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Second Year Biology Semester 2 > Cell and Molecular Biology > Flashcards

Cell and Molecular Biology Flashcards

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1
Q

How are lysosomes formed

A

From endocytic vesicles and vesicles from GA

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2
Q

What are lysosomes

A

organelles responsible for waste processing and recycling in animal cells

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3
Q

What are vacuoles

A

organelles responsible for waste processing and recycling in plant, fungi and algal cells

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4
Q

What receptor is involved in routing of lysosomal enzymes

A

mannose-6-phosphate (M6P)

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5
Q

Name a role of M6P Receptors

A

Synthesis and tagging
Recognition
Transport Vesicle Formation
Delivery to Lysosome
Catalyzation of macromolecule breakdown

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6
Q

Name a function of Lysosomes

A

Endocytosis
Phagocytosis
Autophagy
ER and Golgi transport
Breakdown of macromolecules
Recycling of cellular components
Defense against pathogens

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7
Q

What is Endocytosis

A

Materials from outside the cell being engulfed by the plasma membrane forming a vesicle that fuses with a lysosome for degradation

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8
Q

What is phagocytosis

A

When large particles or cells are ingested forming phagosomes which then fuse with lysosomes

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9
Q

What is Autophagy

A

When damaged organelles or cytoplasmic materials are encapsulated in autophagosomes which fuse with lysosomes for breakdown and recycling

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10
Q

What is the optimum pH of lysosomal enzymes

A

4-5 (acidic) This is due to environment of lysosome being acidic

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11
Q

How is acidity maintained in lysosomes

A

Proton pumps transporting hydrogen ions into lysosome
Membrane permeability - as membrane is impermeable to ions so cant diffuse out

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12
Q

What are some differences between lysosome and vacuole

A

Lysosomes are only found in animal cells
Vacuoles have wider roles including storage, maintaining of turgidity
Vacuoles are larger (only one in cell compared to many lysosomes)

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13
Q

Define In vitro

A

In vitro refers to studies conducted in a controlled environment outside of a living organism e.g. test tube

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14
Q

Define In Vivo

A

In vivo refers to studies or experiments conducted in living organisms

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15
Q

Define Ex Vivo

A

Ex Vivo refers to studies conducted on tissues or organs taken from a living organism but out with the organism itself

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16
Q

Describe a type of in vitro model

A

Cell culture - primary cell culture and immortalized cell line grown under controlled conditions
Organotypic - 3D cultures that maintain some characteristics of original tissue

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17
Q

How are cells cultured in vitro

A

Isolation - cells are isolated from tissues or obtained from cell banks
Culture medium - cells are grown in a nutrient rich medium that provides the necessary growth factors, hormone and gases
Substrate - cells are often cultured on a flat substrate to which they adhere
Environmental control

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18
Q

What are some limitations of in vitro models

A

Lack of complexity, an artificial environment genetic drift and limited longevity

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19
Q

What are some ethical considerations of using animals in experiments

A

The three Rs (Replacement, Reduction, and Refinement) is a good guide. Animals need welfare and care. You need to be able to justify animal use

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20
Q

What are some ethical considerations of using humans in experiments

A

You must receive informed consent, must maintain their privacy, must insure a minimization of risk.

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21
Q

What are some ethical considerations of using in vitro cells in experiments

A

Source of cells
Consent for donated tissue
Use of embryonic stem cells
Replacement of animals /p

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22
Q

Name a function of membranes in eukaryotic cells

A

Compartmentalization
Selective permeability
Signal transduction
Energy transduction
Cell to cell communication

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23
Q

What is selective permeability in membranes

A

Membranes regulate the entry and exit of substances which maintains the internal balance of ions and molecules. Crucial in homeostasis

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24
Q

What is energy transduction

A

Membranes produce ATP in organelles like mitochondria and chloroplasts

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25
Q

Describe the structure of the membrane and phospholipids

A

Made up of a phospholipid bilayer. Phospholipids are made up of hydrophilic (polar) heads and hydrophobic (nonpolar) tails. Membranes are fluid and flexible due to unsaturated fatty acids. The arrangement of lipids forms a selective barrier

