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Flashcards in test 3 Deck (79):
1

what must genetic material be able to do

must contain information
must be capable of replicating itself
must be capable of determining traits
must do some other things

2

must contain info

must have somewhere in molecular structure info that specifies what kind of organism its bearer becomes (directs cellular and organismal processes)

3

must be capable of replicating itself

info stored in dna must be able to be copied to produce 2 molecules with identical base sequence

4

must be capable of determining traits

info coded in base sequence must have meaning that can be decoded (sequence capable of directing cellular activities within organism)
dna directs which proteins are made

5

must do some other things

things such as undergoing chemical and physical changes (mutation) and break apart and join with other dna molecules (as occurs during crossing over)

6

dna replication

watson and crick proposed simple model
hydrogen bonds holding 2 strands of dna are broken and 2 strands come apart (denaturation)
each single stranded molecule now serves as template for synthesis of a new strand which has base sequence that is complementary to template
semi conservative model

7

denaturation

when 2 strands of dna molecule come apart/unwind
occurs when dna molecule heated to 95 degrees C

8

annealing/hybridization

when denatured dna is slowly cooled

9

semi conservative model of replication

each "new" dna double helix actually composed of 1 newly made strand and 1 old strand
original molecule half conserved in new molecule

10

3 possibilities of dna replication

semi conservative
conservative
dispersive

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conservative model

entirely new double helix made from original helix

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meselson and stahl's experiment

in prokaryote (e.coli)
proved semi conservative model

13

taylor, woods, and hughes' experiment

eukaryote
showed that dna was semiconservative in cells of fava bean plant using autoradiography

14

origin of replication

replication fork

15

replication fork

both eukaryotes and prokaryotes
replication starts at replication origin where there is a specific dna sequence

16

prokaryotes replication fork

circular dna so only 1 replication origin
entire chromosome=1 replicon
replication proceeds bidirectionally until 2 replication forks meet on opposite side of chromosome

17

eukaryotes replication fork

replication begins at numerous origins (bc linear molecule)
mammals have about 25000 origins across genome
replication is bidirectional from each origin

18

dna polymerases

main class of enzymes needed for dna replication
can add a nucleotide to 3' OH of primer as directed by template strand
use deoxynucleoside triphosphates (dATP, dGTP, dCTP, dTTP) with pyrophosphate cleaved off during synthesis reaction
phosphodiester bond formed and 3' end of primer extended

19

dna polymerases in prokaryotes

dna polymerase I, II, III
I=primarily repair enzyme
III=main in vivo replication enzyme

20

dna polymerases in eukaryotes

many dna polymerases but sigma primarily responsible for in vivo nuclear dna replication

21

dna helicase

enzyme works at replication fork to break hydrogen bonds and unwind dna

22

SSBs

single stranded binding proteins
bind to denatured single strands to prevent them from collapsing on themselves and help maintain strand in linear form

23

problem of unwinding of helix

unwinding requires rotation of double helix
fixed by topoisomerases like gyrase which allows for rotation

24

problem of dna synthesis only in 5'-->3' direction

replication of 1 strand can proceed without problem but the antiparallel nature of dna means replication must proceed in opposite direction on other strand but there is no primer to attach nucleotide to
solved by primase which attaches primer to allow replication to proceed on antiparallel strand

25

okazaki fragments

short pieces made on discontinuous strand and then joined together

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lagging strand

discontinuous strand
strand with okazaki fragments because bases run in 3'-->5' direction but replication can only go 5'-->3'

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leading strand

continuous strand
strand running in 5'-->3' direction so replication can proceed without okazaki fragments forming

28

5'-->3' exonuclease activity

enzyme with 5'-->3' exonuclease activity must remove rna primer
exonucleases involved in removing rna primer remove 1 nucleotide at a time from 5' end

29

prokaryote exonuclease activity

dna polymerase I (has both 5'-->3' and 3'-->5' exonuclease activity in addition to polymerase activity)
removes rna primer and simultaneously synthesizes new dna to replace it

30

eukaryote exonuclease activity

RNase H (special exonuclease)
appears to work along with other exonucleases to remove rna primer in 5'-->3' direction

31

dna ligase

small gap between okazaki fragments joined and sealed by this enzyme

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eukaryotic telomerase

telomeres (region at end of chromosome) help protect chromosomes from deterioration but they get shorter over time
telomerase repairs telomeres and lengthens them

33

in vitro replication

pcr
used to make many copies of one segment of dna

34

protein synthesis involves

transcription (rna synthesis)
translation (polypeptide synthesis)

35

polypeptides

chains of amino acids joined by peptide bonds

36

gene

dna coding for 1 polypeptide (one gene, one polypeptide)

37

transcription

dna directed rna synthesis
sequence of segment of dna molecule determines sequence of rna
process of making mrna, rrna, trna, and other small rna's

38

rna

rna similar to dna in structure
usually shorter
one stranded
ribose instead of deoxyribose
uracil instead of thymine

39

rna polymerase

enzyme that transcribes dna
uses nucleoside triphosphates (atp, gtp, ctp, utp)
rna polymerization occurs just like dna polymerization
begins at 5' end and new rna molecule grows in 5'-->3' direction
uses 1 strand of dna molecule as template strand to specify which rna nucleotides will be added
newly made rna molecule antiparallel to template dna
DOES NOT NEED PRIMER (can start new rna molecule with single NTP)

