Exam 1 Flashcards
1
Q
Protein Definition
A
Linear unbranched polymer of 50 or more aminos acids
- amino acids are connected by peptide bonds
- proteins linear seq of amino acids fold to form 3D structure
2
Q
Nucleic Acid definition
A
Linear NONbranched polymer of nucleotides
3
Q
Carbohydrate Definition
A
an aldehyde or ketone derivative of a polyhydroxyl cpd
-old def: hydrated carbon (CH2O)n
4
Q
Lipids Definition
A
Heterogenous group of water insoluble (hydrophobic) organic molecules that can be extracted from tissues by non polar solvents (chloroform)
5
Q
Protein Functions
A
ICCE The Muscles Grow
Immune proteins- A highly specific protein-Antibody- detects and removes a foreign substance from cell
Coordinate Motion:
- muscles are made up of mainly proteins
- when muscles contract two proteins slide-actin and myosin
- flagella movement and chromosome movement in mitosis are due to proteins
Control Growth and Differentiation- proteins bind to a specific DNA sequence to express or unexpress another protein
Enzymatic Catalysis- most chemical reactions require enzymes such as globular proteins to increase reactions rate by lowering activation energy
Transport and Storage- small molecules are transported with a cell by transporter proteins
-Hemoglobin carrying oxygen in blood
Mechanical Support- High Tensile strength in bone and skin do to collagen-Fibrous Protein
Generate and Transmission of nerve impulses- sending and receiving signals from nerve cells require a protein that recognizes acetylcholine
6
Q
Nucleic Acid Functions
A
Building Blocks of DNA and RNA
- DNA=genetic material
- RNA= adaptor molecule between DNA and protein
Transport chemical Energy storage within the cell
-ATP
Signaling Molecule
-Cyclic AMP
7
Q
Carbohydrates Function
A
Energy Source (glucose or sucrose)
Energy Storage (Glycogen in animals and starch in plants)
Structural component (DNA and RNA)
Signaling Molecule
Cell to Cell Recognition (Glycosylation of proteins or other biomolecules)
8
Q
Glucogenic vs Ketogenic Amino Acids Define
A
Glucogenic amino acids:
-carbon skeleton converts to Intermediates that can synthesize glucose
Ketogenice amino acids:
- carbon skeleton converts to intermediates (acetyl-CoA or Acetoacetyl-CoA) to form ketone bodies and Fatty acids
- Not substrate of glyconeogenesis
9
Q
Essential vs Nonessential Amino Acids define
A
Essential Amino Acids:
- Organism lacks enzymes to synthesize amino acids
- must be obtained from diet
Nonessential amino acids:
-Organism has the enzymes present to synthesize amino acids
10
Q
Which amino acids are Ketogenic Glucogenic, Both between the nonessential and essential Amino Acids
A
Essential Amino Acids:
Glucogenic: Val and His Thre Methods
Valine, Histidine, Threonin, Methionine
BOTH: Iley trpd BOTH phesants
Isoleucine, tryptophane, phenylalanine
Ketogenic: KETONES in Leu of Lysine
Leucine, Lysine
NONESSENTIAL AMINO ACIDS Glucogenic: Alanine, Arginine, Asparagine, Aspartic Acid Glycerine, Glutamine, Glutamic Acid Cystein, Serine, Proline
BOTH:
Tyrosine
Ketogenic:
NONE
11
Q
Which amino acids have dissociable protons and pka values?
