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176 terms
Biochemistry Lecture 4
What are Lipids?
What enzyme catalyzed the digestion of…
What does Emulsification of dietary li…
What pancreatic enzyme degrades TAG?
Heterogeneous group of water insoluble (hydrophobic) organic…
Lipase
Increases the surface are of the hydrophobic lipid droplets s…
Pancreatic lipase
What are Lipids?
Heterogeneous group of water insoluble (hydrophobic) organic…
What enzyme catalyzed the digestion of…
Lipase
41 terms
Biochemistry Lecture 4
what are protein structures called?
what is there a cost of when a protein…
What are the favorable interactions in…
The peptide bond is a __________ of tw…
native fold
Cost in conformational entropy
-Hydrophobic effect: release of water surrounding... -Hydrogen b…
The peptide bond is a resonance hybrid of two canonical struc…
what are protein structures called?
native fold
what is there a cost of when a protein…
Cost in conformational entropy
26 terms
Biochemistry Lecture 4
Structural features of amino acids
Amino acid ionization
How does amino acid ionization affect…
All amino acids are chiral except?
-a central carbon called the α-carbon ... -one amino group... -one…
-When the pH is more than one unit lower than the pKa, the mo…
Some amino acids have an ionizable side chain (R group) that…
glycine (2 H groups)
Structural features of amino acids
-a central carbon called the α-carbon ... -one amino group... -one…
Amino acid ionization
-When the pH is more than one unit lower than the pKa, the mo…
14 terms
Biochemistry - Lecture 4
What are the stages of catabolism?
What are the other names of the citric…
What are the steps of the citric acid…
What is GTP transformed into? What is…
1. Acetyl CoA is fed into the citric acid cycle... 2. Carbon dio…
• Tricarboxylic Acid Cycle (TCA)... • Krebbs Cycle
1. Pyruvate goes through a monocarboxylic transport protein i…
GTP has the same energetic power as ATP, so it transforms int…
What are the stages of catabolism?
1. Acetyl CoA is fed into the citric acid cycle... 2. Carbon dio…
What are the other names of the citric…
• Tricarboxylic Acid Cycle (TCA)... • Krebbs Cycle
176 terms
Pre-session - Biochemistry Lecture 4
What are Lipids?
What enzyme catalyzed the digestion of…
What does Emulsification of dietary li…
What pancreatic enzyme degrades TAG?
Heterogeneous group of water insoluble (hydrophobic) organic…
Lipase.
Increases the surface are of the hydrophobic lipid droplets s…
Pancreatic lipase.
What are Lipids?
Heterogeneous group of water insoluble (hydrophobic) organic…
What enzyme catalyzed the digestion of…
Lipase.
27 terms
Biochemistry Lecture 4
what are two neg charged a.a common to…
what secondary structural element is t…
path of hemoglobin?
