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Biology 101 > Nucleic acids and the encoding of biological information > Flashcards

Nucleic acids and the encoding of biological information Flashcards

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1
Q

What is the central dogma?

A

Dna to Rna (transcription)

RNA to protein (translation)

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2
Q

What is DNA TO RNA called?

A

transcription

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3
Q

What is RNA TO PROTEIN called?

A

translation

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4
Q

What is the exception to the normal central dogma?

A

a retrovirus

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5
Q

What is DNA (be sure to include the definition of heredity)

A

Genetic material responsible for heredity

Heredity = passing of genetic information from one generation to the next

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6
Q

What is the first step of the central dogma (simple)

A

1) synthesis of mRNA in the nucleus

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7
Q

What is the second step of the central dogma (simple)

A

2) movement of mRNA into the cytoplasm via nuclear pore

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8
Q

What is the third step of the central dogma (simple)

A

3) Synthesis of Protein

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9
Q

What is a gene

A

Sequence of hereditary information in the form of DNA
Functional unit of heredity
Made up of DNA
Many genes code for proteins

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10
Q

What is a genome

A

complete set of genes in an organism

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11
Q

DNA is a polymer of what?

A

Nucleotides

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12
Q

what bond the nucleotides of DNA together to form one strand?

A

Phosphodiester Bonds

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13
Q

What is carbon #5 linked to?

A

Phosphate

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14
Q

How to we read a dna strand?

A

5’ end to 3’ end

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15
Q

How do you know the end of a dna strand

A

it is at the 3’ end with a free hydroxyl group

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16
Q

How do you know the start of a dna strand

A

it is at the 5’ end with a free phosphate group

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17
Q

DNA is parallel or antiparallel

Single or Double stranded

A

Anti Parallel

Double

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18
Q

What are the nitrogenous bases linked by

A

Hydrogen bonds

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19
Q

What links with Adenine

A

Thymine

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20
Q

What links with Guanine

A

Cytosine

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21
Q

What is chargaff’s rule?

A

Chargaff’s rule: 1:1 ratio of A:T & 1:1 ratio of C:G

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22
Q

What are histones

A

: proteins that act as ‘spools’ for DNA

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23
Q

How does DNA condense?

A

Histone proteins

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24
Q

What makes chromatin in eukaryotes

A

DNA associated with proteins that condense it

Eukaryotes: DNA + proteins (histones) = chromatin (makes chromosomes)

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25
Q

What is chromatin

A

coiled ∧ compacted mass of DNA

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26
Q

How can the 4 bases generate so many different combinations

A

They code in 3’s therefore it can make 20 different amino acids which combine so many different ways

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27
Q

What are the 2 strutures of chromatin

A

Euchromatin and Heterochromatin

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28
Q

What are the aspects of Euchromatin

A 
Loosely coiled (DNA is more accessible)
DNA can be transcribed – genes are expressed
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29
Q

What are the aspects of Heterochromatin

A 
Tightly packed (DNA is inaccessible)
DNA cannot be transcribed – genes are not expressed
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30
Q

Difference between euchromatin and heterochromatin

A

EU: loose and dna can be transcribed
Hetero: tight and dna cannot be transcribed

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31
Q

What are the 4 main types of RNA

A 
Ribosomal RNA (rRNA)
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Small nuclear RNA (snRNA)
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32
Q

What is the function of Ribosomal rna

A

Forms Ribosomes with ribosomal proteins

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33
Q

What is the function of messenger rna

A

Template for protein synthesis

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34
Q

what is the function of transfer rna

A

Attaches to correct amino acids and bring them to the Ribosomes

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35
Q

what is the function of small nucleus rna

A

Involved in the processing of mRNA (eukaryotes)

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36
Q

What is the final protein called

A

a polypeptide

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37
Q

Differences in structure between dna and rna

A

dna: longer, acgt, stays in the nucleus, antiparallel, double stranded, double helix formation
rna: shorter, acgu, can leave the nucleus, single stranded

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38
Q

pre-mrna is rearranged to make what?

