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Biology 3/4 > chap 2- nucleic acids > Flashcards

chap 2- nucleic acids Flashcards

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1
Q

What are nucleic acids

A

biomacromolecules. They are like proteins and are essential for all forms of life and are found in all cells

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2
Q

what are biomacromolecules

A

bio- produced by organisms
macro- large
molecules- a group of atoms bonded together

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3
Q

What are the two types of nucleic acids

A

DNA and RNA

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4
Q

nucleic acids are polymers, what are their monomers?

A

nucleotides

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5
Q

What are polymers

A

large molecules made of a chain of monomers that are chemically bonded

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6
Q

What are monomers

A

the building blocks of polymers

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7
Q

What does a nucleotide consist of

A

a phosphate group, a 5- carbon pentose sugar, a nitrogen base

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8
Q

What are the nitrogen bases

A

A,G,C,T,U

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9
Q

Where is uracil found

A

only in RNA

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10
Q

What does uracil replace in RNA

A

thymine

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11
Q

What structure are purines

A

a 2 ring structure. one that is 6 membered the other is 5 membered

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12
Q

what structure are pyrimidines

A

they have a 6 membered ring

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13
Q

what are the purines

A

guanine and adenine

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14
Q

what are pyrimidines

A

cytosine, thymine, uracil

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15
Q

Why is there a base pairing rule

A

so that a smaller pyrimidine will pair with a larger purine. forming hydrogen bonds between them to ensure they have a fixed distance between them

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16
Q

what is a hydrogen bond

A

an attraction between a hydrogen atom and an electronegative atom of nitrogen, oxygen and fluorine.

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17
Q

what is the base pairing rule

A

A-T
C-G

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18
Q

what does condensation polymerization involve

A

the synthesis of a polymer and releases water as a byproduct

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19
Q

what is condensation polymerization

A

how nucleotides join to form nucleic acids

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20
Q

how does condensation polymerization work

A

the hydroxyl (OH) group on the 3’ end of sugar combines with hydrogen from hydroxyl group of the phosphate. creating H2O. holds monomers together

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21
Q

is DNA stable

A

Yes

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22
Q

What does DNA do

A

carry and pass on genetic information of organisms through generations

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23
Q

what do DNA molecules consist of

A

2 strands of nucleotide polymers wound around eachother

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24
Q

what does the order of DNA code determine

A

which products are synthesized

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25
Q

how do you label 3’ and 5’ carbons on DNA

A

count clockwise from oxygen at top of pentose sugar

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26
Q

What sugar does DNA have

A

deoxyribose sugar

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27
Q

What sugar does RNA have

A

ribose sugar

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28
Q

What is the antiparallel nature of DNA

A

one strand will run in the 5’ to 3’ direction with the carbon pointing upwards. the other stand will run 3’ to 5’ direction with the 5’ carbon pointing downwards.

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29
Q

what are histones

A

small proteins that DNA winds around

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30
Q

what are nucleosomes

A

consist of 8 histone proteins which coil DNA

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31
Q

what do nucleosomes do

A

fold up to form chromatin fiber which forms loops

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32
Q

what is the chromatin in a chromosome made up of

A

loops that are compressed folded and tightly coiled

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33
Q

What is the process gene expression for

A

the process which the info used to direct the assembly of a protein molecule

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34
Q

what is a gene

A

a small section of DNA that is a basic unit of heredity

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35
Q

what does gene regulation do

A

conserve energy and materials within a cell

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36
Q

for a gene to be expressed it needs to be:

A

transcribed, processed in the nucleus, translated in the cytoplasm with ribosomes help

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37
Q

what do upstream and downstream sections of DNA indicate

A

where transcription should begin and end

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38
Q

what is the structure of a gene

A

stop/start triplet sequences, promoter regions, exons and introns

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39
Q

what does the start triplet indicate

A

where transcription will begin

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40
Q

what does a stop triplet indicate

A

where transcription ends

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41
Q

where are promoter regions of a gene found

A

before start at the 5’ end of the site where RNA polymerase attaches ready to begin transcription

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42
Q

what are promoter regions

A

binding regions upstream of the gene where RNA polymerase can bind in order for transcription to occur

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43
Q

what are exons

A

regions of the gene that code for an amino acid and are usually expressed as proteins or RNA

