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Biology living cell > Molecule of life > Flashcards

Molecule of life Flashcards

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AP® Biology flashcards Biology 101 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
Q

Protein synthesis RNA

A

mRNA - messenger RNA - read on the templet strand
rRNA - ribosomal RNA - ribosome
tRNA - transfer RNA - Amino acid attachment sit at 3’ & has anticodon

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26
Q

Splicing RNA

A

snRNA - small nuclear RNA

27
Q

-Gene regulation RNA

A

miRNA - micro RNA

siRNA – small interfering RNA

28
Q

The ‘Omics

A

Genomics - Genome (DNA sequences)

Transcriptomics - Transcriptome (RNA expression)

Proteomics - Proteome (Proteins)

29
Q

Genomes and genomics

A

Genome- Organism inheritable genetic instructions library
Studied by large scale DNA sequencing efforts followed by bioinformatics

functional unit : gene.
1 gene = 1 polypeptide.

30
Q

Transcriptomics

A

study of mRNA expression patterns.

Microarrays and gene chips.

Thousands of genes studied simultaneously.

31
Q

Bioinformatics

A

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
Q

Proteins make up % cell weight.

A

~15%

33
Q

Nonpolar amino acids

A

Proline Tryptophan Glycine
Phenylalanine Methionine Alanine
Valine Leucine Isoleucine

34
Q

Uncharged polar amino acids

A

Tyrosine Asparagine Glutamine

Serine Threonine

35
Q

Weakly polar amino acids

A

Cysteine

36
Q

Charged acidic amino acids

A

Aspartic acid Glutamic acid

37
Q

Charged basic amino acids

A

Lysine Arginine Histidine

38
Q

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

A

22

21

20

39
Q

amino acids that have other biosynthetic mechanisms

A

Selenocysteine and pyrrolysine

40
Q

enzyme called ____________ attaches amino acids to their corresponding tRNA molecules using energy from _______

A

aminoacyl tRNA synthetase

ATP

41
Q

how many possibilities of RNA codon

A

64

Only 20 amino acids & “start” and “stop” codes - therefore a lot of redundancy

42
Q

which condon has single codes?

A

Met (start) and Trp

43
Q

Sickle cell hemoglobin

A

Val instead of Glu

44
Q

A protein’s function is determined by

A

its specific conformation.

45
Q

four levels of protein structure

A

Primary / Secondary/ Tertiary / Quaternary

46
Q

Primary protein structure

A

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
Q

Polypeptide backbone

A

Dihedral angles – φ (phi), ψ (psi)

48
Q

Secondary structure

A 
Alpha helices
 Beta sheets (made of strands) - antiparallel / parallel
 Random coils/loops

Often functionally relevant – may become ordered on binding

Protein intrinsic disorder

49
Q

Tertiary structure

A

Overall conformation/ shape

  • Hydrogen bond
  • Disulfide bridge
  • Ionic bond
  • Hydrophobic interaction
50
Q

Quaternary structure

A

Functional protein- 2 or more polypeptides

  • Collagen
  • Hemoglobin
51
Q

The protein folding problem

A

Denaturation Renaturation

52
Q

proteins that help facilitate protein folding

A

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
Q

A protein’s structure is determined only by ____________

A

the sequence of amino acids.

54
Q

Domains

A

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
Q

Domains can be isolated away from the protein as a whole and will ____________

A

fold independently into an active conformation.

56
Q

Different combinations of domains give protein with _______

A

unique properties

57
Q

Eg of single polypeptide made up of different protein domains

A 
Src kinase - with 4 different protein domains:
SH2 domain
SH3 domain
Small kinase domain
Large kinase domain
58
Q

Immunoglobulins are made up of different protein domains T/F

A

F

Immunoglobulins are made up of several copies of the same module.

59
Q

Protein structure can be obtained by _____________

A

X-ray crystallography

60
Q

Protein structure can be modelled on ______________

A

computers using bioinformatics

61
Q

Why predict protein structures

A
  • 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
Q

The protein sequence-structure gap

A

-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
Q

Proteomics

A

Technology driven:

Mass Spectrometry, Structural Genomics, Interactomics, Unfoldomics

…all underpinned with Bioinformatics

Biology living cell (9 decks)

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