Week 3 Flashcards
1
Q
4 classes of macromolecules:
A
- Carbohydrates
- Lipids
- Proteins
- Nucleic acids
2
Q
Biomolecule -
A
any chemical molecule that is a structural or functional component of living organisms
Chemical elements that participate in the synthesis of biomolecules structures: C, H, O, N, S, P
3
Q
polymer and what classes are polymers:
A
- a long molecule consisting of many similar building blocks (monomers)
- Carbohydrates (monosaccharides)
- Proteins (amino acids)
- Nucleic acids (nucleotides)
4
Q
Dehydration reaction (condensation reaction):
A
2 monomers bond together through the loss of a water molecule
5
Q
Enzymes -
A
macromolecules that speed up the dehydration process
6
Q
Hydrolysis -
A
reaction that is the reverse of the dehydration reaction: disassembles polymers to monomers
7
Q
Carbohydrates molecular formula and ex
A
(CH2O)n
ex:
- Pentoses: C5H10O5 (ribose, deoxyribose) (n=5)
- Hexoses: C6H12O6 (glucose, fructose) (n=6)
8
Q
what are biologically important carbohydrates are also called?
A
sugars
9
Q
4 categories of carbohydrates:
A
-
Mοnosaccharides: (CH2O)n where n = 3-7
ex: glucose and fructose -
Disaccharides: made by 2 monosaccharides
ex: maltose, sucrose, and lactose - Οligosaccharides: composed by 20-30 monosaccharides
-
Polysaccharides: composed by many glucose subunits
ex: starch, glycogen, cellulose
10
Q
most common monosaccharide
A
Glucose (C6H12O6)
11
Q
Functions of monosaccharides:
A
- fuel for cells
- raw material for building molecules (ex: glycoproteins, proteoglycans)
12
Q
Monosaccharides are classified by:
A
– The location of the carbonyl group: as aldose (>C=O at the end) or ketose (>C=O in the middle)
– The number of carbons in the carbon skeleton
13
Q
Monosaccharides: structure
A
May be linear but in aqueous solutions many sugars form rings, b/c it’s more E favourable => in the cell it’s rings
14
Q
Disaccharides (Sugars): consist of? name of the bond? examples (3)?
A
- Consist of 2 monosaccharides
- Covalent bond b/w the molecules is called a glycosidic linkage
ex:
Glucose + galactose = lactose (milk)
Glucose + glucose = maltose (beer)
Glucose + fructose = sucrose (sucrose - white sugar)
15
Q
Polysaccharides and their functions:
A
- the polymers of sugars
- have storage and structural roles
- structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages
16
Q
Storage Polysaccharides:
A
- Starch
- Glycogen
– Polymers consisting entirely of glucose monomers
17
Q
Starch
A
- the major storage polysaccharide in plants
- α-glucose polymer
- consists of 2 polysaccharides: amylose (20-30%) and amylopectin (70-80%)
- plants store excess starch as granules within chloroplasts and other plastids (called amyloplasts)
- α-linkage (-OH group at C2 is in the same plane w/ -OH-group at C1) => helical molecule => granules
18
Q
Glycogen
A
- storage polysaccharide in animals
- humans and other vertebrates store glycogen mainly in liver and muscle cells as cytosolic granules
- it is branched - easier f/ hydrolysis, better access f/ enzymes
- α-glucose polymer
- α-linkage (-OH group at C2 is in the same plane w/ -OH-group at C1) => helical molecule => granules
19
Q
Structural Polysaccharides
A
- Cellulose: in plant cell walls
- Chitin: in fungal cell walls and arthropod
20
Q
Cellulose:
A
- found in plant cell wall
- an unbranched β-glucose polymer (-OH group at C2 is in diff side of the plane than the -OH group in C1)
- diff glycosidic linkages from starch: β-linkage = linear molecule => cell wall component
21
Q
Humans can digest ___ but not ___
A
Humans can digest starch but not cellulose => Cellulose in human food passes through the digestive tract as insoluble fiber
22
Q
Chitin (where found? monomer? linkage? clinical correlation?)
A
- Found in the exoskeleton of arthropods and fungal cell walls
- Used to make surgical thread (!)
