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MC Biochem 1 > Exam 1: Chpt 1 review > Flashcards

Exam 1: Chpt 1 review Flashcards

1
Q

Cell Theory

A
  • Organisms consist of one or more cells
  • cell is the basic unit of structure for all organisms
  • all cells arise only from preexisting cells
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2
Q

Prokaryotic vs Prokaryotic and what are 3 domains?

A

Prokaryotic Cells

  • lack nucleus and membrane bound organelles
  • bacteria
  • archaea

Eukaryotic Cells

  • contain a membrane bound nucleus
  • eukarya
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3
Q

Domain Archaea

A

Prokaryotic cells

  • lacks nucleus and membrane bound organelles
  • cell wall lack peptidoglycan
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4
Q

Domain Bacteria

A

Prokaryotic cell

-lack nucleus and membrane bound organelles

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5
Q

Domain Eukarya

A

contain nucleus and membrane bound organelles

4 Kingdoms:

  • Protista
  • Fungi
  • Plantae
  • Animalia
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6
Q

Kingdom protista

A

Domain Eukarya-eukaryotic cell

  • single cellular (with a few multicellular)
  • have groups with characteristics of other three eukaryotic kingdoms
  • Holding kingdom
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7
Q

Kingdom Fungi

A 
Domain Eukarya-eukaryotic cell
Cell:
eukaryotic cell with cell wall containing chitin
Nutrition
-Heterotrophic-absorption
Motility:
-non motile
Life cycle:
-Haplontic
Energy Storage
-Glycogen
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8
Q

Kingdom Plantae

A 
Cell:
-eukaryotic cell with cell wall containing cellulose
Nutrition
-autotrophic: photosynthesis
Motility:
-nonmotile
Life cycle:
-alternation of generations
Energy Storage:
-starch
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9
Q

Kingdom animalia

A 
Cell:
-eukaryotic cell lacking cell wall
Nutrition
-heterotrophic-ingest food
Motility:
-Motile-contraction of muscles
Life cycle:
-Diplontic
Energy Storage:
-glycogen
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10
Q

milli

A

10^-3

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11
Q

micro

A

10^-6

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12
Q

nano

A

10^-9

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13
Q

pico

A

10^-12

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14
Q

Covalent Bond

A

sharing a pair of electrons
-overlapping electron shells

STRONG INTERACTION-do not break under physiological conditions

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15
Q

H bond

A

Sharing of H atom between N, O, or F

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16
Q

Ionic interactions

A

Electrostatic interactions

  • attraction of opposite charges
  • either full + or - or partial charges
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17
Q

Van Der Waal Forces

A

interaction of electron clouds

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18
Q

Hydrophobic interactions

A

interaction of nonpolar substances

-WEAKEST

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19
Q

Water

  • Why is it important
  • characteristics
A

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-

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20
Q

Why does water have such unusual properties?

A

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
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21
Q

Equilibrium Expression Rules

A

gases and aqueous are acceptable

-dont use solids and liquids

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22
Q

Formulas for pH

A 
1x10^-14=[H+][OH]
14=pH+pOH
pH=-log[H+]
pOH=-log[OH]
pH=pKa+ log [Base]/[acid]
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23
Q

pH of human blood

A

pH=7.35-7.45

[H+]=40nm

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24
Q

Strong Acids

A

Dissociate 100% releasing all protons

HCl-hydrochloric acid
HBr-hydrobromic acid
HI- Hydroiodic acid
H2SO4-sulfuric acid
HClO4-perchloric acid
HNO3-nitric acid
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25
Q

Strong Bases

A 
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
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26
Q

Buffer

A

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
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27
Q

Buffer found in humans

A

Carbonic Acid-weak acid that buffers blood

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28
Q

Thermodynamics: Isolated system

A

system does not exchange matter or energy with its surroundings

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29
Q

Thermodynamics: closed system

A

system that exchanges energy but not matter with surroundings

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30
Q

Thermodynamics: open system

A

system that exchanges energy and matter with surroundings (Living organisms-Humans)

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31
Q

Laws of Thermodynamics

A

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

32
Q

Human Genome Project

A

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
33
Q

Protein Definition

A

Linear, unbranched polymer of 50 or more amino acids

34
Q

What type of bond connects amino acids together?

