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Unit 1 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

proteome

A

all the proteins expressed by a genome

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2
Q

why is the proteome larger than the number of genes?

A

alternative RNA splicing and post-translational modification

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3
Q

amino acid link

A

peptide bonds

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4
Q

primary structure

A

the sequence in which amino acids are synthesised into the polypeptide

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5
Q

types of secondary structure

A

alpha helixes, parallel or anti-parallel beta sheets, turns

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6
Q

what holds together the secondary structure?

A

hydrogen bonding in the backbone of the protein strand

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7
Q

classes of R groups

A
  • positively charged (amine nh2)
  • negatively charged (carboxyl)
  • polar (hydroxyl)
  • hydrophobic (hydrocarbon)
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8
Q

ligand

A

substance that can bind to proteins

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9
Q

what happens when a ligand binds to a protein binding site or when a substrate binds to an
enzyme’s active site?

A

the conformation of the protein changes which causes a functional change

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10
Q

prosthetic group

A

non-protein unit bound tightly to a protein which is necessary for its function

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11
Q

what can interations of R groups be influenced by?

A

temperature and pH

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12
Q

possible interactions in tertiary structure

A

hydrophobic interactions, ionic bonds, hydrogen bonds

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13
Q

in which proteins can quartenary structure exist?

A

proteins with several connected polypeptide subunits

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14
Q

in archaea, how do bacteriorhodopsin molecules generate potential differences?

A

by absorbing light to pump protons across the membrane and the resulting
diffusion of hydrogen ions back across the membrane drives ATP synthase.

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15
Q

In plants, what does the light absorbed by photosynthetic pigments within protein
systems do?

A

drives an electron flow that pumps hydrogen ions across the thylakoid membrane of the chloroplast and the resulting diffusion of hydrogen ions back across the membrane drives ATP synthase

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16
Q

what forms rhodopsin?

A

opsin and retinal

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17
Q

what does different forms of opsin do in cone cells?

A

give sensitivity to specific wavelengths of light (red, green, blue or UV)

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18
Q

what does rhodopsin and the protein cascade do in rod cells?

A

absorbs a wider range of wavelengths, and a

greater degree of amplification by the protein cascade results in sensitivity at low light intensities

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19
Q

what amplifies light signals in eyes?

A

a cascade of proteins

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20
Q

Process of a nerve impuulse being generated once rhodopsin is excited by a photon of light

A

Excited rhodopsin activates G-proteins
which activate many enzyme molecules. The enzyme molecules cause the closure of ion channels by catalysing the removal of molecules that keep channels open. The inward leakage of positive ions is halted so the membrane potential increases. Hyperpolarisation (increasing charge) stimulates a nerve impulse.

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21
Q

what are membranes made of?

A

a bilayer of phospholipid molecules and a

patchwork of protein molecules.

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22
Q

where are hydrophyllic R groups in a protein?

A

surface of a soluble protein found in the cytoplasm

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23
Q

where are hydrophobic R groups in a protein?

A

they cluster at the centre of a protein to form a globular structure

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24
Q

peripheral proteins

A
  • proteins that temporarily attach to the cell membrane

- have less hydrophobic R groups interacting with phospholipids

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25
Q

examples of integral transmembrane proteins

A

channels, transporters, receptors

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26
Q

how are integral proteins held in place within the phospholipid bilayer?

A

regions of hydrophobic R groups allow strong hydrophobic interactions that hold the integral proteins in place

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27
Q

in eukaryotes, how is nucleosome packing of DNA in chromosomes formed?

A

positively charged histone proteins bind to negatively charged sugar phosphae backbone of DNA, DNA wraps around histone proteins to form nucleosomes

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28
Q

induced fit

A

correct substrate starts to bind resulting in a temporary change in the shape of the active site increasing the binding and interaction with the substrate, activation energy is lowered for this reaction

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29
Q

where do modulators bind on allosteric enzymes?

A

secondary binding site

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30
Q

effect of modulator binding

A

conformation of the enzyme changes and this alters the affinity of the active site for the substrate

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31
Q

positive and negative modulators effect

A

positive modulators increase the enzyme’s affinity whereas negative modulators reduce the enzyme’s affinity for the substrate.