- monomer: β-NAG (N-acetyl-glucosamine)
- diff glycosidic linkages from starch: β-linkage = linear molecule => cell wall component
23
Q
Lipids
A
- the one class of large biological molecules that do not consist of polymers (of diff types of components)
- hydrophobic
24
Q
Biologically important lipids:
A
- Fats
- Phospholipids
- Steroids
25
Fats (structure, fn)
- structure: glycerol + 3 fatty acids => triglycerides
- storage form of fat
26
Fatty acid structure:
**R- COOH**, where R= long hydrocarbon chain (usually 16-18 carbons)
27
Fatty acids vary in:
- length (number of carbons)
- number and locations of double bonds
28
Saturated fatty acids (formula, characteristics, 3 examples):
- molecular formula: **CH3(CH2)nCOOH**
- have max # of H atoms possible => have no double bonds => solid at room T
- mostly found in animals
ex:
Stearic acid (18:0): 18 C, 0 double bonds
Palmitic acid (16C)
Butyric acid (4 C)
29
Unsaturated fatty acids:
- unsaturated fats or oils
- have 1 or more double bonds => bending => liquid at room T
- mostly found in plants and fish
ex:
Oleic acid - monounsaturated fatty acid (18:1)
Linoleic acid - polyunsaturated fatty acid (18:2)
30
Stearic acid
18 C
saturated
31
Palmitic acid
16 C
saturated
32
Οleic acid
18 C
unsaturated
33
Saturated fats: health risks
diet rich in saturated fats may contribute to cardiovascular disease through **plaque deposits**
34
Diff molecular effects of saturated and unsaturated fats on the liver
- Unsaturated fats actually **reduce LDL-bound (“bad”)** cholesterol levels and **maintain HDL-bound (“good”)** cholesterol (signal to the liver to take up cholesterol from the blood => improve cholesterol levels)
- Saturated fats **directly increase LDL-bound (“bad”)** cholesterol levels
35
Functions of fat:
- energy storage (humans and other mammals - in **adipose cells**)
- cushions vital organs
- insulates the body
36
Phospholipids:
have only 1 or 2 FA & phosphate group instead of 3rd FA
37
2 types of phospholipids:
1. Phosphoglycerides: glycerol + 2 fatty acids + phosphate + organic molecule
2. Phosphosphingolipids: sphingosine + 1 fatty acid + phosphate + organic molecule
38
Phospholipids’ Function:
important components of biological membranes
39
Phospholipid structure in terms of affinity to water
Amphipathic molecules: consist of a hydrophilic “head” and hydrophobic “tails”
40
Common membrane phospholipids and their structures (5):
Phosphatidyl-choline: Glycerol + Choline
Phosphatidyl-ethanolamine: Glycerol + ethanolamine
Phosphatidyl-serine: Glycerol + Serine
Phosphatidyl-inositol: Glycerol + inositol
Sphingomyelin: Sphingosine + choline
41
Bilayer arrangement:
When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior
42
Steroids
- lipids characterized by a carbon skeleton consisting of four fused rings
exs:
*Cholesterol* - steroid found in animal cell membranes, precursor f/ some hormones (steroid hormones - *estradiol* & *testosterone*)
*Ergosterol* - in fungal membrane, target for antimicotic antibiotics
43
Cholesterol: health risks
- Cholesterol circulates in blood bound to lipoproteins:
**HDL** - high density lipoproteins: protein > cholesterol => travels fast into bloodstream and targeted-deposited directly into the liver
**LDL** - low density lipoproteins: cholesterol > protein => travels slower into bloodstream and leaves bits and pieces around => atheromatic plaque formation (**cholesterol+ platelets**)
- Lipoproteins are recognized by their receptor on the PM of liver cells (hepatocytes)
- cells take in the lipoproteins-cholesterol vesicles => *receptor-mediated endocytosis*
44
Proteins’ function (6):
1. structural support by **structural proteins** (ex: collagen, elastin, keratin)
2. storage by **storage proteins** (ex: ovalbumin, casein)
3. transport by **transport proteins** (ex: hemoglobin)
4. cellular communications by **receptor proteins & hormonal proteins** (ex: insulin)
5. movement by **contractile & motor proteins** (ex: actin, myosin)
6. defense against foreign substances (**immune response**) by **defensive proteins** (ex: antibodies)
