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DNA and proteins Flashcards

DNA replication and protein synthesis

1
Q

Griffith, 1928

A

Identified an inheritance factor/gene which caused a transformation, which is a change in genotype and phenotype

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2
Q

Avery

A

Identified that DNA was the inheritance factor

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3
Q

Chargaff, 1947

A

Identified that he composition of DNA differed between species. And that it was consistent within species

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4
Q

Percentages of AT CG

A

A: 31%
T: 29%
C: 20%
G: 20%

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5
Q

A and G
C and T

A

AG: purines
CT: pyrimidines

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6
Q

What are bases attached to?

A

5 carbon sugar 2’deoxyribose
Phosphate group

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7
Q

Identify 3’ and 5’ ends

A

3’ has an OH group attached to deoxyribose group
5’ doesn’t

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8
Q

Who discovered DNA was helical

A

Rosalind Franklin, 1952

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9
Q

Watson and Crick, 1953

A

Specific base pairing within a double helical structure
Width of helix and spacing of nitrogenous bases
Nobel prize 1962

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10
Q

Base pairs of DNA

A

A and T
C and G
dependent on hydrogen bonds

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11
Q

Identify the 3’ and 5’ ends

A

3’ end has OH on the deoxyribose, hydrophilic
5’ end has OH on the phosphate, hydrophobic

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12
Q

Which direction does DNA run/which direction are nucleotides added

A

5’ to 3’

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13
Q

Okazaki fragment

A

The separated chunks of replicated DNA on the lagging strand, joined by primers

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14
Q

DNA polymerase

A

An enzyme that uses ATP to carry out elongation by adding nucleotides to the growing chains.
Adding a nucleotides results in 2 phosphates being released

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15
Q

How many base pairs do humans have?

A

3 x 10^9

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16
Q

mtDNA

A

Mitochondrial DNA
Double stranded and circular
Codes for proteins in respiratory chains
Solely maternal DNA

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17
Q

How does mRNA differ from DNA

A

Uracil instead of thymine
Ribose instead of deoxyribose
No regular 3D structure

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18
Q

Why are proteins translated from mRNA and not DNA?

A

A motile copy means that the original DNA cannot be damaged

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19
Q

What happens to RNA before it leaves the nucleus?

A

A cap is added to the 5’ end
A polyA tail is added to the 3’ end
Splicing

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20
Q

Purpose of cap and tail

A

Protect the mRNA from degradation (eg from RNase)
Aid export from nucleus/across nuclear membrane
Help mRNA anchor to the ribosome at the right start point

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21
Q

Transcription error rate

A

1 in 10^4

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22
Q

Transcription factor (eukaryotes)

A

Differ depending on gene
Orientate RNA polymerase to start at the right place/gene