quaternary structure of hemoglobin vs…
glutamate and aspartate
alpha helices
goes to lungs, picks up oxygen, drops off oxygen to myoglobin…
hemoglobin: 4 functional units ... myoglobin: 1 functional unit
what are two neg charged a.a common to…
glutamate and aspartate
what secondary structural element is t…
alpha helices
162 terms
Biochemistry 3653 lecture 4
Edman degradation is good for
using trypsin, what is the product(s)…
DNA stand for
DNA is composed of
50 amino acids at most
ala-met-val-lys, his-cys-arg, leu,asn,pro
deoxyribonucleic Acid
TWO AN TIPARALLEL strands Hydrogen bonded together
Edman degradation is good for
50 amino acids at most
using trypsin, what is the product(s)…
ala-met-val-lys, his-cys-arg, leu,asn,pro
32 terms
Biochemistry Objective - Lecture 4
Deoxyribonucleic acid (DNA)
Nucleotides
Nucleoside
Purines
Deoxyribonucleic acid (DNA): polymers made of deoxyribonucleo…
Phosphate + Sugar + Base
only the base - 4 bases in total make up DNA
Adenine (A) & Guanine (G)
Deoxyribonucleic acid (DNA)
Deoxyribonucleic acid (DNA): polymers made of deoxyribonucleo…
Nucleotides
Phosphate + Sugar + Base
44 terms
Biochemistry Lecture 4
Hydrophobicity
Hydrophobicity is a defining character…
What generally provides the hydrophobi…
When looking at a fatty acid tail, whi…
Fear of Water
Lipids
Fatty Acids
The carbon on the end of the tail
Hydrophobicity
Fear of Water
Hydrophobicity is a defining character…
Lipids
18 terms
Biochemistry Lecture 4
Oxidoreductases
Transferases
Hydrolases
Lyase
Shuffling Electrons... Oxidation and reduction reactions- indivi…
Moving Chemical Groups... Kinase- transfer phosphate groups; Gly…
Breaking Chemical Bonds with Water... Cleaves chemical bonds (C-…
Breaking Chemical Bonds WITHOUT Water... Similar to hydrolase, j…
Oxidoreductases
Shuffling Electrons... Oxidation and reduction reactions- indivi…
Transferases
Moving Chemical Groups... Kinase- transfer phosphate groups; Gly…
118 terms
biochemistry lecture 4
Proteins are the .... biological macro…
Proteins are the main agents of biolog…
proteins are ... in both structure and…
....are the building blocks of proteins
most abundant, cell
virtually every process
diverse
amino acids
Proteins are the .... biological macro…
most abundant, cell
Proteins are the main agents of biolog…
virtually every process
27 terms
Biochemistry lecture 4 carbohydrates
what are four aldose sugars
what are two ketose sugars
what are the molecules referred to whe…
mutaroation is irrevsersible? true or…
glucose, galactose, mannose, ribose
fructose, sedoheptulose
stereoisomers
false
what are four aldose sugars
glucose, galactose, mannose, ribose
what are two ketose sugars
fructose, sedoheptulose
37 terms
Lecture 4 Biochemistry
Transcriptomics
Quantifying global gene expression
Deep Sequencing of RNA
RNA-Seq analysis
study of the total number and type of transcripts present in…
1. Collect Tissues... 2. Isolate RNA... 3. Convert to cDNA... 4. Clone…
-RNA samples are collected from test tissues... -Poly-A RNA is i…
-Read mapping (sequence reads are directly aligned to the gen…
Transcriptomics
study of the total number and type of transcripts present in…
Quantifying global gene expression
1. Collect Tissues... 2. Isolate RNA... 3. Convert to cDNA... 4. Clone…
145 terms
Biochemistry Lecture 4
Covalent Peptide
Native Conformations
Primary Structure
Primary
Biologically active proteins are polymers consisting of amino…
Many different conformations (three-dimensional structures) a…
The order in which the amino acids are covalently linked toge…
The peptide Leu-Gly-Thr-Val (N-terminal amino acid listed fir…
Covalent Peptide
Biologically active proteins are polymers consisting of amino…
Native Conformations
Many different conformations (three-dimensional structures) a…
51 terms
Biochemistry Lecture 4
Template strand = _______... (+ or - str…
Coding strand = _______... (+ or - strand)
During transcription, RNA is copied fr…
mRNA has the same sequence as which st…
Template = - strand
Coding = + strand
A) - strand
mRNA = same sequence as CODING strand
Template strand = _______... (+ or - str…
Template = - strand
Coding strand = _______... (+ or - strand)
Coding = + strand
51 terms
Biochemistry Lecture 4
Template strand = _______... (+ or - str…
Coding strand = _______... (+ or - strand)
During transcription, RNA is copied fr…
mRNA has the same sequence as which st…
Template = - strand
Coding = + strand
A) - strand
mRNA = same sequence as CODING strand
Template strand = _______... (+ or - str…
Template = - strand
Coding strand = _______... (+ or - strand)
Coding = + strand
23 terms
Biochemistry Lecture 4
What is a dihedral angle?