45
Enzymes - type of protein
that acts as a catalyst, speeding up chemical reactions
46
Polypeptides: Amino Acid Polymers
- monomer - amino acid (each polypeptide has a unique linear sequence of amino acids)
- protein consists of one or more polypeptides
- aminoacids => polypeptides => proteins
47
Amino acid monomer:
- organic molecules possessing both **carboxyl** and **amino groups**
- differ in their properties due to differing side chains, called **R groups**
- general structure: H2N-CHR-COOH
48
Glycine
Gly
nonpolar
49
Alanine
Ala
nonpolar
50
Valine
Val
nonpolar
51
Leucine
Leu
nonpolar
52
Isoleucine
Ile
nonpolar
53
Methionine
Met
nonpolar
54
Phenylalanine
Phe
nonpolar
55
Tryptophan
Trp
nonpolar
56
Proline
Pro
nonpolar
57
Serine
Ser
polar
58
Threonine
Thr
polar
59
Cysteine
Cys
polar
60
Tyrosine
Tyr
polar
61
Asparagine
Asn
polar
62
Glutamine
Gln
polar
63
Glutamine
Gln
64
Aspartic acid
Asp
negatively charged
65
Glutamic acid
Glu
negatively charged
66
Lysine
Lys
positively charged
67
Arginine
Arg
positively charged
68
Histidine
His
positively charged
69
Nonpolar molecules (9):
**G**randma **A**lways **V**isits **L**ondon **I**n **M**ay **F(Ph)**or **P**arty **T**ime
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Methionine (Met)
Phenylalanine (Phe)
Proline (Pro)
Tryptophan (Trp)
70
Polar molecules (6):
**S**anta **T**ook **C**andy **A**fter **G**oing snowball**TH**rowing
Serine (Ser)
Tyrosine (Tyr)
Cysteine (Cys)
Asparagine (Asn)
Glutamine (Gln)
Threonine (Thr)
71
Electrically charged (5):
Aspartic acid (Asp)
Glutamic acid (Glu)
Lysine (Lys)
Arginine (Arg)
Histidine (His)
72
Polypeptides are linked by:
covalent bonds called peptide bonds
73
Four Levels of Protein Structure:
• **Primary structure**: the unique sequence of amino acids
• **Secondary structure**: consists of coils and folds in the polypeptide chain (*α-helices and β-pleated sheets* linked by H-bonds)
• **Tertiary structure**: the 3-dimensional structure (shape) of a protein determined by the interactions among various side chains (R groups linked by van der Waals interactions, H-bonds, ionic bonds, disulfide bridges)
• **Quaternary structure**: results when a protein consists of multiple polypeptide chains (subunits)
74
Tertiary structure: types of interactions (5):
• Disulphide bonds - covalent bonds b/w 2 -SH groups in **cysteine**
• Hydrogen bonds
• van der Waals interactions
• Electrostatic interactions (ionic bonds)
• Hydrophobic interactions
75
Chaperones (chaperonins) -
- proteins that assist and maintain the proper folding of other proteins
- wherever there are ribosomes: cytosol (free ribosomes synthesize cytosolic proteins), mitochondria, chloroplasts, rough ER (bound ribosomes synthesize secreted & membrane-bound proteins).
76
Sickle-Cell Disease:
Example of a disease caused by simple change in primary structure:
Glu (- charged) substitutes f/ Val (nonpolar) => crystallization of hemoglobin into fibers => sickle shape of blood cells => blood clotting
77
Denaturation
the loss of a protein’s native conformation due to unravelling => loss of fn
denaturated protein is biologically inactive
renaturation - reverse of denaturation (sometimes possible, depends on how much damage to the structure is done)
78
Protein denaturation factors:
- pH changes
- salt concentration changes
- temperature changes
- other environmental factors
79
Nucleic acids’ fn:
store and transmit hereditary information
80
genes
- units of inheritance
- program the amino acid sequence of polypeptides
- made of DNA (monomer - nucleotide)
81
2 types of nucleic acids:
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
82
Structure of nucleic acids
- Each polynucleotide consists of monomers called nucleotides
- Nucleotide = nitrogenous base + pentose sugar + phosphate group
- Nucleoside = nitrogenous base + pentose sugar
83
Nitrogenous bases in nucleotides
Pyrimidines:
- cytosine, thymine (DNA), uracil (RNA)
Purines:
- adenine, guanine
84
Sugars in nucleic acids:
deoxeribose
ribose
85
What ends does each DNA strand have?
