Midterm Flashcards
1
Q
Do Kings Play Chess Or Family Games Sometimes
A
domain- archaea, bacteria, eukarya kingdom- eukarya splits to plantae, amnimalia, fungi, protista eubacteria and archaebacteria phylum class order family genus species- most specific level, organisms are so similar they can mate and reproduce
2
Q
what elements make up >96% of living matter
A
C H O P S N
3
Q
covalent bond
A
sharing a pair of valence electrons by two atoms
two or more atoms held together by covalent bonds=molecule
4
Q
ionic bond
A
2 atoms with a very different affinity for valence electrons combine, the electron is transferred from one to the other leaving 2 atoms with a net change in their charge. the oppositely charged cations and anions form an ionic bond
change in charge forms the bonds
compounds formed by ionic bonds are salts not molecules
weak
5
Q
hydrogen bond
A
when hydrogen forms a covalent bond with an electronegative atom. it will have a positive charge allowing it to interact with another negatively charged atom
6
Q
van der waals interactions
A
because of random positioning of electrons in the orbitals, net displacement can occur, creating brief charge differences. the dynamic charge distribution allows the molecules to stick to each other if they are very close.
7
Q
dipole-dipole interaction
A
gecko foot and wall, the geckos feet contain millions of little hairs which stick to many surfaces through van der waals interactions
8
Q
water
A
polar molecule with unique properties
- cohesion of water molecules-allows water molecules to stick (h-bonds)
- moderation of temperature by water- water has high heat of vaporization, water contributes to evaporative cooling
- water solid is more dense than water liquid, crystalline lattice structure makes ice about 10% less dense than liquid
- water is an important solvent- salts dissolve in water, polar molecules are soluble in water (hydrophilic) and non-polar molecules are insoluble in water (hydrophobic)
9
Q
hydrocarbons
A
organic molecules consisting of only H and C
10
Q
isomers
A
- structural (or constitutional) isomers can have a different bond order of atoms, atoms are connected in a different way
- geometric isomers e.g. cis vs. trans isomers, a double bond restricts rotation of the two atoms with respect to each other; trans=different side, cis=same side
- enantiomers, when 4 different atoms (or group of atoms) bind to carbon, an asymmetric arrangement occurs. if the 2 molecules are mirror images, and cannot be superimposed on each other, they are enantiomers
11
Q
Pharmacological Importance of Enantiomers
A
Ibuprofen: S-ibuprofen is effective but R-ibuprofen is not
12
Q
7 functional groups important for biological molecules
A
hydroxyl: OH
carbonyl: C=O
carboxyl: COOH
amino: NH2
sulfhydryl: SH
phosphate: PO4 2-
methyl: CH3
13
Q
macromolecules
A
large molecules that make up living cells, many form by the addition of small monomeric subunits, to make polymers
carbohydrates, proteins, and nucleic acids add nucleotides to form macromolecules, they are polymers
lipids are macromolecules
14
Q
formation of polymers
A
polymers form through dehydration reactions, monomers are attached through the formation of a covalent bond and the simultaneous removal of a water molecule= dehydration reaction
dehydration removes a water molecule and forms a new bond
15
Q
disassembling of polymers
A
polymers are disassembled into monomers by the reverse reaction, or hydrolysis
hydrolysis adds a water molecule, breaking a bond
16
Q
carbohydrates
A
fuel and building material
monosaccharides added to build polysaccharides and disaccharides
most common biological monosaccharides contain either 3, 5, or 6 carbon atoms
molecular monosaccharides are usually multiples of CH2O
e.g. C3H6O3 (glyceraldehyde)
C5H10O5 (ribose)
C6H12O6 (glucose, galactose, and fructose)-structural isomers
17
Q
monosaccharides
A
monosaccharide names end with -ose and can be grouped into general categories based on the number of carbons e.g. trioses, pentoses, hexoses
simple monosaccharides have a linear structure with a carbonyl group (C=O) and multiple hydroxyl groups
glucose is a hexose and it prefers a circular shape
many monosaccharides change dynamically between linear molecules and rings
monosaccharides like glucose are a major nutrient for cells, cells extract glucose via cellular respiration (breaking them down into a series of reactions)
18
Q
disaccharides
A
forms when a dehydration reaction joins two monosaccharides, can form polysaccharides
ex. two glucose molecules joined by an alpha 1-4 glycosidic linkage=maltose
glycosidic linkage is with 2 sugar molecules
19
Q
storage polysaccharides
A
- starch: glucose polymers, each monomer is joined by 1-4 glycosidic linkages with all monomers in the alpha configuration. a simple starch, amylose, is unbranched and helical. amylopectin is a branched starch it uses alpha 1-6 linkages, it is not helical because of the branches.
- glycogen: how we store glucose. animals store glucose in this polysaccharide form and it is structurally similar to amylopectin but with more frequent alpha 1-6 linkages=more branching.
