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Bio/Biochem 1-3 Flashcards

(113 cards)

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1
Q

pyrimidines vs purines bases and shape

A

pyrimidines=CUT (cytosine, uracil, thymine) single 6C ring, purines=Ag “pure silver” (adenine, guanine) double ring- 1 5C and 1 6C

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2
Q

nucleotide vs nucleoside

A

nucleoside=sugar+base, nucleotide=sugar+base+phosphates

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3
Q

prokaryotic DNA protection mechanisms (2)

A

methylation to protect from their own restriction enzymes and supercoiling via DNA gyrase to protect against physical damage

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4
Q

eukaryotic DNA protection mechanisms

A

nucleic acids wrapped around positively charged histones to form nucleosomes which then coils to form chromatin, and telomeres

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5
Q

euchromatin vs heterochromatin

A

euchromatin=lighter in color, looser, heterochromatin=darker in color, wound tighter

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6
Q

stop codons

A

UAA, UGA, UAG (u are annoying, u go away, u are gone)

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7
Q

missense vs nonsense

A

missense=changes codon to a different amino acid, nonsense=premature stop codon

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8
Q

Endogenous damage vs exogenous damage

A

Endogenous=caused by reactive oxygen species or physical damage, inter/intra strand covalent crosslinking between two of the same type (purine or pyrimidine) of bases. Leads to misshapen helix, which leads to polymerase errors, double/single strand breaks. Exogenous=via external radiation or chemicals, forms pyrimidine dimers, double strand breaks, translocation, physical damage, intercalation

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9
Q

Types of transposons- IS element, complex, composite

A

IS element: transposon only takes transposase with it but disrupts a gene. Complex transposon: takes genes with the transposase gene. Composite transposon: takes a central region between two transposase genes with it and inserts it into a new area

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10
Q

topoisomerase

A

cuts strands of DNA to relieve tension up/downstream caused by unwinding helix

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11
Q

prokaryotic DNA polymerase III

A

high processivity, fast polymerase and exonuclease activity for proofreading. adds nucleotides ~400 bp downstream of origin, so not the FIRST enzyme but more efficient

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12
Q

prokaryotic DNA polymerase I

A

low processivity. Slow polymerase and exonuclease to proofread and to remove primer. adds nucleotides starting from RNA primer. Involved in DNA excision repair

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13
Q

prokaryotic DNA polymerase II

A

backup for DNA polymerase III

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14
Q

prokaryotic DNA polymerase IV and V

A

Error prone polymerase because no exonuclease so no proofreading. Functions in DNA repair

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15
Q

telomerase

A

Extends telomeres due to shortening and failure to go all the way to the end in DNA replication. Comes with it own RNA template and has reverse transcriptase activity. Present in spermatogonia, stem cells, and cancer cells

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16
Q

rRNA

A

ribosomal RNA and makes up the ribosome, provides hte catalytic function of ribosome=ribozyme

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17
Q

mRNA

A

messenger RNA- coding RNA and carries genetic information to the ribosome

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18
Q

tRNA

A

carries amino acids from the cytoplasm to the ribosome to be added to a growing protein

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19
Q

hnRNA

A

precursor to mRNA that has not had G-cap, poly-A tail, or splicing of introns/exons

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20
Q

miRNA vs siRNA

A

microRNA and small interfering RNA. Function in post-transcriptional regulation of gene expression by binding to mRNA to increase or decrease translation

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21
Q

monocistronic vs polycistronic

A

Eukaryotes are monocistronic meaning, one gene=one protein, each piece of RNA only encodes one polypeptide. Prokaryotes and viruses are polycistronic, meaning multiple reading frames overlap

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22
Q

eukaryotic RNA polymerase I

A

transcribes most rRNA

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23
Q

eukaryotic RNA polymerase II

A

transcribes most hnRNA (so ultimately mRNA)