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- Glutamic Acid 4.3 K- Lysine 10.8 C-Cysteine 8.3
12
Q
Zwitterion
A
a molecule containing bot a positive and negative charge on the same molecule
13
Q
Peptide Bonds
A
Connect Amino Acids
- Linear, Planar, uncharged
- Fixed due to resonance-has double bond like characteristics
- Trans configuration for carbonyl oxygen and N-H due to steric hindrance
14
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 close
15
Q
Denaturing Protein
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
16
Q
Ramachandran Diagrams
A
- display favored and disfavored phi or psi bond angles
- many conformations are not allowed due to steric hindrance
- L handed helixes are rare
17
Q
What are the 4 Levels of protein structure and describe each
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
18
Q
Loops and Turns in Proteins
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
19
Q
Alpha Helix
A
Secondary Structure of Protein
- orientation-Right (clockwise)
- Stabilized by H-bonding between carbonyl oxygen and N-H every fourth amino acid
- 3.6 amino acids per helical turn
- R groups extend outward
Helix is disrupted by:
- Proline
- Large # of charged amino acids
- Bulky side chains (W)
- Branche R groups (V, I)
20
Q
Proteins that contain Alpha Helixes
A
Ferritin- Iron storage protein
Hemoglobin- Oxygen carrying protein
21
Q
Beta Sheets
A
Secondary structure of protein
- Oreintation- flat, pleated, linear sheets of proteins
- stabilized by H-bonding between carbonyl oxygen and N-H
- amino acids separated by 3.5 A
- can organize into parallel, antiparallel, and mixed
- Beta bends- contain proline and glycine
22
Q
Proteins that contain Beta Sheets
A
Fatty Acid binding protein
Green Fluorescent Protein
23
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
24
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
25
Hydroxylation of Proline and Lysine
Proline:
- enzyme- proly hydroxylase forms hydroxyproline
- requires ascorbate (vit C) and molecular oxygen
- location- 4-hydroxyproline (more); 3-hydroxyproline (less)
Lysine:
- enzyme- Lysyl Hydroxylase
- requires ascorbate (vit C) and molecular oxygen
- HydroyLysine sometimes undergoes glycosylation
BOTTH allow crosslinking of glycogen
26
Biosynthesis of Collagen
- Fxn
- Syntehsized in?
Functions outside the cell so gets secreted into the Extra Cellular matrix
Synthesized in:
Fibroblasts
chondroblasts of cartilage
osteoblasts in bone
27
Collagen Diseases
Ehler's-Danios Syndrome (EDS)
- Heterogenous group of generalized connective tissue disorders (approx 10)
- Heritable defects in Fibrillar Collagen:
1) def in collagen processing enzymes
2) mutations In amino acid seq of collagen I, III, V
Scurvy:
- British Sailors called Lymes
- reduced tensile strength of collagen
1) deficiency in ascorbic acid (Vit C) inhibits propyl hydroxylase and Lysyl hydroxylase thus Collagen lacks cross-links
- Symptoms- Bleeding; leaky capillaries
Osteogenesis Imperfecta (brittle bone disease)
- Due to defects in synthesis of collagen I
- Symptoms: fragile bones, thin skin, abnormal teeth, weak tendons
- Two types
1) Osteogenesis Imperfecta Tarda
- Type I collagen defect
- present in early infancy
- fractures secondary to minor trauma
2) Osteogenesis Imperfect Congenita
- Type II collagen defect
- dies in utero or in neonatal period
28
Protein Folding Diseases
```
Alzheimers-an Amyloidose
Amyloid Plaque
-Involves AB, a 40-43 amino acid peptide
-accumulates in non branching Fibrils with Beta sheets
-neurotoxic
```
Mutant Tau protein
-Tau protein is produced form translation of an alternatively spliced gene called MAPT in humans located on chromosome 17
Transmissible Spongiform Encephalophaties
- Prion Diseases (PrP) proteinaceous infectious particle
- Stanley Prusiner (1997 nobel prize)
- Family of rare progressive neurodegenerative disorders that affect animals and humans,
- Distinguished by: long incubation periods, neuronal loss, lack of inflammatory response
Misfolded prion proteins- normally found in neurons and glial cells, lack posttranslational modifications differences from normal prion proteins, the altered form becomes a template to induce misfiling of normal PrP into altered form
```
Names for various TSEs
Human-kuru
Cattle- Bovine Spongiform Encephalopathies (mad cow's)
Sheep-scrapies
Deer- Chronic Wasting Disease
```
29
Protein Modification
```
Amino acids covalently modified (Usually post translation)
-Hydroxylation
-Carboxylation
-Glycosylation
Attachment of Fatty acids
-Phosphorylation
```
30
Central Dogma of Molecular Biology:
| Where does Replication, Transcription, Translation take place?