20
Q
structural polysaccharides
A
- cellulose: like starch it is a polymer of glucose but with covalent 1-4 linkages which involve beta form of glucose. cellulose forms straight polymers that never branch it is very strong because of the h-bonds between different polymers lying parallel -this forms in microfibrils. most animals cant digest cellulose but cows and other ruminants can because they have special cellulose-digesting bacteria and/or protists that we dont
- chitin: a structural polysaccharide used in arthropods to build their exoskeleton. chitin contains N-acetylglucosamine monomers which are a derivative of glucose. it as an acetyl amine group instead of OH which allows for increased h-bonding between adjacent polymers giving chitin increased strength
21
Q
starch
A
- made of glucose monomers
- used by plants to store surplus glucose
22
Q
glycogen
A
- made of glucose monomers
- more highly branched structure than starch
- used by animals to store glucose
23
Q
cellulose
A
- made of glucose monomers, but different anomeric form of glucose than in starch
- major component of plant cell walls
24
Q
chitin
A
- made of N-acetylglucosamine monomers
- component of arthropod exoskeletons
25
lipids
lipids are hydrophobic because they consist mostly of hydrocarbons which are non-polar
classes: fats, phospholipids, steroids
dont form by polymerization because they dont make long chains
26
fats
fats are not polymers but they are built from monomers that are added by dehydration reactions
a fatty acid has a long chain of 16-18 carbons with a carboxyl group on the end, hence why its and acid
in a fat, 3 fatty acids are joined to glycerol by an ester linkage creating a triacylglycerol or a triglyceride
fatty acids vary in length and the number and location of double bonds
major function is energy storage
humans and other mammals store their fat in adipose cells
adipose tissue cushions vital organs and insulate body
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saturated fat
saturated fatty acids do not have double bonds
all carbons have the maximum amount of hydrogens, making it saturated with hydrogen
the tail of a saturated fatty acid is straight which allows them to be packed tightly therefore making it solid at room temperature
28
unsaturated fat
have one or more double bonds
plant and fish fats are usually unsaturated
carbons do not contain the max amount of hydrogens
the cis double bonds prevent rotation, causes a bend and doesn't allow close packing therefore it is liquid at room temperature
29
fats are essential but,
a diet rich in saturated fats may contribute to cardiovascular disease
trans fats may contribute more than saturated fats
cause arteries to be less flexible and clog
trans fats are found in fried food
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trans fats
trans fats are a biproduct of a reaction
they are unsaturated fats
the kinks found in the structures of unsaturated fats is removed so it will be solid at room temperature
the double bonds are saturated by adding H atoms
makes plant oil solid at rt, increases shelf life, and can be used as butter substitute
the process creates a lot of trans fat as a by-product i.e. some cis 2 bonds in the plant oil become rearranged rather than saturated, our bodies aren't used to this
31
phospholipids
two fatty acids and a phosphate group attached to glycerol
phosphate group is hydrophilic the 2 fatty acid tails are hydrophobic
phospholipids are amphipathic molecules, having both a hydrophilic polar end and a hydrophobic non polar end
because of their amphipathic nature, when phospholipids are added to water, they can rearranged into various structures
phospholipids are the major component of all cell membranes
32
liposome
=spherical lipid bilayer with aqueous middle
| hydrophilic heads interact with H2O and hydrophobic tails interact with each other, away from water
33
steroids
steroids are amphipathic
lipids with a carbon skeleton consisting of 4 fused rings
cholesterol is an important component of animal cell membranes it provides strength and flexibility
too much cholesterol leads to cardiovascular disease
some steroids include cortisol and testosterone
34
proteins
form by addition of amino acids
lots of variability
proteins are involved in every biological task
polymers of amino acids (there are 20 biologically relevant amino acids)
vary extensively in structure
e.g. enzymes, antibodies, storage proteins, hormones, transporters, structural cytoskeletal proteins, intracellular machines
35
amino acid
amino acids can exist as different enantiomers but all proteins use L-enantiomers
side chains are what make them different
amino with carboxyl
linked by peptide bonds
can be put together to form macromolecules, a polymer
ribosomes make peptide bonds
36
3-main categories of amino acids
1. non-polar side chains (hydrophobic)
2. polar side chains (not charged) (hydrophilic)
3. electrically charged side chains (+ or -) (hydrophilic)
37
polypeptide
a polymer of amino acids
polypeptides have an NH3+ (amino) end and a COO- (carboxyl) end and they can be composed of a few to more than a thousand monomers
each polypeptide can have a unique linear sequence of amino acids with an amino end (N-terminus) and a carboxyl end (C-terminus)
38
primary level of protein structure
linear sequence of amino acids
primary structure is determined by the inherited genetic information
amino terminus in the start and carboxyl terminus is the end
change in primary structure can affect a proteins function
39
secondary structure
the formation of alpha helices or beta pleated sheets due to hydrogen bonding between the O of a carboxyl group and the H of the amino group
h-bonds make the structure stable
depending on how the amino acids line up different structures will form
beta pleated sheet forms when peptide sequences lie next to each other in antiparallel orientation or parallel orientation
beta strand is shown as a flat arrow pointing towards the carboxyl end
40
tertiary structure
the arrangement of the peptide chain due to interactions between R groups that gives the protein its distinctive shape
involves reactive groups
hydrophobic "pockets" that exclude water and push other amino acids to the outside
van der waal interactions
ionic bonds
h-bonds
disulphide bonds
41
quaternary structure
results from the aggregation of 2 or more polypeptide subunits
not all proteins exhibit quaternary structure
42
denaturation
loss of a protein's native structure
| denatured protein is biologically inactive
43
protein folding
chaperonins are proteins that assist proper folding of other proteins
a specific protein may or may not require a chaperonin to assist its folding.