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44
Q

what do exons make up when joined together

A

mature mRNA

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45
Q

what are introns

A

non-coding regions of a gene

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46
Q

when are introns taken out of mRNA

A

during RNA processing

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47
Q

What is protein synthesis

A

a smaller single stranded mRNA molecule is created through transcription so that a section of DNA can leave the nucleus

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48
Q

what is RNA structure

A

single stranded, ribose sugar, uracil,

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49
Q

what are the 3 types of RNA

A

mRNA, rRNA, tRNA

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50
Q

when/where are mRNA molecules formed

A

in the nucleus during transcription

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51
Q

what is mRNA responsible for

A

carrying a copy of the nucleotide sequence of DNA that specifies the amino acid sequence out of the nucleus to a ribosome where the message can be translated

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52
Q

what structure does tRNA have

A

folded structure

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53
Q

what does tRNA do

A

match an mRNA codon with the amino acid it codes for

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54
Q

where is rRNA synthesised

A

in the nucleolous

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55
Q

what does rRNA do

A

with help of proteins forms organelle ribosome

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56
Q

what do ribosomes do

A

where info in mRNA is translated into chain of amino acids which can then be folded into a protein

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57
Q

what is the template strand of DNA

A

RNA polymerase reads template strand during transcription so that mRNA is same as DNA coding strand but it has U instead of T

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58
Q

what does transcription do

A

make an RNA copy of the DNA code

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59
Q

what are the 3 steps of transcription

A

initiation, elongation, termination

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60
Q

what happens during initiation (transcription)

A

RNA polymerase attaches to promoter region and unwinds DNA strand by breaking hydrogen bonds that hold the 2 strands together exposing nitrogenous bases

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61
Q

What happens during elongation (transcription)

A

RNA Polymerase moves along template strand in 3’ to 5’ direction. free nucleotides are attached to their complimentary base pairs and as RNA P moves along strand mRNA is produced

62
Q

at what end are nucleotides added

A

3’ end

63
Q

what happens during termination (transcription)

A

when RNA polymerase reaches stop tiplet transcription ends. this releases chemicals that signals termination and the RNA polymerase detaches releasing the mRNA strand and allowing DNA to reform

64
Q

what does the finished product of transcription carry

A

the same base sequence as coding strand of DNA except U instead of T

65
Q

What does RNA processing do

A

turns pre-mRNA into mature mRNA which is ready to leave the nucleus.

66
Q

what is step 1 of RNA processing

A

methyl cap added to 5’ end of pre-mRNA

67
Q

what is step 2 of RNA processing

A

spliceosome removes introns from pre-mRNA strand and joins the exons together to make mature mRNA.

68
Q

what is step 3 of RNA processing

A

poly-A-tail is added to 3’ end of mRNA molecule

69
Q

what increases mRNA’s stability and prevents it from degrading

A

5’ methyl cap and 3’ poly-A-tail

70
Q

what does a poly-A-tail consist of

A

a chain of up to 250 adenine nucleotides

71
Q

What is alternative splicing

A

RNA processing, many ways to splice out the introns. results in different proteins arising from the same gene

72
Q

what happens during translation

A

translating the message (mRNA) into a protein

73
Q

what happens during inititation (translation)

A

small ribosomal subunit attaches to 5’ of a mature mRNA strand &moves along till it reaches start codon. tRNA molecule brings amino acid Met to mRNA &joins to mRNa start codon. large ribosomal subunit also attaches to tRNA & small ribosome subunit which allows 3 sites for the tRNA to bind

74
Q

what happens during elongation (translation)

A

after Met has attached, another tRNA molecule with complimentary anticodon to next codon on the mRNA strand attaches by a peptide bond &adds its amino acid to the growing chain, ribosome releases tRNA molecule &moves further along mRNA strand &process repeats

75
Q

what happens during termination (translation)

A

attachment of amino acids continues until stop codon is reached, & a release factor attaches. polypeptide chain is then released from ribosome into cytoplasm or ER.

76
Q

What is ribosome A site

A

A site accepts incoming tRNA molecules with associated amino acid to match the anticodon that complementary pairs with the mRNA codon.

77
Q

What is ribosome P site

A

P site where its associated amino acid is joined by peptide bonds into growing polypeptide chain

78
Q

What is ribosome E site

A

E site is where tRNA molecules that have added their amino acids to the polypeptide chain move before they exit ribosome.