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32
Q

cooperativity

A

changes in binding at one subunit alter the affinity of the remaining subunits

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33
Q

cooperativity in oxygen in haemoglobin

A

In haemoglobin, when one of the subunits binds a molecule of oxygen, the
second binds more easily, and so on

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34
Q

main factors which will affect haemoglobin’s ability to bind oxygen

A

temperature and pH

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35
Q

kinase

A

phosphorylation- attaches a phosphate group to a protein

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36
Q

phosphatase

A

dephosphorylation- removes a phosphate group from a protein

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37
Q

process of muscle contraction

A

-Myosin has heads that act as cross bridges as they bind to actin
-When ATP binds to myosin, the myosin head detaches from actin, swings forwards and rebinds
-The rebinding releases the ADP and a
phosphate and drags the myosin along the actin filament.

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38
Q

what uses ATP for phosphorylation?

A

ATPases

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39
Q

what can the addition or removal of phosphate from particular R groups can be used to cause?

A

reversible conformational changes in proteins, common form of post-translational modification

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40
Q

what does the phospholipid bilayer act as a barrier to?

A

ions and most uncharged polar molecules

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41
Q

where are the receptor molecules for hydrophyllic proteins?

A

on the surface of the cell

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42
Q

where are the receptor molecules for hydrophobic proteins?

A

within the nucleus as hydrophobic signals can pass through membranes

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43
Q

small molecules that can pass through the phospholipid bilayer

A

carbon dioxide and oxygen

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44
Q

how do cells perform specialised functions?

A

different cell types and different cell compartments have different channel and transporter proteins

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45
Q

passage of molecules through channel proteins is

A

passive

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46
Q

types of gated channels

A
  • ligand gated channels- controlled by specific ligand binding to protein
  • voltage gated channels- controlled by changes in voltage
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47
Q

types of transporter proteins

A
  • facillitated transport- simultaneuosly transports 2 types of molecules
  • active transport- transports molecules against concentration gradient
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48
Q

examples of gated channels

A

sodium channel and potassium channel

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49
Q

examples of transporter proteins

A

facilitated- glucose symport

active- Na/K-ATPase

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50
Q

transcription factor

A

proteins that have binding sites that are specific to particular sequences of DNA and when bound to can either stimulate or inhibit initiation of transcription

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51
Q

where does the energy for conformational change in active transport come from?

A

hydrolysis of ATP

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52
Q

Functions of the sodium-potassium pump

A

◦ maintaining the osmotic balance in animal cells;
◦ generation of the ion gradient for glucose symport in the small intestine
◦ generation and long-term maintenance of the ion gradient for resting potential in neurons
◦ generation of the ion gradient in kidney tubules

53
Q

signal transduction can result in:

A

activation of enzymes or G-proteins,
a change in uptake or secretion of molecules, rearrangement of the
cytoskeleton or activation of proteins that regulate gene transcription

54
Q

Process of sodium potassium pump

A

-The sodium-potassium pump has high affinity for sodium ions inside the cell, therefore binding occurs.
-Phosphorylation by ATP causes the conformation of the protein to change.
-The affinity for ions changes, resulting in sodium
being released outside of the cell.
-Potassium ions from outside the cell bind to the sodium-potassium pump.
-Dephosphorylation occurs, which causes the conformation of the protein to change.
-Potassium ions are taken into
the cell and the affinity returns to the start.

55
Q

resting potential

A

membrane potential of a neuron that is not transmitting signals

56
Q

depolarisation

A

membrane potential of neuron increase

57
Q

action potential

A

a signal that carries information along axons, is achieves if depolarisation change is big enough

58
Q

Process of Nerve Transmission

A

-An appropriate signal molecule like neurotransmitter, triggers the opening of ligand-gated ion channels.
-If sufficient ion movement occurs, then voltage-gated ion channels will open and the effect travels along the length of the nerve.
-Once the wave of depolarisation has passed, these channel proteins close and others open to allow the movement of ions in the opposite direction to
restore the resting potential.