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24
Q

eukaryotic RNA polymerase III

A

transcribes tRNA

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25
eukaryotic vs prokaryotic ribosome components size
prokaryotic=50+30=70 s. eukaryotic=60+40=80s
26
lac operon
lactose binds to repressor and deactivates it so that it can't bind to the operator and repress. Instead, lactase can be transcribed/translated
27
amount of ATP needed to make a polypeptide
4 ATP per amino acid
28
lytic vs lysogenic cycle
lytic=bacteriophage inserts its DNA into the cell, degrades the hosts genome, create new genome copies from viral genome and assembles new viruses. Hosts cell wall then bursts and progeny viruses are released to infect other cells. Lysogenic=viral DNA inserts itself into hosts genome and remains dormant, replicating as part of normal DNA replication in the host cell. When its ready, that part of the sequence excises itself along with a "stolen" part of the host DNA. It then starts the lytic cycle
29
difference between animal and baterical viruses (phages)
animal cells have specific receptors on their cell surfaces for viruses to bind and be endocytosed, while phages have to puncture the cell wall of bacteria and inject their DNA- leaving the protein capsid on the outside. Also animal viruses don't destroy their host cells since they bud through the membrane instead of lysing it. Animal viruses make envelopes and bud through the membrane during the PRODUCTIVE CYCLE, while bacteriophages do not do this.
30
How do HIV and retroviruses work?
inject RNA into the cell and encode a reverse transcriptase that converts it back into DNA
31
prions
misfolded proteins that are very hard to destroy and that cause the destruction of neurons and degeneration of nervous system
32
hydrolase
early gene that is transcribed from the viral genome to destroy the host cell genome to conserve energy and to produce a pool of dNTPs to use for viral genome replication
33
lysozyme
late gene that is transcribed to punch holes in bacteria cell walls, causing the bacterial cell to burst and release all of the replicated viruses
34
Transduction
upon excision of viral genome from host genome, the virus accidentally "steals" part of the hosts genome, causing some host genes to transfer to other cells, including mutations
35
Endergonic/exergonic vs endothermic/exothermic
-gonic=delta G, spontaneous/nonspontaneous. -thermic=enthalpy (delta H), heat of formation
36
How are terpenes named?
prefix assigned for treating 2-isoprene units as 1. ie. 4 isoprene units=Diterpene
37
Which has more branches? glycogen or starch
glycogen
38
Why can't humans digest cellulose?
because it has large numbers of β(1,4) glycosidic linkages and we can't digest these β linkages
39
what is dietary fat (triglycerides/triacylglycerol) broken down into?
1 monoglyceride and 2 fatty acids
40
Feedback inhibition
the decrease in activity of an enzyme by binding to a downstream product
41
feedforward stimulation
stimulation of an enzyme by its substrate or by a molecule use in the synthesis of the substrate
42
ways to regulate enzyme activity
phosphorylate it to activate/deactivate enzyme, activated when cleaved by a protease, binding to other protein subunits causing catalysis or activation, feedback inhibition, or allosteric regulation
43
function of cholesterol
Cholesterol is an important component of plasma membranes, increasing fluidity of the membrane. It is also the precursor to steroid hormones and bile. Energy storage is NOT a function of cholesterol, rather it is a function of triglycerides.
44
positive cooperativity
binding of a substrate to one subunit's active site increases the affinity of other subunits for substrate, sigmoidal curve
45
when can wobble base pairing occur
G, U, I on the 5' end
46
these 3 common disaccharides are made up of... maltose=?, sucrose=?, lactose=?
maltose=glucose+glucose, sucrose=glucose+fructose, lactose= glucose+galactose
47
cysteine vs cystine
cysteine=individual amino acid, cystine=disulfide bonded cysteines
48
what acts as the final electron acceptor if O2 is unavailable?
pyruvate
49
amount of enzyme or substrate DOES/DOESN'T affect rate of reaction?
DOES
50
aldose vs ketose
The position of the carbonyl (C = O) group classifies the sugars into aldoses and ketoses. If the sugar has an aldehyde group, meaning that the carbonyl group (C=O) is at the end of the carbon chain, it is known as an aldose. If it has a ketone group, meaning that the carbonyl group is in the middle of the carbon chain, it is known as a ketose.
51
where do glycogenesis and glycogenolysis occur?
liver and skeletal muscle
52
where does gluconeogenesis occur?
liver, NOT skeletal muscle
53
what gluconeogenesis enzyme does skeletal muscle lack?
glucose-6-phosphatase, so charged/phosphorylated glucose cannot leave the cell
54
where does glycolysis occur?
in the cytoplasm of all cells of all organisms
55
what happens when diabetes is unregulated?
Too much glucose in the blood but not being taken up by the cells. Either no insulin to trigger it to take glucose into the cells or receptors are desensitized. Reduced glycolysis so other pathways are required to make acetyl CoA
56
Reducing end on glycogen
The end of the molecule containing a free carbon number one on glucose is called a reducing end. The other ends are all called non-reducing ends. Non-reducing residues within sugars are those that do not have an OH at the anomeric carbon (C1), or alternatively those that are linked to other monosaccharides or carbon groups
57
order of ribosome active sites in order of binding to releasing tRNAs
APE
58
direction of protein synthesis
N--\>C (N attacks the previous C)
59
open complex vs unpackaged DNA
open complex means DNA strands are separated, unpackaged means not wrapped around histones
60
repressable vs inducible enzymes
repressable means that transcription of the enzyme is negatively inhibited by the product (default ON) whereas transcription of inducible enzymes is stimulated by the presence of substrate (default OFF)
61
CAP protein's role in lac operon
