Bio/Biochem Flashcards
(133 cards)
1
Q
chirality and configuration of amino acids
A
L (except glycine is not chiral), and S (except cysteine)
2
Q
nonpolar nonaromatic amino acids (7)
A
glycine, alanine, valine, leucine, isoleucine, methionine, proline
3
Q
aromatic amino acids
A
tryptophan (W), phenylalanine (F), tyrosine (Y)
4
Q
negatively charged amino acids
A
aspartatic acid (D), glutamic acid (E)
5
Q
positively charged amino acids
A
lysine (K), histidine (H), arginine (R)
6
Q
general pI’s of amino acids
A
acidic anions ~3 polar, uncharged ~5 aromatic ~5.5 nonpolar, aliphatic ~6 basic cations ~9
7
Q
peptide bond formation is a _____ rxn with a nuc amino group attacking an electrophilic carbonyl. Peptide bonds are broken by _____
A
condensation (dehydration); hydrolysis
8
Q
actin
A
Microfilament that mysosin will crawl along
9
Q
tubulin
A
Microtubule that kinesins walks along
Spindle fibers
10
Q
Cell Adhesion Molecules (CAMs)
A
bind cells to other cells or surfaces. Include cadherins, integrins, and selectins
11
Q
antibodies
A
Y shaped things released by B cells that recognize antigens on the cell surface of pathogens
12
Q
Three types of ion channels
A
ungated, voltage gated, ligand gated
13
Q
Enzyme-linked receptors
A
Participate in cell signaling through extracellular ligand binding and initiation of 2nd messenger cascades
14
Q
GTPase
A
1) ligand binds and induces conformational change
2) GDP –> GTP
3) alpha subunit separates to activate protein/enzyme (eg. adenylate cyclase)
4) protein/enzyme works as 2nd messenger
15
Q
Cyclic AMP 2nd Messenger System
A
1) adenylate cyclase converts ATP –> cyclic AMP
2) cyclic AMP activates PKA
3) PKA phosphorylates (activates) downstream targets
16
Q
Enzymes do what?
A
Lower the activation energy of a reaction
17
Q
Ligases
A
Join two large biomolecules
eg. DNA Ligase joins Okazaki fragments
18
Q
Lyases
A
Cleave without water and without the transfer of e-
The reverse reaction (synthesis) is usu. more important
19
Q
Hydrolases
A
Cleave with water
20
Q
Transferases
A
Move functional groups
21
Q
Competitive Inhibitor
A
Binds to active site
No change Vmax, Increase Km
22
Q
Noncompetitive Inhibitor
A
Binds allosterically
Decrease Vmax, No change Km
23
Q
Uncompetitive Inhibitor
A
Binds to [E-S] Complex
Decreases Vmax, Decreases Km
24
Q
A high Km means
A
Low binding affinity
25
A high Ka means
High binding affinity (its an association constant)
26
triose
Three carbon sugar
27
aldose
sugar with an aldehyde
28
ketose
sugar with a ketone
29
D and L forms of the same sugar are called
enantiomers
30
Diastereomers
Differ at at least one, but not all, chiral centers
31
Chiral
4 different substituents attached to a carbon
CANNOT be where there is a double bond.
usually where there is an oxygen
32
Epimers
Differ at one chiral carbon
33
Anomers
Differ at one chiral carbon, the anomeric one
34
Anomeric Carbon
The carbon to the right on the oxygen
35
β-sugar
Where the anomeric carbon points up (cis as the CH2OH group)
36
α-sugar
Where the anomeric carbon points down (trans to the CH2OH group)
37
Mutarotation
Interconversion between alpha and beta anomers
| measured by a change in specific rotation
38
Monosaccharides can undergo 3 main reactions:
1) Oxidation/Reduction
2) Esterification (OH > O- > attack of acetic anhydride > H's replaced with acetals)
3) Glycoside Formation (glycosidic bond/ stabilized by oxocarbenium ion)
39
Deoxy sugar
When an OH group is replaced with an H (deoxyribose in DNA vs ribose in RNA)
40
Sucrose
glucose α 1,2 fructose
41
lactose
galactose β 1,4 glucose
42
maltose
glucose α 1,4 glucose
43
glycogen main chain
α 1,4 linkages
44
glycogen branching
α 1,6 linkages
45
stereoisomers
2^n chiral carbons
46
reducing sugar
Any monosaccharide with a hemiacetal ring
aka reducing agent (helps reduce something)
detected by Tollens and Benedict's reagents
47
hemiacetal/hemiketal
C bonded to OR, OH, H, R
| C bonded to OR, OR, H, R
48
Recombination
Crossing over during meiosis
49
Prophase
chromatin condenses into chromosomes
| centrosomes move to opposite poles of the cell
50
Metaphase
chromosomes line up on plate
51
Anaphase
chromosomes start to separate
52
Telophase
opposite of prophase
53
Metastasis
traveling cancer
54
mismatch repair
proofreading that happens in G2
| aka after replication
55
nucleotide excision repair
proofreading that fixes T=T binding within the same strand as a result of UV radiation
endonuclease used
56
base excision repair
proofreading that fixes an incorrect base (the backbone is correct)
57
recombination
When you take DNA and stick some other DNA inside and you get recombinant DNA
58
What happens in starvation?