59
Q

receptor molecules of target cells

A

proteins with a binding site for a signal molecule

60
Q

in a multicellular organism, can different cell types show a tissue-specific response to the same signal?

A

Yes

61
Q

Hydrophobic signalling molecules examples

A

steroid hormones and the thyroid

hormone thyroxine

62
Q

How does thyroxine increase metabolic rate?

A

When thyroxine binds to the receptor protein, conformational change prevents the protein binding to
the DNA, allowing transcription of the gene for Na/KATPase, resulting in an increase in metabolic rate

63
Q

How does thyroxine decrease metabolic rate?

A

Thyroxine receptor protein binds to DNA in the absence of thyroxine and inhibits transcription of the gene for Na/K-ATPase

64
Q

Process of hormone signalling

A

The receptor proteins for steroid hormones are transcription factors. Once the hormone signal has bound to the receptor can the transcription factor bind to gene regulatory sequences of DNA which allows transcription to occur

65
Q

hydrophyllic signalling molecules examples

A

peptide hormones and neurotransmitters

66
Q

cause of Type 1 diabetes

A

lack of insulin production

67
Q

cause of Type 2 diabetes

A

loss of insulin receptor function

68
Q

Transduced hydrophilic signals often involve

A

cascades of G-proteins or phosphorylation by kinase enzymes

69
Q

transmembrane receptor signalling process

A

transmembrane receptors change conformation when the ligand binds outside the cell; the signal molecule does not enter the cell, but the signal is transduced across the membrane of the cell

70
Q

effect of binding of the peptide hormone insulin to its receptor

A

triggers recruitment of GLUT4 glucose transporters to the cell membrane of fat and muscle cells which facilitates the uptake of glucose into the cells

71
Q

another thing that can trigger GLUT4 recruitment

A

exercise, can help people with Type 2 diabetes

72
Q

where is the receptor for ADH?

A

collecting duct of kidney

73
Q

effect of ADH binding to it’s receptor

A

triggers recruitment of the channel protein aquaporin 2 (AQP2)

74
Q

aquaporins provide

A

highly efficient route for water to move across membranes

75
Q

Recruitment of AQP2 allows

A

control of water balance in terrestrial vertebrates

76
Q

what can failure to produce ADH or insensitivity of it’s receptor lead to?

A

diabetes insipidus

77
Q

what does the cytoskeleton of a cell do?

A

provides mechanical support and shape to cells

78
Q

what are microtubulins made of?

A

hollow straight rods of globular proteins called tubulins

79
Q

what do microtubules do and form?

A

govern the location and movement of membrane-bound organelles and other cell components and form spindle fibres

80
Q

where do microtubules and spindle fibres radiate from?

A

centrosome

81
Q

the cell cycle

A

interphase (G1, S, G2), prophase, metaphase, anaphase, telophase, cytokinesis

82
Q

prophase

A

each duplicated chromosome appears as two identical

sister chromatids which are joined at the centromere

83
Q

metaphase

A

the chromosomes line up on the metaphase plate in the middle of the cell and each of the sister chromatids in each chromosome is attached to microtubules from opposite ends of the parent cell the kinetochore

84
Q

anaphase

A

the paired centromeres of each chromosome separate

and the chromatids begin moving apart as the spindle shortens

85
Q

telophase

A

the cell lengthens and a nuclear membrane forms around each set of chromosomes, the chromosomes start to uncoil

86
Q

cytokinesis

A

takes place during telophase, involves the separation of the cytoplasm into two daughter cells

87
Q

checkpoints in cell cycle

A

G1, G2 and M

88
Q

what happens if go ahead signal is not reached at G1 checkpoint?

A

the cell switches to a nondividing state called the G0 phase

89
Q

uncontrolled decrease in the rate of cell cycle leads to

A

degenerative disease

90
Q

uncontrolled increase in the rate of cell cycle leads to

A

tumour formation

91
Q

proliferation gene

A

codes for proteins that promote cell division eg. cyclin dependant kinase (CDK)

92
Q

anti-proliferation gene

A

codes for proteins that restrict cell division eg. retinoblastoma (Rb) and p53

93
Q

biological control

A

includes using more suitable strain of microorganism eg. less virulent

94
Q

dilution series

A

stepwise dilution of a stock dilution, often performed by diluting 1cm3 with 9cm3 of water and then repeating the process with newly produced solution

95
Q

standard curve

A

used to determine the concentration of an unknown solution

96
Q

pH buffer

A

solution whose pH changes very little when strong acid or base is added

97
Q

equipment that can be used to measure liquid volumes

A

cylinders, pipettes, burettes, syringes, autopipetters

98
Q

how to measure pH?