proteins aren't functional until they're completely folded
44
nucleic acids
contain code for a species
coded information that cells transmit to future generations and the messages that determine protein production
2 types: DNA and RNA
DNA stores hereditary info and transmits information to cell descendants
mRNA transmits information within the cell
amino acid sequence of a polypeptide is programmed by a region of DNA called a gene
45
nucleotide
consists of 3 different molecules joined together, phosphate, 5-carbon sugar, and nitrogenous base
(nucleoSide is without the phosphate and nucleoTide has a phosphate)
46
5-carbon sugar
in ribonucleic acid (RNA) the sugar is ribose
| in deoxyribonucleic acid (DNA) the sugar is deoxyribose and there is no oxygen hence the deoxy-
47
features of a nucleotide
5'C - attaches to phosphate group "five-prime phosphate"
3'C - OH important for polymer formation "three-prime OH"
2'C - OH in RNA "two-prime OH"
2'C - H in DNA
1'C - attaches to the base
prime indicates its in the sugar ring not the nitrogenous base ring
48
nitrogenous base
2 types:
1. Pyrimidines (single 6-sided ring), cytosine, thymine, uracil
2. Purines (6- and 5-sided rings fused), adenine, guanine
49
structure of DNA
2 polynucleotides spiralling around an imaginary axis, forms a double helix
DNA double helix: 2 backbones run in opposite 5'->3' directions from each other in an antiparallel arrangement
nitrogenous bases for H-bonds
complementary base pairing
A-T and G-C
50
structure of RNA
usually a single nucleotide chain
complementary base paring can occur between RNA and DNA, other RNAs, or itself
A-U and G-C
51
plasma membrane
a boundary that separates the living cell from its surroundings
exhibits selective permeability allowing some substances to cross more easily that others
52
integral membrane proteins
embedded in the bilayer at least one portion of the protein is hydrophobic
53
peripheral membrane proteins
attached loosely to the surface of the membrane (usually interacting with an integral protein)
54
glycoproteins
membrane proteins that have a sugar attached
| important function in cell recognition
55
glycolipids
membrane lipids that have a sugar attached
56
cholesterol
inserts between phospholipid molecules
| influences membrane permeability and fluidity
57
membranes
fluid at physiological temperature
like an oil, is flexible, moves, is dynamic
phospholipids and some proteins in the membrane can move
high temperature increases fluidity, gaps form if the temperature is too high
cholesterol has an effect on membrane fluidity
58
6 major functions for membrane proteins
1. transport of molecules into or out of the cell
2. enzymatic reactions near the membrane
3. signalling via receptors
4. cell-cell recognition
5. intercellular attachment
6. attachment of the cell to extracellular matrix proteins
59
Diffusion (passive transport)
occurs best with small hydrophobic molecules like O2
these are soluble in the bilayer and can pass through quickly
when a molecule is more concentrated on one side of a membrane, diffusion occurs until equilibrium is reached
i.e. molecules diffuse down their concentration gradient
called passive transport because no energy is required
60
Osmosis (special case of passive transport)
diffusion of water across a selectively permeable membrane
| water moves from high to low free water concentration (or lower to higher solute concentration)
61
tonicity
the relative concentration of a solute in two solutions separated by a membrane that it cannot cross
if water can pass freely, the solute [ ] difference determines whether cells gain or lose water
62
hypotonic
= less [solute] outside cell
animal cells: lysed, the cell bursts, too much water
plant cells: turgid(normal) plant cell prefers the pressure of the water
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isotonic
= equal [solute]
animal cells: normal
plant cells: flaccid, starts to lose some pressure, less strength so plants start to wilt
64
hypertonic
=more [solute] outside cell
animal cell: shrivelled
plant cell: plasmolyzed, plasma membrane pulls away from cell wall and can tear membrane, cell also shrinks (plasmolysis)
65
facilitated diffusion (passive transport aided by proteins)
specific molecules that are impeded by the membrane diffuse passively with the aid of a transport protein
66
channel proteins
- a specific channel protein usually allows only one type of molecule or ion to pass through
cellular conditions determine if the channel is open or closed
e.g. aquaporins are a type of channel protein that facilitates osmosis. water moves across the membrane faster if it goes through a channel
e.g. ion channels allow specific ions through (usually a different protein for each ion)
channel proteins can be "gated", turned on or off by different stimuli
67
carrier proteins
these undergo a subtle change in shape (conformational change) to translocate a solute across the membrane
specific for the molecule being transported
solute also diffuses down its [ ] gradient
protein has the same affinity for target molecule on both sides of the membrane i.e. movement can occur in any direction
68
active transport
used to move a substance against the concentration gradient
requires energy usually in the form of ATP
why do cells do this?