DNA->RNA->protein
Nucleus:
replication- DNA directed DNA synthesis
Transcription- DNA directed RNA synthesis
Cytoplasm:
Translation: RNA directed Protein Synthesis
31
What are the different classes of Nucleic Acids
DNA- 2' deoxyribonucleic acid
| RNA- ribonucleic acid
32
Nucleotide vs Nucleoside
Nucleotide
-Nitrogenous Base + Pentose Sugar+ Phosphate Group (one or more)
Nucleoside
-Nitrogenous Base + Pentose Sugar
33
Phosphodiester Bonds
connect nucleotides 3' to 5'
34
Nitrogenous Base Categories
Pyrimidines: TCU
Thymine (T)
5-methyl-2,4-dioxypyrimidine
DNA only
Cytosine (C)
4-amino-2-oxypyrimidine
DNA and RNA
Uracil (U)
2,4-dioxypyrimidine
RNA only
PURINES:
Adenine (A)
6-aminopurine
DNA and RNA
Guanine (G)
2-amino-6-oxypurine
DNA and RNA
35
Beta Glycoside Linkage
Bases are attached to Sugar by Beta Glycosidic Bonds
36
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
37
Sugar Phosphate Backbone
-nucleotides connect 3' to 5' by phosphodiester bonds
Impart Uniform negative charge to DNA and RNA
-negative charge repels nucleophilic species (OH) thus phosphodiester bonds resist hydrolytic attack
-Seperation by agarose gel electrophoresis
Creates Directionality
38
DNA
Organized into Genes:
- discrete functional unit of DNA
- when expressed (translated) yields functional produce
1) rRNA, tRNA, snRNA
2) mRNA- translated to polypeptide sequence
- open reading frame
Double Stranded
3 forms: B, A, and Z
Held together by H-bonds between Base Pairs and Hydrophobic interactions between base stacking
39
B Form, A form, and Z form of DNA
```
B FORM:
Normal form/ Watson and Crick Used
(Intermediate)
Diamter of Helix- 20 A
10.4 BP per helical turn
BP 3.4 A apart
-Right handed Helix
-Complementary Base pairing
-Major/Minor Groove
-Antiparallel
-Hydrogen bonding Between complementary BP
```
A FORM: (Broadest)
- dehydrated B form
- nucleotide tilted 20 degrees relative to helical axis
- R handed helix
Z FORM (elongated)
- zig zag
- stretches of alternating purine and pyrimidines
- BP flip 180 degrees
- L handed Helix
40
Karyotype
- photographs of chromosomes from a single organism
- arranged by size/Named (largest #1 to smallest #22 #23=Y)
- Homo sapiens 43 chromosomes-23 pairs
41
Chromosome contains
Centromere- site that connect sister chromatids
Kinetochore- site that spindle connects to chromosome
Telomere- nucleotide Repeat at end of linear chromosome
-TTAGGG x1000 synthesized by telomerase
42
Properties of DNA
melt/reanneal/ anneal
- Hyperchromic effect
- Super coiled/relaxed
43
Hyperchromic effect
HEATING DNA What happens?
