Frequent Mistakes Flashcards
At what C does galactose differ from glucose?
C4
At what C does mannose differ from glucose?
C2
How does fructose compare to glucose?
same as glucose but with a ketone group on C2
What is maltose?
2 glucose (alpha)
What is sucrose?
fructose + glucose (alpha)
What is lactose?
galactose + glucose (beta)
What kind of glycosidic linkages are not digesteable by humans?
Beta (opposite sides)
What is urea’s chemical structure?
H2N-C=O-NH2
What is a sphingolipid?
Sphingoside backbone + fatty acid chains + polar head group
What are the 4 types of sphingolipids?
- Ceramide
- Sphingomyelins = sphingophospholipids
- Glycosphingolipids
- Gangliosides
What are the 2 types of glycosphingolipids?
- Cerebrosides
2. Globosides
What is a sphingoside backbone?
Long C chain + HO-C-C-NH3-C-OH (with a double bond near the polar head group)
The NH3 is also bound to a O=C-R –> the fatty acid residue
What is a sphingomyelin? Does the head group have a net charge?
Sphingolipid with a phosphocholine group bound by a phosphodiester bond
Phosphocholine group = phosphatidylethanolamine or phosphatidylcholine
No net charge!
Is a glycosphingolipid a phosphosphingolipid?
No
Is a sphingomyelin a phosphosphingolipid?
Yes
What is a cerebroside? Does it have a net charge?
Glycosphingolipid with a single sugar as a head group
No net charge
What is a globoside? Does it have a net charge?
Glycosphingolipid 2 or more sugars as a head group
No net charge
What is a ganglioside? Does it have a net charge?
Sphingolipid with an oligosaccharide + 1 or more N-acetylneuraminic acid (NANA = sialic acid) as a head group
Yes, it is negatively charged
Is a ganglioside considered a glycosphingolipid?
Yes, because it has a glycosidic bond
What elements does a phospholipid contain?
Fatty acid tail + head: phosphate + alcohol
Linked by phosphodiester bonds
What is the difference between primary and secondary active transport?
Primary: requires ATP hydrolysis to move substances across their chemical gradients
Secondary: makes use of concentration gradients set up by primary active transport
What does a hydrolase enzyme do?
catalyze hydrolysis
What does a lyase enzyme do?
enzyme that catalyzes a catabolic reaction without water
What is facilitated diffusion? What molecules utilize this?
spontaneous passive transport → large, polar, and/or charged molecules through ion channels (proteins)
What is a nucleosidic bond?
bond between the nitrogenous base and the pentose sugar at the 1’ Carbon –> C-N bond forms
What bond forms in a peptide bond?
C-N
What is required for an amino acid to act as a buffer?
the pH needs to be near one of its pKas
What is the molecular weight of a peptide bond?
18
What kind of molecules will cluster around disulfide bonds?
HYDROPHOBIC molecules will cluster around disulfide bonds because they form the nucleus of the hydrophobic core of the folded protein.
Are allosteric interactions covalent?
No
Describe competitive inhibition
Km increases
Vmax stays the same
Lines intersect on the y-axis
Overcome by: increasing [S]
Describe noncompetitive inhibition
Km stays the same
Vmax decreases
Lines intersect on the x-axis
Overcome by: increasing [E]
Describe uncompetitive inhibition
Km decreases (due to better binding efficiency - prevent release of substrate = This makes it look like the substrate has greater affinity for the enzyme than it would otherwise, which lowers Km- as a result of Le Chatelier's principle and the effective elimination of the ES complex thus decreasing the Km which indicates a higher binding affinity). Vmax decreases (as a result of removing activated complex) Lines do not intersect, they are parallel
Described mixed inhibition
Km will increase or decrease (depending on binding affinity)
Vmax decreases
Lines will intersect at neither axis
Which is an organic molecule: coenzyme or cofactor?
Coenzyme
Can heat denature fatty acids?
NO
What 3 processes are endonucleases used for?