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26
Q

What are the polymer components of membranes

A

Integral and peripheral membranes
Carbohydrates (glycolipids + glycoproteins)
Lipids (other than phospholipids) such as cholesterol

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27
Q

How does sterols such as cholesterol affect membrane fluidity

A

At high temperatures they stabilize the membrane and at low temperatures make it more fluid

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28
Q

Name a function of proteins in membranes

A

Integral proteins function as channels and carriers for ions and molecules across the membrane.
Proteins act as receptors for signaling molecules

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29
Q

What are the functions of carbohydrates in the plasma membrane

A

Cell recognition - important in immune responses and tissue formation
Protect the cell surface from mechanical and chemical damage

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30
Q

What molecules require membrane transport proteins

A

Some ions due to their charge cannot diffuse through the lipid bilayer (Na+, K+, Ca2+, Cl- etc.)
Large polar molecules due to size and polarity (e.g. glucose, amino acids)
Water can diffuse through to an extent aquaporins facilitate its transport to make it faster

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31
Q

Define Membrane potential

A

The voltage difference across a membrane resulting from the unequal distribution of ions across the cell membrane. This potential energy influences the movement of charged substance across the membrane.

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32
Q

Define electrochemical gradient

A

The combined effect of both the concentration gradient and the electric potential gradient on the movement of ions across membranes. It dictates the direction ions will move.

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33
Q

Define what a channel is

A

Channels allow molecules to pass through by diffusion acting as pores that can open or close

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34
Q

Define what a transporter is

A

They bind to specific molecules on one side of the membrane and change shape to release them on the other side

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35
Q

Define what passive transport is

A

Transport that does not require energy allowing substances to move according to concentration gradient

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36
Q

Define active transport

A

transport that requires energy to move substances against concentration gradients

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37
Q

Define coupled transport

A

Transport that involves the simultaneous transport of two different molecules where the movement of one is directly coupled with the movement of another.

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38
Q

Define uncoupled transport

A

transport of a single molecule without the direct coupling to the transport of another molecule

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39
Q

Define the cytoskeleton

A

A complex network of protein filaments that plays a vital role in both plant and animal cells. It is also integral to the structure and function of plant cell walls

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40
Q

What are the functions of the cytoskeleton in animal cells

A

Support/shape - Provides mechanical support and maintains cell integrity and shape
Intracellular transport - serves as tracks for the transport of neurotransmitters and other molecules between the cell body and synaptic terminals
Cell division - mitotic spindle ensures accurate chromosome segregation
Cell movement - actin filaments and myosin motor proteins facilitate muscle contraction
Signal transduction - cytoskeletal elements participate in signal transduction pathways that control cell growth differentiation and apoptosis

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41
Q

What are the functions of the cytoskeleton in plant cells

A

Support/shape - directs the desposition of cellulose fibres to cell wall synthesis
Cell Division - for the preprophase band and later phragmoplast
Signal transduction - plays a role in growth, development and stress response
The cytoskeleton is also vital in integration of cell wall components

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42
Q

Name the three principal components of the cytoskeleton

A

Actin filaments, Microtubules, intermediate filaments

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43
Q

Define Actin Filaments

A

Thinnest filament (7nm diameter), primarily involved in cell shape and movement. Found just beneath the cell membrane and in areas requiring strength or movement and composed of actin monomers.

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44
Q

Define Microtubules

A

Thickest filament (25nm in diameter), crucial for cell division, intracellular transport and cell structure. THey radiate from the cell centre. Composed of alpha and beta tubulin.