What are characteristics of a dihedral…
Why are phi and psi torsion angles of…
Are there usually violations of the Ra…
A dihedral (torsion) angle is made up of three bonds or four…
There is free rotation around the central bond and counter-cl…
They are restricted by steric clashes
No, the observed phi and psi angles are rarely observed outsi…
What is a dihedral angle?
A dihedral (torsion) angle is made up of three bonds or four…
What are characteristics of a dihedral…
There is free rotation around the central bond and counter-cl…
24 terms
Biochemistry Lecture 4
Three stages of catabolism
What were Krebs two cycles?
What instrument was used to measure re…
What is currently used to measure resp…
1. Hydrolysis... 2. Conversion to Acetyl CoA... 3. Oxidation of Ace…
The Urea cycle... The Citric Acid Cycle
The Warburg Manometer
Oxygraph with Clark type electrode
Three stages of catabolism
1. Hydrolysis... 2. Conversion to Acetyl CoA... 3. Oxidation of Ace…
What were Krebs two cycles?
The Urea cycle... The Citric Acid Cycle
21 terms
biochemistry lecture 4
what are proteins?
what are proteins made of?
what is the relationship between prote…
why do we continuously require protein…
- peptides that are made from at least 50 joined amino acids…
- formed by the linkage of amino acids via peptide bonds
- amino acids are obtained from breaking down proteins we eat…
- the body continuously breaks down proteins... - proteins are u…
what are proteins?
- peptides that are made from at least 50 joined amino acids…
what are proteins made of?
- formed by the linkage of amino acids via peptide bonds
biochemistry lecture 4
what is a proteome?
how is a proteome different from a gen…
what do proteins require to be purified?
how does an assay work?
The proteome is the entire set of proteins expressed and modi…
Unlike the genome, the proteome is not a fixed characteristic…
Protein purification requires an assay that determines whethe…
The assay is based on some unique identifying property of the…
what is a proteome?
The proteome is the entire set of proteins expressed and modi…
how is a proteome different from a gen…
Unlike the genome, the proteome is not a fixed characteristic…
44 terms
Biochemistry, Lecture 4
What features does a plasmid have?
Which steps in gene expression can be…
How many stages does transcription have?
Describe the steps of transcription in…
An origin of replication, an antibacterial marker, and a rest…
Any step, from transcription to protein transport.
6
1. RNA polymerase core binds to the DNA promoter region.... 2. T…
What features does a plasmid have?
An origin of replication, an antibacterial marker, and a rest…
Which steps in gene expression can be…
Any step, from transcription to protein transport.
27 terms
Biochemistry Lecture 4
How many amino acids per turn in alpha…
What handed turn is the alpha helix?
What is the distance of one turn in th…
What amino acid produces a kink in alp…
3.6
right handed
5.4 Angstroms
proline
How many amino acids per turn in alpha…
3.6
What handed turn is the alpha helix?
right handed
31 terms
Biochemistry Lecture 4 (8/17/15)
Definition of SIBLINGs?
What are the SIBLINGs?
Kinetic Thermal Energy
Kinetic Radiant Energy
Small Integrin-Binding LIgand, N-linked Glycoproteins: compon…
1) Osteopontin (OPN)... 2) Bone Sialoprotein (BSP)... 3) Dentin Sia…
Energy of motion, heat energy. Thermal regulation in warm blo…
Energy of light (photons) may be converted to heat energy. Ma…
Definition of SIBLINGs?
Small Integrin-Binding LIgand, N-linked Glycoproteins: compon…
What are the SIBLINGs?