A

functional mRNA

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39
Q

What is the anatomy of a gene (3 parts)

A

Promoter:
Intron:
Exon:
DIAGRAM IN NOTES

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40
Q

What is a the promoter

A

5’ region of DNA ‘Upstream’ of gene

Where RNA Polymerase binds

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41
Q

What is the intron

A

Non-coding region (do not encode protein product)

must get rid of introns

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42
Q

what is the exon

A

Coding region

Becomes part of mature RNA

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43
Q

What happens in the promoter region

A

Where RNA polymerase binds and splits dna to be ready to code

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44
Q

What does the rna polymerase do (firstly)

A

RNA polymerase recognizes a region (promoter) upstream of (before) the gene that will be transcribed
DNA strands separate

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45
Q

Are both dna strands used in transcription?

A

No, only one is used

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46
Q

What is the dna strand used in transcription called, what is the other one called?

A

Used: Template

Non-used: Coding

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47
Q

What does the rna polymerase do (secondly)

A

RNA polymerase assembles (Transcribes) mRNA with nucleotides that are complementary to the DNA
Forms mRNA in 5’  3’ direction

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48
Q

What do terminators do? and where are they located?

A

Terminators (regions at the end of the gene) cause release of RNA

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49
Q

what are the 2 dna strands?

A

Template strand

Coding strand

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50
Q

What is the template stand

A

Template for transcription

Also called ‘anti-sense’ strand

51
Q

what is the coding strand

A

Same sequence as mRNA
Also called ‘sense’ strand
5’ to 3’ direction

52
Q

what direction does the rna polymerase read the dna template?

A

3’ to 5’

53
Q

what direction is newly transcribed rna formed sythesize in?

A

5’ to 3’

54
Q

what is the simplified 3 step process of transcription?

A

Initiation
Elongation
Termination
DIAGRAM IN NOTES*****

55
Q

What are the 2 ways of modifying mRNA

A

RNA splicing

adding cap and tails

56
Q

How is the mRNA modified right after the strand is made?

A

Addition of a cap
modified Guanine nucleotide at the 5’ end

Addition of a poly-A tail
50-250 Adenine nucleotides at the 3’ end

57
Q

What is the function of added caps and tails

A

Protects mRNA
Facilitates export from nucleus
Helps recognition by ribosomes
DIAGRAM IN NOTES

58
Q

What is RNA splicing?

A

Removal of Introns
(Intervening sequences removed)

Splicing of Exons
(Sequences that will be expressed pasted together)
DIAGRAM IN NOTES

59
Q

what determines the structure of proteins

A

the order of bases

60
Q

how many bases code for an amino acid?

A

3

61
Q

during protein synthesis does the DNA read in 1 direction or 2 and why?

A

1, to determine the ordering of the amino acids in protein

62
Q

What is the triplet code?

A

3 nucleotide bases on DNA that specify a given amino acid

63
Q

What is a codon?

A

same information (3 bases that specify a given amino acid) on mRNA

64
Q

What reads a codon

A

ribosomes

65
Q

Why is the genetic code almost universal?

A

All organisms use the same base sequences to code for the same amino acids

66
Q

is there less or more codes than amino acids

A

more

67
Q

Explain redundancy of codes

A

One amino acid can be coded by more than one code

68
Q

Why do we need start and stop codes?

A

To have the right reading frame

69
Q

explain the start codon and what is it

does it code for an amino acid?

A

First codon of mRNA to be translated by Ribosome
AUG (methionine)
YES

70
Q

Explain the stop codon and name them and does it code for an amino acid?

A 
Signals termination of translation
Do not code for an Amino Acid
UAA
UAG
UGA
71
Q

Do the stop codons code for an amino acid?