-to concentrate nutrients in the cell
-to expel waste
-to establish voltage/chemical gradients
proteins involved in this type of transport are all carrier proteins, specific protein for each substance
sodium-potassium pump is one type of active transport system
active transport allows cells to establish and maintain concentration gradients that might not occur naturally
69
sodium potassium pump
1. cytoplasmic Na+ binds to the pump
2. Na+ binding stimulates phosphorylation by ATP, ATP is hydrolyzed energy so it causes a change in shape
3. phosphorylation causes the protein to change its shape Na+ is expelled to the outside
4. K+ binds to extracellular side and triggers release of the phosphate group
5. loss of phosphate restores the protein's original shape
6. K+ is released and the cycle repeats
70
cotransporters
couple the "downhill" transport of a solute to the "uphill" transport of a second substance against its own concentration gradient
71
bulk transport
big molecules like polysaccharides must be transported using a bulk transport mechanism
involves formation of vesicles
membrane is flexible and can bend into different shapes including pinching off into vesicles, this requires energy
72
exocytosis (secretion)
exporting substances out of the cell
73
endocytosis
3 main types:
1. phagocytosis (cell eating)
2. pinocytosis (cell drinking)
3. receptor-mediated - a mechanism involving receptors to import specific things
74
lipoproteins
transport fats to cells via the blood stream
75
LDL
low density lipoprotein, low in density, but high in cholesterol
LDL cholesterol is often referred to as bad cholesterol
76
HDL
high density lipoprotein, highest density due to high protein/lipid ratio
these particles can remove excess cholesterol from blood vessels (for transport to the liver)
HDL cholesterol is often referred to as good cholesterol
77
uniporters
those that transport only one type of molecule
78
symporters
transport two different molecules in the same direction
79
antiporters
transport two different molecules in the opposite direction
80
membranes and transport
- cellular membranes are fluid mosaics of lipids and proteins
- membrane structure results in selective permeability
- passive transport is diffusion of a substance across a membrane with no energy
- active transport uses energy to move solutes against gradients
- bulk transport across plasma membranes uses exocytosis and endocytosis
81
cell membrane
fluid barrier that separates cell interior from the exterior but it is not very strong so cells typically have additional structures that reinforce the membrane
82
bacterial cell walls
provide shape and protection from bursting in hypotonic environments
like animal cells they contain a much higher concentration of many molecules compared with their environment
allows them to stay the same size and resist pressure due to osmosis
almost all bacterial cells walls contain peptidoglycan
2 major classes of bacteria that are defined by their cell wall structure:
gram positive- simple cell wall, thick peptidoglycan, don't have outer membrane
gram negative- complex cell wall structure, thinner peptidoglycan, has an outer membrane, has lipopolysaccharides which can elicit a strong immune response in animals, endotoxins, can cause fever
83
peptidoglycan
a thin sheet composed of:
1. chains of a repeating disaccharide unit composed of two monosaccharides:
i) N-acetylgucosamine (NAG) and ii) N-acetylmuramic acid (NAM)
2. small peptides, attached to NAM subunits of the chains, bonds formed between peptides on adjacent chains cross-link the chains and gives strength to the structure
crosslinking reaction is called transpeptidation and it adds strength to the layer
84
antibiotics
there are many naturally occurring antibiotics, some are specific to certain types of bacteria based on their ability to target prokaryote-specific structures
two common targets are:
1. prokaryotic ribosomes (responsible for protein synthesis)
2. prokaryotic cell walls
a) lysozyme = antimicrobial present in our bodily fluids (tears, milk, saliva, mucous) enzyme that catalyzes hydrolysis of beta 1-4 linkages between NAG and NAM, peptidoglycan falls apart, cells lyse
b) penicillin
85
penicillin
petri plate with solid agar media streaked with staphylococcus bacteria was left to grow and a mold growth from something that landed on the plate formed and a zone of inhibited growth formed around it
86
how does penicillin work
as bacterial cells grows it synthesizes more peptidoglycan
transpeptidation reaction is catalyzed by a specific enzyme
the enzyme is inhibited by penicillin, inhibition leads to a weakened peptidoglycan, works best on gram positive cells
as the cell grows no new peptidoglycan is formed so eventually cell bursts
87
capsule
mostly polysaccharides
further protects cell from environment
can be used to stick bacteria to surface
capsule is rare in archaea
88
pili
2 types:
1. fimbriae (attach to surfaces or host cells) e.g. gonorrhoea uses fimbriae to attach itself to mucus membranes
2. sex pilus (for transfer of DNA between bacteria cells) DNA is transferred to another bacteria (bacterial conjugation) the pilus is a tube of protein for plasmid transfer between bacteria
89
plasmid
small circular DNA, distinct from the chromosome
90
taxis and chemotaxis
taxis: ability to move towards or away from a stimulus
chemotaxis: the movement towards or away from a chemical stimulus
91
how do bacteria move
motile bacteria move in a series of runs and tumbles
| duration of the run is longer if the concentration of the attractant increases during the run
92
flagella
for movement
flagella of bacteria, archaea, and eukaryotes are composed of different proteins and likely evolved independently (analogous structure)
rotation can be clockwise or counterclockwise (to allow changes in direction)
