Biochem Test 1 Flashcards
(140 cards)
1
Q
Key properties of proteins
A
- linear polymers composed of amino acids
- wide variety of functional groups
- interact with one another and with other macromolecules to form complexes
- some are rigid, some are flexible
2
Q
myocin
A
thick filaments
3
Q
actin
A
thin filament
4
Q
What covers active site of G actin molecules?
A
tropomyosin
5
Q
what are the 4 complexed of hemoglobin
A
alpha, alpha 2, beta, beta 2
6
Q
low iron=
A
low hemoglobin= low RBC (anemia)
7
Q
sickle cell anemia
A
RBC are crescent shaped
8
Q
what happens when you’re missing complexes of hemoglobin?
A
- missing 1 = produce 75% of amt of normal blood
- if missing 2= produce 50% of blood, don’t gain weight, spleen can become inactive
9
Q
how many amino acids are there
A
20
10
Q
what isomer is found in proteins
A
L isomer
11
Q
how do the amino acids differ
A
contain side chains that vary in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity
12
Q
Xeroderma Pigmentation
A
inability to repair DNA pyrimidine dimers caused by UV exposure
- S/S: dry skin, skin cancer, extreme light sensitivity
13
Q
AUG
A
start codon
14
Q
PKU (Phenyl Ketone Urea)
A
- autosomal recessive: mutation of the gene that codes for phenylalanine hydroxylase
- S/S: eczema, musty body odor, growth retardation
- Rx: Inc Tyr in diet
15
Q
which amino acids are hydrophobic
A
glycine, alanine, proline, valine, leucine, isoleucine, tryptophan, phenylalanine,
16
Q
characteristics of hydrophobic amino acids
A
- have side chains that lack the ability to interact with polar substances like water
17
Q
Tryptophan is only amino acid with what group
A
indole group (double ring)
- tryptophan is bulkiest amino acid
18
Q
Which amino acids are polar
A
serine, threonine, tyrosine, asparagine, glutamine, cysteine
19
Q
which amino acids are positively charged
A
lysine, arginine, histidine
20
Q
what group does arginine contain
A
guanidinium
21
Q
special characteristics of histidine
A
- contains an imidazole group
- pKa of 6 (near physiological pH)–> can accept/donate protons readily
22
Q
negatively charged amino acids
A
aspartate, glutamate
23
Q
which seven amino acids have readily ionizable side chains
A
aspartic acid, glutamic acid, histidine, cysteine, tyrosine, lysine, arginine
24
Q
why did these amino acids become “protein alphabet”
A
- provide chemical versatility
- may have been available for prebiotic reactions
- larger amino acids may be too reactive
25
primary structure
amino acids are linked by peptide bonds to form polypeptide chains
26
peptide bond formation
linking of two amino acids, accompanied by the loss of a water molecule
27
polypeptide directionality
- has directionality/polarity
- amino terminal end is considered to be the beginning of the polypeptide chain
28
polypeptide consists of...
a repeating part called the main chain or backbone and a variable part consisting of the distinctive amino acid side chains
29
why does the backbone have hydrogen bonding potential
because of the carbonyl groups and hydrogen atoms that are bonded to the nitrogen of the amine group
30
what is the mean molecular mass for an amino acid?
110 g/mol
31
how are disulfide bonds formed
two cysteines are cross-linked (by oxidation)
32
why is knowing amino acid sequence important?
