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2: Molecular biology 2 Flashcards

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1
Q

What is metabolism?

A

All of the enzyme-catalysed reactions in a cell or organism.

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2
Q

What is anabolism?

A

The synthesis of complex molecules from simpler molecules. Requires the input of energy. Occurs by condensation reactions.

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3
Q

What is catabolism?

A

The breakdown of complex molecules into simpler molecules. Releases energy. Occurs by hydrolysis reactions.

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4
Q

What is condensation?

A

The reaction in which two smaller organic molecules combine to form a larger molecule with the accompanied formation of water or some other simple molecule.

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5
Q

What is hydrolysis?

A

The breaking of chemical bonds by the addition of water molecules.

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6
Q

What are the properties of water?

A

Cohesion, adhesion, thermal and solvent

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7
Q

What is cohesion (in water)?

A

Interaction between water molecules due to hydrogen bonding. Responsible for surface tension of water.

Allows water to be pulled up from roots to leaves in plants and permits insects to walk on water.

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8
Q

What is adhesion (in water)?

A

Interaction between water molecules and a surrounding material or surface due to dipolarity. Responsible for capillary action.

Assists the pumping of blood through vessels, and helps water move against gravity from the roots to the leaves (by adhering to the xylem).

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9
Q

What are the thermal properties (in water)?

A

Hydrogen bonding causing high specific heat capacity and high latent heat of vaporization due to large amount of energy needed to break them. Responsible for water being stable and a great coolant.

Evaporation of sweat from body surfaces involves heat loss, bringing a cooling effect.

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10
Q

What are the solvent properties (in water)?

A

Polarity allows many substances to dissolve in water, including those composed of ions or polar molecules.

Water in blood plasma dissolves a range fo solutes and gases, which makes it possible for blood to transport nutrients and gases around the body.

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11
Q

Modes of transport for biological molecules

A
  • Glucose and amino acids: polar, soluble due to positive and negative charges
  • Sodium chloride: polar, transported as ions (split by water)
  • Cholesterol: non-polar, attaches to polar proteins, hydrophilic end is soluble
  • Lipids: non-polar, attaches to polar proteins, carried by lipoprotein complexes
  • Oxygen: non-polar, carried by haemoglobin
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12
Q

What is cellulose?

A

The structural component of plant cell walls.

Linear form, alternating orientation, beta-D-glucose subunits, 1-4 bonds

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13
Q

What is starch?

A

Forms energy stores in plants.

Linear and helical form (amylose) / highly branched form (amylopectin), same orientation, alpha-D-glucose subunits, 1-4 bonds (amylose) / 1-4 and 1-6 (amylopectin)

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14
Q

What is glycogen?

A

The storage form of carbohydrates. Found in animals in the liver and muscles.

Highly branched form, same orientation, alpha-D-glucose subunits, 1-4 and 1-6 bonds

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15
Q

What are the key features of cis isomers?

A
  • Commonly occur in nature
  • Two hydrogen atoms attached on the same side of the double bond
  • Lipids of this form have lower melting points
  • Healthier, promote good cholesterol (HDL)
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16
Q

What are the key features of trans isomers?

A
  • Produced artificially (polyunsaturated fatty acids being ‘partially hydrogenated’)
  • Hydrogen atoms on opposite sides of the double bond
  • Lipids of this form have higher melting points
  • Dangerous for cardiovascular system, promote bad cholesterol (LDL)
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17
Q

What are the key properties of lipids?

A
  • More energy per gram than carbs or proteins
  • Less dense than water
  • Non-polar, which dissolves non-polar compounds
  • Excellent heat insulation
  • Water-insoluble
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18
Q

The three-dimensional conformation of a protein

A
  • Primary structure: order of the amino acid sequence
  • Secondary structure: alpha helices (coiled) and beta-pleated sheets (directionally-oriented staggered strand) resulting from hydrogen bonds forming between amine and carboxyl groups
  • Tertiary structure: determined by the interactions between the variable side chains
  • Quaternary structure: proteins that consist of more than one polypeptide chain linked together
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19
Q

What is a proteome?

