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Biomolecules and Cells > What is Life > Flashcards

What is Life Flashcards

1
Q

All living things.. (9)

A
  1. composed of common set of chemical compounds
  2. made up of cells
  3. use molecules obtained from environment to make news molecules
  4. extract energy from environment to use it to do work
  5. regulate internal environment
  6. contain genetic information
  7. use universal molecular code to build proteins from genomic information
  8. grow and change
  9. exist in population that evolve over time
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2
Q

What are prions

A

prions are misfolded proteins which transmit their misfolded shape onto normal variants of the protein

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3
Q

Characteristics of prions (3)

A
  • no DNA
  • survive being boiled
  • treated with disinfectants
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4
Q

Prions are

A

non living

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5
Q

Characteristics of viruses (2)

A
  • Contain genetic material (DNA/RNA)

- Replicate and evolve

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6
Q

Viruses are

A

not living (need host to replicate + no metabolic processes)

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7
Q

What are the 3 theories on how life began

A
  1. Prebiotic synthesis experiment model early earth
  2. Life came outside from earth
  3. RNA may have been first biological catalyst
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8
Q
  1. Prebiotic synthesis experiment model early earth
A

hot - early atmospheric gases struck by spark cause chemical reaction to make new compounds
cold - 27 years of gases -78c caused chemical reactions to speed and accumulate

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9
Q
  1. Life came outside from earth
A

meteorite carried different amino acid (L/D- isomers earth usually has L)
isotope ratio of carbon and hydrogen different in sugars

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10
Q
  1. RNA may have been first biological catalyst
A

catalytics RNAs - ribozymes
speed up reactions involve their own nucleotides
RNA catalyst for its own replication + protein synthesis

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11
Q

What does reverse transcriptase do in retroviruses

A

catalyse RNA –> DNA

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12
Q

What is a protocell

A

Molecules form a bilayer and polar heads are near water and non polar tails are interior
Prebiotic water filled structures

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13
Q

How did first cells with membrane come to exist

A

Fatty acids are amphipathic
Stabilise structure in aq. makes lipid bilayer - protocell
nucleic acids inside protocell would replicate using nucleotides from outside
limited replication

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14
Q

What is the cell theory (4)

A
  1. cells are fundamental unit of life
  2. all living organisms are composed of cells
  3. all cells from pre existing cells
  4. modern cells evolved from common ancestors
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15
Q

What do similarities among living organisms indicate?

A
  • all live on earth has common ancestry
  • evidence for origin of life 4 billion years ago
  • organisms go through evolution from past years
  • organisms are related sharing same genetic code/chemical composition/cellular structure
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16
Q

Describe evolution by Charles Darwin

A

Species change over time by natural reproduction of some individuals due to fitness
Descent with modification - divergent species share common ancestor

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17
Q

Definition of evolution by Charles Darwin

A

Changes of genetic composition of population over time

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18
Q

What is lysozyme protein held by

A

Water molecules

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19
Q

How did stromatolites form banded iron

A

oxygen from photosynthesis organisms react with iron in water

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20
Q

how did chloroplasts form

A

photosynthetic organisms symbiotic relationship with eukaroytes

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21
Q

what is cyanobacteria

A

group of bacteria forming oxygen
biofilms of cyanobacteria die and other take layers
thrive in salty ass water

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22
Q

effect of increase ozone (O3) on earth

A

life able to grow + adapt since lesson UV rays

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23
Q

effect of oxygen for animals

A

larger and more complex organisms + diversify

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24
Q

what is the cambrian explosion

A

the appearance of major animal groups and rapid diversification + little fossils form

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25
Q

what are stomatolites

A

evidence of early life

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26
Q

compare and contrast the features of DNA and RNA

A 
DNA: deoxyribose nucleic acid
double stranded
no oxygen on 2-carbon
RNA: ribonucleic acid
single stranded
OH on 2-carbon
can have complementary binding to its own nucleotide - folded shape
(mRNA/tRNA/rRNA)
Uracil instead of Thymine
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27
Q