- phosphate 5’-end
- -OH 3’-end
86
nucleotides are connected with a covalent bond to create a polymer (name of bond)
phosphodiester bond (the–OH group on the 3´ carbon of one nucleotide is linked to the phosphate on the 5´ carbon on the next nucleotide)
87
Cellular DNA molecules consist of
2 antiparallel polynucleotide strands that form a double helix
Strands are antiparallel: each strand runs in an opposite direction to the other one: one runs 5’→3’ and the other 3’→5’
88
Double helix is connected by:
nitrogenous bases in DNA form hydrogen bonds in a complementary fashion:
A-T
G-C
89
Microscopy is used f/ studying
cell structure & morphology
90
Cell fractionation is __ and is used f/ studying__
- isolation of subcellular structures
- f/ studying cell function
91
Light microscopes (LM) principle of work:
– Visible light passes through a specimen
– Magnification of cellular structures using lenses
92
Electron microscopes (EM) principle of work:
Focus a beam of electrons through a specimen (TEM) or onto its surface (SEM) by applying a
strong magnetic field
93
What can be seen w/ light microscope:
objects from 1 mm to 200 nm (most plant & animal cells, nucleus, most bacteria, mitochodrion)
We CAN’T see: smallest bacteria, viruses, ribosomes, proteins, lipids, atoms
94
Comparison of the size of cellular and acellular forms of living organisms
Virus 0.05 μm < Phage 0.1 μm < Bacterium (0.1 - 10 μm) < Eukaryotic cell (10-100 μm)
95
Magnification
ratio of an object’s image size to its real size
96
Resolution
measure of the clarity of the image (minimum distance of two distinguishable points)
97
Contrast
visible differences in parts of the sample
98
5 types of LM
1. Brightfield
2. Phase-contrast
3. Differential-interference-contrast (Nomarski)
4. Fluorescence
5. Confocal
99
Brightfield
1a - unstained specimen: Passes light directly through specimen. Unless cell is naturally
pigmented or artificially stained, image has little contrast.
1b - stained specimen: Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved)
result is **2D**
100
Phase-contrast
Enhances contrast in unstained cells by amplifying variations in density within specimen;
especially useful for **examining living unpigmented cells** (e.g. dividing cells).
results is **2D**
101
Differential-interference-contrast (Nomarski)
Like phase-contrast microscopy, it uses optical modifications to exaggerate differences in density, making the image appear almost 3D, but **result is still 2D**
102
Fluorescence
Shows the locations of specific molecules in the cell by tagging the molecules with fluorescent dyes or antibodies. These fluorescent substances absorb ultraviolet (UV) radiation and emit visible light
result is **2D**
103
Confocal
Uses lasers and special optics for “optical sectioning” of fluorescently-stained specimens. Only a single plane of focus is illuminated; out-of-focus fluorescence above and below the plane is subtracted by a computer.
result is **3D**
104
Two types of EM:
1. Transmission electron microscope (TEM): focus a beam of electrons **through** a specimen => used mainly to study the internal structure of cells. Result is **2D**
2. Scanning electron microscope (SEM): focus a beam of electrons **onto the surface** of a specimen => used to study of the surface of the specimen. Result is **3D**
105
Cell fractionation:
- enables isolation of subcellular components and determination of the organelle functions
- fractionates cells and separates the major organelles from one another, based on size and density
106
Centrifugation
used to fractionate cells into their component parts (e.g. ultracentrifuges)
107
Differential vs Density gradient centrifugation
Differential centrifugation:
- stabilizing solvent gradient (stable solvent C; e.g. 0.5 M sucrose)
- multiple centrifugation steps (increasing acceleration and time)
-separation is based on **size**
Density gradient centrifugation:
- steep solvent C
- single centrifugation step
- separation is based on **Density (size & shape)**
108
Which cells appeared firs and what’s the time diff b/w the two?