40

what does first nucleotide of rna molecule have

3 phosphates on 5' end

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template strand

strand of dna used to make rna

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non-template strand

strand of dna not used to make rna

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transcript

rna molecule made by transcription

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promoter

site where rna polymerase binds and begins transcription

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termination site

where transcription stops

46

rna processing

in eukaryotes pre-mrna molecules undergo considerable processing before leaving nucleus and directing translation
3 parts of rna processing:
5' cap
poly-A tail
splicing

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poly-A tail and cap

addition of cap on 5' end
poly-A tail on 3' end (made up of many A bases)

48

splicing

removal of introns and leaving of exons

49

translation

follows transcription
meaning of informational rna molecule decoded
process by which rna base sequence used to direct synthesis of specific polypeptide with specific amino acid sequence

50

eukaryote translation

follows rna processing and occurs after mrna leaves nucleus through nuclear pore and travels to cytoplasm
2 processes are temporally and spacially separated

51

prokaryote translation

translation begins before transcription is finished (occur simultaneously) and occur in same place

52

things that must be present for translation to occur

mrna molecule
ribosome
charged transfer rna's (trna)

53

transfer rna (trna)

single stranded rna 70-80 bases in length
all have common sequences
at least 1 trna for every amino acid
amino acid covalently bonds to trna creating charged trna
each trna designated with a superscript that indicates which amino acid it will bind
trna have various modified bases

54

trna 3-D structure

all have same general shape
cloverleaf shape with internal base paring holding cloverleaf in place (cloverleaf actually folds in on itself producing more complex 3-D structure)

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3' CCA

all trna's have trinucleotide CCA at 3' terminus
amino acids attach here
3' CCA at one end of folded trna and anticodon on other end

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anticodon

3 bases in the middle of trna sequence make up anticodon (actually on 1 end after cloverleaf forms and folds up)
3 bases unique for each trna and hydrogen bond to codon of mrna during translation

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aminoacyl-trna synthetases

catalyst for attachment of an amino acid to the trna
specific enzyme for each amino acid/trna pair

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ribosomes

sites where actual protein synthesis occurs
similar in composition in prokaryotes and eukaryotes
large and small subunit which come together

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mrna

already undergone extensive processing in eukaryotes
mrna used in translation has several features
untranslated region, cap, poly-A tail

60

untranslated region

region before beginning of coding sequence and after coding sequence end
front=5' untranslated region (5' UTR)
end=3' untranslated region (3' UTR)

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polycistronic mrnas

prokaryotes often have long mrnas that code for more than 1 polypeptide

62

translation 3 stages

initiation
elongation
termination

63

initiation

same in prokaryotes and eukaryotes
special charged trna and 5' end bind to small ribosomal subunit
involves various protein factors
assembled ribosome has 3 potential trna binding sites: A (aminoacyl site), P (pepitdyl site), and E (exit site)

64

elongation

polypeptide grows from amino to carboxyl end as new amino acids arrive at the A site bound to their respective trnas
several ribosomes (polysome/polyribosome) may be translating a given mrna at any time

65

termination

when codon for which there is no trna with complementary anticodon comes into A site translation terminates
terminator codons: UAA, UAG, UGA (also called nonsense codons)
instead of trna binding to open A site a release factor binds there and stops protein synthesis

66

genetic code

table of codons showing which codons specify which amino acids

67

features of genetic code

triplet: 3 bases per 1 amino acid
standard: same code used in all organisms
non-ambiguous: given codon always encodes same amino acid
degenerate: more than 1 codon possible for most amino acids (64 codons, 20 amino acids)--accomplished primarily through wobble pairing at third codon position

68

gene expression

process of gene producing certain functional gene product (such as a protein)
all genes are present in all cells but not all genes are expressed all the time in all tissues (gene expression regulated)
regulation mostly occurs at transcription

69

gene regulation in prokaryotes

set of 3 genes encoded by single polycistronic mrna are turned on when lactose is present in the medium (lac operon)
3 genes produce proteins needed to utilize lactose as nutrient
turning on these genes means their polycistronic mrna is being transcribed (3 proteins being made)
when lactose absent 3 genes are turned off (not made)
negative control (bc something binds to dna and prevents transcription)
regulation of expression in lac operon was first to be described and serves as model for expression of many other prokaryotic genes

70

eukaryotic transcriptional regulation

histones
positive and negative transcriptional control
epigenetic changes

71

histones

dna tightly bound by histones cannot be transcribed so histones must be removed for transcription to occur
may involve conversion of heterochromatin to euchromatin as well as chromatin remodeling (removal of histones)

72

heterochromatin

extremely tight coiling of dna

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euchromatin

more relaxed but still coiled dna

74

positive transcriptional control

regulation of gene expression may involve enhancer and specific transcription activator proteins
enhancer is dna segment to which transcriptional activator (protein) binds and causes rna plymerase to bind to promoter (turning on transcription)

75

negative transcriptional control

proteins that can bind to dna and block transcription (like repressor protein of prokaryotic lac operon)
regulation occurs by interplay between repressor protein, promoter, and operator

76

epigenetic changes

methylation of dna suppresses transcription and is a common method the cell uses to turn off gene
methyl can be passed on in replication

77

post transcriptional regulation

alternate splicing of pre-mrna
sirnas and mirnas

78

slternate splicing of pre-mrna

splicing doesn't always occur the same way so 1 gene may code for more than 1 polypeptide

79

siRNA and miRNA

bind to mrna and prevent translation of rna from occuring