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Lecture 2: Eukaryotic cells, amino
acids
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Prokaryotic cell features
Eukaryotic cell types
Amino acids
Quiz next Wed. on Amino Acids-you need to
know the structures, names, single letter
symbols, and pKas of the functional groups.
You will have 30 min to take this quiz.
General schematic for a prokaryote cell
Prokaryotic cell structures
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Cytoplasmic membrane/Inner membrane
– About 45% lipid and 55% protein, forming a bilayer
– Similar in structure and composition to the eukaryotic plasma membrane and
mitochondrial membrane.
• Highly selective pemeability barrier, transport-facilitated diffusion, active
transport, group translocation
• Electron transport and oxidative phosphorylation
• Energy production
• Motility
• Replication
Cytosol - not just water- 20% protein by weight
– Site of intermediary metabolism and energy production
– Precursors necessary for biosynthesis
Nucleoid - Chromosomal DNA
– Haploid genome.
– Smaller than eukaryotic chromosomes, encodes ~ 3500 genes
– No nucleus or nuclear membrane
Ribosomes
– About 15,000 ribosomes per cell. Sites of protein synthesis
Prokaryotic cell structures
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Capsule (slime layer), K antigen-another layer on the outside of the cell.
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Glycocalyx-extracellular polysaccharide; biofilms; not a capsule
Flagella (H-antigen) for motility and chemotaxis
Pili (fimbriae) - Hair-like; protein
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Metabolically inactive, resistant to heat (boiling), dessication, formed inresponse to stress
Storage granules - Storage forms of polymerized metabolites
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Adherence
Genetic exchange (fimbriae)
Fibrillar layer (protein coat, virulence)
Spores (Gram-positive bacteria only)
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Both gram-positive and gram-negative bacteria can make capsules
Polysaccharide (exception is Bacillus anthracis (anthrax) which makes a poly-glutamate
capsule).
Virulence-inhibits complement and phagocytosis
Poly-3-hydroxybutyrate
sugars
Plasmids - non-chromosomal DNA
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Usually circular, independently replicating, can be transmissible between cells by genetic
exchange (conjugation), can encode antibiotic resistance
Archaea
• Discovered as third or ‘intermediate’ branch of the
tree by Carl Woese
– Equidistantly related to both bacteria and eukaryotes (Eukarya)
– Three main groups of Archaea
• Methanogens - obligate anaerobes that produce methane (marsh
gas) by reducing CO2 with H2.
• Halobacteria - live only in concentrated brine solutions (>2M)
• Thermoacidophiles - inhabit acidic hot springs
• Many others found (~40% of ocean microorganisms!)
The Tree of Life has 3 primary branches:
Bacteria, Archaea, and Eukaryotes
Eukaryotes
• Larger than prokaryotic cells (10-100 µm)
• Structural organization more complex than prokaryotes
– Cell volumes 103-104 times larger than prokaryotic cells
• Compartmentalization
– Membrane bound nucleus
– Internal membranes differentiated into specialized structures
• Endoplasmic reticulum (ER)
• Golgi apparatus
• Animal vs. Plant cells
General schematic of an animal cell
Eukaryotic animal cell structures
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Cell membrane/plasma membrane
– About 50% lipid and 50% protein, ~5 nm thick
– Similar in structure and composition to the prokaryotic inner membrane and highly selective
pemeability barrier.
• Pumps and channels
• Enzymes
• Reception of extracellular information
Nucleus- Separated from cytosol by nuclear envelope (double membrane)
– DNA is complexed with histones (basic proteins) forming chromatin fibers
– DNA organized into chromosomes
Nucleolus- Distinct region in the nucleus
– Synthesizes rRNA
– Site of ribosome assembly
Endoplasmic reticulum (ER) and ribosomes
– Most extensive membrane in the cell
– ER studded with ribosomes called rough ER
– Synthesis of proteins and membranes
Eukaryotic animal cell structures
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Golgi apparatus - Packages and processes macromolecules
– Secretion
– Delivery to other cellular compartments
Mitochondria - Separated from cytosol by double membrane
– Markedly different in protein and lipid composition compared to the rest of the cell
– 1 µm ~ same size of bacteria
– Inner membrane and matrix contain many enzymes for energy metabolism.