Prokaryotic =>109 years=> eukaryotic
109
All cells have several basic features in common (4):
– bounded by a plasma membrane
– contain a semifluid substance called the cytosol
– contain chromosomes
– have ribosomes
110
Prokaryotic cells (3 characteristics):
– Do not contain a nucleus (no nuclear membrane)
– Have their DNA located in an unbound region called the **nucleoid**
– Do not have any membrane-bound organelles
111
Eukaryotic cells (3 characteristics):
– Contain a nucleus bounded by a membranous nuclear envelope
– Generally bigger than prokaryotic cells (10-100 times)
– have internal membranes that compartmentalize their functions (e.g. ER, Golgi) and membrane-bound organelles (e.g. mitochondria, chloroplasts)
112
Structures common f/ all prokaryotic cells (3):
- Nucleoid: region where the cell’s DNA is located (not enclosed by a membrane)
- Ribosomes: organelles that synthesize proteins
- Plasma membrane: membrane enclosing the cytoplasm
- Cell wall: rigid structure outside the plasma membrane
113
Structures common only f/ some prokaryotic cells:
- Pili: attachment structures on the surface of some prokaryotes
- Capsule: jelly-like outer coating of many prokaryotes
- Flagella: locomotion structure of some bacteria
114
nucleolus in nucleus of eukaryotic cells is responsible f/
r-RNA synthesis
115
Golgi complex vs ER in the pictures: how to differentiate?
Golgi: faces plasma membrane and ER
ER: faces Golgi and nucleus
116
Cytoplasm
region b/w the plasma membrane and nucleus => includes all the subcellular structures **except the nucleus**
117
Cytosol
intracellular fluid component of cytoplasm => **excludes** organelles and other subcellular membranes, **contains** ribosomes, proteasomes, cytoskeletal filaments, soluble molecules, and water
118
Plant cells (4) vs Animal cells (3):
Plant cells have:
- Chloroplasts
- Central vacuoles (instead of lysosomes)
- Cell wall
- Different cell junctions (plasmodesmata)
Animal cells have :
- Lysosomes
- Centrosome (composed of centrioles)
- Some have a flagella (e.g. sperm cell)
119
Plasma membrane (Cytoplasmic membrane)
- selective barrier that allows sufficient passage of oxygen, nutrients, and waste in and out of the cell
- consists of phospholipid bilayer
- semi-permiable
120
The Nucleus
- contains most of the DNA in eukaryotic cell
121
chromatin
- complex of proteins and DNA
- condensation of chromatin => discrete chromosomes
122
Central dogma of transfer of genetic information:
DNA =>transcription=> mRNA =>translation=> protein
transcription - in nucleus
translation - in cytoplasm
123
What processes take place in the nucleus?
- DNA is replicated before every cell division (in nucleus)
- DNA is transcribed to mRNA in the nucleus
124
Nucleolus
- denser area in the nucleus
- here ribosomal rRNA is synthesized, it after is assembled w/ proteins => subunits exit the nucleus & form ribosomes in the cytoplasm
125
Ribosomes:
– particles made of ribosomal RNA (rRNA) and protein
– consist of a small and a large subunit which are assembled in the nucleolus
– fn: translation - protein synthesis
– 2 cellular locations: free ribosomes in cytosol => cytosolic proteins, bound ribosomes in RER => secreted or membrane-bound proteins
126
ER:
- Network of membranous tubules and sacs
- Inside space - **lumen**
- ER membrane: continuous with the nuclear envelope
- 2 distinct regions: smooth ER, rough ER
127
SER (fns: 4)
- doesn’t have any bound ribosomes
Fns:
- **Synthesizes lipids**
- Metabolizes carbohydrates
- Stores *calcium*
- Detoxifies poisons
128
RER fns (3):
- has bound ribosomes
Fns:
- synthesis of secreted proteins or membrane-bound proteins
- Some post-translational modifications
- Protein targeting (sorting): transports and distributes proteins to other cell compartments (e.g. Golgi) by producing membrane-bound transport vesicles (cell trafficking)
129
Post-translational modifications that occur in the RER (4):
- Polypeptide cleavage: some polypeptides are activated by enzymes that cleave them in order to become **functional** (ex: *insulin*)
- Protein folding (**tertiary structure**): e.g. *disulphide bond formation*.