1) Osteopontin (OPN)... 2) Bone Sialoprotein (BSP)... 3) Dentin Sia…
15 terms
Medical Biochemistry Lecture 4
Hyperuricemia is due to
CYP genes encode
Relevance of CYP SNPs
Grapefruit juice interactions
Also known as gout. Due to 3x increased activity of PRPP synt…
Encode the drug metabolizing enzymes in the cytochrome P450 p…
Variation in metabolization of drugs. Results in the having "…
Inhibitor of CYP3A4 which metabolizes >1/3rd of commonly pres…
Hyperuricemia is due to
Also known as gout. Due to 3x increased activity of PRPP synt…
CYP genes encode
Encode the drug metabolizing enzymes in the cytochrome P450 p…
95 terms
Biochemistry Lecture 4 - Lipids
What are the functions of lipids?
In what form are lipids a key componen…
True/False: Lipid molecules are mainly…
What are the two essential fatty acids?
1. Essential for energy storage and transport (triglycerols/t…
as phospholipids, glycolipids, and cholesterol
True... -they are chemical compounds that possess both hydrophil…
1. a-Linolenic acid (ALA)... 2. Linoleic Acid (LA)
What are the functions of lipids?
1. Essential for energy storage and transport (triglycerols/t…
In what form are lipids a key componen…
as phospholipids, glycolipids, and cholesterol
22 terms
Biochemistry Lecture 4 - JHus
Enzymes are catalysts
Activation Energy
Rate Enhancement in enzyme catalysis
Example of an aspartyl or acid protease
They lower activation energies, thus increasing rate.... They ar…
The amount of energy needed in a reaction for the reactants t…
Rate of catalyzed reaction/Rate of uncatalyzed reaction... Bigg…
HIV protease, pepsin*... KNOW THESE
Enzymes are catalysts
They lower activation energies, thus increasing rate.... They ar…
Activation Energy
The amount of energy needed in a reaction for the reactants t…
68 terms
Biochemistry 2 Lecture 4
Oxidation
Alkylation
hydrolysis of DNA
Radiation
reactive oxygen species and hydrogen peroxide; loss of electr…
methyl or ethyl groups covalently added to bases
damage to the phosphodiester backbone
UV radiation causes pyrimidines to clump together covalently…
Oxidation
reactive oxygen species and hydrogen peroxide; loss of electr…
Alkylation
methyl or ethyl groups covalently added to bases
12 terms
Biochemistry Lecture 4
measures the degree of disorder
total heat content of a system
exothermic
endothermic
Define entropy
Define enthalpy
Negative delta H
Positive delta H
measures the degree of disorder
Define entropy
total heat content of a system
Define enthalpy
42 terms
Biochemistry Lecture 4
Urea Cycle (2)
Warburg manometer and citrate
Warburg manometer
What happened to citrate?
1. cyclical, intermediates didn't disappear... 2. several interm…
more citrate added, faster the respiration was
as oxygen is used up, soda lime absorbs carbon dioxide, and t…
did not vanish, instead the intermediates remain and are not…
Urea Cycle (2)
1. cyclical, intermediates didn't disappear... 2. several interm…
Warburg manometer and citrate
more citrate added, faster the respiration was
12 terms
Lecture 4 Biochemistry
dissociate completely in dilute soluti…
don't dissociate
more
larger
strong acids and bases
weak acids and bases
Stronger weak acids will dissociate ______ than weaker acids
Weak acids (stronger) will have a ______ dissociation (equili…
dissociate completely in dilute soluti…
strong acids and bases
don't dissociate
weak acids and bases
83 terms
Biochemistry Lecture 4
Actinomycin D
Rifamycin/Rifampicin
Streptolydigin
Werner
Binds DNA Duplex/Intercalates GC
Binds B subunit RNA Pol (prevents 1st bond)
Blocks RNA elongation
Autosomal Recessive
Actinomycin D
Binds DNA Duplex/Intercalates GC
Rifamycin/Rifampicin
Binds B subunit RNA Pol (prevents 1st bond)