First glycogenolysis
Then, 12 hrs later, gluconeogenesis. Depleting supplies of aa, ketones, oaa
59
How do proofreading enzymes distinguish between the correct and incorrect strand?
The correct, template strand has been in the nucleus for longer so it is more heavily methylated
60
miRNA
silence translation
61
postranslational modifications
1) folding assisted by chaperone proteins
2) quaternary structure
3) cleavage of proteins/signal sequences
4) addition of biomarkers (phosphorylation, glycosylation, carboxylation, prenylation)
62
posttranscriptional modification
1) intron/exon splicing
2) poly A tail
3) 5' guanine cap
63
regulation of gene expression at DNA level
promoter
64
convergent evolution example and structure
sharks and dolphins
| paired with analogous structures
65
homologous structures
similar structure, different function
indicate a common ancestor
// divergent evolution
eg. arms/flippers/wings
66
analogous structures
```
different structure
similar function
not common ancestors
//convergent evolution
eg. bird wing/fly wing
```
67
osmotic pressure
the pressure created by water moving across a membrane due to osmosis
water follows solute
```
pi = iMRT
i: vant hoff's factor (# of ions of solute that form when dissolved in water)
M: mol/L [conc]
R: ideal gas constant .08 Latm/molK
T: temp (K)
```
68
If you have 1/4 the osmotic pressure, you will have ___ [solute]
1/4
69
Helicase
catalyzes the separation of parent DNA strands at the origin of replication
70
ssDNA binding protein
stabilizes unwound template strand to keep it from coming back together
71
Primase
synthesizes RNA primer. RNA primer is spliced out and replaced with DNA by DNA Polymerase I
72
DNA Polymerase
III: synthesizes DNA 5' > 3' (reads 3>5)
I: replaces RNA primer with DNA
73
Leading and lagging strands
Leading strand requires one primer. lagging strand requires many and okazaki fragments are annealed together with ligase
74
Retrovirus aka HIV
Contains ssDNA and reverse transcriptase enzymes to make more DNA from host RNA
75
Viral DNA or RNA is contained in a
capsid
76
mRNA will have the same sequence as the DNA ____ strand (3 names)
Coding//sense//nontemplate
77
mRNA is coded from the template strand also known as the ___ or ___
noncoding strand/antisense strand
78
protease
cleaves by hydrolysis (usu. peptide bonds)
79
renin/angiotensin
vasoconstrictive system that raises blood pressure. inhibited by ACE inhibitors. (angtiotensin converting enzyme)
80
aldosterone
steroid hormone released from adrenal glands. increases sodium reabsorption in the distal tubules and water follows, raising BP
81
Calcium's role in muscle contraction
Ca++ binds to troponin (nail) and causes it to change it's conformation, denailing the tropomyosin from the actin, allowing myosin to crawl
contained in sarcoplasmic reticulum. acts in cytoplasm of muscle cell
82
tropomyosin
blocks the myosin from crawling along the actin. nailed in my troponin. moves out of the way when Ca++ binds troponin
83
troponin
nail tropomyosin into actin. released by ca++ binding
84
early stages of development from egg to ball of cells
oocyte, zygote(fertilized egg), embryo (zygote post mitotic cleavage), morula (ball of cells), blastula(hollow ball of cells)
85
ADH does what and is released when?
Stimulates movement of aquaporins in the collecting duct and distal convoluted tubule to increase water reabsorption. Decreases blood osmolarity and need to pee. Raises BP.
