Exam 1: Chpt 1 review Flashcards
Cell Theory
- Organisms consist of one or more cells
- cell is the basic unit of structure for all organisms
- all cells arise only from preexisting cells
Prokaryotic vs Prokaryotic and what are 3 domains?
Prokaryotic Cells
- lack nucleus and membrane bound organelles
- bacteria
- archaea
Eukaryotic Cells
- contain a membrane bound nucleus
- eukarya
Domain Archaea
Prokaryotic cells
- lacks nucleus and membrane bound organelles
- cell wall lack peptidoglycan
Domain Bacteria
Prokaryotic cell
-lack nucleus and membrane bound organelles
Domain Eukarya
contain nucleus and membrane bound organelles
4 Kingdoms:
- Protista
- Fungi
- Plantae
- Animalia
Kingdom protista
Domain Eukarya-eukaryotic cell
- single cellular (with a few multicellular)
- have groups with characteristics of other three eukaryotic kingdoms
- Holding kingdom
Kingdom Fungi
Domain Eukarya-eukaryotic cell Cell: eukaryotic cell with cell wall containing chitin Nutrition -Heterotrophic-absorption Motility: -non motile Life cycle: -Haplontic Energy Storage -Glycogen
Kingdom Plantae
Cell: -eukaryotic cell with cell wall containing cellulose Nutrition -autotrophic: photosynthesis Motility: -nonmotile Life cycle: -alternation of generations Energy Storage: -starch
Kingdom animalia
Cell: -eukaryotic cell lacking cell wall Nutrition -heterotrophic-ingest food Motility: -Motile-contraction of muscles Life cycle: -Diplontic Energy Storage: -glycogen
milli
10^-3
micro
10^-6
nano
10^-9
pico
10^-12
Covalent Bond
sharing a pair of electrons
-overlapping electron shells
STRONG INTERACTION-do not break under physiological conditions
H bond
Sharing of H atom between N, O, or F
Ionic interactions
Electrostatic interactions
- attraction of opposite charges
- either full + or - or partial charges
Van Der Waal Forces
interaction of electron clouds
Hydrophobic interactions
interaction of nonpolar substances
-WEAKEST
Water
- Why is it important
- characteristics
1) Liquid a physiological temps
2) Water has an unusually high boiling point for its molecular weight
3) Good thermal regulator-large amount of heat is required to change its temp
4) provides very effective heat dissipation
-70% of cell mass
-Matrix of life due to unique physical properties
-High Specific Heat
-High Heat (enthalpy) of Vaporization
-Universal Solvent
-High surface tension
-Density of solid water is less dense than liquid water
(ice floats on water)
-Water ionizes H2O-> H+ + OH-
Why does water have such unusual properties?
Shape of the Molecule and hydrogen bond
Hydrogen bond explain:
- High BP/Freezing point
- High heat of vaporization
- Universal solvent
- High surface tension Adhesive/cohesive forces
- Density of solid water is less than liquid water
Equilibrium Expression Rules
gases and aqueous are acceptable
-dont use solids and liquids
Formulas for pH
1x10^-14=[H+][OH] 14=pH+pOH pH=-log[H+] pOH=-log[OH] pH=pKa+ log [Base]/[acid]
pH of human blood
pH=7.35-7.45
[H+]=40nm
Strong Acids
Dissociate 100% releasing all protons
HCl-hydrochloric acid HBr-hydrobromic acid HI- Hydroiodic acid H2SO4-sulfuric acid HClO4-perchloric acid HNO3-nitric acid
Strong Bases
dissociate 100% in water LiOH-lithium hydroxide NaOH-sodium hydroxide KOH-potassium hydroxide Ca(OH)2-calcium hydroxide Sr(OH)2-Strontium hydroxide Ba(OH)2-Barium hydroxide
Buffer
Substance that tends to resist pH changes in a solution thus stabilizing relative pH
- weak acids and conj bases
- works one pH unit either side of pKA
Buffer found in humans
Carbonic Acid-weak acid that buffers blood
Thermodynamics: Isolated system
system does not exchange matter or energy with its surroundings
Thermodynamics: closed system
system that exchanges energy but not matter with surroundings
Thermodynamics: open system
system that exchanges energy and matter with surroundings (Living organisms-Humans)
Laws of Thermodynamics
Zeroth Law:
-If two systems are in thermal equilibrium with a third system, they must be in thermal equilibrium with each other
1st law:
- Total energy of a system and its surrounds is constant
- energy can neither be created nor destroyed. It can only change forms
2nd Law:
-Entropy is a measure of randomness or disorder
3rd Law:
-the entropy of a perfect crystal at absolute zero is zero
Human Genome Project
15 year project to sequence the entire genome
- started 1990 and completed in 2003
- 3 billion haploid base pairs
- 20,500 genes down from 100,000
Protein Definition
Linear, unbranched polymer of 50 or more amino acids
What type of bond connects amino acids together?
