Nucleic acids and the encoding of biological information Flashcards
1
Q
What is the central dogma?
A
Dna to Rna (transcription)
RNA to protein (translation)
2
Q
What is DNA TO RNA called?
A
transcription
3
Q
What is RNA TO PROTEIN called?
A
translation
4
Q
What is the exception to the normal central dogma?
A
a retrovirus
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
6
Q
What is the first step of the central dogma (simple)
A
1) synthesis of mRNA in the nucleus
7
Q
What is the second step of the central dogma (simple)
A
2) movement of mRNA into the cytoplasm via nuclear pore
8
Q
What is the third step of the central dogma (simple)
A
3) Synthesis of Protein
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
10
Q
What is a genome
A
complete set of genes in an organism
11
Q
DNA is a polymer of what?
A
Nucleotides
12
Q
what bond the nucleotides of DNA together to form one strand?
A
Phosphodiester Bonds
13
Q
What is carbon #5 linked to?
A
Phosphate
14
Q
How to we read a dna strand?
A
5’ end to 3’ end
15
Q
How do you know the end of a dna strand
A
it is at the 3’ end with a free hydroxyl group
16
Q
How do you know the start of a dna strand
A
it is at the 5’ end with a free phosphate group
17
Q
DNA is parallel or antiparallel
Single or Double stranded
A
Anti Parallel
Double
18
Q
What are the nitrogenous bases linked by
A
Hydrogen bonds
19
Q
What links with Adenine
A
Thymine
20
Q
What links with Guanine
A
Cytosine
21
Q
What is chargaff’s rule?
A
Chargaff’s rule: 1:1 ratio of A:T & 1:1 ratio of C:G
22
Q
What are histones
A
: proteins that act as ‘spools’ for DNA
23
Q
How does DNA condense?
A
Histone proteins
24
Q
What makes chromatin in eukaryotes
A
DNA associated with proteins that condense it
Eukaryotes: DNA + proteins (histones) = chromatin (makes chromosomes)
25
What is chromatin
coiled ∧ compacted mass of DNA
26
How can the 4 bases generate so many different combinations
They code in 3's therefore it can make 20 different amino acids which combine so many different ways
27
What are the 2 strutures of chromatin
Euchromatin and Heterochromatin
28
What are the aspects of Euchromatin
```
Loosely coiled (DNA is more accessible)
DNA can be transcribed – genes are expressed
```
29
What are the aspects of Heterochromatin
```
Tightly packed (DNA is inaccessible)
DNA cannot be transcribed – genes are not expressed
```
30
Difference between euchromatin and heterochromatin
EU: loose and dna can be transcribed
Hetero: tight and dna cannot be transcribed
31
What are the 4 main types of RNA
```
Ribosomal RNA (rRNA)
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Small nuclear RNA (snRNA)
```
32
What is the function of Ribosomal rna
Forms Ribosomes with ribosomal proteins
33
What is the function of messenger rna
Template for protein synthesis
34
what is the function of transfer rna
Attaches to correct amino acids and bring them to the Ribosomes
35
what is the function of small nucleus rna
Involved in the processing of mRNA (eukaryotes)
36
What is the final protein called
a polypeptide
37
Differences in structure between dna and rna
dna: longer, acgt, stays in the nucleus, antiparallel, double stranded, double helix formation
rna: shorter, acgu, can leave the nucleus, single stranded
38
pre-mrna is rearranged to make what?
functional mRNA
39
What is the anatomy of a gene (3 parts)
Promoter:
Intron:
Exon:
DIAGRAM IN NOTES
40
What is a the promoter
5’ region of DNA ‘Upstream’ of gene
| Where RNA Polymerase binds
41
What is the intron
Non-coding region (do not encode protein product)
| must get rid of introns
42
what is the exon
Coding region
| Becomes part of mature RNA
43
What happens in the promoter region
Where RNA polymerase binds and splits dna to be ready to code
44
What does the rna polymerase do (firstly)
RNA polymerase recognizes a region (promoter) upstream of (before) the gene that will be transcribed
DNA strands separate
45
Are both dna strands used in transcription?
No, only one is used
46
What is the dna strand used in transcription called, what is the other one called?
Used: Template
| Non-used: Coding
47
What does the rna polymerase do (secondly)
RNA polymerase assembles (Transcribes) mRNA with nucleotides that are complementary to the DNA
Forms mRNA in 5’ 3’ direction
48
What do terminators do? and where are they located?
Terminators (regions at the end of the gene) cause release of RNA
49
what are the 2 dna strands?
Template strand
Coding strand
50
What is the template stand
Template for transcription
| Also called ‘anti-sense’ strand
51
what is the coding strand
Same sequence as mRNA
Also called ‘sense’ strand
5’ to 3’ direction
52
what direction does the rna polymerase read the dna template?
3' to 5'
53
what direction is newly transcribed rna formed sythesize in?
5' to 3'
54
what is the simplified 3 step process of transcription?
Initiation
Elongation
Termination
DIAGRAM IN NOTES*****
55
What are the 2 ways of modifying mRNA
RNA splicing
| adding cap and tails
56
How is the mRNA modified right after the strand is made?
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
What is the function of added caps and tails
Protects mRNA
Facilitates export from nucleus
Helps recognition by ribosomes
DIAGRAM IN NOTES
58
What is RNA splicing?
Removal of Introns
(Intervening sequences removed)
Splicing of Exons
(Sequences that will be expressed pasted together)
DIAGRAM IN NOTES
59
what determines the structure of proteins
the order of bases
60
how many bases code for an amino acid?
3
61
during protein synthesis does the DNA read in 1 direction or 2 and why?
1, to determine the ordering of the amino acids in protein
62
What is the triplet code?