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45
Q

define Intermediate filaments

A

Intermediate thickness (10nm in diameter), providing mechanical support and resilience against stress. Found throughout the cell often surrounding the nucleus and made of various proteins

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46
Q

What circumstances require cell death

A

Damaged DNA
Infection
Developmental processes
Maintaining homeostasis
Disease prevention

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47
Q

Define Apoptosis

A

Programmed cell death, characterized by cell shrinkage, DNA fragmentation

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48
Q

Define necrosis

A

Accidental cell death resulting from external factors like trauma or infection leading to swelling and rupture

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49
Q

Define Autophagy

A

A process where cells degrade their own components through lysosomal machinery often as a survival mechanism

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50
Q

Define Proptosis

A

A form of programmed cell death associated with inflammation, involving cell swelling and lysis to release pro-inflammatory mediators

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51
Q

Define Ferroptosis

A

AN iron dependent form of cell death characterized by the accumulation of lipid peroxides

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52
Q

Name the 3 stages of apoptosis

A

Initiation phase, execution phase phagocytosis

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53
Q

Define Phagocytosis

A

The cell beaks apart into apoptotic bodies and then phagocytosed and digested by neighboring cells

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54
Q

Name the 4 stages of necrosis

A

Onset, Cell swelling, organelle swelling and dysfunction, rupture

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55
Q

What are the consequences of uncontrolled cell death

A

Tissue damage, autoimmune disease, cancer (insufficient cell death), degenerative disease

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56
Q

Define anoikis

A

a form of apoptosis that is induced when cells lose their attachment to the extracellular matrix

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57
Q

Define contact-depended signalling

A

Signalling that requires direct physical contact between cells through membrane bound receptors and ligands

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58
Q

Define paracrine signalling

A

Signalling molecules released by a cell that affect nearby cells

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59
Q

Define synaptic signalling

A

signalling where neurotransmitters released from neurons cross synaptic gaps to target cells

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60
Q

Define endocrine signalling

A

hormones released into the bloodstream affecting distant target cells

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61
Q

Define what a receptor is

A

A protein molecule on the cell surface or inside a cell that binds to a specific ligand to initiate a cellular response

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62
Q

What is a ligand

A

A molecule that binds specifically to a receptor to trigger a signal transduction pathway or cellular response

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63
Q

Define, intercellular, intracellular and extracellular

A

Intercellular - occurring between cells
Intracellular - occurring within a cell
Extracellular - occurring outside a cell(s)

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64
Q

What are the main cell surface receptors

A

Ion Channel-linked receptors
G-Protein-Linked Receptors
Enzyme Linked Receptors

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65
Q

How does an Ion Channel linked receptor work

A

Opens or closes in response to ligand binding allowing ions to pass through membrane

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66
Q

How does a G Protein linked receptor work

A

They activate G proteins which in turn activate other intracellular signalling pathways

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67
Q

How does an enzyme linked receptor work

A

They function as enzymes or re associated with enzymes that are activated upon ligand binding

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68
Q

What is autocrine signalling

A

Signalling molecules that interact with receptors on same cell

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69
Q

What is paracrine signalling

A

When signalling molecules interact with receptors on nearby cells

70
Q

What are gap junctions

A

Direct cytoplasmic connections between cells that allow molecules and ions to pass directly from one cell to another

71
Q

What are second messengers

A

Second messengers are produced in response to the activation of cell surface receptors. These amplifications lead to the activation of multiple signalling proteins which creates a cascade effect

72
Q

What are kinases

A

Enzymes that transfer phosphate groups from atp to specific substrates, often activating or deactivating target proteins

73
Q

What is phosphatase

A

Phosphatase removes phosphate groups from proteins, often reversing action of kinases

74
Q

What does the balance between kinase and phosphatase effect

A

The balance of activities regulates many processes including cell growth, differentiation and apoptosis

75
Q

Why do cells need to divide

A

Growth, repair and regeneration, reproduction, maintenance

76
Q

Describe the structure of chromosomes

A

a long DNA molecule with part or all of the genetic material of an organism. DNA wraps around histones which makes the structure chromatin which condenses to form chromosomes

77
Q

Describe the function of chromosomes

A

they carry genes

78
Q

How many chromosomes are in the human body

A

In humans there is 23 pairs (46). Varies between organisms

79
Q

What are the phases of the cell cycle

A

G1 phase - cell grows and works as normal. Decision to divide occurs at G1 checkpoint
S phase - synthesis phase where DNA replication occurs
G2 phase - cell continues to grow and prepare for division. Integrity of DNA checked here
M phase - mitosis, cell divides its duplicated DNA into two sets of chromosomes which are separated into two daughter cells