- DNA can melt and reanneal, if seq are similar they will reanneal or hybridize
- Breaks Hydrogen Bonds between base pairs
- Tm=melting temperature- when half the helical structure is lost
- Single stranded DNA absorbs light more efficiently than dsDNA
44
DNA Linear or Circular Molecules
Eukaryotic DNA- Linear
Prokaryotic DNA, Chloroplast, and Mitochondrial- Circular molecules and may exist in topological isomers
45
ssDNA can form complex structures
STEM LOOPS
- produced by hydrogen bonding between complimentary regions of DNA and RNA
- H-bonding stabilizes complex structure
- mismatches occur
- often observed in ribosomal RNA
46
DNA Replication
```
DNA directed DNA synthesis (nucleus)
Semiconservative
DNA polymerase
-adds deoxyribonucleotide to an existing DNA molecule in a template fashion 5' to 3'
-requires:
1) dNTPs
2) divalent cation (Mg2+)
3) template strand
4) Primer- 3' OH
```
DNA polymerase Rxn Mech:
- nucleophilic attack by the 3' OH on the alpha phosphate group of dNTP (NTP for RNA polymerase)
- PPi (pyrophophosphate) hydrolyzes to Pi + Pi (orthophosphate)
47
Types of RNA
ribosomal RNA- rRNA- part of ribosome
transfer RNA- tRNA-
messenger RNA- mRNA-translated to polypeptide sequence
small nuclear RNA-snRNA- involved in splicing (spliceosome)
micro RNA- miRNA- small RNA complimentary of to mRNA that inhibits translation of the mRNA
small interfering RNA-siRNA-small RNA that binds to mRAN causing destruction of mRNA
48
Transcription
DNA directed RNA synthesis (Nucleus)
RNA polymerase
- add ribonucleoside triphosphate to an Existing DNA molecule in a template directed fashion 5' to 3'
- requires
1) Four NTPS (A, U, G, C)
2) Template Strand
3) Divalent Cation (Mg2+)
4) No primer needed
5) no Endo or exo nuclease activity
RNA polymerase Rxn Mechanims
1) Nucleophilic attack by 3' OH on the alpha phosphate group of NTP
2) PPi (pyrophophosphate) hydrolyzes to Pi + Pi (orthophosphate)
```
PROKARYOTIC PROMOTER
1)Pribnow Box (TATA Box)
5' TATAAT 3'
-centered at -9/-10
2) -35 Sequence
```
EUKARYOTIC PROMOTER
- class II genes- those synthesized by RNA polymerase II
- TATA or Hogness Box
- GC box
- CAAT Box
Transcription TERMINATION
Rho dependent- use rho protein
Rho independent-involves stem loop structure in mRNA followed by UUU
Prokaryotic RNA polymerase: RNA poly I
Eukaryotic RNA polymerase: RNA poly I, RNA poly II, mRNA, RNA poly III
Genes may or may not be transcribed depending on the cells need
49
mRNA eukaryotic vs prokaryotic
Prokaryotic mRNA is polycistroinic
-can encode more than one protein
Eukaryotic mRNA are monocistronic
- encodes only one protein
- contains exons and introns
- post translationally modified by
1) capping-attachment of 7-methylguansine using 5' to 5' triphosphate linkage
2) Poyadenylation- add 40 to several hundred adenines to 3' end of mRNA
3) Splicing- removal of introns
50
Translation
Stages:
1) Initiation
- assemble and align ribosome, mRNA, tRNA^fmet
2) elongation
- symthesis of proteins
3) Termination
- termination factors halt protein synthesis
- ribosome, mRNA, and new protein dissociate
Translation Start Site
AUG encodes Met-Start Codon
-Prokaryotics use SHINE DALGARNO sequence to align an align a ribosome upstream on mRNA
-eukaryotes use 5' cap to align ribosomes on the mRNA
51
Genetic Code
- Specific
- Universal
- Redundant (degenerate)
- No overlapping and comma less
52
Fatty Acids
1) Contain:
- Hydrocarbon (12C to C24)
- Saturates/unsaturated-contain DB-Cis or trans
2) As fatty acid length increases, solubility decreases
- carbohydrates way more soluble
53
Fatty acids need to know
Fuck All Principles BioChem Lectures
PeoPole Should Only Lecture-essentially At Late Night
```
Formic Acid 1:0
Acetic Acid 2:0
Propionic Acid 3:0
Butyric acid 4:0
Capric acid 10:0
Lauric acid 12:0
```
Palmitic Acid 16:0
Palmitoleic Acid 16:1 cis (delta 9)
Stearic acid 18:0
Oleic acid 18:1 cis (delta 9)
Linoleic acid 18:2 cis, cis (delta 9, 12)
Linolenic acid 18:3 cis, cis, cis (Delta 9, 12, 15)