Peptide bonds
Functions of proteins
ICCE The Muscles Grow
1) Immune Support
- antibodies are highly specific proteins that identify and remove foreign antibodies
2) Coordinate Motion
- muscle are made mostly of proteins
- contraction of muscles rely on two proteins sliding which are myosin and actin
3) Control of growth and differentiation
- proteins turn the expression of other proteins on or off by binding to specific sequences of DNA
4) Enzymatic catalysis
- most chemical reactions in the cell are carried out by enzymes, which are globular proteins
- increase rate of chemical reactions by reducing activation energy
5) Transport and Storage
- small molecules are moved throughout the cell by specific transporters
- Ex: Hemoglobin transport oxygen throughout the blood
6) Mechanical support
- high tensile strength of bone and skin due to a fibrous protein-collagen
7) Generate and Transmission of Nerve impulses
- sending and receiving messages between nerve cells requires receptor proteins that detect acetylcholine
Glucogenic Amino Acids and Ketogenic amino acids Definition
Glucogenic amino acid
-carbon skeleton is converted into intermediates that can be used to synthesize glucose
Ketogenic amino acids
- carbon skeleton is converted into intermediates (acetyl-CoA and acetoacetyl-CoA) that can form ketone bodies and Fatty acids
- not substrate for glyconeogenesis
Nonessential amino acids vs essential amino acids defintino
Essential Amino acids
- organism lack the enzymes to synthesize the amino acids
- obtain from diet
Nonessential
-organim has the enzyme to synthesize the amino acids
Which amino acids are:
Glucogenic vs Ketogenic
Essential vs Nonessential
Essential-Glucogenic Val and His Three Methods -valine -histidine -threonin -methionine
Essential-BOTH glycogenic and ketogenic iley Trped BOTH pheasants -isoleucine -tryptophane -phenylalanine
Essential-Ketogenic
- Lysine
- Leucine
Nonessential-Ketogenic
NONE
Noneessential-BOTH
Tyrosine
Nonessential-Glucogenic
- alanine
- asparagine
- arginine
- Aspartic acid
- cysteine
- glutamate
- glycine
- proline
- serine
Cyclic Amino Acids
Proline (P, Pro)
- associated with bends kinks or tight turns in proteins
- often followed by glycine in hair pin turns
- often hydroxylated on C3 or C4 of side chain
Amphatic Amino Acids
-characteristics of group
Aliphatic-Nonaromatic hydrocarbon
- nonpolar/hydrophobic
- G, A, V, I, L
- participate in hydrophobic reactions
- usually found inside proteins, away from aqueous solvent
Sulfur containing Amino acids
-characteristics of group
Cysteine
- may for disulfide bridges which stabilize tertiary proteins
- Polar
Methionine:
-Start Codon-first amino acid incorporate in growing peptide structure during translation
Nonpolar
Aromatic Amino acids
-characteristics of group
W, F, Y
- may participate in hydrophobic bonding
- Absorbe ultraviolet light at approx 280nm
- Tyrosine may hydrogen bond or donate a proton in catalysis (aromatic and Oh counting group)
Hydroxyl Containing amino acids
-characteristics of group
S, T
Proton donors
-Ser is at active site of some enzymes
-attachment of O-linked carbohydrates to proteins
Acidic amino acids
-characteristics
D, E
- polar-acidic(charged), hydrophilic
- Found at surface of proteins
- often at active site of enzymes to donate/accept protons
Neutral Amide amino acids
-characteristics of group
N, Q
- Polar-uncharged
- paricipates in h bonding
Basic amino acids
-characteristics of group
K, R, H
- Polar-charged (Basic), hydrophilic
- located on the surface surface of proteins
- may be involved in catalysis or metal bonding
Zwitterion
molecule with a positive and negative charge making it neutral overall
Which amino acids have dissociable R groups?