3 nucleotide bases on DNA that specify a given amino acid
63
What is a codon?
same information (3 bases that specify a given amino acid) on mRNA
64
What reads a codon
ribosomes
65
Why is the genetic code almost universal?
All organisms use the same base sequences to code for the same amino acids
66
is there less or more codes than amino acids
more
67
Explain redundancy of codes
One amino acid can be coded by more than one code
68
Why do we need start and stop codes?
To have the right reading frame
69
explain the start codon and what is it
| does it code for an amino acid?
First codon of mRNA to be translated by Ribosome
AUG (methionine)
YES
70
Explain the stop codon and name them and does it code for an amino acid?
```
Signals termination of translation
Do not code for an Amino Acid
UAA
UAG
UGA
```
71
Do the stop codons code for an amino acid?
NO
72
explain translation (only up til tRNA)
- 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
Explain transfer RNA
Carries Amino Acid to Ribosome
Anticodon matches to the mRNA codon
Adds Amino Acid to growing peptide chain
SEE DIAGRAM
74
What is the anticodon
the opposite bases of the mRNA strand
75
Explain translation (before completing protein)
- 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
can messenger rna be used again
yes, as long as its not degraded
77
How does the cell decide to re use the rna
Depends on how much protein needs to be produced
78
Does this process require a lot of energy?
Yes
79
What are the last steps of translation
- Protein folding
- post-translational modifications
- targeting polypeptides to specific locations
80
examples of post translational modifications
e. g., attachment of sugars, lipids
| e. g., bonding of 4 polypeptides to make haemoglobin
81
examples of genes that must be regulated
Insulin
| e.g. Matrix Metalloproteinases (MMPs)
82
do cells express all their genes?
No, only 3-5%
83
why do Cells of multicellular organisms need to turn specific genes on and off at specific times in specific places
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
What can de-regulation of gene expression result in
cancer, heart disease
85
explain differential gene expression
expression of different sets of genes in cells that have the same genome
86
what determines the structure of a cell
the genes expressed in the cell
87
what are mutations and. what do they affect
Mutations affect protein structure and function
Changes in the genetic material of a cell
Affect amino acid sequence → may modify protein structure & function
88
How are mutations passed on in a somatic cell
passed to daughter cells
89
HOW Are mutations passed on in a gamete cell (or cell that gives rise to gametes)
may be transmitted to offspring and subsequent generations
90
define phenotype
the physical and physiological traits of an organism (determined by its genetic makeup)
91
how do mutations affect phenotype
genetic disorder or hereditary disease
92
what are the 4 types of point mutations?
silent substitution
neutral substitution
missense subsitution (potentially serious)
nonsense substitution
93
What is. a silent substitution
when it has no impact on the strand
when the mutation codes for the same amino acid
SEE SLIDES FOR EXAMPLE
94
what is a neutral substitution
when the mutation codes for different amino acids but with the same charge/properties
SEE SLIDES FOR EXAMPLE
95
what is missense substitution ?
when the mutation codes for different amino acids, one being polar and the other being non polar
SEE SLIDES FOR EXMAPLE
96
what is non sense substitution?
when the mutation codes for a stop codon
| will make a non functional protein
97
What happens if it it not a multiple of 3 bases
frame shift
98
what are Base pair insertions or deletions and what happens to the protein if that happens
adding or removing a codon
| ends in nonsense (termination of translation) which gives a non functional protein
99
what happens to the nucleotides after the mutation and what does this cause?
All nucleotides downstream of mutation improperly grouped into codons
usually ending in nonsense (termination of translation) non-functional protein
100
Explain what the Avery, Macleod and McCarty experiment did
Determined that DNA was the blueprint for different properties within an organism:
101
what are the 3 proposed methods for DNA strand separation and which was the right one
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
how does dna "unzip"
helicases
103
where does dna unzipping start
at the origin of replication
104
what is primer and what does it do
Short RNA strand added by Primase
| Converted into DNA
105
what are the functions of the 2 dna polymerases
1st: adds nucleotides at 3’ end of RNA strand
2nd: replaces RNA (primer) with DNA
106
explain the dna ligase
Follows behind 2nd DNA polymerase
Catalyses phosphodiester bonds where there are breaks
(fixes holes in strand)
107
which direction do the new strands form in
5' to 3'
108
If dna replication is semi conservative what does that mean
each has:
1 parent strand
1 daughter strand
109
are the two sides in the replication fork copied differently or the same
if differently name the two strand names
differently
| leading strand vs lagging strand
110
why is it called the lagging strand (ie. whats the problem)
direction of unzipping is 3' to 5'
111
what is the solution to fix the lagging strand
okazaki fragments
112
can ligases and polymerases start replication on their own?
no
113
What do okazaki fragments do
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
are errors ever made in replication, if so, what is the initial rate of error
yes, 1 mistake per 10000 nucleotides
115
how to fix the errors in dna replication and what is the final error rate>
DNA polymerase does proof-reading
| Enzymes swoop in & remove incorrectly paired nucleotides - the correct ones are then added
116
What are 3 ways damage to Dna can arise
```
Reactive chemicals (e.g. Reactive Oxygen Species)
Radiation (X-rays, ultraviolet light, etc.)
Spontaneous nucleotide changes
```
117
are cells vigilant when looking for errors and how
yes, they are always old the lookout for damage occurring after dna synthesis
we have 130 report enzymes in humans
118
Explain the repair process of dna replication
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
initiation:
initiator trna goes to psite, others start at a site
| this step needs energy
120
elongation:
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
termination
there is a release factor and the stop codon
| polypeptide chain is free and detatched
122
explain polyribosomes
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
what is the end of translation (ie. completing the protein)
- 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