A

NO

72
Q

explain translation (only up til tRNA)

A
  • mRNA moves to Cytoplasm
  • Ribosome attaches to a sequence at the start (5’) of mRNA (reads 5’ to 3’)
  • Ribosome moves along the mRNA until it reaches the Start Codon (Methionine)
  • Enter the tRNA…
73
Q

Explain transfer RNA

A

Carries Amino Acid to Ribosome
Anticodon matches to the mRNA codon
Adds Amino Acid to growing peptide chain
SEE DIAGRAM

74
Q

What is the anticodon

A

the opposite bases of the mRNA strand

75
Q

Explain translation (before completing protein)

A
  • mRNA moves to cytoplasm and ribosome attaches to sequence at the start (reads 5’ to 3’)
  • Ribosomes move along mRNA until it reaches the start codon (methionine)
  • enter the tRna
  • tRNA carrying methionine diffuses into a special tunnel in the ribosome and its anticodon attaches to the mRNA codon
  • Ribosome moves down by one codon (3 nucleotides that codes for an amino acid)
  • Another tRNA drifts into the ribosome and attaches to the second codon

-Translation continues until the Ribosome reads a Stop Codon
DIGRAM IN NOTES

76
Q

can messenger rna be used again

A

yes, as long as its not degraded

77
Q

How does the cell decide to re use the rna

A

Depends on how much protein needs to be produced

78
Q

Does this process require a lot of energy?

A

Yes

79
Q

What are the last steps of translation

A
  • Protein folding
  • post-translational modifications
  • targeting polypeptides to specific locations
80
Q

examples of post translational modifications

A

e. g., attachment of sugars, lipids

e. g., bonding of 4 polypeptides to make haemoglobin

81
Q

examples of genes that must be regulated

A

Insulin

e.g. Matrix Metalloproteinases (MMPs)

82
Q

do cells express all their genes?

A

No, only 3-5%

83
Q

why do Cells of multicellular organisms need to turn specific genes on and off at specific times in specific places

A

because All the cells in an organism contain the same genes

But these cells are different therefore a heart cell should not code for a hair protein

84
Q

What can de-regulation of gene expression result in

A

cancer, heart disease

85
Q

explain differential gene expression

A

expression of different sets of genes in cells that have the same genome

86
Q

what determines the structure of a cell

A

the genes expressed in the cell

87
Q

what are mutations and. what do they affect

A

Mutations affect protein structure and function
Changes in the genetic material of a cell
Affect amino acid sequence → may modify protein structure & function

88
Q

How are mutations passed on in a somatic cell

A

passed to daughter cells

89
Q

HOW Are mutations passed on in a gamete cell (or cell that gives rise to gametes)

A

may be transmitted to offspring and subsequent generations

90
Q

define phenotype

A

the physical and physiological traits of an organism (determined by its genetic makeup)

91
Q

how do mutations affect phenotype

A

genetic disorder or hereditary disease

92
Q

what are the 4 types of point mutations?

A

silent substitution
neutral substitution
missense subsitution (potentially serious)
nonsense substitution

93
Q

What is. a silent substitution

A

when it has no impact on the strand
when the mutation codes for the same amino acid
SEE SLIDES FOR EXAMPLE

94
Q

what is a neutral substitution

A

when the mutation codes for different amino acids but with the same charge/properties
SEE SLIDES FOR EXAMPLE

95
Q

what is missense substitution ?

A

when the mutation codes for different amino acids, one being polar and the other being non polar
SEE SLIDES FOR EXMAPLE

96
Q

what is non sense substitution?

A

when the mutation codes for a stop codon

will make a non functional protein

97
Q

What happens if it it not a multiple of 3 bases

A

frame shift

98
Q

what are Base pair insertions or deletions and what happens to the protein if that happens

A

adding or removing a codon

ends in nonsense (termination of translation) which gives a non functional protein

99
Q

what happens to the nucleotides after the mutation and what does this cause?