what is the pka of the n terminus and c terminus
Ryan Harris Do You Even Know Connor R-Arginine-12.5 H-histidine-6.0 D-Aspartic Acid-3.9 Y-Tyrosine-10.9 E-Gluatmic acid-4.3 K-Lysine-10.8 Cysteine- 8.3
C terminus- 3.1
N terminus-8.0
Peptide bonds
Connect amino acids together
- linear and planar, uncharged
- not free to rotate due to double bond like character from resonance
- Trans configuration is favored between H-N and C=O due to steric hindrance
- Exception- Proline is cis
Protein folding
-due to Change conformation in the N-Calpha and Calpha-C single bonds in the PROTEIN BACKBONE
Phi- angle of rotation of N-Calpha (-80)
Psi- angle of rotation of Calpha-C (+85)
- amino acid sequence contains all the info needed for a protein to fold into 3D structure
- Different secondary structures contain different amounts of amino acids
- “All or none process” due to COOPERATIVE TRANSITION. Rapid transition from folded (native) to unfolded (denatured) state
- Brings amino acids R-groups together at the active sites, R groups come from far and
Ramachandran Diagram
displays favored and disfavored phi and psi bond angle combinations
-many combinations aren’t allowed due to steric hindrance
Protein Denaturing
- unfolding and disorganization of a protein secondary or tertiary structure
- DOES NOT involve hydrolysis of peptide bond
Denaturing Agents
- Heat
- organic solvents
- Guanidium Chloride
- Urea
- Detergents (SDS)
- Changes in pH (strong acids or bases)
- Heavy Metals (Hg or Pb)
Reducing Agents
-Beta-mercaptoethanol- reduces disulfide bonds
Four Levels of Protein structure
Primary
-linear sequence of amino acids
Secondary
- alpha helix, Beta sheets, Beta turns, Omega Loops
- H bonding between carbonyl oxygen and N-H of the BACKBONE
Tertiary
- folding of peptide chains as a result of interactions between R-groups
- Interactions: Disulfide bonds, Hydrophobic interactions, Hydrogen Bonding, Ionic Bonding
- Domains: Units of tertiary Structure-> Helix turn Helix, Helix Loop Helix, Leucine Zipper, Zinc Fingers
Quarternary
-interaction of different polypeptide chains (subunits) to form functional protein
Alpha Helix
Secondary Protein Structure Orientation: -Right Handed (Clockwise) -3.6 amino acids per turn of helix -R groups extend outward
Stabilized by h-bonding between carbonyl oxygen and NH group of peptide-EVERY FOURTH AMINO ACID
Helix is disrupted by:
- Proline
- Large number of charged amino acids
- amino acids with bulky side chains
- Amino acids with branched R groups
Ferritin
Protein that contains only alpha helix
-An iron storage protein
Hemoglobin
Protein that contains only alpha helixes
-oxygen caring protein
Beta Pleated Sheet
Secondary Structure
Orientation:
-flat or pleated linear sheets of proteins
-parallel, antiparallel, mixed
-adjacent amino acids are separated by 3.5 amino acids
Stabilized by hydrogen bonding by carbonyl oxygen and NH group of peptide
Beta bends:
-contain proline and glycine
Fatty acid binding protein
contains mostly beta sheets
Green fluorescent protein
contains mostly beta sheets
Proteins: Loops and Turns
Connect secondary structures to form Domains of tertiary structures
Beta Turn
- stabilized by H-bonding between Carbonyl Oxygen and N-H bond three amino acids down
- on the surface of proteins
Omega Loops
- Well Defined and rigid
- no repeating structure
- usually on surface of proteins
Post translation modifications
RNA->Protein
Hydroxylation-add hydroxyl group Carboxylation- add carboxylate Glycosylation-add carbohydrate Attach Fatty Acids Phosphorylation: add PO4-
Alpha Keratin
- Primary component of hair, wool, horns, claws, and hooves
- composed of TWO RIGHT HANDED ALPHA HELIXES intertwined to forma coiled:coiled structure resulting in a L handed helix