79
Q

why is DNA considered universal

A

every known living organisms has genes make of DNA, and the 20 amino acids are the same in all organisms

80
Q

what is the genetic code based off

A

triplets of nucleotides called codons which specify individual amino acids in a polypeptide or a stop signal

81
Q

how many possible combinations of nucleotide sequences are there

A

64, 3 of which are stop codons

82
Q

why is genetic code redundant/degenerate

A

as there is 61 codons but there are only 20 amino acids. some code for the same amino acid

83
Q

what is the protein secretory pathway

A

1-nucleous (stores DNA, controls and regulates activities of cell)
2- Rough ER (production, folding, quality control and dispatch of proteins
3- Smooth ER (synthesis of lipids and steroid hormones)
4- Golgi (process/packages proteins and lipid molecules into vesicles to then be transported

84
Q

what is exocytosis

A

the release of substances from inside to outside of the cell

85
Q

how does exocytosis occur

A

fusion of vesicle membrane with plasma membrane

86
Q

what is a protein

A

a type of biological polymer that has a diverse range of functions

87
Q

what are proteins made of

A

amino acids, nitrogen, carbon, hydrogen and oxygen, some also contain sulphur & phosphate

88
Q

motility protein function

A

allow movement of cells and their organelles

89
Q

structural protein function

A

provide support, strength and protection

90
Q

transport protein function

A

carry molecules from one location to another or across plasma membrane

91
Q

cellular signaling protein function

A

signal between different cell types: stimulation or inhibition

92
Q

cell-surface reception protein function

A

receive signals such as hormones and growth factors, transmission of nerve impulse

93
Q

defense protein function

A

recognize and protect against foreign organisms

94
Q

enzymes function

A

catalyze, or actively assist biochemical reactions

95
Q

structure of amino acid

A

amino refers to NH2.
Acid refers to COOH
R group is part of molecule that varies and has a different chemical structure in different amino acids

96
Q

what are polar amino acids

A

hydrophilic and tend to be on the surface of the protein

97
Q

what are non-polar amino acids

A

hydrophobic and tend to fold away from the water molecules in the cell environment

98
Q

what do the R groups of amino acids do

A

distinguish one amino acid from another and give them different chemical properties, some r groups make regions of the protein molecule polar or non-polar

99
Q

how are the 9 essential amino acids obtained

A

from our diet

100
Q

how are amino acids joined together

A

peptide bonds in condensation polymerization. The OH part of one amino acid joins with a H atom from the other amino acid

101
Q

what does condensation polymerization produce

A

a growing polypeptide chain

102
Q

what is the primary structure of a protein

A

linear sequence of amino acids in the polypeptide chain

103
Q

what is the secondary structure of a protein

A

the coiling and folding of a protein chain

104
Q

when is secondary structure deemed random coiling

A

when not alpha helices or beta pleated sheets

105
Q

what are alpha helices

A

secondary structure. hydrogen bonds form between adjacent amine and carboxyl groups within the polypeptide chain causing it to coil and form a helical shape

106
Q

what are beta pleated sheets

A

secondary structure, hydrogen bonds formed between amine and carboxyl parts of adjacent polypeptide chains causing the chains to fold back on each other

107
Q

What is tertiary structure of a protein

A

the total irregular folding pattern of a protein forming a complex shape. now considered biologically functional as its a complex 3D shape

108
Q

what is quaternary structure of a protein

A

two or more polypeptide chains interacting to form a single functioning protein

109
Q

What are conjugated proteins

A

chains of amino acids join with other chemical groups. attached by covalent bonds or weak interactions

110
Q

What is a proteome

A

the complex range of proteins produced by a single cell or organism in a particular environment

111
Q

What is proteomics

A

the study of proteomes

112
Q

what does denaturation do

A

results in the loss of function of a protein

113
Q

are fully denatured proteins reversible

A

no

114
Q

when is a protein said to be denatured

A

when the bonds that create the tertiary structure of the protein are broken and the shape of the protein is altered causing it to lose its function

115
Q

what is a regulatory sequence capable of

A

increasing or decreasing the expression of specific genes within an organism.

116
Q

what is the promoter region for

A

found before the start triplet on the 5’ end where RNA polymerase binds (determines site of transcription.

117
Q

What is the enhance/silencer

A

region where transcription factors can bind

118
Q

what does UTR stand for

A

Untranslated Region

119
Q

Where is the UTR located

A

each side of a coding sequence, this section is transcribed not translated.

120
Q

What is the 5’ UTR for

A

recognized by the ribosome allowing it to bind to it but not translate it.

121
Q

What is the 3’UTR for

A

plays a role in polyadenylation adding poly-A-tail and terminating translation.