How do polynucleotides (RNA/RNA) form (DNA replication)

A

3’ OH on sugar forms a phosphodiester bond with phosphate group
Two phosphate groups released
Hydrolysis of pyrophosphate to its individual phosphates releases energy for polymerization
Nucleic acids elongate 5’ → 3’ for the sugar phosphate backbone
Include RNA molecule that function as primers to allow duplication of RNA
RNA regulate expression of genes (transcription), DNA used to amplify (translation)
Hydrogen bonds form between (A=T/C triplebond G)
Hydrogen bonds form due to the polar C=O/N-H so the hydrogen and oxygen has delta +/- → lots of hydrogen bonds provide large attraction but not strong so it can be broken/made

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28
Q

nucleic acids/nucleotides/polynucleotides/nucleoside? explain

A

sugar + phosphate group (no base) = nucleoside
nucleoside + base = nucleotide
nucleotide + nucleotide = polynucleotide
polynucleotide (2) = nucleic acid (DNA)

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29
Q

what’s the name of DNA nucleosides

A

DEOXY-adenosine etc

RNA doesn’t have

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30
Q

what are the pyrimidine bases

A

C/U/T

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31
Q

what are the purine bases

A

A/G

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32
Q

nucleotide components

A

base (ribose/deoxyribose) + pentose sugar + phosphate group

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33
Q

what are proteins for (8)

A 
Structural
Defence 
Hormones
Muscles
Transport
Storage
Enzymes
Mucilage
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34
Q

amino acid components

A

basic amino group
r group side chain
carboxyl acidic group

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35
Q

non polar means

A

hydrophobic

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36
Q

polar, uncharged means

A

hydrophilic

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37
Q

charged means

A

hydrophilic

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38
Q

peptide bond formation type of reaction

A

condensation

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39
Q

definition of primary structure

A

sequence of amino acids in straight chain

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40
Q

definition of secondary structure

A

consist of regular and repeating patterns in polypeptide chain - involved hydrogen bonding

  • alpha helix
  • B-pleated sheets
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41
Q

what is an alpha helix

A

R groups extend outwards of the helix
Hydrogen bonding between C=O and N-H of amino acids throughout segments
Coiling right hand

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42
Q

what is b pleated sheets

A

Two or more polypeptide aligned side by side/completely extended
Hydrogen bonding between C=O and N-H on separate polypeptide cains

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43
Q

definition of tertiary sturcture + types of bonds

A 
3D structure formed from the interaction of R groups with itself and environment
Covalent disulfide bridges
Hydrogen bonds
Ionic bonds
Hydrophobic/van der waals
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44
Q

definition of quarternary structure

A

Contains two or more polypeptides folded and bind together and interact

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45
Q

what are carbohydrates for (5)

A 
Source of chemical energy
Form structural components
Abundant organic compounds in nature
(CH2O)n
Subunit is a monosaccharide
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46
Q

glycosidic bonds reaction?

A

condensation reaction between monosaccharides

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47
Q

examples of monosaccharides

A

glucose
galactose
fructose

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48
Q

glucose + glucose ->

A

maltose

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49
Q

galactose + glucose ->

A

lactose

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50
Q

fructose + glucose ->

A

sucrose

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51
Q

polysaccharides (3)

A

starch
glycogen
cellulose

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52
Q

describe glycogen

A

Water insoluble
Highly branched polymer of glucose
Store glucose in liver in form of glycogen

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53
Q

describe starch

A

A-1,4 and a-1,6 glycosidic bonds
Amylose unbranched
Amylopectin branched
Energy storage in plants

54
Q

cellulose

A

More stable due to b-glycosidic bonds
Structural for cell wall - can withstand harsh conditions
Linear polysaccharide

55
Q

describe lipids

A

Insoluble in water
Dissolve readily in organic solvents
Composed of C,H,O
Differ from carbohydrates due to smaller proportion of oxygen
Contain other elements (P/N)
Unsaturated = double bond form a kink = liquid in r.t.p
Saturated = single bond throughout = solid in r.t.p