A

Peptide bonds

35
Q

Functions of proteins

A

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

36
Q

Glucogenic Amino Acids and Ketogenic amino acids Definition

A

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
37
Q

Nonessential amino acids vs essential amino acids defintino

A

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

38
Q

Which amino acids are:
Glucogenic vs Ketogenic
Essential vs Nonessential

A 
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
39
Q

Cyclic Amino Acids

A

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
40
Q

Amphatic Amino Acids

-characteristics of group

A

Aliphatic-Nonaromatic hydrocarbon

  • nonpolar/hydrophobic
  • G, A, V, I, L
  • participate in hydrophobic reactions
  • usually found inside proteins, away from aqueous solvent
41
Q

Sulfur containing Amino acids

-characteristics of group

A

Cysteine

  • may for disulfide bridges which stabilize tertiary proteins
  • Polar

Methionine:
-Start Codon-first amino acid incorporate in growing peptide structure during translation
Nonpolar

42
Q

Aromatic Amino acids

-characteristics of group

A

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)
43
Q

Hydroxyl Containing amino acids

-characteristics of group

A

S, T
Proton donors
-Ser is at active site of some enzymes
-attachment of O-linked carbohydrates to proteins

44
Q

Acidic amino acids

-characteristics

A

D, E

  • polar-acidic(charged), hydrophilic
  • Found at surface of proteins
  • often at active site of enzymes to donate/accept protons
45
Q

Neutral Amide amino acids

-characteristics of group

A

N, Q

  • Polar-uncharged
  • paricipates in h bonding
46
Q

Basic amino acids

-characteristics of group

A

K, R, H

  • Polar-charged (Basic), hydrophilic
  • located on the surface surface of proteins
  • may be involved in catalysis or metal bonding
47
Q

Zwitterion

A

molecule with a positive and negative charge making it neutral overall

48
Q

Which amino acids have dissociable R groups?

what is the pka of the n terminus and c terminus

A 
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

49
Q

Peptide bonds

A

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
50
Q

Protein folding

A

-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
51
Q

Ramachandran Diagram

A

displays favored and disfavored phi and psi bond angle combinations
-many combinations aren’t allowed due to steric hindrance

52
Q

Protein Denaturing

A
  • 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

53
Q

Four Levels of Protein structure

A

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

54
Q

Alpha Helix

A 
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
55
Q

Ferritin

A

Protein that contains only alpha helix

-An iron storage protein

56
Q

Hemoglobin

A

Protein that contains only alpha helixes

-oxygen caring protein

57
Q

Beta Pleated Sheet

A

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

58
Q

Fatty acid binding protein

A

contains mostly beta sheets

59
Q

Green fluorescent protein

A

contains mostly beta sheets

60
Q

Proteins: Loops and Turns

A

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
61
Q

Post translation modifications

RNA->Protein

A 
Hydroxylation-add hydroxyl group
Carboxylation- add carboxylate
Glycosylation-add carbohydrate 
Attach Fatty Acids
Phosphorylation: add PO4-
62
Q

Alpha Keratin

A
  • 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
63
Q

Collagen

A

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
64
Q

Biosynthesis of Collagen

A

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)

65
Q

what is Collagen is synthesized in?

A

Fibroblasts
osteoblasts of bone
chondroblasts of cartilage

66
Q

Degradation of collagen

A

Highly stable

Remodels due to growth and injury

Breakdown due to collagenases called metalloproteinases

67
Q

Function of nucleic acids

A

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

68
Q

Nucleic Acid Definition

A

linear, NONbranched polymer of nucleotides

69
Q

Classes of nucleic acids

A

DNA-2’ deoxyribonucleic acid

RNA-ribonucleic acid

70
Q

Sugar Phosphate backbone consists of:

A

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
71
Q

What bonds Nitrogenous bases to Pentose sugars?

A

B-Glycosidic Linkage

  • N-9 of purine
  • N-1 of pyrimidine
72
Q

Watson and Crick

A 
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

73
Q

Gene

A

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
74
Q

Karyotype

A

photograph of chromosomes from a single organism

-arranged and names by size (smallest to largest)

75
Q 
Homo sapiens (Humans) 
-# of chromosomes and pairs of chormosomes
A

46 chromosomes

-23 pairs

76
Q

Stem loops

A

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

MC Biochem 1 (30 decks)

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