CCW=run CW=tumble
the flagella spins
93
archaea cell walls
no outer membrane
various coverings surrounding the plasma membrane (depends on species)
no true peptidoglycan but related molecules have been found in some species
some archaea are covered in archaea specific lipopolysaccharides
in general they have stronger membranes due to a number of unique differences e.g. an ether linkage rather than an ester in their triacylglycerols
94
eukaryotic cells walls
animal cells do not have cell walls but plants and fungi do
cell wall function: provides shape and protection, strong cell walls of plants help hold them up
cellulose chains embedded in a matrix of other polysaccharides and proteins
95
plant cell walls
young plant cell secretes a thin cell wall outside the plasma membrane
the primary cell wall as cell matures, cell wall is strengthened, some secrete hardening substances into the primary cell wall
others add a secondary cell wall
a cell may have many layers made of a matrix of strong materials
between the primary cell walls of adjacent plant cells is the middle lamella
96
middle lamella
composed of sticky polysaccharides called pectins, this effectively glues the adjacent cells together
97
plasmodesmata
pores, tunnels, between plant cells to allow communication between them due to the thick cell wall and middle lamella
allows passage of H2O and small solutes between cells
thus interior of all cells can be connected
98
animal cells
```
no cell wall but they secrete proteins and polysaccharides =extra cellular matrix (ECM)
some cells attach to the ECM using additional specialized proteins, most common is fibronectin (interacts with collagen)fibronectin also binds to a specific class of integral membrane proteins called integrins
```
99
collagen
glycoproteins and protein fibres
100
proteoglycans
collagen is embedded in a network of these glycoproteins
| bind non-covalently to long polysaccharides
101
connectivity between collagen and cells (holds down cell)
cells - microfilaments - integrins - fibronectin - collagen
102
tight junctions
membranes of neighbouring cells are essentially fused
bands of protein in plasma membrane
tight seals are formed
prevents absorption of materials from one side of cells into the intercellular region between them
103
desmosomes
provide strength for cells to keep them close together and resist mechanical forces
tightly fastens cells together at certain points
made of strong protein filaments
104
gap junctions
allow cells to communicate with each other and pass ions back and forth
multi-subunit structures form a channel between cells
allow free exchange of small molecules
allows tissues to coordinate responses to stimuli
105
connexon
6 protein subunits
| 2 connexons form a gap junction that spans the membranes of both cells
106
cytoplasm
interior of a prokaryotic or eukaryotic cell
107
cytosol
the fluid portion of the cytoplasm
108
organelle
any membrane bound structure in an eukaryotic cell
109
prokaryotic cells
no nucleus
DNA in an unbound region called the nucleoid
no membrane bound organelles
cytoplasm bound by plasma membrane
cell walls (bacteria and archaea but composition is different)
110
eukaryotic cell
most recent common ancestor arose around 2.1 billion years ago
evolved a way to fold their membrane to increase surface area
metabolic requirements set upper limits on size
111
endosymbiont hypothesis
mitochondria and chloroplasts arose in eukaryotes by endosymbiosis
a mutually beneficial relationship derives from one cell living inside another cell
mitochondria are descended from an ancient bacterium
chloroplasts are descended from an ancient cyanobacterium
112
evidence for the hypothesis
mitochondria and chloroplasts have their own DNA, their genes are organized like prokaryote genome and they have their own ribosomes
ribosomes are big complexes of proteins and RNA molecules
eukaryote and prokaryote ribosomes differ in size and components (70S vs. 80S)
113
endomembrane system
contains: nuclear envelope, ER, vacuoles, vesicles, lysosomes, golgi, plasma membrane
114
membrane-bound organelles not part of the endomembrane system
peroxisomes, mitochondria, chloroplasts
115
nucleus
stores DNA, is the site of transcription (produces RNA), contains multiple liner chromosomes
116
nucelar envelope
double membrane, each is a phospholipid bilayer, separates the nucleoplasm from the cytoplasm
117
nuclear pore
complexes span both bilayers
| regulates movement of substances in and out of nucleus
118
nuclear lamina
provides structural support for the nucleus
| composed of an intermediate filament called lamin which assembles on the inner surface of the nuclear envelope
119
chromatin
DNA and protein, associated together because of electrostatic interaction (DNA is - histones are +)
can be highly condensed
120
nucelosome
DNA + histone octamer
121
histone H1
provides stability and protection to DNA and it is involved in the packaging of nucleosomes into the 30 nm fibre
122
nucleolus
ribosome production factory
this is a visible sub compartment of the nucleus (not bound by membrane)
site of ribosomal RNA (rRna) synthesis
site of assembly of ribosome protein subunits, each half of the ribosome enters the nucleus separately via pores
123
endoplasmic reticulum
cells that produce a lot of proteins will have more rough ER
| cells that produce a lot of lipids (fats) and steroid hormones will have more smooth ER
124
rough ER
covered in ribosomes
associated with the translation of proteins that are destined for the endomembrane system
site of protein synthesis and assembly
site of protein quality control
e.g. many chaperones assist with protein folding in the rER misfolded proteins are either refolded or degraded
125
ribosomes
protein factories
particles made of ribosomal RNA and protein
ribosomes assemble all peptides (using amino acid monomers)