A

The unique set of proteins that an organism possesses.

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20
Q

What are examples of globular proteins?

A

Rubisco, insulin, immunoglobulin, and rhodopsin.

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21
Q

What are examples of fibrous proteins?

A

Collagen and spider slik.

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22
Q

What is rubisco?

A

An enzyme involved in the fixation of CO2 in chloroplasts.

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23
Q

What is insulin?

A

A hormone produced by the beta cells of the pancreas, which is involved in glucose uptake from the blood.

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24
Q

What is immunoglobulin?

A

These are large Y-shaped proteins, also called antibodies, involved in fighting infections by specifically recognising and binding to antigen molecules.

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25
Q

What is rhodopsin?

A

A protein linked to pigment, found on the membrane of rod (photoreceptor) cells of the retina, where it allows very low light intensities to be detected.

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26
Q

What is collagen?

A

A structural protein, found in muscles, tendons and ligaments, where it gives tensile strength. It also occurs in skin and bones, where it prevents tearing and fractures, respectively.

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27
Q

What is spider slik?

A

A fibrous protein produced by spiders for their webs. It can be extended and is very resistant to breaking

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28
Q

What is denaturation?

A

A process in which proteins lose their secondary and tertiary structures (in some cases also quaternary)

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29
Q

How can you denature proteins?

A
  • Exposing the protein to higher temperatures

- Changing the pH of a surrounding solution

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30
Q

What are enzymes?

A

Globular proteins that catalyse biochemical reactions.

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31
Q

What is the induced fit model?

A
  • When substrate enters active site, 3D-shape of enzyme changes
  • Due to flexibility of protein molecules in enzyme
  • When enzyme and substrate fit together tightly, the enzyme induces the weakening of bonds within the molecules of the substrate
  • Reduces activation energy needed for reaction
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32
Q

What is activation energy?

A

The minimum energy that reacting particles should possess in order for a reaction to occur. An enzyme-substrate complex lowers the activation energy needed to catalyse a reaction.

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33
Q

What affects the rate of activity of enzymes?

A

Temperature, pH, substrate concentration, and enzyme concentration

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34
Q

What is the graph of the effects of temperature on enzyme activity?

A
  • Graph does not start at the origin, but a bit above 0 on the y-axis
  • Steady rise until optimum at 37C
  • Rapid decrease until 51C
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35
Q

What is the graph of the effects of substrate concentration on enzyme activity?

A
  • Graph begins at origin

- Rate rises gradually before plateauing

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36
Q

What is the graph of the effects of pH on enzyme activity?

A
  • Graph begins at origin

- Steady rise until optimum at around 7, then steady decrease

37
Q

What causes the denaturation of enzymes?

A

Extreme pH values, heat and the presence of heavy metals

38
Q

How are lactose free products made?

A
  • Lactase is an enzyme that can break down lactose into monosaccharides
  • Some people lack lactase, causing lactose to build up and remain in the digestive system
  • Lactose-free products are produced by adding lactase to milk
  • Lactase can be immobilised in alginate beads, which converts lactose into glucose and galactose as the milk flows through
39
Q

What is immobilisation (of an enzyme)?

A

A process of attaching an enzyme to a material so that its movements are restricted

40
Q

Why do industries prefer immobilised enzymes?

A
  • Permits higher concentrations of enzymes to be used
  • Allows immediate separation of the enzymes from the reaction mixture
  • Allows enzymes to be recycled, reducing production costs
41
Q

What is the Watson-Crick model of DNA?

A
  • Four-base code
  • Double helix structure
  • How the structure enables replication and transcription
  • Discovered by x-ray diffraction patterns
42
Q

Which nitrogenous bases are pyramidines?

A

Thymine, cytosine and uracil

43
Q

Which nitrogenous bases are purines?

A

Adenine and guanine

44
Q

What are the differences between DNA and RNA?

