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Biology living cell > Molecule of life > Flashcards

Molecule of life Flashcards

1
Q

Most of living matter is composed of

just 4 elements. Which

A

Carbon, Hydrogen, Nitrogen, Oxygen

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2
Q

elements of remaining 4%

A 
Calcium
 Phosphorus
 Potassium
 Sulphur
 Sodium
 Chlorine
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3
Q

Key molecular constituents of cells

A 
Water (cells typically 60-85% water)
Proteins
Nucleic acids
Lipids
Carbohydrates
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4
Q

Water is polar

A

O is more electro-negative than H, therefore, the electrons that make up the bonds between O and H are not shared equally – they are pulled towards the O.

As a result, O has a slight negative charge (2δ−) and H has a slight positive charge (δ+).

excellent solvent for ions

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5
Q

Hydrophilic interactions

A

Water loving - Readily associates with water.

Solutes dissolved to form an aqueous solution.

Cytoplasm - water plus complex mixture of organic and inorganic compounds

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6
Q

Hydrophobic interactions

A

Water hating - Water insoluble

Non polar molecules

Membranes - lipid bilayer formation driven by hydrophobic forces

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7
Q

Simple Membranes

A

Monolayer / Bilayer

Composed of amphipathic phospholipids
Energetically favorable, form spontaneously

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8
Q

Polymerisation

A

Polymers are long molecules consisting of many similar or identical building blocks (monomers) linked by covalent bonds.

Polymers are broken down by dehydration

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9
Q

Biological macromolecules

A

Monomers Polymers

Nucleotides Nucleic acids

Amino acids Proteins

Sugars Carbohydrates

Acetyl CoA Fatty acids

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10
Q

Polymers are broken down by

A

hydrolysis

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11
Q

In liquid water the hydrogen bonds between water molecules are

A

fluid and constantly breaking and forming

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12
Q

____________ stabilise protein interactions and in _______

A

Hydrogen bonds

in DNA

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13
Q

DNA

A

Deoxyribonucleic acid

Double stranded- The double helix
Inherited material
Deoxyribose- absence of the OH group at the 2 position carbon.

Cytosine - Guanine & Adenine - Thymine

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14
Q

RNA

A

Ribonucleic acid

Mainly single stranded
Many different functions
Ribose- presence of the OH group at the 2 position carbon.
Cytosine- Guanine & Adenine - Uracil

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15
Q

nucleic acid

Difference between Nucleotide & Nucleoside

A

RNA / DNA

nitrogenous bases - purines & pyrimidines (inside for pairing in DNA, held by hydrogen bond)
pentose sugars  (backbone)
phosphate groups  (outside)

nitrogenous bases - purines & pyrimidines
pentose sugars

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16
Q

purines

A

double ring nitrogenous bases

adenine & guanine

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17
Q

pyrimidines

A

Single ring nitrogenous bases

Cytosine / Uracil / Thymine

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18
Q

Nucleic acid strands have __________ and are synthesised from __ to ___

A

polarity

from 5’ to 3’.

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19
Q

In DNA, the 2 strands run in _______ directions relative to each other

A

opposite [antiparallel]

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20
Q

DNA is replicated _____________

A

semi-conservatively

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21
Q

Extending the nucleic acid polymer

A

nucleoside triphosphate attach to the OH on pentose and lose pyrophosphate

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22
Q

DNA replication

A

DNA [transciption] mRNA [translation] Protein

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23
Q

different RNA

A 
mRNA - messenger RNA
rRNA - ribosomal RNA
tRNA - transfer RNA
snRNA - small nuclear RNA
miRNA - micro RNA
siRNA – small interfering RNA
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24
Q