- determine the 3D structures of proteins
- alterations in amino acid sequence can lead to abnormal protein function and disease
- the sequence of a protein reveals much about its evolutionary history
33
features of the peptide bond
- peptide bond is uncharged
- essentially planar
- PARTIAL double bond character because of resonance--> rotation about double bond is prohibited
34
what form of peptide bond is favored
in most cases, trans is favored
35
proline unique geometry
when proline is after another amino acid, the peptide bond between them is equally likely to be cis or trans due to prolines unusual geometry
36
phi bond
N-alpha carbon bond; rotation is permitted
37
psi bond
alpha carbon-carbonyl bond; rotation is permitted
38
rotation around phi and psi bond called
torsion angle--> determines path of polypeptide chain
39
maple syrup urine disease
- blocked degradation of branched AA (ex: leucine, isoleucine, valine), dec alpha-ketoacid deficiency (B1), which leads to an inc in alpha-ketoacids in blood
- autosomal recessive
- S/S: urine smells like maple syrup/burnt sugar, CNS severe defect, intellecual disability
- Rx: B1 (thiamine), restriction of Leu, Tle, and Val
40
Secondary structure
polypeptide chains can fold into regular structures such as the alpha helix, the beta sheet, and turns and loops
-3D structure formed by hydrogen bonds between peptide NH and CO groups of amino acids that are near one another in the primary structure
41
alpha helix
- tightly coiled structure stabilized by Intrachain Hydrogen Bonds
- rodlike structure
- R groups emanate out from the axis of the helix
- all of the backbone CO and NH groups form hydrogen bonds except those at the end of the helix
- right handed
42
beta sheet
- stabilized by hydrogen bonding between polypeptide strands
- secondary structure
- formed by adjacent beta strands
- polypeptide is fully extended
43
types of beta sheets
- hydrogen bonds link the strands in a beta sheet
- the strands of a beta sheet may be parallel, antiparallel, or mixed
- may be flat or may adopt a twisted conformation
44
myoglobin
highly compact, globular, mainly helical protein with a heme prosthetic group
45
distribution of amino acids (folding)
-Surface= charged amino acids
- interior= tightly packed with mostly hydrophobic amino acids
46
protein motif
- supersecondary structures
- common combinations of secondary structure that are present in many proteins and frequently exhibit similar functions
47
protein domains
- independently folding regions within a polypeptide, connected by a short, flexible linker segment
48
two right handed alpha helixes intertwine to form a
left handed super helix
- stabilized by ionic and van der Waals interactions
49
collagen
- useful as a structural protein in skin, bone, tendons, cartilage, and teeth
- Gly has to be every third residue for it to be normal
- consists of three intertwined helical polypeptide chains that form a superhelical cable, interact via H-bonds
- only Gly can fit in the interior
50
collagen defects
- result in pathalogical conditions
- osteogenesis imperfecta (brittle bone disease) occurs if a mutation results in the subsitution of another amino acid in place of glycine
51
Osteogenesis Imperfecta
- autosomal dominant
- blue sclera
- soft bone
- multiple fractures and bone deformities after minimal trauma
- conductive hearing loss
- may be confused with child abuse
52
quaternary structure
polypeptide chains assembled into multisubunit structures
53
reestablishing disulfide bonds
- can regain enzyme activity
- slow formation and breakage of disulfide bonds over the course of several hours until the lowest-energy, most stable active form is finally regenerated
54
Amyloidoses
diseases that result from the formation of protein aggregates, called amyloid fibrils or plaques
- ex: Alzheimers disease
55
Alzheimers
-chromosome 21
- dendrite recieves info that goes down it
- plaques prevent info from being transmitted
- Once CNS is damaged, its irreversible
- space on brain= lateral ventrical
- this is filled with cerebrospinal fluid
- this gets bigger in Alzheimers disease--> less circulated, brain becomes atrophied, neurons die, leading to dementia
56
lack of Vitamin C
prevents hydroxylation of proline in collagen, which can lead to scurvy
- bleeding gums--> eat green vegetables
- problem with collagen-> brittle bone disease
57
lack of vitamin K
prevents carboxylation of clotting proteins, which can lead to hemorrhaging
- Vitamin K is lipid/fat soluble (factor 2,7,9,10 need to be in vit K)
58
Vitamin C
- ascorbic acid
- antioxidant, facilitates iron absorptionby reducing it to Fe2+ state
- necessary for hydroxylation of proline and lysine in collagen synthesis
- necessary to dopamine beta-hydroxylation which converts dopamine into NE (norepinephrine)
- deficiency: scurvy, swollen gums, hemarthrosis(bleeding in joints), anemia, poor wound healing, weakened immune response
59
protein purification requires a...