A
  • DNA has deoxyribose, whereas RNA has ribose
  • DNA has A,T,G,C whereas RNA has A,U,G,C
  • DNA is double stranded whereas RNA is single stranded
45
Q

How are nucleotides bonded together?

A

By phosphodiester bonds. They are always formed between the phosphate group attached to the 5’ end of one sugar and the OH-group on the 3’ end of another sugar.

46
Q

What is the complementary base pairing rule?

A

G always pairs with C, and A always pairs with T

47
Q

How are two DNA strands held together?

A

Hydrogen bonds (3 between G and C, and 2 between A and T)

48
Q

What does it mean to be antiparallel (in terms of DNA structure)?

A

The two strands run in opposite directions. One strand runs from 5’ to 3’ and the opposite strand runs from 3’ to 5’.

49
Q

What did Meselson and Stahl prove about DNA replication?

A
  • That it is replicated semi-conservatively
  • The two strands are separate and each serves as a temple for the synthesis of a new strand
  • Results in two new DNA molecules, both containing one parental strand and a new strand
50
Q

What is DNA replication?

A

A semi-conservative process whereby pre-existing strands act as templates for newly synthesised strands

51
Q

Explain DNA replication.

A
  • Helicase uncoils DNA into two strands
  • Primase adds short length of RNA
  • DNA polymerase III copies DNA
  • Adds nucleotides in the 5’ to 3’ direction
  • Uses deoxynucleoside triphosphates that are free in the cell
  • Two phosphates are removed to release energy
  • Complementary base pairing of A with T and G with C
  • Leading strand replication towards the replication fork
  • Okazaki fragments on lagging strand
  • DNA polymerase I removes RNA primers and replaces them with DNA
  • Ligase joins short fragments by making sugar-phosphate bond
52
Q

What was the Meselson and Stahl experiment?

A
  • Cultured E. coli bacteria in 15N
  • All bacterial DNA had 15N in its bases
  • Transferred bacterial culture into fresh medium with 14N
  • Bacteria allowed to grow for several generations
  • DNA samples extracted and subjected to centrifugation
  • DNA moved to different positions based on density (15N denser than 14N)
  • Band after one generation (half 14N and half 15N) was between those of only 14N and 15N
  • Shows that DNA replicates semi-conservatively
53
Q

Explain the process of transcription.

A
  • RNA polymerase binds to a promoter on the DNA to form mRNA strand
  • Unwinds the DNA strands
  • Binds nucleoside triphosphates to the antisense strand of DNA as it moves along in a 5’ to 3’ direction
  • Uses complementary base pairing where A is with U and C is with G
  • Loses two phosphates to gain required energy
  • Occurs until terminator signal is reached
  • RNA detaches from the template strand
  • DNA rewinds
  • RNA polymerase detaches from DNA
  • Introns must be removed to form mature mRNA
54
Q

What is the sense strand?

A

The DNA strand that is not transcribed. Also has the same sequence of bases as the mRNA molecule (except T is U)

55
Q

What is the antisense strand?

A

The transcribed strand. Also complementary to the mRNA molecule

56
Q

What is translation?

A

The synthesis of polypeptides on ribosomes according to the genetic code

57
Q

Explain the process of translation.

A
  • Translation involves initation, elongation and termination
  • mRNA binds to the small sub-unit of the ribosome
  • Ribosome slides along mRNA to start codon
  • Anticodon of tRNA pairs with codon on mRNA
  • Complementary base pairing between codon and anticodon
  • tRNA with methionine pairs with start codon AUG
  • second tRNA pairs with next codon
  • Peptide bond forms between amino acids
  • Ribosome moves along mRNA by one codon
  • Moves in 5’ to 3’ direction
  • Large ribosomal subunit aligns with tRNA molecule at the P site and forms a complex with the small subunit
  • tRNA that has lost its amino acid detaches
  • Another tRNA pairs with next codon
  • tRNA activating enzymes link amino acids to specific tRNA
  • Stop codon reached
58
Q

Outline the roles of the different binding sites for tRNA on ribosomes during translation.