Released when blood is very salty, when blood volume is low, when BP is low, when RAAS system tells you that BP is low
86
histone acetylation
removes the positive charge on histones, weakening the interaction with negatively charged phosphate groups of DNA, increasing transcription
87
Why is DNA negatively charged
negatively charged phosphate groups on the 5' end
88
pentose phosphate pathway
anabolic pathway for generating NADPH and pentoses for nucleotides. Offshoots from glycolysis at G6P
89
Adrenal Medulla
Inner part of the adrenal glands. releases epinephrine and norepinephrine
90
Adrenal Cortex
Outer part of adrenal glands. releases gluco/mineralcorticoids
91
Anterior Pituitary releases which hormones
FSH, LH, ACTH, TSH, Prolactin, Endorphins, GH
92
Thyroid produces which 3 hormones
T3, T4, and calcitonin (decreases blood Ca2+)
93
Pancreas produces which 3 hormones
glucagon (@ low gluc)
insulin (@ high gluc)
somatostatin (inhibits gluc/insulin)
94
Key event of follicular phase
FSH causes growth of a follicle
95
Key event of ovulation
LH surge causes follicle to rupture and release egg
96
key event of luteal phase
corpus luteum forms
97
Restriction Enzyme
PALINDROMES
98
NADH/Ubiquinone Oxidoreductase, NADH-CoQ reductase, or NADH dehydrogenase
Complex I of ETC
99
Succinate Dehydrogenase
Complex II of ETC
100
Cytochrome C Reductase
Complex III of ETC
101
Cytochrome C Oxidase
Complex IV of ETC
102
In the ETC, protons are transfered from the ___ to the ___
mitochondrial matrix, intermembrane space
103
The proton-motive force is the electrochemical gradient generated by the electron transport chain across the inner mitochondrial membrane. The ___ has a higher conc. of protons than the ___. The energy of this gradient helps form ATP in a process called _____
intermembrane space, matrix, chemiosmotic coupling
104
Where is translated protein cleaved?
in the endomembrane system
105
y-linked gene
never occurs in females, will occur in all male decendants
106
x-linked gene
common in males
107
autosomal dominant
will never skip generations
108
autosomal recessive
all offspring of two affected parents will be affected
109
imprinted gene
epigenetic phenomenon that causes genes to be expressed in a parent specific manner
110
inflation of the lungs is accomplished by
negative pumping action. a negative pressure (less than atm) is created in the alveolar sacs when the diagragm contracts and pulls to expand the lungs
111
efferent
away (from CNS, from organs)
112
afferent
towards (CNS, organs)
113
cardiac output
stroke volume x heart rate
114
blood pressure can be measured by examining
cardiac output x resistance
// Ohms Law V=IR
115
Accumulation of DDT in the testes may cause reduced fertility in males because the uncoupling of oxidative metabolism from ATP production may reduce
sperm motility
116
nuclear envelope
lipid bilayer that contains the nucleus, nuclear cytosol, DNA
117
proteolysis
breakdown of proteins or peptides into amino acids by the action of enzymes.
118
Would an increase in the level of plasma aldosterone be expected to follow ingestion of excessive quantities of NaCl?
No; aldosterone causes Na+ reabsorption by kidney tubules.
119
How does aldosterone affect volume and osmolarity of blood?
Increases volume. Does not affect osmolarity.
It makes blood more salty, pulling Na+ out of nephron and back into blood, but water follows. so no net effect on blood concentration
120
How does ADH affect volume and osmolarity of blood?
ADH increases volume and decreases osmolarity of blood
121
neurulation
germ layers develop a nervous system
122
gastrulation
endoderm, ectoderm, and mesoderm form
123
bile is produced in the ____, stored in the ____, and acts on ____ in the ____
liver, gallbladder, fats(emulsifying them), small intenstine
124
Gene regulation in eukaryotes vs prokaryotes
In eukaryotes, 1 promoter (DNA) upregulates the transcription of 1 gene that ends up on 1 mRNA (monocistronic mRNA)
In prokaryotes, an operon (DNA) regulates the transcription of multiple genes that end up on 1 mRNA (polycistronic mRNA)
125
Prokaryotes
have cell walls
circular, uncondensed DNA in the cytosol
DNA transcribed and translated at the same time
no membrane bound organelles
operons though!
polycistronic mRNA (multiple genes on 1 mRNA)
126
calcitonin
increases blood calcium. activates osteoclasts
127
parathyroid hormone
decreases blood calcium. activates osteoblasts.
128
When do you use a radiolabel and when do you use an antibody?
radiolabel for nucleotides, antibodies for proteins
129
how does breathing affect blood pH?
increased respiration leads to the loss of CO2 which makes the blood more basic via Le Chatlier's principle and bicarbonate buffer system:
H+ (aq) + HCO3- (aq) ↔ H2CO3 (aq) ↔ H2O (l) + CO2 (g)
130
immunoglobulin
class of proteins present in the serum and cells of the immune system, which function as antibodies. Responsible for "humoral immunity" as opposed to cell based immune function. Also known as IgG
131
Where might you find histidine in a protein
at the active site. Due to its pKa of 6.5, it is close to physiological pH and can either be protonated or deprotonated easily. t4 it can play a role in stabilizing or destabilizing substrate
132
Which amino acids disrupt the alpha helix
proline (b/c bulky secondary amino group) and glycine (b/c flexible from two H's)
133
Zymogen (example?)
a proenzyme that is activated by irreversible cleavage
| eg. pepsinogen --> pepsin