22 terms
Biochemistry Lecture 4
Trans
Cis
Torsion angle (omega)
Phi bond
Steric clash unlikely; predominates over cis configuration =…
Steric clash more likely
Alpha carbon-carbon-nitrogen-alpha carbon; refers to amide bond
Carbon-nitrogen-alpha carbon-carbon; free rotation occurs
Trans
Steric clash unlikely; predominates over cis configuration =…
Cis
Steric clash more likely
19 terms
Biochemistry Lecture 4
palindrome
restriction enzymes
polymerase chain reaction
hemoglobin
a sequence that reads the same from left to right as it does…
special enzymes (restriction endonuclei) that recognized spec…
powerful technique to amplify any target sequence from the en…
carries oxygen from the lungs to the rest of the body and CO2…
palindrome
a sequence that reads the same from left to right as it does…
restriction enzymes
special enzymes (restriction endonuclei) that recognized spec…
Biochemistry Lecture 4
Cells
Intermediates
Amino acids
Fireflies
amino acids are structural constituents of ___
amino acids serve as ____ in biosynthesis of many physiologic…
lack of these in humans leads to disorders; defects in their…
reaction involving the protein luciferin and ATP, catalyzed b…
Cells
amino acids are structural constituents of ___
Intermediates
amino acids serve as ____ in biosynthesis of many physiologic…
51 terms
Biochemistry Lecture 4
The Cell Theory
Prokaryote
Coccus
Spirrilius
1) All living organisms are composed of one or more cells... 2)…
Lack membrane bound organelles: ... 1) Mitochondria... 2) Nucleus (…
Round
Spiral
The Cell Theory
1) All living organisms are composed of one or more cells... 2)…
Prokaryote
Lack membrane bound organelles: ... 1) Mitochondria... 2) Nucleus (…
47 terms
Biochemistry Lecture 4
Enzyme
Substrate Specificity
Reaction Specificity
(1.)
A biological catalyst
Only accept 1 particular substrate
Producing only one particular product
Oxidoreductases
Enzyme
A biological catalyst
Substrate Specificity
Only accept 1 particular substrate
biochemistry lecture 4
how are amino acids joined together
Free amino acids are
"Residue"
properties of the peptide bond
through condenstation
zwitterions near neutral pH
means part of AA retained in protein polymer
C-O & C-N bonds fall between single & double bond lengths. th…
how are amino acids joined together
through condenstation
Free amino acids are
zwitterions near neutral pH
11 terms
Biochemistry Lecture 4?
Rho (ρ) termination factor is a ____-d…
____________ termination is Rho indepe…
Transcriptional regulation in which th…
Transcriptional regulation in which th…
ATP, helicase, G:C
intrinsic, G:C
induction, co-inducers
repression, co-repressor
Rho (ρ) termination factor is a ____-d…
ATP, helicase, G:C
____________ termination is Rho indepe…
intrinsic, G:C
13 terms
Biochemistry lecture 4 (exam 1)
Secondary Structure
Tertiary structure
Quaternary structure
peptide bonds
-contains a-helix and b-helix sheet
- all proteins have this structure... -three dimensional form of…
-largely noncovalent but can include covalent disulfuide bond…
-covalent link by which amino acid residues are joined to one…
Secondary Structure
-contains a-helix and b-helix sheet
Tertiary structure
- all proteins have this structure... -three dimensional form of…
36 terms
Biochemistry lecture 4: enzymes
Biological catalyst that enhances chem…
For a reaction to occur spontaneously,…
Reaction rates (kinetics) depend on
If activation energy falls, reaction r…
enzyme
<
activation energy
rise
Biological catalyst that enhances chem…
enzyme
For a reaction to occur spontaneously,…
<
49 terms
Biochemistry Lecture 4
Transcription
Translation
Three-dimensional structure of protein…
Side chain defines...