DNA repair, Southern blotting and gene therapy
What is proofreading? When does it happen? To whom? What is the key enzyme?
happens in the S phase for both prokaryotes and eukaryotes
fixes mismatched base pairs
key enzyme: DNA polymerase (distinguishes between strands thanks to methylation)
What is mismatch repair?When does it happen? What is the key enzyme?
happens in the G2 phase
fixes mismatched base pairs that were missed by the proofreading process
key genes: MSH2 and MLH1
What is nucleotide excision repair? When does it happen? What is the key enzyme?
happens in G1 and G2
repairs dimers
key enzyme: excision endonuclease
What is base excision repair? When does it happen? What is the key enzyme?
happens in G1 and G2
no double helix deformation (no base pair mismatch) but still not the base you want. ex: uracil inserted in DNA; take the one base out, then the whole thing and then reinsert the whole thing
key enzyme: glycosylase and AP endonuclease
What do primers do in PCR?
complementary to the DNA that attach at the 3’ end of each strand
What enzyme is involved in PCR?
DNA polymerase
What is Southern blotting?
: DNA is cut by restriction enzymes and then separated by gel electrophoresis → then DNA fragments are transferred to a membrane and probed with many copies of single stranded DNA sequences → probes are labeled and will indicate when they have bound to the complementary DNA strand
What happens during DNA sequencing?
uses ddNTPs → modified N+sugar nucleotides that contain a hydrogen at C-3’ rather than OH → once one of these bases is added, the polymerase can no longer add to the chain → sample will contain many fragments → separated by gel electrophoresis by size, so the sequence can then be read
Nucleotides vs nucleoside?
nucleoside = pentose + base nucleotide = nucleoside + phosphate group
3 Differences between prokaryotic and eukaryotic gene control?
Multiple transcription factors are necessary for eukaryotes
In eukaryotes RNA undergoes further modifications before translation
In eukaryotes, alternative splicing occurs so that multiple different proteins can be translated from the same primary message
1 similarity between prokaryotic and eukaryotic gene control?
both depend upon specific protein-DNA interactions
2 features of fatty acids found in eukaryotes?
EVEN number of Cs!
cis double bonds, never trans!
Effects of cholesterol on fluidity of plasma membrane?
At physio temperatures: increasing cholesterol content would decrease fluidity
At cold temperatures: increasing cholesterol would increase fluidity because it keeps the phospholipids from clumping together
From where does exhaled CO2 derive its O2?
from carbohydrates
What is the difference between synthase and synthesaze enzymes?
Synthase does not require outside energy
What does a dehydrogenase enzyme do?
transfers H- to an electron acceptor (NAD+, FAD, …etc.) → oxidizes its substrate
What does a reductase enzyme do?
reduces its substrate
What does a carboxylase enzyme do?
COOH is added to the molecule
What is the effect of uncouplers?
Uncouplers inhibit ATP synthesis without affecting the ETC, which means that the body will need to burn more fuel (like glycogen and use more O2) to maintain the H+ gradient!
Why is acetyl-CoA so energetic?
has very high energy thioester bonds.
Can acetyl-CoA be converted to glucose?
No!
Can fatty acids be converted to glucose?
Those with an odd number of Cs, yes!
What organ is most sensitive to O2 deprivation?
Brain
What kind of molecules are stored within the cell?
Polar
What is hyperplasia?
increased cell production in a normal tissue or organ.
What is an agonist?
binds to a receptor to increase what the receptor does; stimulate it
What does mitosis always produce?
Diploid cells
What is necessary for a gas to flow from one place to the other?
the partial pressure of the gas in the first place must be higher than that in the place it’s going to.
What is a test cross?
Always with a homozygous recessive genome
What does polymorphism mean?
phenotypic variations within the same species of the same population
What are the conditions for the Hardy Weinberg equilibrium? 5
- Large pop
- No mutations
- Random mating
- No migrations
- Equally successful genes
What did the Griffith experiment show?
bacteria can acquire new genetic material
What did the Avery-McLeod experiment show?
DNA is the genetic material (DNA degradation)
What did the Hershey Chase experiment show?
Confirmed DNA is the genetic material: radiolabeled DNA in infected bacteria
What is genetic leakage?
Flow of genes between species through hybrid offspring that are fertile
What is a monohybrid cross? What is the genotype ratio?
crossing 2 heterozygotes with complete dominance
1:2:1
What is hybrid breakdown?