- Helixes are cross linked by: Van Der Waals, Ionic Interactins, Disulfide Bonds
- Heptid Repeat
- 3.5 amino acids per turn
- Hair and wool have less disulfide bonds-stretchy
- Horns, claws, and hooves have more disulfide bonds-hard
Collagen
A fibrous protein
- most abundant protein in the human body
- composed of LONG RIGID ALPHA CHAINS wrapped around in a L HANDED TRIPLE HELIX
Triple Helix:
- 1000 amino acids in length
- 3 amino acids per turn
- Repeated Triplet-> Gly-Pro- X
- Proline and Lysine often hydroxylated
- Proline facilitated formation of helix by introducing kink in chain. 100% trans orientation
Biosynthesis of Collagen
rER:
1) translation on bound ribosome to produce pre-proalpha chain and contains a cleavable N-terminal signal sequence
2) 4 Post translational modifications occur
- signal peptidase removes signal sequence to form pro alpha chain
- hydroxylation of proline or glycine in Y position (Gly-x-y)
- glycosylation of some hydroxylysine residues
- Protein disulfide Isomerase bind pro alpha chains together by disulfide bonds to form Procollagen
3) Transported to Golgi where it is enters the secretory pathway by vesicles and enters the plasma membrane
4) undergoes exocytosis and is secreted into the extracellular matrix (outside cell)
5) N and C collagen peptidases cleave the N and C terminal procollagen peptides to form mature collage-tropocollagen
6) undergoes different types of crosslinking which produces collagen fibrils (insoluble)
what is Collagen is synthesized in?
Fibroblasts
osteoblasts of bone
chondroblasts of cartilage
Degradation of collagen
Highly stable
Remodels due to growth and injury
Breakdown due to collagenases called metalloproteinases
Function of nucleic acids
1) building blocks for DNA and RNA
-DNA-Genetic material
-RNA-adaptor molecule between DNA and protein
2) Transport chemical E within cell
-ATP
3) Signaling molecule
cAMP
Nucleic Acid Definition
linear, NONbranched polymer of nucleotides
Classes of nucleic acids
DNA-2’ deoxyribonucleic acid
RNA-ribonucleic acid
Sugar Phosphate backbone consists of:
Nucleotides are connected by 3’ to 5’ phosphodiester bond
- impart uniform negative charge to DNA/RNA
a) negative charge repels nucleophiles thus phosphoeiste bonds are resistant to hydrolytic attack
What bonds Nitrogenous bases to Pentose sugars?
B-Glycosidic Linkage
- N-9 of purine
- N-1 of pyrimidine
Watson and Crick
Determined to structure of DNA by: 1) X-ray diffraction photograph of DNA crystals -Maurice Wilkins and Rosalind Franklins -2 chains formed a helical structure 2) Chargraff's Rule -Edwin chargraff determined the composition of DNA -[A]=[T] -[G]=[C] 3) Bond Angles in Reference Books Complementary base pairing 4) Built Models -nucleotide content determines DNA melting point or number of hydrogen bonds G to C has 3 h bonds A to T has 2 h bonds
Nobel Prize in 1962 of Physiology or Medicine
Maurice Wilkins, Francis Crick, James Watson
DNA structure
Gene
DNA is organized into genes
Gene:
- discrete functional unit of DNA
- when expressed/transcribed yields a functional product
a) rRNA, snRNA, tRNA
b) mRNA-translated into polypeptide sequence - open reading frame-No stop codons, consist of a long stretch of nucleotides that encode polypeptides
Karyotype
photograph of chromosomes from a single organism
-arranged and names by size (smallest to largest)
Homo sapiens (Humans) -# of chromosomes and pairs of chormosomes
46 chromosomes
-23 pairs
Stem loops
ssDNA for this complex structure
- produced by hydrogen bonding between complimentary regions in DNA and RNA
- h-bond stabilizes structure
- mismatches are observed
- often found in rRNA