Creates a complementary RNAcopy (messenger RNA, mRNA) of a se…
MRNA is decoded by the ribosome and tRNA is used to produce a…
Function by interaction
Amino acid type
Transcription
Creates a complementary RNAcopy (messenger RNA, mRNA) of a se…
Translation
MRNA is decoded by the ribosome and tRNA is used to produce a…
44 terms
Biochemistry Lecture 4
Hydrophobicity
Hydrophobicity is a defining character…
What generally provides the hydrophobi…
When looking at a fatty acid tail, whi…
Fear of Water
Lipids
Fatty Acids
The carbon on the end of the tail
Hydrophobicity
Fear of Water
Hydrophobicity is a defining character…
Lipids
51 terms
Biochemistry Lecture 4
Template strand = _______... (+ or - str…
Coding strand = _______... (+ or - strand)
During transcription, RNA is copied fr…
mRNA has the same sequence as which st…
Template = - strand
Coding = + strand
A) - strand
mRNA = same sequence as CODING strand
Template strand = _______... (+ or - str…
Template = - strand
Coding strand = _______... (+ or - strand)
Coding = + strand
11 terms
Biochemistry Lecture 4
Describe the basics of Protein separat…
What is specific activity?
What is in the toolkit for protein sep…
What are the stationary phases in Chro…
•You start with Crude extract -> fractions ->pure protein... • Y…
specific activity = units of activity / mg protein = (umol/ti…
• Salt, organic acids and bases • Chromatography... • Electropho…
-Ion-exchanges: Polymer beads with negatively charged functio…
Describe the basics of Protein separat…
•You start with Crude extract -> fractions ->pure protein... • Y…
What is specific activity?
specific activity = units of activity / mg protein = (umol/ti…
31 terms
Biochemistry Lecture 4
Collagen, elastin, and keratin are all…
Fibrous proteins have (high/low) alpha…
What are the 3 classes of molecules in…
Collagen types I, II, and III are....
Fibrous
High
Structural proteins, protein-polysaccharide complexes (to emb…
Fibril-forming
Collagen, elastin, and keratin are all…
Fibrous
Fibrous proteins have (high/low) alpha…
High
68 terms
Biochemistry 2 Lecture 4
Oxidation
Alkylation
hydrolysis of DNA
Radiation
reactive oxygen species and hydrogen peroxide; loss of electr…
methyl or ethyl groups covalently added to bases
damage to the phosphodiester backbone
UV radiation causes pyrimidines to clump together covalently…
Oxidation
reactive oxygen species and hydrogen peroxide; loss of electr…
Alkylation
methyl or ethyl groups covalently added to bases
Lecture 4- Intro to Biochemistry
__ covalent bonds to every Carbon
same molecular formula, different stru…
Simple Sugars. Cannot be broken down
2 monosaccharides. Can be broken down.
4
Structural Isomers
Monosaccharides
Disaccharides
__ covalent bonds to every Carbon
4
same molecular formula, different stru…
Structural Isomers
23 terms
anatomy lecture 4- biochemistry
biochemistry
what is the most abundant inorganic co…
polarsolvent
salts
the study of chemical composition and reactions of living mat…
water- accounting for 60-80% of the volume of living cells
dissolves ionic substances and forms hydration layers around…
ionic compounds that dissolve into separate ions in water
biochemistry
the study of chemical composition and reactions of living mat…
what is the most abundant inorganic co…
water- accounting for 60-80% of the volume of living cells
20 terms
Lecture 4 and 6 biochemistry
Cross linking protein in parallel bund…
Cross linking protein in contractile b…
Actin 3D network cross linking protein
GTP hydrolysis activity
Fimbrin
Alpha-actin
Filamin
Microtubules
Cross linking protein in parallel bund…
Fimbrin
Cross linking protein in contractile b…
Alpha-actin
34 terms
Biochemistry II: Lecture 4
Is DNA synthesis slower or faster in e…
What is an ORC or Origin of Replicatio…
What are ARS?
When the correct proteins are in place…
Slower
A set of conserved proteins that binds to origins.
They are autonomously replicating sequences, which are the or…
lisenced
Is DNA synthesis slower or faster in e…
Slower
What is an ORC or Origin of Replicatio…
A set of conserved proteins that binds to origins.
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