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23
Q

Polyadenylation signal

A

AAUAAA
Trigger for RNA polymerase to pop off and for mRNA to come away

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24
Q

Types of RNA

A

m(essenger)RNA
r(ibosomal)RNA
t(ransfer)RNA
small nuclear RNA

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25
Exons and introns
Exons: coding regions also correspond to a distinct folded unit of a protein with a particular function Introns: non-coding regions
26
Splicing
Removal of introns in immature mRNA and joining of exons by snRNPs
27
snRNPs
Small nuclear ribonucleoproteins Join exons Identify splice sites at ends of introns
28
Purpose of splicing
Increase the range of possible protein products from a given gene May assist creation of new modular proteins
29
Codon
3 nucleotides on mRNA
30
tRNA
transfer RNA transfers amino acids to the site of protein synthesis/ribosome
31
Anti-codon
The 3 distinct bases on tRNA that correspond to one of the 20 amino acids
32
Wobble
The site of attachment for the amino acid is remote from the anti-codon. Some anti-codons can pair with more than one codon
33
How is tRNA activated?
Aminoacyl-tRNA synthetase (enzyme) binds the amino acid to the tRNA There are 20 of these enzymes, one for each amino acid Specific
34
What makes up a ribosome
rRNA and proteins
35
Ribosomal sites
Binding mRNA P E A
36
P ribosomal site
Binds the growing peptide chain
37
Start codon
AUG on mRNA
37
E ribosomal site
Exit site to allow the discharged tRNA to leave the ribosome
37
A ribosomal site
Binds the incoming aminoacyl-tRNA
38
Sickle-cell mutation
CAT instead of CTT CAT becomes GUA Valine amino acid produced instead of Glutamine
38
What happens to the polypeptide chain?
1. Protein folding 2. Components added (sugars/lipids) or removed (amino acids) 3. Moved to correct location
39
Protein bonds
Non-covalent bonds for flexibility Hydrogen bonds Ionic bonds Hydrophobic bonds
40
Non-covalent bonds
Allows the backbone/sidechains to contact the target molecule precisely
41
Hydrogen bonds
Individually weak electrostatic bonds formed because N and O are more electronegative than H
42
Ionic bonds
Electrostatic interactions between full positive and negative charges
43
Hydrophobic interactions
Determine 3d structure non-polar sidechains cluster together excluding water, allowing water molecules to form H bonds between themselves
44
Van der waals interactions
weak forces between adjacent neutral atoms
45
Enzymes
Catalyse all the chemical reaction is a cell
46
Importance of proteins
Communication Movement Defence
47
Fact 1 about proteins
Proteins are polymers of L-alpha amino acids linked by peptide bonds
48
Fact 2 about proteins
They contain 20 different amino acids with different sidechains
49
Fact 3 about proteins
Each one has a unique amino acid sequence determined by the DNA sequence of its gene
50
Conformation
Each polypeptide chain folds into a specific 3d structure defined by its amino acid sequence, allowing them to bind specifically to other molecules
51
Peptide bond
Formed by condensation (loss of water) between alpha-amino group of one amino acid and the carboxyl group of the next Planar, stable
52
Protein ends
Start: N- / amino terminus End: C- / carboxy terminus
53
Hydrophobic core
Nonpolar sidechains cluster together due to hydrophobic interactions
54
Sidechains
Charged sidechains form ionic bonds Polar sidechains form H bonds
55
Primary structure
The amino acid sequence
56
Why are sickle cells misshapen
Glutamine (the normal amino acid) is polar, whilst Valine is non-polar. Non-polar chains cluster in the centre, so the protein folds in on itself
57
How can protein structures be determined
X-ray crystallography NMR cryo-EM
58
Secondary structure
ways in which the backbone folds regularly Stabilised by H bonds between C=O and N-H groups
59
Tertiary structure
The way is which the polypeptide chain folds into a compact 3D shape Stabilised by H bonds, ionic bonds, hydrophobic interactions and disulphide bonds involving backbone or sidechain groups
60
Quaternary structure
Doesn't apply to every protein The arrangement of subunits in proteins containing 2 or more polypeptide chains Same stabilisation as tertiary structure
61
Alpha helix
forms a rigid rod with the sidechains around the outside
62
Beta sheet
forms a flat surface that can be twisted into a cylinder. Side chains alternate above and blow the plane of the sheet The chains in the sheet can be either parallel or anti-parallel
63
Disulfide bonds
Form between 2 cysteines Proteins have hydrophobic groups inside and polar groups outside
64
Why are proteins held together by weak bonds?
Flexibility, to change conformations Conformation can easily be destroyed Changes in conformation regulate proteins
65
How do proteins catalyse reactions?
By binding substrates at the active site and reducing activation energy
66
What are the two main types of chains in antibodies?
Antibodies consist of 2 heavy and 2 light chains joined by disulfide bridges.
67
What is the role of globins?
Globins are proteins that facilitate the transport and storage of oxygen in the body.
68
Induced fit
The process by which enzymes change shape when binding to a substrate
69
What is the significance of the active site in enzymes?
It is where substrates bind and reactions are catalysed
70
True or False: Most enzymes are absolutely specific for their substrates.
True
71
What is end product inhibition in enzymes?
Regulation of enzyme activity by the end product of a reaction
72
Arnold
Generated enzyme variants with desirable properties for the chemical industry.
73
What is an epitope?
A small part of the antigen recognized by an antibody Antibodies are specific to particular epitopes.
74
What is the significance of the sigmoid O2 saturation curve of hemoglobin?
It allows hemoglobin to efficiently bind O2 in lungs and release it in capillaries High metabolic activity reduce pH and enhances unloading of O2.
75
What are the types of protein domains in hexokinase?
Catalytic domain and regulatory domain
76
What are the membrane-spanning parts of membrane proteins usually composed of?
α-helices or β-barrels, These structures allow proteins to interact with both the hydrophobic membrane and the aqueous environment.
77
What is the structure of collagen in connective tissue?
Three collagen helices coiled together
78
Vitamin...
Vitamin C is required for the formation of hydroxyproline in collagen
79
What happens when protein folding goes wrong?
Amyloid diseases can occur, These diseases include Alzheimer's and type 2 diabetes.
80
How do enzymes speed up reactions?
By reducing activation energy, Enzymes can increase reaction rates by factors of up to 10^12.
81
Fill in the blank: Antibodies are ______ molecules.
defence
82
True or False: Membrane proteins can play many functions.
True, Functions include cell-cell recognition, signal transduction, and transport.
83
What are the components of the sweet taste receptor?
A dimer of TAS1R2 and TAS1R3, These are examples of 7-transmembrane helix proteins.
84
What is hexokinase activity inhibited by?
Glucose 6-phosphate.
85
Purpose of induced fit
This change in shape enhances the enzyme's ability to catalyse the reaction.
86
Chaperone proteins
Help with the folding of certain proteins by creating a hydrophilic environment
87
Domain
Independently stable part of a polypeptide chain, usually with a specific function
88
How many chromosomes does a human have?
23 pairs of homologous chromosomes
89
Helicase
Unwinds DNA at replication fork
90
Single-strand binding protein
Binds to and stabilises single-stranded DNA until it can be used as a template
91
Topoisomerase
Corrects overwinding ahead of replication forks by breaking, swivelling and re-joining DNA strands
92
Primase, leading
Synthesises a single RNA primer at the 5' end of the leading strand
93
Primase, lagging
Synthesises an RNA primer at the 5' end of each Okazaki fragments
94
DNA pol III, leading
Continuously synthesises the leading strand, adding on to the primer
95
DNA pol III, lagging
Elongates each Okazaki fragment, adding on to its primer
96
DNA pol I, leading
Removes primer from the 5' end of the leading strand and replaces it with DNA, adding on to he adjacent 3' end
97
DNA pol I, lagging
Removes the primer from the 5' end of each fragment and replaces it with DNA, adding on to the 3' end of the adjacent fragment
98
DNA ligase, leading
Joins the 3' end of the DNA that replaces the primer to the rest of the leading strand
99
DNA ligase, lagging
Joins the Okazaki fragments

Biology 1B (6 decks)

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