122
Q

Where is the 5’UTR found

A

between promoter and start triplet where the gene is transcribed not translated.

123
Q

do eukaryotes contain both exons and introns

A

yes

124
Q

do prokaryotes have introns

A

No, which is why their translated mRNA doesn’t need to undergo RNA processing before its translated.

125
Q

What is gene expression

A

where the info in a gene is used to synthesise a functional gene product such as a protein or RNA.

126
Q

why is the info in a gene being expressed.

A

the info in a gene is being expressed in the form of the product that is produced.

127
Q

What is gene regulation

A

the process that controls gene expression by determining which genes are switched on and which genes are switched off

128
Q

why is gene regulation important

A

for efficiency as otherwise every protein would be produced regardless of whether the cell needs it or not.

129
Q

What are structural genes

A

genes that code for proteins that become pat of the structure and functioning of an organism

130
Q

What are regulatory genes

A

involved in controlling the expression of one or more other ones. turns genes on or off determining the rate in which their products are made.

131
Q

what do regulatory genes

A

proteins that do not control other genes

132
Q

how do regulatory genes work

A

code for transcription factors that control gene expression at the transcription stage.

133
Q

how do transcription factors work

A

bind to DNA sequences close to the promoter region of a gene or to the RNA polymerase to activate or repress the expression of specific genes.

134
Q

what are transcription factors

A

proteins or functional pieces of RNA

135
Q

What is E.Coli

A

a simple prokaryotic bacteria

136
Q

what happens if trp is unavailable to E.Coli

A

produces enzymes for trp synthesis, otherwise they aren’t produced.

137
Q

What is an operon

A

a group of genes transcribed as a single unit from one promoter

138
Q

Are operons found in both prokaryotes and eukaryotes

A

found in prokaryotes but not eukaryotes

139
Q

which direction does the trp operon move

A

left to right (5’ to 3’)

140
Q

What is trp R

A

a regulatory gene, upstream of the operon that codes for a transcription factor called trp repressor. Expressed all the time which is why the trp repressor is always present

141
Q

what is the operater

A

short DNA segment that forms the binding site for a transcription factor

142
Q

what is the leader

A

a sequence of nucleotide bases with regulatory activity

143
Q

what is the attenuator

A

a mRNA transcription termination site made up of multiple uracil-adenine base pairs.

144
Q

What are trp e,d,c,b,a

A

structural genes that code for the enzymes needed for the biosynthesis of trp.

145
Q

What happens during transcription repression when tryptophan is present

A

binds to repressor protein & alters its shape, so that is repressor can bind to the operator. repressor then covers part of the promoter, preventing RNA polymerase from binding to promoter & blocking transcription of the structural genes in the operon.

146
Q

are structural genes made/transcribed during transcription repression when tryptophan is present

A

No

147
Q

What happens during transcription repression when tryptophan is absent

A

repressor protein is inactive, and cant bind to operator. RNA polymerase can bind to the promoter & transcribe the 5 genes into a mRNA transcript. This in turn is translated into 5 enzymes used in the synthesis of trp.

148
Q

what is attentuation

A

the 2nd regulatory mechanism in the trp operon. reduces expressiom of the trp operon when the levels of trp are high. doesn’t block initiation of transcription, it prevents the completion of transcription.

149
Q

what happens in attenuation when trp is present on tRNA molecules

A

1- ribosome reads mRNA strand & quickly passes through region 1 where the 2 trp codons are located.
2- ribosome stops when it reaches stop codon 1&2 of the leader.
3- as ribosome is partially covering region 2, allows regions 3/4 to form a hairpin via complimentary base pairing
4- hairpin classed as terminator as it puts pressure of attenuator & breaks the hydrogen bonds holding together A&U.
5- causes mRNA to break away from DNA being transcribed & the ribosome detaches. RNA polymerase also detaches from DN strand ending transcription. the structural genes of the trp operon are therefore not produced.

150
Q

what happens in attenuation when trp is absent

A

1- ribosome stalls/pauses in region 1 waiting for trp molecules to be carried by tRNA.
2- allows regions 2&3 to form a hairpin via complementary base pairing
3- hairpin is known as anti-terminator as its further away from the attenuator region meaning that the mRNA does not pull away from DNA.
4- means that RNA polymerase can continue transcribing the structural genes of the operon into an mRNA strand and translation of the enzymes needed for synthesis of trp will proceed.

Biology 3/4 (22 decks)

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