- Subunit assembly (protein **quaternary structure**): Some polypeptides come together to form the subunits of a functional protein (ex: *haemoglobin*)
- Some chemical modifications: addition of chemical groups to proteins (e.g. *glycosylation, hydroxylation*) => formation of **glycoproteins** (some in RER but most in Golgi apparatus).
130
The Golgi Apparatus
- Consists of flattened membranous sacs (cisternae)
- TGN (trans Golgi network) faces the PM
- CGN (cis Golgi network) faces the ER
- transfers the vesicles that it receives from RER
131
Fns of the Golgi Apparatus (3):
1. **Protein and macromolecule processing** (chemical modifications): Receives and modifies protein and other macromolecule products of the ER by addition of chemical groups to proteins (e.g. glycosylation, phosphorylation, hydroxylation => production of glycoproteins, glycolipids, lipoproteins)
2. **Macromolecule sorting and targeting**: Sorts and packages biomolecules into transport vesicles and sends them to other parts of the cell or the organism (targeting= transport to their cellular destination)
3. **Manufacture of certain macromolecules** ex: polysaccharides
132
Proteins
Lipids
Carbs
are produced in which structures of the cell?
Proteins - RER
Lipids - SER
Carbs - Golgi
133
Lysosomes -
- membranous vesicles containing hydrolytic enzymes, which function at pH=4
134
Fns of lysosomes:
1. **digestion of macromolecules** (or even microorganisms)
- *phagocytosis*: intracellular digestion, human macrophages use lysosomes to ingest pathogenic microorganisms (immune cells)
- *autophagy*: destruction of damaged organelles, recycling of cell’s organic material
2. **recycling**: release simple sugars, aminoacids, nucleotides and FA to be reused by the cell for building new macromolecules
135
Types of vacuoles (3):
- Food vacuoles (phagosomes): formed by phagocytosis
- Contractile vacuoles: pump excess water out of protist cells (ex: Paramecium)
- Central vacuole: in plant cells
136
The endomembrane system function (3):
- important role in the cell’s compartmental organization
- regulates protein traffic (trafficking)
- performs metabolic functions in the cell
137
Endomembrane system components:
– Nuclear envelope
– Endoplasmic reticulum
– Golgi apparatus
– Lysosomes/vacuoles
– Plasma membrane
• Components are either continuous or connected via vesicle-mediated transfer
138
Semi-independent organelles:
**mitochondria & chloroplasts**
- not part of endomembrane system
- have a double membrane
- contain their own DNA (circular double -stranded mtDNA)
- their proteins are made by their own free ribosomes (in mitochondrial matrix and chloroplast stroma)
139
Mitochondria and chloroplasts fn:
- change energy from one form to another
mitochondria:
- sites of cellular respiration
- found in nearly all eukaryotic cells (both animal & plant)
chloroplasts:
- sites of photosynthesis
- only found only in plant cells and algae
140
Plastids
plant organelles:
- Chloroplasts: contain chlorophyll
- Chromoplasts: contain other pigments (e.g. carotenoids)
- Amyloplasts (leucoplasts): contain starch granules
141
Peroxisomes and their fns (3):
- specialized membrane-bound metabolic compartments
Fns:
1. produce hydrogen peroxide (H2O2) and convert it to H2O by their enzymes (*catalase and oxidase*)
2. Detoxification: e.g. *liver peroxisomes detoxify alcohol and other harmful compounds*
3. FA breakdown (β-oxidation of very long fatty acids)
142
Proteasomes and their fns:
- giant protein complexes that bind to protein molecules and degrade them
Fn - protein degradation of *short-lived cytosolic proteins* & *non-functional (misfolded) proteins*: these are attached to ubiquitin (ubiquitination) => targeted to the proteasome f/ degradation in order to be recycled
143
Where are long-lived proteins degraded?
in **lysosomes**
144
Resolution of microscopes:
LM - 200 nm
EM - 2 nm
the lower the resolution - the higher the magnification