A
  • A, P and E binding sites are on the large sub-unit of the ribosome
  • Initiation of translation starts with binding of methionine tRNA to the start codon
  • Large subunit binds with start tRNA in the P site
  • A binding site holds tRNA with the next amino acid to be added
  • Peptide bond is formed between the amino acids of the A sit and the polypeptide at the P site
  • Polypeptide is transferred to the tRNA in the A site
  • the tRNA with the polypeptide in the A site is moved to the P site
  • E binding site is the exit where the tRNA from the P site without the amino acid leaves the ribosome
59
Q

What is PCR?

A

A technique that allows for the rapid production of multiple copies of DNA using Taq DNA polymerase

60
Q

Describe the PCR, including the role of Taq DNA polymerase.

A
  • PCR is a process by which a small sample of DNA can be amplified
  • PCR involves repeated cycling through high and lower temperatures to promote melting and annealing of DNA strands
  • DNA and Taq DNA polymerase are heated to high temperatures to break hydrogen bonds between strands of DNA
  • Taq DNA polymerase can withstand high temperatures without denaturing
  • Primers bind to targeted DNA sequences at lower temperatures
  • Taq DNA polymerase forms new double-stranded DNA by adding complementary nucleotides
61
Q

What is PCR useful for?

A

Gene transfer and forensic analysis

62
Q

What is mRNA?

A

Carries the DNA code from the nucleus to the ribosomes in the cytoplasm

63
Q

What is rRNA?

A

Provides a large percentage of the ribosome composition

64
Q

What is tRNA?

A

Carries one of the 20 possible amino acids to the mRNA-ribosomal complex

65
Q

How is human insulin produced (in terms of gene transfer)?

A
  • The genetic code is universal
  • The same codons code for the same amino acids in all living things
  • Genetic information is transferrable
  • The gene responsible for insulin production is extracted from a human cell
  • It is spliced into a plasmid vector (becoming a recombinant plasmid) before being inserted into a bacterical cell
  • The transgenic bacteria (E. coli) are selected and cultured in a fermentation tank
  • The bacteria now produce insulin
  • Harvested, purified and packaged for human use
66
Q

What is a transgenic organism?

A

A unicellular organism that carries a specific gene from another organism

67
Q

What is cellular respiration?

A

The controlled release of energy by breaking down organic compounds to produce ATP. Occurs as a series of oxidation reactions which is controlled by enzymes.

68
Q

Explain anaerobic respiration (glycolysis)

A
  • Takes place in the cytoplasm
  • Takes place without the presence of oxygen
  • Begins with breakdown of glucose by glycolysis
  • Breaks glucose (6C) into two molecules of pyruvate (3C) using 2 ATP
  • Also produces NADH and 4 ATP
  • Generates a smaller amount of ATP (only 2 ATP) than aerobic respiration
  • In yeast, it produces alcohol and CO2
  • In animal muscle cells, it produces lactate
69
Q

Explain aerobic cell respiration (krebs cycle).

A
  • Requires oxygen
  • Gives large yield of ATP from oxidation of glucose
  • Occurs in the cytoplasm and mitochondria
  • Consists of the link reaction, krebs cycle and the electron transport chain
  • Two pyruvate molecules produced by glycolysis move into the mitochondrion
  • Two pyruvates enter the Krebs cycle one at a time and are broken down into water, CO2 and a large amount of ATP
70
Q

Anaerobic respiration in baking

A
  • Yeast is used in bread
  • Yeast rapidly uses up all O2 in dough and produces CO2 and ethanol
  • CO2 forms bubbles, causing dough to rise and increase in volume
  • When dough is baked, ethanol evaporates
71
Q

Anaerobic respiration in brewing and biofuel industries

A
  • Yeast used to produce ethanol by fermentation
  • Yeast is cultured in a liquid containing sugar and other nutrients, but no oxygen
  • Ethanol concentration of fluid around yeast rises to around 15% by volume before killing the yeast and ending the fermentation
  • CO2 bubbles out into the atmosphere
72
Q