56
Q

purpose of lipids

A

Insulation
Phospholipid membrane
Energy reserve
Buoyancy

57
Q

what is triglyceride made of

A

3 fatty acids + glycerol

58
Q

what are the fundamental elements of biomolecules

A

C,H,O,N

59
Q

general formula for carbohydrates

A

(CH2O)n

60
Q

size of prokaryotes

A

1-10um

60
Q

size of eukaroytes

A

10-100um

61
Q

characteristics of prokaryotes

A 
Capsule
Cytoplasm
Nucleoid
Cell membrane
Flagellum
Pili (protein hairlike structures)
Cell wall (peptidoglycan)
62
Q

characteristics of eukaryotes

A 
Compartmentalisation is important to cell
Nucleus (DNA held inside)
Endoplasmic reticulum
Mitochondria
Vacuole
Golgi apparatus
(cell membrane + cytoplasm)
63
Q

ribosomes present in prokaryotes

A

70S (50 + 20)

2 rRNA molecules

64
Q

describe the great oxygenation event

A

High levels of methane/CO2/ammonia gas + radiation

cyanobacteria form oxygen to allow ozone layer

65
Q

how do prokaryotes divide

A

binary fission exponentially

66
Q

describe binary fission in prokaryotes

A

replication of circular DNA at origin of replication
cell elongates and FtsZ protein migrate to middle of cell
duplicated chromosome move to opposite ends
FtsZ proteins form ring at midpoint - directs formation of septume
cell wall and plasma membrane accumulate there
septum complete - cell pinched into two daugher cells

67
Q

ribosomes are used as

A

drug targets

antibiotic targets ribosomes - inhibit protein synthesis to make bad protein

68
Q

difference between archaea and bacteria

A

Morphologically (physically) are similar
Achaean genes new - more closely related to eukaryotes
Archaea and eukarya millions of years apart
RNA polymerase in Archaea has multiple - bacteria has one
Genetic transcription and translation more similar to eukaryotes than bacteria
Features of archaean lipids and membrane unusual and lack of peptidoglycan wall
More archaea are extremophiles
Many are thermophilic/acidophilic
Maintain internal pH of 5.5-7 sitting in pH 2-3
Pyrolobus fumarii found in deep sea hydrothermal vents 106 degrees - metabolically inactive below 90 degrees
No production of resting spores - no long term state of immortality
No archaean pathogens - no disease affecting humans
Bacteria causes many diseases

69
Q

what are prokaryotes used for

A

recycling and nitrogen fixing bacteria and GM bacteria and primary producers

70
Q

2 features of prokaryotes

A

small genome and rapid cell division

metabolically diverse and found everywhere

71
Q

when did eukaryotes evolve

A

2.1 billion years ago

72
Q

how did eukaryotes come about

A

through spirally coiled photosynthetic algae

73
Q

what is linker DNA

A

double stranded DNA which holds two nucleosome cores

73
Q

describe nucleus

A

Surrounded by double membrane/nuclear envelope
Presence of nuclear pores (50 nm)
Allows movement of ribosomes in and out
Nucleolus: subregion containing ribosomal genes

74
Q

definition of chromosome

A

threadlike structure containing protein

75
Q

what is nucleosome

A

histone + DNA packing protein

76
Q

what is heterochromatin

A

highly condensed - gene poor

77
Q

euchromatin

A

easily condensed - gene rich

78
Q

Describe the structure and function of the mitochondrion.

A

Double membrane
Inner and outer membranes
Inner membrane is highly convoluted - high surface area for protein complex → ATP synthesis/reactions
Carry anaerobic respiration in eukaryotic cells

79
Q

reactions in the mitochondria matrix

A

TCA cycle and B-oxidation occur in the matrix

80
Q

Describe the structure and function of the chloroplast.