different RNA roles

A
  • Protein synthesis
  • RNA splicing
  • Gene regulation
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25
Protein synthesis RNA
mRNA - messenger RNA - read on the templet strand rRNA - ribosomal RNA - ribosome tRNA - transfer RNA - Amino acid attachment sit at 3' & has anticodon
26
Splicing RNA
snRNA - small nuclear RNA
27
-Gene regulation RNA
miRNA - micro RNA | siRNA – small interfering RNA
28
The ‘Omics
Genomics - Genome (DNA sequences) Transcriptomics - Transcriptome (RNA expression) Proteomics - Proteome (Proteins)
29
Genomes and genomics
Genome- Organism inheritable genetic instructions library Studied by large scale DNA sequencing efforts followed by bioinformatics functional unit : gene. 1 gene = 1 polypeptide.
30
Transcriptomics
study of mRNA expression patterns. Microarrays and gene chips. Thousands of genes studied simultaneously.
31
Bioinformatics
field of research which strives to make sense of the explosion of biological data in recent years fusion of computer science and molecular biology
32
Proteins make up % cell weight.
~15%
33
Nonpolar amino acids
Proline Tryptophan Glycine Phenylalanine Methionine Alanine Valine Leucine Isoleucine
34
Uncharged polar amino acids
Tyrosine Asparagine Glutamine | Serine Threonine
35
Weakly polar amino acids
Cysteine
36
Charged acidic amino acids
Aspartic acid Glutamic acid
37
Charged basic amino acids
Lysine Arginine Histidine
38
no of standard amino acids no of amino acids found in eukaryotes no of amino acids are common and encoded by the universal genetic code
22 21 20
39
amino acids that have other biosynthetic mechanisms
Selenocysteine and pyrrolysine
40
enzyme called ____________ attaches amino acids to their corresponding tRNA molecules using energy from _______
aminoacyl tRNA synthetase ATP
41
how many possibilities of RNA codon
64 Only 20 amino acids & “start” and “stop” codes - therefore a lot of redundancy
42
which condon has single codes?
Met (start) and Trp
43
Sickle cell hemoglobin
Val instead of Glu
44
A protein’s function is determined by
its specific conformation.
45
four levels of protein structure
Primary / Secondary/ Tertiary / Quaternary
46
Primary protein structure
the linear sequence of amino acids joined by polypeptide bonds and a water molecule made written from the N (amino) terminus to C (carboxyl) terminus
47
Polypeptide backbone
Dihedral angles – φ (phi), ψ (psi)
48
Secondary structure
``` Alpha helices Beta sheets (made of strands) - antiparallel / parallel Random coils/loops ``` Often functionally relevant – may become ordered on binding Protein intrinsic disorder
49
Tertiary structure
Overall conformation/ shape - Hydrogen bond - Disulfide bridge - Ionic bond - Hydrophobic interaction
50
Quaternary structure
Functional protein- 2 or more polypeptides - Collagen - Hemoglobin
51
The protein folding problem
Denaturation Renaturation
52
proteins that help facilitate protein folding
chaperones unfold polypeptide enters the hollow cylinder. Cap attach and cylinder changes shape to create a hydrophilic environment for folding. Cap opens and folded protein released
53
A protein’s structure is determined only by ____________
the sequence of amino acids.
54
Domains
regions of a protein with a discrete fold and/or function. Most proteins are found to be made up of a number of identifiable domains.
55
Domains can be isolated away from the protein as a whole and will ____________
fold independently into an active conformation.
56
Different combinations of domains give protein with _______
unique properties
57
Eg of single polypeptide made up of different protein domains
``` Src kinase - with 4 different protein domains: SH2 domain SH3 domain Small kinase domain Large kinase domain ```
58
Immunoglobulins are made up of different protein domains T/F
F Immunoglobulins are made up of several copies of the same module.
59
Protein structure can be obtained by _____________
X-ray crystallography
60
Protein structure can be modelled on ______________
computers using bioinformatics
61
Why predict protein structures
- Bridge gaps in knowledge, coping with data deluge - Fast, cheap, accurate! (Experimental methods are expensive and time consuming) - Inform and direct experimental work - Useful for mutagenesis studies - Protein design - How will this protein fold? - Some proteins are difficult to resolve experimentally e.g. intrinsic protein disorder, membrane proteins - Understanding protein evolution - Inferring function! - Close the protein sequence-structure gap
62
The protein sequence-structure gap
-Tens of millions of protein sequences, but only tens of thousands of protein structures >32,000,000 non redundant protein sequences (NCBI) Only 87,00 protein structures (PDB)
63
Proteomics
Technology driven: Mass Spectrometry, Structural Genomics, Interactomics, Unfoldomics ...all underpinned with Bioinformatics

Biology living cell (9 decks)

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