Arachidonic acid 20:4 cis, cis, cis, cis (delta 5,8,11,14)
Lignoceric acid 24:0
Nervonic acid 24:1 cis (delta 15)
54
2 essential Fatty acids in humans
```
Linoleic Acid (omega 6 Fatty acid)
18:2 cis, cis (delta 9, 12)
cis, cis-9, 12-octadecadienoic acid
precursor for arachidonic acid
def-arachidonic becomes essential
```
Linolenic Acid (Omega 3 Fatty Acid)
18:3 cis, cis, cis (delta 9,12,15)
cis, cis, cis-9,12,15-octandecatrienoic acid
precursor for other omega 3 fatty acids
deficiency- decreased vision and altered learning behavior
55
Types of Lipids
```
1)Phospholipid (Phosphoglycerides)
decribed as Amphipathic
contains:
-Glycerol Group
-Polar Head Group (ex phosphate)
-Two non polar tails (2 Fatty Acids)
```
```
2) Glycolipid
contains:
-substituted serine (similar to sphingosine) -NO glycerol
-Polar head group-carbohydrate (glucose)
-2 non polar tails (2 fatty acids)
```
3) Triacylglycerides
accumulates as fat in cytoplasm
-Glycerol Groupo
-3 fatty acids
56
Common Phospholipids
Head groups- Serine, ethanolamine, choline, inositol
Sphingomylin **
- no glycerol containing phospholipid
- contains sphigosine (mod serine)
57
Cholesterol
multiring, nonpolar structure with hydroxyl
- component of cell membrane
- 27 carbons
- Four rings-A, B, C, D form steroid nucleus
Substituents
- Hydroxyl Group (3)
- one Double bond (5-6)
- 2 methyl groups (10 and 13)
- a branched 8 carbon chain (17)
58
Micelle
formed by ionized fatty acids
| -Phospholipids and glycolipids can't form due to steric constraints but do form vesicles (phospholipid bilayer)
59
Phospholipid Bilyaer
(or vesicles)
- Liposome (lipid vesicle)-in aqueous compartment surround by phospholipid bilayer
- contains phospholipids, glycolipids, and cholesterol
contain membrane proteins:
Transmembrane proteins:
-passes through both layers of membrane
-cross membrane by hydrophobic alpha-helixes and sometimes by beta sheets (BETA BARRELS)
-hydrophobic alpha helixes can be identified by HYDROPATHY index-> 20 amino acids at a time and must reach critical/criterion level to be. Beta Barrels are not recognized
-extraction requires organic solvent or detergent
Peripheral proteins
- attached to one side of membrane: associated with polar head groups or transmembrane proteins
- anchored by: Lipid anchors, GPI anchors, sometimes hydrophobic alpha-helixes act like anchors
- extraction by increasing ionic strength or change in pH
60
Fluid Mosaic Model
1) Membranes are 2D solution of Lipids and Globular Proteins
2) Membranes are Asymmetric
3) Membrane fluidity is controlled by fatty acid and cholesterol composition (solid vs liquid state)
- Tm=change of state between solid and liquid
- Lower Tm=shorter fatty acid or DB
- Cholesterol-membrane antifreeze
4) Movement of phospholipids and proteins
Phospholipids
-lateral-rapid
-transverse (flip flop)-VERY SLOW
Proteins:
- lateral- some proteins move as fast as phospholipids other do not due to being anchored to cytoskeleton
- Transverse-do not exhibit-orientation is established at protein synthesis
61
Proteins in Phospholipid Bilayer
1) Bacteriohodopsin
- Arachael protein
- uses light E to transport protons out fo cell to create proton gradient
- 7 alpha helixes span membrane
2) Glycophorine
- RBC membrane protein
- single alpha helix span membrane
3) Porin
E. coli and Rhodobacter capsulatus
-allows movement of material across membrane
62
Ways to classify Carbohydrates
```
1) Repeating structural repeat
Monosaccharides-one
disaccharides-two
Oligosaccharides- >9
Polysaccharides- ALOT
```
2) Monosaccharides- Aldose or Ketose
- Aldose contain a aldehyde group
- ketose contain a ketone group
3) Monosaccharides- Cyclic
- greater than 5 carbons=cyclic -->In vivo less than 1% exist in linear form
- cyclization forms anomeric carbon-new chiral carbon
- Alpha HYDROGEN Above; Beta HYDROGEN Below
4) Monosaccharides- Furanos and Pyranose by hemiacetal and hemiketal
- Hemiacetal- aldehyde reacts with alcohol and forms a 6 membered ring=Pyranose