– Carbohydrates, fats, and amino acids are oxidized to CO2 and H2O.
– Energy is converted to high-energy phosphate bonds (ATP)
Lysosomes - Intracellular digestion of materials
– 0.2 - 0.5 µm single-membrane bounded vessicle
– Contain hydrolytic enzymes such as proteases and nucleases
– Formed from Golgi apparatus
– Degrade cellular constituents targeted for destruction
Peroxisomes
– 0.2 - 0.5 µm single-membrane bounded vessicle
– Contain oxidative enzymes that use molecular oxygen and generate peroxides
– Formed from smooth ER
General schematic of a plant cell
Plant cell structures
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Cell wall
– Cellulose fibers embedded in a polysaccharide/protein matix
– >0.1 µm thick
– Rigid and porous to small molecules.
Cell membrane - similar to animal cell membrane
ER, Golgi apparatus, ribosomes, lysosomes, peroxisomes
– Similar to animal cells
Chloroplasts - site of photosynthesis
– Light energy is converted to chemical energy (ATP)
– Double membrane, inner volume is called stroma
– Rich in membrane and encloses the thylakoid lumen
– Photosynthetic reactions take place on the thylakoid membranes
– Formation of carbohydrate from CO2 takes place in stroma
– Much larger than mitochondria
Mitochondria
– Similar to animal cells, responsible for energy generation in the dark
Vacuole - functions in transport and storage of nutrients andd cellular waste products
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Most obvious part of plant cell
Enclosed by a single membrane called the tonoplast
Amino acids
• The origins of biochemistry are tied to protein research
• Why proteins?
– Amino acids-the building blocks of proteins
– The most well-defined physicochemical properties
– Easier to isolate and characterize than nucleic acids, polysaccharides,
or lipids
– Proteins had easily recognizable functions (enzymes)
• Amino acids
– The building blocks of proteins
– Diversity of function in proteins arises from the intrinsic properties of
only 20 commonly occurring amino acids.
– Can be polymerized
– Novel acid-base properties
– Varied structure and chemical functionality in amino acid side
chains
– Chirality
General structure for amino acids
Except for proline, all amino acids possess the following
structure:
R
H
R
Side
chain
C
+
H3N
Amino
group
COO
-
H
Carboxyl
group
NH3
C
COO-
Amino acids are tetrahedral structures
Ionic forms of amino acids
R
H
H+
R
H
C
+
H3N
COO
Zwitterion
pH 7 Net charge 0
H+
C
+
H3N
R
H
C
COOH
pH 1 Net charge +1
H2N
COO -
pH 13 Net charge -1
Amino acids can join via peptide bonds
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The amino (-NH3+) and carboxyl (-COO-) groups allow amino acids to
polymerize.
Amino acids react in a head-to-tail fashion
– Elimination of a water molecules
– Formation of covalent amide linkage (peptide bond)
– Peptide bond formation is thermodynamically unfavorable-so reaction is
coupled
Peptides
– 2 amino acid (aa) residues - dipeptide
– 3 aa residues - tripeptide
– A few aa residues - oligopeptide
– Many aa residues - polypeptide
• Proteins are molecules that consist of one or more polypeptide
chains
– Polypeptides range from 40 to 33,000 amino acids (most about 1500
aa)
Condensation of two amino acids to form
peptide bond
Polypeptides
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Polypeptides are linear polymers
20 standard amino acids
– 3 main groups (note there are crossovers) based on R-groups (side
chains)
– Nonpolar (hydrophobic) side chains
• Simple aliphatics
• Aromatics
• Proline
– Uncharged polar side chains
• Alcohols
• Sulfur containing
• Amides
– Charged polar side chains
• Acidic
• Basic
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From these 20 choices we get diversity
– For a dipeptide, 202 = 400 possible dipeptides
– For a tripeptide, 203 = 8000 possible tripeptides
– For a 100 aa polypeptide, 20100 = 1.27 X 10130 possible polypeptides!