80
Q

Define mitosis

A

the process by which a cell divides its nucleus and duplicated chromosomes into two nuclei each with an identical set of chromosomes

81
Q

Describe the phases of mitosis

A

Prophase - chromosomes condense and become visible, nuclear envelope breaks done, mitotic spindle begins to form
Metaphase - chromosomes align at the cell equator, the spindle fibres attach to centromere of each chromosome
Anaphase - sister chromatids separated and pulled to opposite poles.
Telophase 0 chromatids arrive at opposite poles. nuclear envelop reform around each set of chromosomes which begin to decondense

82
Q

Define cytokinesis

A

the process of dividing the cells cytoplasm into two daughter cell following mitosis

83
Q

What is the role of cyclins

A

Proteins that act as regulatory subunits that activate CDKs with different cyclins being synthesized and degraded at specific stages of the cell cycle

84
Q

What is the role of Cyclin-Dependent Kinases

A

CDKs are serine/threonine protein kinases that when activated by binding to cyclins, phosphorylate specific target proteins to regulate cell cycle progression. Their activation is essential for the cell to transition from one phase to the next in cell cycle

85
Q

What do cyclin-CDK complexes effect

A

They ensure that cell cycle does not proceed if the conditions are not favorable or if errors are detected. They are tightly regulated by phosphorylation and dephosphorylation.

86
Q

What is thought to be the origin of mitochondria

A

a symbiotic relationship between eukaryotic cell and proteobacterium

87
Q

What is thought to be the origin of chloroplast

A

endosymbiotic engulfment of photosynthetic cyanobacterium by a eukaryotic cell

88
Q

Describe the permeability of outer mitochondrial membrane

A

The OMM is highly permeable to small molecules and ions due to presence of porin protein channels.

89
Q

Describe the permeability of inner mitochondrial membrane

A

The IMM is selectively permeable with a tight barrier to most ions/molecules. Transport requires transport proteins

90
Q

Describe the electron transport chain

A

The ETC is a series of complexes that transfer electrons from electron donors to acceptors via redox reaction. This produces an electrochemical gradient that ATP synthase uses to produce ATP

91
Q

Describe oxidative phosphorylation

A

Synthesis of ATP from ADP and inorganic phosphate driven by ETC

92
Q

Describe Krebs cycle (citric acid cycle)

A

a series of reactions that oxidize acetyl-CoA to CO2 generating NADH and FADH2 which are used in electron transport chain

93
Q

What processes occur in IMM

A

Electron transport chain and oxidative phosphorylation

94
Q

What processes occur in Mitochondrial Matrix

A

Citric acid cycle

95
Q

Define cellulose

A

long chain polysaccharide that forms microfibrils providing tensile strength

96
Q

define Hemicellulose

A

a matrix of polysaccharides that bind to cellulose contributing to wall flexibility

97
Q

Define pectin

A

a group of polysaccharides that are rich in galacturonic acid contributing to porosity and hydration of the wall

98
Q

define the cell wall

A

a complex dynamic structure that surrounds the plasma membrane of the cell

99
Q

what are the function of the cell wall

A

It provides support, protection and acts as a filtering mechanism.

100
Q

Define the extracellular matrix

A

a network of extracellular components that provides structural and biochemical support to the surrounding cells in animal tissue

101
Q

Name the key components of extracellular matrix

A

Collagen, elastin, proteoglycans, fibronectin and laminin

102
Q

What are some similarities between the cell wall and ECM

A

Both provide structural support
both offer protection against pathogens, mechanical stress and osmotic pressure changes
both play roles in regulating external environments

103
Q

What are some differences between the cell wall and ECM

A

They are made of different things
their functionality is different
the EMC is more involved in regulation of biochemical environment

104
Q

How does the ECM interact with integrins

A

Integrins are transmembrane receptors that facilitate cell-EMC adhesion acting as a critical mediators of cell signalling and mechanical transduction.