in the cytosol there are free ribosomes
on the outside of the ER there are bound ribosomes
126
smooth ER
ion storage
phospholipid, steroid synthesis
detox of drugs and alcohol
carbohydrate metabolism
127
golgi apparatus
shipping and receiving centre
consists of flattened membranous sacs called cisternae
cis face = receiving side of golgi (faces nucleus)
trans face = shipping side of golgi (faces away from nucleus)
vesicles form and leave the golgi carrying products to different membranous organelles or the plasma membrane
golgi cisternae move from cis to trans
modifies products of ER
sorts and packages materials into transport vesicles
manufactures some macromolecules
enzymes in golgi add tags to protein for lysosome and no tag for proteins for the plasma membrane
128
lysosomes
digestive compartments
cell stomach
membranous sac of hydrolytic enzymes that can digest macromolecules
lysosomal enzymes work best in an acidic environment inside the lysosome
lysosome enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids
important for recycling various structures and organelles
129
autophagy
cell eats itself or parts of itself
130
vacuoles
variable function depending on cell
plant cell or fungal cell may have one or several derived from ER and golgi
1. food vacuoles (formed by phagocytosis)
2. contractile vacuoles, pump excess water out of cells
3. central vacuole (specific to plants) holds organic compounds and water, helps maintain turgor pressure, usually largest compartment in a plant cell
131
mitochondria and chloroplasts
both are bound by double membrane
both contain several copies of their own DNA (mtDNA and cpDNA)
mitochondria does ATP production
chloroplast does photosynthesis
both contains ribosomes that synthesize a few components but most of the components in each organelle are encoded by genes in the nucleus
132
peroxisomes
microbodies
single membrane bound organelles
perform reactions, breakdown of molecules or assembly, in which H2O2 is a by-product
133
cytoskeleton
provides support
isn't always rigid, can be dynamic and formed into different shapes
network of 3 sizes of protein filaments: microtubules (thick), actin/microfilament (thin), and intermediate filaments
acts as a system of cables throughout cell
organelles may attach to the cables and some move along them
134
microtubules
straight, hollow tubes
walls constructed with proteins called tubulins
alpha and beta tubulin combine to form a dimer
dimers assemble end to end into microtubule protofilaments
many protofilaments interact to form tubes usually around 13 per tube
tubulin dimers continue to add to protofilaments at one end of the tube, the plus end, this end grows and shrinks
minus end is connected to microtubule organizing centres
135
microtubule organizing centre (MTOC)
an organized structure composed of many different proteins
one of these proteins is a specific type of tubulin, gamma-tubulin
for each microtubule a ring of gamma tubulin forms a stable platform for it to anchor to
136
centrosome
primary MTOC in most animal cells
| at the centre of chromosomes are 2 smaller structures, centrioles
137
centrioles
have microtubules
arranged around a cylinder composed of other proteins
number and appearance of centriolar microtubules can vary depending on organism and cell type
centrioles are not present in plants or fungi and are missing in some animal cells
138
dynein
microtubule motor protein that walks along microtubules
this one walks towards the minus end of the microtubule
each step requires ATP
carries cargo
produces force for ciliary movement
139
kinesin
microtubule motor protein that walks along microtubules towards the plus end
carries cargo
140
cilia
usually present in large numbers on cell surface
they act in unison like oars
can be used to move the cell or to move fluids past the membrane
beat using an active power stroke followed by a relaxed recovery stroke
141
actin filaments
abundant in eukaryotic cells
first found in skeletal muscle where actin filaments slide along filaments of myosin to make the cells contract
support and strengthen the plasma membrane from inside the cell
made of identical actin proteins arranged in a long chain which spirals around a second chain to form a filament
actin filaments have a + and - end more growth at + end
can form thick bundles
major component of muscle
thicker filaments composed of myosin interdigitate with the thinner actin fibres
myosin is a type of motor protein that interacts with actin
kinesin and dynines don't work here
can form a variety of structures
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intermediate filaments
strong and rope-like
less dynamic than actin or microtubules
all cells have intermediate filaments but the protein subunits of the structures vary
do not have a + or - end
not as dynamic, more permanent structures
polypeptide-dimer-tetramer-protofilament-filament
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neurofilaments
in neurons
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desmin
in muscles
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keratins
in epithelial cells
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vimentin
in a broad range of cell types
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lamins
on inside of nuclear membrane
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metabolism
the totality of an organism's chemical reactions managing the materials and energy resources of the cell
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anabolism
building molecules
requires energy
e.g. synthesis of protein from amino acids
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catabolism
breaking down molecules
releases energy
e.g. breakdown of glucose in the presence of oxygen
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energy