- Hemiketal- ketone reacts with alcohol and forms a 5 membered ring=Furanose
* * Fructose forms BOTH pyranose and Furanose
63
6 Membered Ring Conformations
IN Carbohydrates (Sugars)
Chair conformation is more stable than Boat conformation due to Steric Hindrance
*Furanose forms enveloped form- C-2 and C-3 carbon are above the plane in same direction as C-5
64
Reducing vs Nonreducing sugars
- reducing sugars have a free aldehydes or form a aldehyde by ring opening, tautomerization, or isomerization
- Ketones can sometimes be reducing sugars when they undergo tautomerization
Tests for reducing Sugars:
1)Benedicts Reagent (CuSO4/Citrate)
2)Fehlings Solution (CuSO4/Tartrate)
-reducing sugars reduce Copper (II) to Copper (I). The product Copper (I) oxidized, forms red precipitate
3) Tollen's Reagent (Silver mirror test)
Tollen's reagent when exposed to free aldehyde precipitates silver metal
65
Carbohydrate modifications
Monosaccharide modifications
- Hydroxyl group attach by O-linked glycosidic bonds
- Amine Groups (NR2) Attach by N-linked Glycosidic bonds
- Phosphorylation (PO32-)***
1) key metabolic intermediates
2) sugar becomes more negative (anionic)
3) Locks intermediate inside the cell or other membrane bound compartment
4) Intermediate is activated
Proteins are modified by attachment of Carbohydrates (Glycosylation)
1) N-linked carbohydrates are attached to R group of Asparagine
- Glycosylation sites: Asn-X- Ser/Thr; X can't be provine
2) O-linked carbohydrates are attached to R group of serine or threonine
66
Glycosidic Bonds
connect Monosaccharides (cyclic sugars)
- connects monosaccharides into dimers, trimers, oligosaccharides, or polysaccharides
- orientations are A or B; N-linked or O-linked glycosidic bonds when it comes to modifications
- Glycosyltransferases- class of enzymes that catalyzes the formation of glycosidic bonds by using sugar nucleotide intermediates
67
Disaccharides and Polysaccharides you need to know
```
Disaccharides:
1)Maltose
Glucose alpha-1,4 Glucose
Breakdown of glycogen and starch
2)Lactose
Galactose B-1,4 Glucose
Milk Sugar
3) Sucrose
Glucose A-1,2 Fructose
```
Polysaccharides
Glycogen and Starch are branched polymers of glucose connected by A-1,4 bonds with A-1,6 Branches
-Glycogen is Animal E (glucose) storage found in the liver and muscles
-Starch is Plant E (glucose) storage
Cellulose- Linear polymers of glucose connected by A-1,4 bonds.
- Plant Structural fiber
68
Proteoglycans
Proteoglycans- glycosylated proteins that serve as joint lubricants and structural component of connective tissue
69
Glycosaminoglycans
are the carbohydrate component of proteoglycans
70
Mucopolysaccharidoses
- disease caused by the inability to degrade glycosaminoglycans
- can result in skeletal deformities and reduced life expectancy
71
Osteoarthritis
caused by breakdown of proteoglycans
72
ABO Blood Type
due to different carbohydrates on RBCs
O antigen (foundation)
-contains four carbohydrates- Fucose, 2x Galactose, N-actylglucosamine
-A and B modified from
A antigen
N-actylgalactosamine
B antigen
Galactose
73
Erythropoietin
```
(EPO)
function is to stimulate RBC production and is glycoprotein hormone secreted by the kidneys
```
Structure
-165 amino acid
3 N-linked
1 O-linked
Uses
- treats anemia cancer pts
- Performance enhancers for athletes
74
Digestion of Carbohydrates
Mouth
-mastification mixes salivary alpha amylase with dietary starch
Stomach
-digestion halts due to low pH
Small Intestine
- acid neutralized by bicarbonate (pancreas)
- alpha amylase resumes digestion (pancreas)
Mucosal Lining of upper jejunum
- disaccharidases and oligosaccharidases-isomaltase, maltase, sucrase
- secreted by luminal side of brush border of intestinal mucosal cells
75
Biosynthesis of Collagen-Pathway
r. E.R
1) Translation (protein synthesis) on bound ribosome, prepro alpha chain has cleavable N-terminal signal sequence
2) Post translational modification
- signal peptidase removes signal sequence to form alpha pro chain.
