole sets of chromosomes

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point mutation

mutation result in change of single base pair in DNA

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types of point mutation

(1) missense mutation

(2) silent mutation

(3) frameshift mutation

(4) nonsense mutation

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missense mutation

point mutation that changes 1 amino acid for another w/in protein sequence

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silent mutation

point mutation that changes codon sequence w/out changing amino acid that is specified

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frameshift mutation

addition or deletion of nucleotide in a coding sequence that shifts the reading frame of mRNA
- alters meaning of all subsequent codons

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nonsense mutation

point mutation that converts an amino-acid specifying codon into a stop codon
- large effect
- causes early termination of polypeptide chain
- often results in a non-fcnal protein

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mutation categories

(1) beneficial

(2) neutral

(3) deleterious

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beneficial mutation

mutation ↑ org fitness (ability to survive/reproduce) in certain environ

(ie) G-to-A mutation (beach habitats) camouflages mice

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neutral mutation

mutation has no effect on fitness

(ie) silent mutation

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deleterious mutation

mutation, allele, or trait that ↓ individual’s fitness
- harmful

(ie) cancerous cell chromosomes = aneuploidy + inversions + translocations + deletions + duplications

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changes in chromosomes

(1) inversion

(2) translocation

(3) deletion

(4) duplication

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inversion

mutation in which chromosome segment breaks from rest of chromosome, flips & rejoins in reversed orientation

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translocation

attached to a different chromosome

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deletion

chromosome segment is lost

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duplication

additional copies of segment present