105
Q

What triggers anoikis

A

the loss of cell-EMC interactions (especially ones mediated by integrins

106
Q

Define immunology

A

the branch of biology that studies the immune system its functions, disorders and mechanisms in protecting the body

107
Q

Define viruses

A

intracellular pathogen that hijack the host cellular machinery to replicate

108
Q

Define prions

A

Misfolded proteins that can induce other proteins to misfold

109
Q

Define adaptive immunity

A

Characterized by specificity and memory. It adapts its response to specific pathogens and improves upon repeated exposure

110
Q

What are B cells

A

Cells that produce antibodies that neutralize pathogens

111
Q

Define T cells

A

Cytotoxic T cells kill infected cells
Helper T cells coordinate the immune response

112
Q

Define innate immunity

A

First defense, providing immediate but non specific responses to pathogen. Includes physical barriers, phagocytic cells and NK cells

113
Q

What are the tasks of the immune system

A

Detection and elimination, Discrimination, regulation, memory

114
Q

Where do immune cells originate from

A

All immune cells originate from hematopoietic stem cells in the bone marrow

115
Q

What are progenitors

A

Lymphoid progenitors give rise to B, T, and NK cells
Myeloid progenitors develop into granulocytes, monocytes and other cells involved in innate immune response

116
Q

What are the cell types of the innate immune system

A

Macrophages
Neutrophils
Dendritic cells
NK cells
Eosinophils and Basophils

117
Q

How do Macrophages work

A

Engulf and digest pathogens, present antigens to T cells

118
Q

What do neutrophils do

A

Phagocytose bacteria and fungi

119
Q

What do dendritic cells

A

present antigens to T cells linking innate to adaptive immunity

120
Q

WHat do NK cells do

A

Kill virus infected cells and tumor cells

121
Q

What are eosinophils and basophils involved in

A

allergic reactions and parasitic infection

122
Q

What are the responses to an infectious agent

A

Recognition, activation, elimination and resolution

123
Q

Define Cytokine

A

small proteins important in cell signalling in the immune system. THey modulate balance between humoral and cell based responses

124
Q

Define chemokine

A

type of cytokine that specifically induces chemotaxis in nearby responsive cells. THis directs immune cells

125
Q

Define chemotaxis

A

The movement of an organism or cell along a chemical gradient toward higher concentration (often towards site of infection/injury)

126
Q

What are neutrophils

A

primary responders to infection. Phagocytose pathogens and release antimicrobial peptides and enzymes

127
Q

What are eosinophils

A

mainly involved in parasitic infection they contribute to dealing with allergic reactions
They release cytotoxic granules and inflammatory mediators to kill parasites and modulate inflammation

128
Q

Define basophils

A

involved in allergic reactions and parasitic infections. They release histamine and other mediators that contribute to inflammation and allergic reaction

129
Q

What are the types of granules in neutrophils

A

Azurophilic (primary) granules
Specific (secondary) Granules
Gelatinase (tertiary) granules

130
Q

Define monocytes

A

Monocytes circulate in the blood and migrate into tissue to differentiate into macrophages and dendritic cells

131
Q

Define Macrophages

A

Macrophages phagocytose pathogens and dead cells

132
Q

How do immune cells activate

A

Immune cells are activated by recognition of pathogens or by cytokines and chemokines produced by other immune cells

133
Q

What are the key characteristics of the adaptive immune response

A

Specificity
Diversity
Memory
Self-nonself recognition (ability to distinguish own cells to foreign cells

134
Q

What cell types are responsible for adaptive immune response

A

B cells
T cells

135
Q

What are the key features of immunological memory

A

Longevity, rapid response, enhanced affinity

136
Q

What is MHC class I

A

Presented by all nucleated cells allowing cytotoxic T cells to monitor for pathogens

137
Q

What is MHC class II

A

Presented by professional antigen presenting cells (dendric cells, mactophages etc.)