Anaerobic respiration in lactate production

A
  • Anaerobic respiration can supply ATP are a more rapid overall rate due to not being limited to the supply of oxygen
  • Used in muscles carrying out rigorous exercise
  • Maximises power of muscle contractions
  • Produces lactate and hydrogen ions
  • Beyond 2 minutes, hydrogen ion concentrations would make the pH of the blood too low
  • High-intensity exercise must be stopped without oxygen
73
Q

What is photosynthesis?

A

The reaction of carbon dioxide and water using energy from light to produce carbohydrates and releasing oxygen as a waste product

74
Q

What is the electromagnetic spectrum?

A

The range of all possible frequencies of electromagnetic radiation. Exists in the range 400-700nm.

75
Q

What is chlorophyll?

A

A green pigment found in photosynthetic organisms that is responsible for light absorption. When it absorbs light, it releases electrons which are used to synthesis ATP

76
Q

What types of light does chlorophyll absorb and reflect?

A
  • Absorbs light most strongly in the blue and red portions of the visible spectrum
  • Reflects light most strongly in the green portion of the visible spectrum
77
Q

What is the action spectrum?

A

Shows the rate of photosynthesis achieved over the various wavelengths of light from the visible spectrum

78
Q

What is the absorption spectrum?

A

Shows which wavelength of visible light is absorbed by a particular photosynthetic pigment such as chlorophyll a or b measured by a spectrometer

79
Q

How do you draw the action spectrum?

A
  • X-axis labelled light wavelength
  • Y-axis labelled rate of photosynthesis
  • Curve increases, decreases, increases and decreases again
  • One peak at 425 nm
  • Second peak at 670 nm
  • First peak higher than second peak
80
Q

How do you draw the absorption spectrum?

A
  • X-axis labelled light wavelength
  • Y-axis labelled rate of absorption
  • Curve increases, decreases, increases and decreases again
  • For chlorophyll a: peaks at 440 nm and 660 nm
  • For chlorophyll b: peaks at 470nm and 630nm
  • Higher first peak for chlorophyll b than ch. a, lower second peak for chlorophyll b than ch. a
81
Q

What is photolysis?

A

When the energy in photons is used to split water molecules

82
Q

What are the limiting factors of photosynthesis?

A

Light intensity, carbon dioxide, and temperature

83
Q

How to draw the graph of the effect of light intensity on photosynthesis?

A
  • Starts at the origin
  • X- axis labelled light intensity
  • Y-axis labelled CO2 uptake
  • Steady rise into plateau
84
Q

How to draw the graph of the effect of CO2 on photosynthesis?

A
  • Starts at the origin
  • X- axis labelled CO2 concentration
  • Y-axis labelled rate of photosynthesis
  • Steady rise into plateau
85
Q

How to draw the graph of the effect of temperature on photosynthesis?

A
  • Starts at the origin
  • X- axis labelled temperature
  • Y-axis labelled rate of photosynthesis
  • Steady rise until max, before rapid decrease
86
Q

How did photosynthesis change the Earth’s atmosphere, oceans and rock deposition?

A
  • Little to no oxygen in the atmosphere about 3.5 billion years ago
  • Only bacteria present
  • Caused banded iron formations
  • O2 content rose due to photosynthesis
  • O2 levels rose more due to the evolution of multicellular algae and land plants
87
Q

What is chromatography?

A

A technique used to separate mixtures of substances based on the movement of the different substances on a piece of paper by capillary action

88
Q

Explain the process of chromatography.

A
  • A mixture is dissolved in a fluid (called the mobile phase) and passed through a static material (called the stationary phase)
  • The static material can be paper or silica gel
  • The different components of the mixture travel at different speeds
  • Causes them to separate
  • A retardation factor can be calculated (Rf value = distance component travels / distance solvent travels)

Biology (3 decks)

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