CAP binds to cAMP, which binds to the promoter of the lac operon and recruits RNA polymerase to stimulate transcription when glucose levels are low. In the presence of glucose, cAMP levels are low so CAP doesn't bind to it
62
Lac operon repressor protein
in high lactose conditions, lactose binds to the repressor protein, causing a conformational change and making it fall off of the operator so that the DNA can be transcribed
63
when is the lac operon being transcribed the most
glucose absent, lactose present
64
Where is the START codon bound in a ribosome? Where is each new tRNA bound in a ribosome?
Start binds to P site. Each new tRNA binds to A site
65
peptidyl transferase
enzyme that catalyzes the formation of a peptide bond between the amino acids in the ribosome
66
Hydrolases
enzymes that hydrolyze chemical bonds (catalyze cleavage of bonds in the presence of water)
67
Lyases
enzymes that cleave bonds without the addition of water
68
Kinases
enzymes that transfer a phosphate group to a molecule from a high energy carrier like ATP
69
oxidoreductases
enzyme that catalyzes redox reactions
70
phosphatases
removes a phosphate group from a molecule
71
phosphorylases
transfers a phosphate group to a molecule from inorganic phosphate
72
transferases
enzymes involved in the transfer of a functional group from a donor molecule to an acceptor molecule
73
protease
enzyme that hydrolyzes/cleaves peptide bonds in the presence of water
74
vitamins serve what role in reactions?
cofactors
75
medulla oblongata
controls autonomic processes ie. blood pressure, blood flow, respiratory rate, heart rate, swallowing, vomitting. relays sensory info to the cerebellum and the thalamus.
76
pons
relay station to the cerebellum and thalamus and balance
77
cerebellum
movement coordination, balance, spatial equilibrium
78
midbrain
eye movement, visual and auditory reflexes, wakefulness and consciousness
79
thalamus
integrating center and relay station for conscious (somatic) sensation except olfactory input between spinal cord and cerebral cortex
80
hypothalamus
homeostasis and behavior, controls homeostatic functions via neural and hormonal regulation, controls pituitary gland, primitive emotions like anger, rage, and sex drive
81
basal nuclei (ganglia)
regulates body movement and muscle tone, subconscious coordination of rhythmic and learned movements like walking
82
limbic system
emotion, memory, and learning
83
cerebral cortex
4 lobes: frontal, parietal, temporal, and occipital. Perception, skeletal muscle movement, memory, attention, intellectual processes, thought, language, consciousness, personality
84
corpus callosum
connects left and right cerebral hemispheres
85
white matter
myelinated axons in CNS, called a tract in spinal cord, called a tract or column in PNS, called a nerve
86
grey matter
myelinated neuronal cell bodies deep in brain, called nucleus surface of brain, called cortex spinal cord, called horn in PNS, called ganglion
87
How is sympathetic nervous activated?
adrenal medulla releases epinephrine into the bloodstream
88
reciprocal inhibition
ie. quads contract, hamstrings relax
89
simple/monosynaptic vs complex reflex arc
monosynaptic: sensory neuron sends info to dorsal root ganglion and stimulates motor neurons which control muscle complex: sensory neuron sends info through dorsal root ganglion to inhibitory interneuron which then synapses with a motor nueorn which inhibits activity
90
temporal summation vs spatial summation
temporal=from 1 synapse where EPSPs or IPSPs pile up on top of one another during rapid action potential firing spatial summation=EPSPs and IPSPs are summed from all synapses
91
afferent vs efferent neurons
afferent: "**a**pproaching" CNS, "**a**ffective"=sensory neurons efferent: "exiting" CNS, efferents go to effectors (muscles and glands), motor neurons
92
acetylcholine (ACh)
neurotransmitter that is released at neuromuscular junction, binds to receptor which opens ligand gated sodium channels, causing depolarization. Acetylecholinesterase (AChE) degrades acetylcholine in synaptic cleft so that sodium channels don't always stay open
93
equilibrium potential for Na+ and K+
Na+ is around +50 mV, K+ is around -90mV
94
absolute vs relative refractory period
absolute=Na+ channels are inactivated and cell is too positive, impossible to fire another action potential relative refractory period= K+ channels are at equilibrium potential (-90mV) and cell is too negative, very difficult to fire a second action potential
95
How fast is a usual action potential?
2-3 msec
96
Progression of channels opening/closing during action potential
-70 mV (resting potential maintained via Na+/K+ ATPase pump) Na+ channels open and pull sodium in until threshold potential is reached (-50 mV) voltage gated Na+ channels open +35 mV is reached and voltage gated Na+ channels are inactivated. voltage gated K+ channels are now fully open and K+ flows back out of the axon, making the membrane potential more negative voltage gated K+ channels continue to allow K+ to flow out and hyperpolarize the axon until around -90 mV. Voltage gated calcium channels close at -90 mV Normal axon membrane function of Na+/K+ ATPase pump works to restore the potential to normal resting potential (-70 mV).
97
colored part of the eye
iris
98
biconvex structure that focuses light on the retina
lens
99
external transparent layer of the eye
cornea
100
black opening in the middle of the eye
pupil
101
muscles that regulate the curvature of the lens
ciliary muscles
102
responsible for extreme visual acuity in the retina, comprised entirely of cones, no rods here
fovea centralis
103
layer at the back of the eye sensitive to light
retina
104
blind spot, on retina where optic nerve forms
optic disk
105
optic nerve
106
rod cells
process light
107
cone cells
respond to high light intensity, concentrated on fovea centralis, red, green, and blue cones
108
white part of the eye
sclera
109
perception of light. which amino acid is released?
glutamate is released in the dark, less/none released in light
110
emmetropia
normal vision
111
myopia
near sightedness
112
hyperopia
far sightedness
113

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