A

Cells contain one or many chloroplasts per cell
Surrounded by two membranes - out and inner to form thylakoids
Photosynthetic pigments located in thylakoids
Chloroplasts responsible for photosynthesis - light energy → chemical energy

81
Q

why do mitochondria and chloroplast have double membrane

A
  • nucleus formed from invagination of plasma membrane around the nucleoid of an ancient prokaryote
  • mitochondria arise from primary endosymbiosis from purple bacteria
  • chloroplasts arise from primary endosymbiosis from photosynthetic cyanobacteria
82
Q

evidence of endosymbiotic from mitochondria/chloroplasts

A
  1. organelles morphologically similar
  2. outer membrane/inner membrane
  3. semi-autonomous - retain own genome
  4. make their own stuff (protein/ribosomes)
  5. metabolism like existing prokaryotic organisms
  6. some chloroplasts have bacterial peptidoglycan
83
Q

definition of primary endosymbiosis

A

engulfing and absorbing of a prokaryotic cell by a eukaryotic cell

84
Q

steps of primary endosymbiosis

A

Aerobic bacteria enters in the eukaryote as a prey/parasite → becomes a cell living in a cell (endosymbiont)

Endosymbiont releases oxygen to allow the cell to survive - eventually turns into a mitochondrion

Eukaryotic cell may go on to obtain more endosymbionts (cyanobacteria) which will become chloroplasts

Outer membrane disappears

85
Q

definition of secondary endosymbiosis

A

engulfing and absorbing of a eukaryotic cell (undergone primary endosymbiosis) by a eukaryotic cell

86
Q

how many genomes do plants and animals have

A

plants - 3 (+ chloroplasts)

animal - 2

87
Q

definition of endomembrane system

A

system of compartments that include all membrane bound components of cell except for mito/chloro/microbodies

88
Q

describe the endoplasmic reticulum

A

Cisternae (enclosed membrane) → internal compartments and channels
Changing in structure and function
Rough endoplasmic reticulum
Ribosomes attached
Protein synthesis
Smooth endoplasmic reticulum
Synthesis for glycoproteins/carbohydrates/lipids
Biomolecules secreted throughout the cell

89
Q

describe the golgi apparatus

A

collection/packaging/distribution of molecules, then secreted
Biochemically modified (addition of sugars etc)
Polysaccharides formed
Consists of Golgi stacks (flattened sacs of membrane)
Receive vesicles from ER
Golgi polar structures
Vesicles arrive at cis face
Vesicles leave at trans face
Many molecules (hormones/digestive enzymes) exit the Golgi in secretory vesicles (exocytosis)

90
Q

describe the lysosomes

A

Break down material ingested by endocytosis or recycle old organelles
Surrounded by single membrane
Acidic interior - hydrolytic enzymes

91
Q

describe the plant vacuole

A

Surrounded by single membranes (tonoplast)
Contain hydrolytic enzymes
Storage of nutrients/pigments/maintenance
Maintain cell turgor pressure

92
Q

describe microbodies

A

Surrounded by single membrane
Found in animal and plant cells
Contain enzymes from free ribosomes in cytoplasm (not in RER)
Neutral pH
Oxidative enzymes release hydrogen peroxide
Enzyme catalase breaks down hydrogen peroxide
Peroxisomes (break down amino acids) and glyoxysomes (break down fatty acids)

93
Q

describe cytosol

A

Site of numerous biochemical processes
Space between organelles and endomembrane
Protein biosynthesis - protein synthesis begins in the cytosol and proteins made passed to nucleus/mitochondria etc
Cytoskeleton
Glycolysis reaction starts in the cytosol → mitochondria

94
Q

what is cytosol

A

fluid in cytoplasm, cytoplasm is the entire content within cell membrane

95
Q

describe cytoskeleton

A

Composed of protein (made in cytosol)

Act as form of structural elements within cytoplasm in cell (actin/microtubules)

96
Q

what are cytoskeleton components

A

microtubules + actin filaments

97
Q

describe the microtubules and actin filaments in cytoskeleton

A

Tubulin makes up microtubules (25nm diameter)
Actin makes up actin filaments (7nm diameter)
Form stiff structures don’t branch or contract
Polar and dynamic structures (one side negative/positive/one way)
polymerise/depolymerise to satisfy cell needs (forming polymer)
Cell movement generated by motor proteins (by actin filaments + microtubules)