Aliphatic nonpolar amino acids: Gly, Ala,
Met, Val, Leu, and Ile
+
H3N
COOC
H
Glycine
Gly
G
+
H H3N
COO- H +N
3
C H
CH3
Alanine
COOC
H
CH2
CH2
+
H2N
C
Proline
CH3
Pro
Methionine
P
Met
M
H
CH2 CH2
CH2
S
Ala
A
COO-
Aliphatic nonpolar amino acids: Gly, Ala,
Met, Val, Leu, and Ile
+
H3N
COOC
H
COO-
+
H3N
C
CH2
CH
CH3
CH3
H
Valine
CH
H
C
H
C CH3
CH2
CH3
CH3
+
H3N
COO-
CH3
Val
Leucine
Isoleucine
V
Leu
Ile
L
I
Aromatic nonpolar amino acids: Tyr, Trp
and Phe
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H3N
COOC
H
COO-
+
H3N
C
H
CH2
CH2
+
H3N
COOC
H
CH2
C
OH
Tyrosine
Tyr
Y
N
H
CH
Phenylalanine
Tryptophan
Phe
Trp
F
W
Amino acids
• Nonpolar amino acids
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All amino acids with alkyl R-groups (Ala, Val, Leu, and Ile)
Pro, Met, and Gly
Aromatic amino acids Phe, Tyr, and Trp
Generally hydrophobic
• Exceptions are Pro, Gly, Tyr and Trp
Uncharged polar side chains
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H3N
+
H3N
COOC
H
COOC
CH2
OH
COO-
+
H H3N
C
H
H
C
OH
+
H3N
COO-
C
H
CH2
CH3
Serine
Threonine
H
Ser
Thr
Glycine
S
T
OH
Tyrosine
Gly
Tyr
G
Y
Uncharged polar side chains
+
H3N
COOC
H
R-SH
R-S- + H+
R-OH
R-O- + H+
CH2
SH
Cysteine
Cys
C
Formation of cystine
Uncharged polar side chains
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H3N
COOC
+
H3N
H
Asparagine
Asn
N
H
CH2
C
NH2
C
CH2
CH2
O
COO-
C
O
NH2
Glutamine
Gln
Q
Amino acids
• Polar, uncharged amino acids
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Contain R-groups that can form hydrogen bonds with water
Includes amino acids with alcohols in R-groups (Ser, Thr, Tyr)
Amide groups: Asn and Gln
Usually more soluble in water
• Exception is Tyr (most insoluble at 0.453 g/L at 25 C)
– Sulfhydryl group: Cys
• Cys can form a disulfide bond (2 cysteines can make one cystine)
Charged polar (acidic) side chains
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H3N
COOC
H
+
H3N
O
Aspartic acid
D
H
CH2
C
Asp
C
CH2
CH2
O
COO-
C
O
O
Glutamic acid
Glu
E
Amino acids
• Acidic amino acids
– Amino acids in which R-group contains a carboxyl
group
– Asp and Glu
– Have a net negative charge at pH 7 (negatively
charged pH > 3)
– Negative charges play important roles
• Metal-binding sites
• Carboxyl groups may act as nucleophiles in
enzymatic interactions
• Electrostatic bonding interactions
Charged polar (basic) side chains
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H3N
COOC
H
+
H3 N
COOC
H
CH2
CH2
CH2
CH2
CH2
CH2
Lysine
CH2
NH
C
NH2+ NH2
Lys
Arginine
K
Arg
NH3+
R
COO-
+
H3N
C
H
CH2
C
HC
H+N
NH
CH
Histidine
His
H
Amino acids
• Basic amino acids
– Amino acids in which R-group have net positive charges at pH 7
– His, Lys, and Arg
– Lys and Arg are fully protonated at pH 7
• Participate in electrostatic interactions
– His has a side chain pKa of 6.0 and is only 10% protonated at
pH 7
– Because His has a pKa near neutral, it plays important roles as a
proton donor or acceptor in many enzymes.
– His containing peptides are important biological buffers
Nonstandard amino acids
• 20 common amino acids programmed by genetic code
• Nature often needs more variation
• Nonstandard amino acids play a variety of roles: structural,
antibiotics, signals, hormones, neurotransmitters, intermediates in
metabolic cycles, etc.
• Nonstandard amino acids are usually the result of modification of a
standard amino acid after a polypeptide has been synthesized.
• If you see the structure, could you tell where these nonstandard
amino acids were derived from?
Nonstandard amino acids
Nonstandard amino acids