- Hydroxylation of Proline or Lysine in "Y" position: Gly-x-y
- Glycosylation of (some) hydroxylysine residues-glucose and glycosyl-galactose
- PRO COLLAGEN FORMED BY WRAPPING TOGETHER Pro alpha chains
- transported to Golgi-transports in vesicles to plasma membrane
- where its secreted to the extracellular matrix by exocytosis and undergoes cleavage of C and N terminal pro collagen peptides to form TROPOCOLLAGEN (mature collagen)
- it can now under go crossing by:
1) Deamination of lysine and hydroxylysine produces allysine and hydroxyallysine
2) aldol condensation
3) Schiff Base
-Collagen fibrils form that are insolube
76
Histones
Proteins (H1, H2A, H2B, H3, and H4) that pack DNA due to presence of the amino acids Arginine and Lysine which cause the proteins positive charge at physiological temp
77
Biochem Definition
the study of the chemistry of life processes
78
Cell Theory
- organisms are composed of one or more cells
- cells are the basic unit of life
- cells arise from preexisting cells
79
Domains of Life
Bacteria-Prokaryotic, lack nucleus and membrane organelles
Arachaea-Prokaryotic, lack nucleus and membrane bound organelles
-lack peptidoglycan in cell wall
Eukarya- contain nucleus
Kingdoms
1) Protista- single cellular (sometimes multicellular); similar characteristics to other eukarya kingdoms; holding kingdom
2) Fungi- cell wall composed of chitin; heterotrophic-absorption; no motile; haplontic life cycle; glycogen E storage
3) Animalia- lack cell wall, heterotrophic-ingest food, motile, life cycle-diplontic, Glycogen E storage
4) Plantae-cell wall contains cellulose, autotrophic-photosynthesis, non motile, nonmotile, Starch E storage
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Water
Water important:
- liquid at physiological temps
- unusually high BP for molecular weight
- good thermal regular. large amount of heat required to change Temp
- Very effective heat dissipation
H-bonding:
- High Boiling Point/Freezing point
- High heat of vaporization
- Universal Solvent
- High surface tension adhesive/cohesive forces
- Density of solid water (ice) is less than density of solid liquid
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Strong Acids and Strong Bases
```
Strong Acids
HCl- hydrochloric acid
HBr- Hydrobromic acid
HI- Hydroiodic acid
H2SO4-sulfuric acid
HClO4-perchloric acid
HNO3-Nitric acid
```
```
Strong Bases
LiOH-Lithium Hydroxide
NaOH- Sodium Hydroxide
KOH- Potassium Hydroxide
Sr(OH)2- Strontium Hydroxide
Ca(OH)2- Calcium Hydroxide
Ba(OH)2- Barium Hydroxide
```
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Buffer
substance that resist changes in pH in a solution thus stabilizes relative pH
- weaks acids and conj bases
- range 1 unit of pKa
- Bicarbonic Acid is buffer in our bodies
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Thermodynamics
```
DH=DG+tDS
-deltaG=spontaneous reaction
S=Entropy-randomness or disorder
H=Enthalpy-heat content
G=Gibbs free energy
```
Laws
0th- if two systems are in thermal equilibrium w/a third system. Then they must be in equilibrium
1st- E can neither be created nor destroyed
2nd-Total entropy (S) of a system plus that of surrounds always increases (spontaneous)
3rd- entropy of a perfect crystal @ absolute zero is zero
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Human Genome Project
15 year project
-started 1990 ended 2003
3 million bases
20,500 genes
homo sapiens plus other model organisms were sequenced