138
Q

Where do B cells mature

A

Bone marrow

139
Q

Where do T cells mature

A

the thymus

140
Q

Define the nuclear envelope

A

A double-layered membrane that encloses the nucleus, separating its contents from the cytoplasm

141
Q

Define nuclear pores

A

Openings in the nuclear envelope that allow for the exchange of materials
(like RNA and proteins) between the nucleus and cytoplasm

142
Q

define nucleoplasm

A

The gel-like substance within the nucleus, containing the chromatin and
nucleolus

143
Q

Define chromatin

A

complex of DNA and histones

144
Q

What is the nucleolus

A

dense region within nucleus where rRNA is synthesised

145
Q

What are the functions of the nucleus

A

Genetic info storage, gene expression regulation, ribosome assembly

146
Q

define semi-conservative replication

A

Each new DNA molecule consists of one original strand and
one newly synthesized strand

147
Q

define Conservative Replication

A

The original DNA molecule is conserved, and an entirely new
molecule is synthesized

148
Q

define dispersive replication

A

Both strands of the new DNA molecules are a mix of old and new
DNA

149
Q

What is the function of DNA polymerase

A

Removes RNA primers from the fragments and replaces them with DNA
nucleotides

150
Q

What is the replication fork

A

A Y-shaped region where the DNA double helix is unwound into two single
strands for replication to occur.

151
Q

What is the continuous strand

A

Synthesized continuously towards the replication fork
because the DNA polymerase can add nucleotides in the direction of unwinding

152
Q

what is the fragmented strand

A

Synthesized discontinuously away from the replication
fork in short segments known as Okazaki fragments, because DNA polymerase can only
synthesize DNA in one direction (5’ to 3’), necessitating this backstitching process.

153
Q

What are some examples of DNA proofreading

A

Exonuclease activity, mismatch repair, post-replication repair

154
Q

What is the DNA helicase

A

enzyme that unwinds DNA double helix

155
Q

what is gene mutation

A

permanent alteration in DNA sequence

156
Q

Describe what base pair substitution is and what the types are

A

Type of mutation where one nucleotide is replaced by another
Silent mutations, missense mutations, nonsense mutations

157
Q

What is frame shift

A

caused by addition or subtraction of base leads to entire reading frame being off causing wrong codons and potential early termination

158
Q

What are induced mutations

A

mutations caused by exposure to mutagens (physical - UV or xray, chemical - alkylating agents, biological agents - viruses)

159
Q

What is transcription

A

copying a sequence of DNA into RNA

160
Q

define translation

A

process in which mRNA is used to synthesis protein

161
Q

What is the central dogma

A

Describes flow of genetic information
DNA->RNA->Protein

162
Q

describe mRNA

A

single stranded, serves as template for protein synthesis during translation

163
Q

describe tRNA

A

cloverleaf structure with a anticodon arm and amino acid attachment site. Transfers amino acid to growing polypeptide chain

164
Q

describe splicing

A

removal on non coding introns anf joining of coding exons

165
Q

what is tRNA synthase

A

enzyme that provides tRNA with the correct amino acid

166
Q

what are the 3 stages of translation

A

Initation - ribosome assembles around target mRNA. First tRNA is attached at start codon
Elongation - ribosome continues to translate each codon in turn adding amino acid to growing peptide chain
termination - process ends when a stop codon is reached

167
Q

What are the functions of the A, P and E sites of ribosomes

A

A (aminoacyl) site is the entry site for the aminoacyl tRNA
P (peptidyl) site holds tRNA carrying the growing polypeptide chain
E (exit) site is where tRNA no longer bound to amino acid leaves ribosome

168
Q

Describe rough ER

A

characterized by presense of ribosomes
primarily involved in synthesis of proteins

169
Q

Describe Smooth ER

A

lacks attach ribosomes
involved in lipid synthesis, carbohydrate metabolism, ion storage and other functiona

170
Q

Describe the GA

A

an essential organelle. Plays role in modifying sorting and packaging protein and lipids for secretion and delivery

Second Year Biology Semester 2 (4 decks)

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