A

meter or indicator

99
Q

colorimeter

A

used to quantify the concentration of a pigmented solution

100
Q

substances can be separated according to

A

solubility, size, shape, or charge

101
Q

centrifugation

A

allows substances to be separated according to their size and density, largest and densest separate first and form a pellet at the bottom and liquid above the pellet is called the supernatant

102
Q

chromatography types

A
  • paper chromatography- seperates components using a solvent drawn up chromatography paper
  • thin layer chromatography
  • affinity chromatography- relies on binding interactions between the protein of interest and ligand
103
Q

protein electrophoresis

A

uses current flowing through a buffer to seperate proetins according to size and charge

104
Q

iso-electric point

A

overall neutral net charge and precipitate out of solution

105
Q

ELISA

A

uses antibodies that are linked to reporter enzymes to cause a colour change in the presence of a specific antigen

106
Q

applications of ELISA

A

diagnostic tests for HIV and food allergens

107
Q

protein blotting

A

proteins are separated and transferred to a membrane which is probed for the protein of interest using a specific antibody that is linked to a detectable label, this label may be a reporter enzymes to cause a colour change in the presence of a the target protein

108
Q

immunohistochemistry

A

antibodies are used to detect the presence of a particular antigen within a tissue sample

109
Q

how are hybridomas formed?

A

fusion of a B lymphocyte with a myeloma cell using polyethylene glycol

110
Q

fluorescence microscopy

A

specific protein structures have fluorescent markers added to them and structures are visualised using a fluorescent microscope

111
Q

haemocytometry

A

known volume of cell culture is added to haemocytometer which is viewed under a microscope to perform cell counts to estimate the number of cells in a sample

112
Q

flow cytometry

A

allows scientists to detect, count and analyse cells one by one as they flow past a detector in solution

113
Q

what dyes can be used to show cells for cell counts (viable and total)?

A

methlyne blue or trypan blue dye

114
Q

comparison of primary cell lines to tumour cell lines

A

primary cells have limited lifetimes whereas tumour cells grow and divide indefinitely in cell culture

115
Q

culture media contains

A

requirement of a cell

116
Q

complex culture media contains

A

growth factors from serum

117
Q

aseptic technique aim

A

keep bacteria free from contamination by microorgansims such as bacteria

118
Q

examples of aseptic technique

A

sterilisation of equipment, containers and materials, disinfection of the working area and wearing a lab coat

119
Q

event that triggers p53

A

DNA damage

120
Q

what happens as cell size increases during G1?

A

cyclin proteins accumulate and combine with Cdks and activate them

121
Q

what do active Cdks cause?

A

phosphorylation of proteins that stimulate the cell cycle, if a sufficient threshold of phosphorylation is reached the cell cycle moves on to the next stage, if not the cell is held at a checkpoint

122
Q

how does active G1 Cdks cause DNA replication in the S phase?

A

G1 Cdk phosphorylates a transcription factor inhibitor, Rb protein

123
Q

what can p53 cause?

A

stimulate DNA repair, arrest the cell cycle or cause

apoptosis

124
Q

caspases

A

DNAases and proteinases

125
Q

apoptosis is triggered by

A

cell death signals that activate inactive forms of caspases that destroy the cell

126
Q

cell death signals that originate outwith the cell (eg from lymphocytes)

A

bind to a surface receptor protein to activate a protein cascade that produces active caspases

127
Q

absence of cell growth factors can

A

initiate apoptosis

128
Q

action of caspases in cell destruction

A

activate other caspases and digest other proteins

129
Q

tertiary structure

A

folded polypeptide shape

Advanced Higher Biology (3 decks)

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