98
Q

what are microtubule associated proteins

A

kinesin and dynein

99
Q

describe kinesin and dynein in microtubules

A

Kinesin motor move towards + end of microtubules
Dynein motors move towards - end of microtubules
May consume ATP for movement

100
Q

what does myosin do

A

pulls organelles along actin filament

responsible for cytoplasmic streaming (plant) and muscle contraction (mammals)

101
Q

3 things to remember about membranes

A
  1. always enclose a space
  2. membranes never open ended unless damaged cell
  3. phospholipid bilayer
102
Q

describe phospholipid bilayer

A

semi permeable
selective
water passed by osmosis

103
Q

difference between simple and facilitated diffusion

A

both passive diffusion facilitated sometimes use some carrier protein etc for fac.

104
Q

describe primary active transport

A

Na/K pump (antiporter)
ATP required against gradient
2K in cell
3Na out of cell

105
Q

describe secondary active transport

A

cotransporter (symport)
Using the electrochemical gradient formed from primary active transport
Coupling molecules

106
Q

why do cells need to divide

A

Cellular maintenance

Growth and development

107
Q

Cell division rates are highly variable

A

yes

108
Q

what is the cell cycle of eukaryotes

A

G1
S phase - dna synthesis
G2
M - mitosis

109
Q

describe g1 phase

A 
Unreplicated DNA (spent most time here)
G0 = resting phase
g1 cyclin
110
Q

describe s phase

A

DNA replication 5-6 hours

s cyclin

111
Q

describe g2 phase

A

Preparation for mitosis 3-4 hours

g2-m cyclin

112
Q

describe m phase

A

Nuclear division 2 hours → cytokinesis = 2 daughter cells

m cyclin

113
Q

describe the cell cycle

4 steps

A
  1. Internal signal trigger events to progress a cell through phases of cell cycle
    Cyclins and cyclin-dependent kinase (Cdk)
    If they come together → form activated complex
    Phosphorylate target - phosphate group from ATP to protein substrate
    = Phosphorylated protein (active) + ADP
    Regulation of cell cycle
  2. R (restriction points) regulated by different cyclin-cdk complex
  3. Cyclins are transient proteins (proteins can form and broken easily) during cell cycle
    RB protein stop movement of cell out of G1 to S
    Synthesis of G1/S cyclin
    DNA → mRNA → G1/S cyclin + CDK (active complex)
    Deactivates RB by phosphorylating it stop blocking cell into moving into S phase
    Breakdown of cyclin
  4. If checkpoints not meant = cyclin-Cdk interact with signalling pathways to prevent progression
114
Q

describe the cell cycle

4 steps

A
  1. Internal signal trigger events to progress a cell through phases of cell cycle
    Cyclins and cyclin-dependent kinase (Cdk)
    If they come together → form activated complex
    Phosphorylate target - phosphate group from ATP to protein substrate
    = Phosphorylated protein (active) + ADP
    Regulation of cell cycle
  2. R (restriction points) regulated by different cyclin-cdk complex
  3. Cyclins are transient proteins (proteins can form and broken easily) during cell cycle
    RB protein stop movement of cell out of G1 to S
    Synthesis of G1/S cyclin
    DNA → mRNA → G1/S cyclin + CDK (active complex)
    Deactivates RB by phosphorylating it stop blocking cell into moving into S phase
    Breakdown of cyclin
  4. If checkpoints not meant = cyclin-Cdk interact with signalling pathways to prevent progression
115
Q

look at page 37 cell cycle graphs ok

A

ok

116
Q

what is the cell cycle in prokaryotes

A

B phase - gap phase
C phase - replication
D phase - division

117
Q

conditions for C phase in prokaryotes

A

A lot of DnaA-ATP
Little of DnA-ADP

DnaA-ATP responsible for C phase → high affinity for DnaA binding region at the origin of replication (oriC region) in bacterial genome
Can bind and unwind

118
Q

conditions for D phase in prokaryotes

A

Little of DnaA-ATP

A Lot of DnA-ADP

119
Q

Cell cycle progression in bacteria regulated by initiation DNA replication DnaA-ATP - define oriC region/DnaA-ATP

A

(single origin of replication)

DnaA is a protein that activates initiation of DNA replication in bacteria, bound to ATP

120
Q

how does DnaA-ATP –> DnaA- ADP

A

DnaA-ATP opens and pulls apart DNA
Helicase pulls apart DNA → attract DNA polymerase III
DNA polymerase replicate DNA
ATPase converts DnaA-ATP → DnaA-ADP

121
Q

dna synthesis is semi conservation because?