test (assay) that determines whether the protein of interest is present
60
homogenate
a mixture of sll of the components of the cell
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salting in
most proteins require some salt to dissolve in water
62
salting out
as salt concentration is increased, different proteins will precipitate at different characteristic cell concentrations
63
dialysis
- removes salt from protein
- protein solution placed in a cellophane bag with pores too small to allow the protein to diffuse, but big enough to allow the salt to equilibrate with the solution surrounded by the dialysis bag
64
which amino acids are used in Isoelectric focusing (and when are they uncharged)
= Asp and Glu have carboxyl groups and are uncharged when they are protonated
- Lys, Arg, and His have N-containing groups and are uncharged when deprotonated
65
how is the effectiveness of protein purification evaluated
measured by calculating the specific activity after each separation technique
66
specific activity
ratio of enzyme activity to total protein concentration; should inc with each step of the purification process since total protein is being removed, while desired enzyme is being retained
67
how is protein purification easier with recombinant DNA technology
- large quantities of proteins can be obtained
- proteins can be modified with affinity tags that allow purification of the protein or visualization of the protein in the cell
- proteins with modified primary structure can be generated
68
Immunology
antibodies to a specific protein can be generated
69
antibody
protein synthesized in response to the presence of a foreign substance called an antigen
70
antigenic determinant/epitope
antibody recognizes this particular structural feature of the antigen
71
What are the 5 antibodies
IgA, IgG, IgM, IgE, IgD
72
Ig
immunoglobin
73
IgG
only one that crosses placenta(from mom to baby)
74
IgM
produced as soon as the baby is born (produced first)
75
IgA
comes from saliva, mom's milk
76
IgE
least produced, causes asthma/allergies
77
antobody-producing cell sythesizes...
antibodies that recognize only one epitope
- each antibody-producing cell synthesizes monoclonal antibody
78
any antigen can have...
multiple epitopes
- antibodies produced to the antigen by different cells are said to be polyclonal
79
immortal cell lines
- produce monoclonal antibodies
- generated by fusing normal antibody-producing cells with cells from a type of cancer called multiple myeloma
80
multiple myeloma
- increased igG and IgA (both are inc but IgG more)
- S/S: anemia, bone lytic lesions (punched out x-ray), back pain, hyper calcemia
- UA(urine analysis): high protein in urine-> Bence-Jones protein uria
- Complication: high risk of infection, high risk of amyloidosis
81
ELISA
Enzyme-linked immunosorbent assay
- quantifies the amount of protein present because the antibody is linked to an enzymee that produces a readily identified colored product
82
SNOW
DROP
southern=DNA
Northern=RNA
Western=Protein
83
Information provided by the Amino Acid Sequence
- can be compared to identify similarities
- evolutionary info from comparing same protein from different species
-reveal the presence of internal repeats
- can identify signals that determine the location of the protein or processing signals
- can be used to generate antibodies for the protein
- can be used to generate DNA probes specific for the gene encoding protein
84
purpose of synthesizing peptides
- as antigens to produce antibodies
- to isolate receptors
- as drugs
- to understand protein folding
85
Central dogma
DNA->RNA->Protein
86
nucleic acids
long, linear polymers constructed from four types of monomers
- each monomer consists of a sugar, a phosphate, amd a nitrogenous base
- information content is the sequence of bases
87
deoxyribose
a ribose with the 2' hydroxyl replaced with a hydrogen
88
backbone of DNA/RNA
consists of sugars linked by phosphodiester bridges between the 3' hydroxyl of one sugar and the 5' hydroxyl of the other
89
purines
adenine, guanine
90
pyrimidines
cytosine, thymine(DNA), or uracil(RNA)
91
nucleoside
nitrogenous base bound to a sugar
92
nucleosides of DNA
deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine (thymidine)
93
nucleosides of RNA
adenosine, guanosine, cytidine, and uridine
94
nucleotide
nucleoside with one or more phosphoryl groups
95
nucleoside triphosphates
building blocks of DNA and RNA
96
beta-glycosidic bond
C-1 of the sugar is attached to the N-9 of the purine or the N-1 of the pyrimidine
97
nucleic acid directionality
one end has phosphoryl group attached to the 5' carbon atom of the sugar, and one end has a free hydroxyl attached to the 3' carbon of the sugar
- typically written in 5' to 3' direction
98
double helical structure
pair of nucleic acid strands with complementary sequences
- stabilized by hydrogen bonds