A

All nucleotides downstream of mutation improperly grouped into codons
usually ending in nonsense (termination of translation)  non-functional protein

100
Q

Explain what the Avery, Macleod and McCarty experiment did

A

Determined that DNA was the blueprint for different properties within an organism:

101
Q

what are the 3 proposed methods for DNA strand separation and which was the right one

A

Conservative:
One copy is made up of entirely new ‘daughter’ strands

Semi-conservative: USEDD
Each copy is made from an old ‘parent’ & new ‘daughter’ strand

Dispersive:
Each strand has a mix of old & new

102
Q

how does dna “unzip”

A

helicases

103
Q

where does dna unzipping start

A

at the origin of replication

104
Q

what is primer and what does it do

A

Short RNA strand added by Primase

Converted into DNA

105
Q

what are the functions of the 2 dna polymerases

A

1st: adds nucleotides at 3’ end of RNA strand
2nd: replaces RNA (primer) with DNA

106
Q

explain the dna ligase

A

Follows behind 2nd DNA polymerase
Catalyses phosphodiester bonds where there are breaks
(fixes holes in strand)

107
Q

which direction do the new strands form in

A

5’ to 3’

108
Q

If dna replication is semi conservative what does that mean

A

each has:
1 parent strand
1 daughter strand

109
Q

are the two sides in the replication fork copied differently or the same
if differently name the two strand names

A

differently

leading strand vs lagging strand

110
Q

why is it called the lagging strand (ie. whats the problem)

A

direction of unzipping is 3’ to 5’

111
Q

what is the solution to fix the lagging strand

A

okazaki fragments

112
Q

can ligases and polymerases start replication on their own?

A

no

113
Q

What do okazaki fragments do

A

Leapfrog’ in direction of unzipping (towards 3’)
DNA ligase catalyses phosphodiester bonds (fills in breaks)
okazaki are short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.

114
Q

are errors ever made in replication, if so, what is the initial rate of error

A

yes, 1 mistake per 10000 nucleotides

115
Q

how to fix the errors in dna replication and what is the final error rate>

A

DNA polymerase does proof-reading

Enzymes swoop in & remove incorrectly paired nucleotides - the correct ones are then added

116
Q

What are 3 ways damage to Dna can arise

A 
Reactive chemicals (e.g. Reactive Oxygen Species)
Radiation (X-rays, ultraviolet light, etc.)
Spontaneous nucleotide changes
117
Q

are cells vigilant when looking for errors and how

A

yes, they are always old the lookout for damage occurring after dna synthesis
we have 130 report enzymes in humans

118
Q

Explain the repair process of dna replication

A

DNA polymerase does proof-reading
If it finds a mistake, it backs up & a nuclease cuts out the incorrect nucleotide(s), then the polymerase replaces it/them

SEE NOTES FOR DIAGRAM

119
Q

initiation:

A

initiator trna goes to psite, others start at a site

this step needs energy

120
Q

elongation:

A

Codon-anticodon recognition of new tRNA at A-site

Peptide bonds form between Amino Acids on tRNAs at P-site & A-site
Pass the chain along to the next tRNA

Ribosome moves up 1 codon:
tRNA at P-site goes to E-site
tRNA at A-site goes to P-site
New tRNA starts Step 1

121
Q

termination

A

there is a release factor and the stop codon

polypeptide chain is free and detatched

122
Q

explain polyribosomes

A

single mRNA can be used to make copies of the same protein simultaneously.
Once a ribosome is passed the start codon a 2nd ribosome can attach. This enables many copies of a polypeptide very rapidly

123
Q

what is the end of translation (ie. completing the protein)

A
  • Protein folding
  • Post-translational modifications
    e. g., attachment of sugars, lipids
    e. g., bonding of 4 polypeptides to make haemoglobin
  • Targeting polypeptides to specific locations

Biology 101 (15 decks)

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