in physics it is defined as the capacity to do work
in biochem it is useful to think of energy as a capacity for change
in reactions energy changes are associated with changes in the chemical structures and properties of molecules
energy comes in many forms: chemical, electrical, heat, light, mechanical
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kinetic energy
energy of motion
heat - increase molecular motion and/or break bonds
moving objects - cars, running water down a mountain, kinesin walking on microtubule
radiant energy of light
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potential energy
stored energy
chemical energy - stored in bonds that hold atoms together
concentration gradients
electrical potential - batteries, membranes
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first law of thermodynamics
energy can change its form but energy is never created nor destroyed, the amount of energy in the universe is constant
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free energy
G - energy available to do work
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second law of thermodynamics
in a closed system with multiple energy transformations, free energy (G) decreases and unuseful energy increases
referred to as an increase in entropy
entropy of universe is always increasing
S = a measure of disorder in the universe, unuseful energy (energy not available to do work)
every energy transfer or transformation makes the universe more disordered
randomness of universe increases over time = increase in entropy
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heat
considered the lowest grade of energy
heat increases the random unordered movement of molecules
heat is difficult to store or harness to do work
can use heat for work but it must be concentrated in one location
when heat is used to do work it comes from burning something and using it immediately
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systems with high free energy
are complex, organized, non-random, and low in entropy
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systems with low free energy
are disordered, random, and have high entropy
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how can we calculate change in free energy for a chemical reaction?
```
G = H - TS
H = total energy of a system (enthalpy)
T = temp. on degrees K
S = entropy
```
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G < 0
spontaneous, a change that does not require energy
magnitude of energy change indicates the amount of energy available to work
exergonic - proceeds with a net release of free energy
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G = 0
equilibrium
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G > 0
not spontaneous
| endergonic - absorbs free energy from its surroundings
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ATP
most energy coupling in cells is mediated by ATP (adenosine triphosphate) the energy currency of the cell
made in cell respiration, used in most cell reactions
stores potential energy due to bond position and composition
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catalyst
chemical agent that speeds up a reaction without being consumed
an enzyme is a catalytic protein
catalyst lowers activation energy
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catalysis
1. substrates enter active site, enzyme changes shape to enfold substrates
2. substrates held in active site by weak interactions
3. active site can lower energy of activation and speed up a reaction
4. substrates are converted to products
5. products are released
6. active site is available for 2 new substrate molecules
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enzymes lower activation energy by
1. bringing reactant together
2. physically stressing the substrate bonds
3. providing favourable microenvironment for the reaction
4. direct participation in the chemical reactions
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factors that affect enzyme function
1. temperature
2. pH
3. cofactors and coenzymes
4. enzyme inhibitors
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competitive inhibitor
mimics
have a similar shape to the normal substrate and can bind to the active site of the enzyme
they do not participate in any reaction
compete with the real substrate for access to the enzyme
can be out-competed by increasing the amount of substrate
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non-competitive inhibitor
inhibit the function of the enzyme by binding to a different location (not the active site)
inhibitor binding can affect:
1. the shape of the active site (prevents substrate docking)
2. the function of the active site, without interfering with substrate docking
cannot be out competed
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allosteric regulation
when a protein's function at one binding site is affected by the binding of a molecule to another site
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feedback inhibition
the synthesis of isoleucine
| feeds back on first enzyme and inhibits it from creating more, stopping the reaction
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autotrophs
survive without anything derived from other organisms
| use inorganic C as carbon source to produce organic molecules
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heterotrophs
consumers
consume plants (direct) or animals (indirect)
use organic C as their carbon source
most depend on photoautotrophs for food and O2
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photoautotrophs
use light energy to fix carbon
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stomata
where CO2 enters and O2 exits
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chlorophyll
a green pigment