- base pairing rules (A-T and C-G)-> one strand determines other strand
- can be seperated and complementary sequences synthesized to generate two identical daughter strands
99
Watson-Crick Model of DNA
- two helical, antiparallel strands, right-handed helix
- sugar-phosphate backbone on outside, purine/pyrimidine bases on inside
- bases are nearly perpendicular to axis
100
"base stacking interactions"
van der Waals interactions that help stabilize DNA
101
A form of double helix
- shorter and wider than B form (normal DNA)
- bases at an angle to axis
- sugar of C-3 in in endo configuration
- seen in RNA double helixesand in RNA-DNA hybrid helixes
102
Z-DNA
left-handed
- zigzagged backbone
103
stem-loop
- most common in RNA
- occurs when complementary sequences in the same strand form a double helix
104
helicase
splits DNA
105
single strand binding proteins
keeps strands seperate
106
leading strand
coding strand
107
DNA Polymerase III
synthesizes from 5->3 direction
108
RNA primer
5' end
109
DNA Polymerase I
puts fragments together
110
DNA ligase
seals fragments together
111
daughter helix
one parent strand and one newly synthesized strand (semiconservative replication)
112
Denaturation/melting
when DNA strands are seperated by heating a solution of DNA
113
melting temperature (Tm)
temp at which half of the DNA molecules are denatured
114
hypochromism
bases stacked in a double helix absorb less ultraviolet light than bases in a single stranded molecule
115
reannealing
when the two strands bind to each other to reform the double helix
116
DNA Polymerase
catalyzes phosphodiester bridge formation
117
Characteristics of DNA synthesis
four deoxynucleoside triphosphates and Mg2+ are required
- template strand used to direct DNA synthesis
- primer must be present
- Many DNA Polymerases have nuclease activity that allows for the removal of mimatched bases
118
Retroviruses
have single-stranded RNA genomes that are converted into DNA double helices by the action of reverse transciptase
119
most abundant type of RNA
rRNA
120
least abundant form of RNA
mRNA
121
RNA Polymerase
synthesizes RNA from DNA template (transcription)
- initiates and elongates the RNA product with chain growing in the 5 to 3 direction
- no primer needed
122
Requirements for transcription
- DNA template
- activated precursors in the form of the four ribonucleoside triphosphates
- divalent metla ions (usually Mg2+ or Mn2+
123
promoters
specific DNA sequences that direct RNA polymerase to the proper initiation site
124
consensus sequence
- often variation in the sequence of a promoter for different genes
- this is the average of the variation
125
Pribnow box
-10
prokaryotes
126
CAAT box
-75
eukaryotes
127
TATA Box
-25
eukaryotes
128
termination of transcription in prokaryotes
- stop signal is transcribed of a segment of palindromic DNA
- RNA complement of the DNA stop signal forms a hairpin structure, followed by several uracil residues
- synthesis of hairpin, polymerase stalls, RNA product is released, DNA double helix reforms
129
modification of Eukaryotic mRNA
- after transcription
- 5' end of mRNA is modified by attachment of 7-methylguanicine cap and 3' end aquires poly(A) tail
130
tRNA
react with specific amino acids in a reaction cctalyzed by aminoacyl-tRNA synthetases
131
anticodon
- part of tRNA
- template recognition site
- consists of three bases, recognizes a complementary 3 base sequence on the mRNA called the codon
- ends in CAA
132
translation
nucleic acid squence information is translated into amino acid sequence information
- genetic code links these two types of information
133
characteristics of genetic code
- 3 nucleotides(codon) encode an amino acid
- code is nonoverlapping
- no punctuation
- has directionality (read from 5' end of the mRNA to the 3' end)
- code is degenerate (come amino acids are encoded by more than one codon (minimizes deleterious effects of mutations
134
nomRNA
- contains start and stop signals for protein synthesis
- translated on ribosomes
- first codon is almost always AUG
- Formyl-Met-tRNA binds to the initiator codon
- in prokaryotes, the AUG si preceded by Shine-Dalgarno sequence
- in eukaryotes the AUG nearest 5' end is the initiator codon
135
Shine-Dalgarno
in prokaryotes
- purine-rich sequence, precedes AUG
136
initiator codon
location establishes the reading frame
137
exons
coding regions of eukaryotic genes
- often encodes discrete structural and functional units of proteins
138
introns
noncoding regions of eukaryotic genes
- almost always begin with GU and end with AG
139
processing mature mRNA
-pre-messenger RNA contains exons and introns
- first modified by the addition of 5' cap and the poly(A) tail at eh 3' end
- introns are spliced out by splicosomes to generate mature/pure mRNA
140
alternative splicing
allows generation of multiple proteins from a single gene