A

→ Daughter cell will get old strand from parental DNA and new strand

122
Q

reference to replication origin on prokaryotes and eukaryotes

A

Prokaryote have single origin of replication along their DNA

Eukaryotes have multiple origins of replication along the chromosome

123
Q

describe DNA replication

A

Leading strand (continuous) from 3’ to 5’
DNA polymerase works from 5’ to 3’
Lagging strand (discontinuous)
Primase makes short RNA primer on the lagging strand template (on empty space)
DNA polymerase add to 3’ on the RNA primer to form okazaki fragment (RNA primer 5’ + okazaki fragment 3’)
Primase will land on random bits of lagging strand
DNA synthesis requires a primer
RNA primer synthesised before DNA polymerase attachment
Primase makes RNA primer
DNA helicase unwinds DNA
DNA ligase removes RNA primer and patches up between okazaki fragments
Single stranded binding proteins prevent DNA from winding back together

124
Q

describe chromosome/sister chromatids

A

G1 phase have single copy
S phase replication to form sister chromatids
End of S phase, chromosomes are held together by centromere
Before mitosis, DNA and histones form tightly packed structures
DNA double helix into nucleosomes (core of 8 histone molecules) - DNA wrapping around histones [10:1]
Nucleosomes wrap together to form super coles [50:1]
Chromatin forms loop domains on protein scaffold [250:1]
Condensed heterochromatin
Compacted chromosome

125
Q

what do kinetochores do

A

Kinetochores (specialised protein structure) important for movement
Connect microtubules to centromere region

126
Q

describe mitosis - IPMAT

A

Interphase
S phase - DNA replication
Prophase
Chromatin coils and supercoils to form visible chromosomes (paired sister chromatids)
Prometaphase
Nuclear envelope breaks down
Kinetochore and microtubules form and connect to poles
Cohesin holds sister chromatids together
Cohesin removed but held by by some cohesin in centromere
M cyclin + Cdk + APC + ATP → actives separase by phosphorylation
Metaphase
Centromeres align
Anaphase
Paired sister chromatids separate and move toward opposite poles
Daughter chromosomes separated
Telophase
Chromosome reach pole
Nuclear envelope forms
Decondensed chromatin

127
Q

cytokinesis in plant vs animals

A

In animal cells: plasma membrane contractile ring forms to pulling two membranes together to form separate cells
In plant cells: cell plate forms from cell wall membrane - endomembrane form vesicles of carbohydrates to form cell plate

128
Q

describe binary fission in prokaryotes

A

Double stranded circular DNA
DNA replication initiation (DnaA-ATP) in C phase
Daughter DNAs - DNA polymerase/helicase/ligase etc action
Cytokinesis
Forming of Z ring
FtsZ protein (filament temperature sensitive)
Forms protein fibres that constricts the cell
Similar to protein tubulin
Involved in division of chloroplasts/mitochondria

129
Q

what does mutation in FtsZ protein do

A

Mutation in FtsZ alter bacterial shape and frequency and control chloroplasts division

  • filament temp sensitive
  • form protein fibres constricting the cell
  • homologue of protein tubulin
  • involved in division of chloroplasts/mitochondria
129
Q

what does mutation in FtsZ protein do

A

Mutation in FtsZ alter bacterial shape and frequency and control chloroplasts division

  • filament temp sensitive
  • form protein fibres constricting the cell
  • homologue of protein tubulin
  • involved in division of chloroplasts/mitochondria

Biomolecules and Cells (5 decks)

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