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stroma
the dense interior fluid (cytosol of the chloroplast)
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photosynthesis outline
1. redox reactions
2. process of photosynthesis divided into:
A) the light reactions (convert energy in light to ATP and NADPH)
-light
-pigments
-structures involved
-the photosynthesis reactions
B) carbon fixation reactions
-utilize energy stores in ATP and NADPH to derive fixation of CO2 molecules into carbohydrates
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redox reactions
various reactions in which electrons are transferred from one molecule to another
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reduction
the gain of one ore more electrons by an atom, ion, or molecule
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oxidation
the loss of one or more electrons by an atom, ion, or molecule
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reducing agent
gives electron, gets oxidized
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oxidizing agent
accepts electron, gets reduced
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photosynthesis is what type of reaction
endergonic - it requires energy in order to convert low energy CO2 to high energy glucose
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NAD and NADPH
electron carriers
187
pigments
substances that absorb visible light
different pigments will absorb and reflect different wavelengths
the reflected light is the colour of the thing
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chlorophyll a
the main photosynthetic pigment
189
chlorophyll b
broadens spectrum used for photosynthesis
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carotenoids
absorb excessive light that can damage chlorophyll
191
structures involved in photosynthetic electron transfer
```
inside the thylakoid membrane
many small molecules and large enzyme complexes are involved:
photosystem II
water splitting enzyme
cytochrome b6f complex
photosystem I
NADP reductase
```
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photosystem I and II
a photosystem consists of a reaction-centre complex surrounded by light harvesting complexes
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reaction centre
energy from absorption of photons in all other pigment molecules in a photosystem is transferred to a pair of chlorophyll a molecules in the reaction centre
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special pair of chlorophyll a
molecules in the reaction centre that absorb a characteristic wavelength of light (max=680nm)
195
photosystem
1. photon strikes a pigment molecule in PSII
2. electron is transferred to primary e- acceptor (pheophytin)
3. H2O is split and its electrons are transferred one at a time to P680+ (reducing it to P680) the 2 protons are then released into the thylakoid space
4. PSII photo-excited electrons move to PSI via an electron transport chain (Pq, cytochrome b6f, Pc)
5. e- fall to a lower energy level (exergonic) proton pumping driven by electrons moving through cytochrome b6f complex
6. light-harvesting PSI pigments independently cause P700 to lose electrons and become photo-oxidized P700+
7. P700+ accepts electrons that arrive via the e- transport chain of PSII
8. NADP+ reductase catalyzes the transfer of electrons from Ferredoxin (Fd) to NADP+. 2 e- and 1H+ (from stroma) are required to make NADPH
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linear electron flow
```
primary electron acceptor (pheophytin)
plastoquinone (Pq)
cytochrome b6f complex
plastocyanin (Pc)
PSI
(creates ATP and NADPH)
```
197
ATP synthase
a molecular mill
198
chemiosmosis
the use of energy in a proton (H+) gradient to drive cellular work
gradient has PE
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cyclic electron flow
only PSI
no production of NADPH
no release of oxygen
makes ATP from protons
1. electrons end up back to fill holes in the PSI reaction centre
2. the transfer of electrons is from ferredoxin to plastoquinone instead of NADP+
3. proton pumping at cytochrome b6f complex from stroma to thylakoid space creates H+ gradient (used by ATP synthase to create ATP from ADP + Pi
4. in this manner ATP is produced via cyclic photophosphorylation
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light reactions in the thylakoids
- split H2O
- release O2
- reduce NADP+ to NADPH
- generate ATP from ADP by photophosphorylation (linear or cyclic)
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main points of calvin cycle
CO2 is fixed in the first step of cycle:
-don't need ATP or NADPH for this step; they are required later to regenerate RuBP, which serves as a substrate for further carbon fixation
CO2 fixation occurs via a cyclic process:
-carboxylation products of the Calvin cycle are 3-carbon compounds (plants that use this pathway are referred to as C3 plants)
-as the cycle repeats some fixed carbon gets siphoned off for other uses
-glyceraldehyde-3-phosphate (G3P) triose sugar can be used for different purposes including the synthesis of 6-carbon glucose
generation of one usable molecule of G3P consumes: 9 ATP and 6 NADPH
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photorespiration
a phenomenon in plants that works against carbon fixation
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why would a low CO2/O2 ratio ever occur
can develop within the plant on very bright hot days:
1) plants photosynthesize at high rates
- CO2 consumed, O2 produced
2) pores on leaves (stomata-pairs of cells that make little pores in the leaf to allow gas exchange) close to prevent loss of H2O
- normally CO2 enters and O2 exits through stomata
- since neither of these can occur with stomata closed internal O2 [ ] goes up and CO2 [ ] goes down, rubisco will bind to O2 instead