2nd generation is inviable or sterile
What is gene flow?
gene flow (also known as gene migration) is the transfer of alleles or genes from one population to another
What is the basolateral membrane?
Faces toward the interstitium and away from lumen
What is the order from blood vessel to tissue?
Blood vessel Capillary endothelial cell Interstitium (with fluid) Basolateral membrane Epithelial cell Apical membrane Lumen
What is Mendel’s first law?
Segregation: alleles segregate during meiosis
What is Mendel’s second law? What is the problem with it?
Independent assortment
Problem: linked genes
Skeletal muscle: multi or uninucleated?
Multi
What are the differences between red and white muscle fibers?
Red: slow-twitch: carry out ETC
White: fast twitch: rely on anaerobic metabolism
Smooth muscle: multi or uninucleated?
Uni
Cardiac muscle: multi or uninucleated?
Uni (sometimes bi)
Describe muscle contraction? 12 steps
- Acetylcholine release at the neuromuscular junction
- Ach binds to sarcolemna = depolarization
- Depolarization spreads through T-tubules
- Ca2+ is released by the sarcoplasmic reticulum
- Ca2+ binds to troponin
- Shift in tropomyosin= exposure of myosin binding sites on actin
- Myosin binds to actin
- Myosin releases ADP + Pi = contraction
- Ach is degraded at synapse
- Ca2+ is resorbed by sarcolemna
- ATP binds to myosin= actin release
- ATP is hydrolyzed to ADP + Pi = recocking of myosin head
What is the relationship between the thymus and Ach?
Thymus has Ach receptors
What are the 5 cell types that do not undergo mitosis?
- Neurons
- Red and white blood cells
- All muscle cells (3 types)
Out of all of the endocrine system hormones, which ones are steroid hormones? 5
Glucocorticoids Aldosterone Estrogen Progesterone Testosterone
What happens in the proximal convoluted tubule of the nephron? 2
- Bulk resorption of glucose, aas, vitamins, salt, and water
- Absorption of HUNK: H+, urea, NH3, and K+
What happens in the descending limb of the loop of Henle of the nephron?
Water resorption
What happens in the ascending loop of Henle of the nephron? What about in the diluting segment?
Salt resorption
Loop is thicker in diluting segment (mito) and can give extra salt to blood: active transport
What happens in the distal convoluted tubule of the nephron? 2
- Salt resorption
2. Waste product (HUNK) absorption
What part of the nephron is responsive to aldosterone?
DCT and collecting duct
What part of the nephron is responsive to ADH?
Collecting duct
What happens in the collecting duct of the nephron? What does it control?
Water resoption; controls urine concentration
What is another name for coenzyme Q?
Ubiquinone
Which involves crossing over: meiosis or mitosis?
Meiosis
During which phase do the centrosomes migrate to the poles of the cell?
Prophase
During which phase do the chromatids or chromosomes migrate to the poles of the cell?
Anaphase
Where does prokaryotic transcription take place?
Cytoplasm
In what phase of the cell cycle does eukaryotic trasncription occur?
G1 and G2
What does RNA polymerase I synthesize in eukaryotes?
rRNA
What does RNA polymerase II synthesize in eukaryotes?
mRNA
What does RNA polymerase III synthesize in eukaryotes?
tRNA
What enzyme synthesizes RNA in prokaryotes?
RNA polymerase: only 1 for all types of RNA
What are the 2 actions to process hnRNA after transcription in prokaryotes?
- 5’ cap = methylguanosine
2. 3’ poly A tail
What is the H zone of the sarcomere?
Thick filaments ONLY
What is the A band of the sarcomere?
Thick filaments in their entirety
What is the M line in the sarcomere?
Cuts the thick filaments in half
What is the I band of the sarcomere?
Thin filaments ONLY
What is GABA? What is its other name?
Neuron inhibitor both pre and post synaptically
gamma-aminobutyric acid
What does a GABA deficiency usually cause?
Stress, panic, anxiety
What can cause a downregulation of GABA receptors?
Chronic alcohol consumption –> seizures and tremors once you stop drinking
What is the pathway of a newly synthesized protein?
rough ER → cis side of Golgi apparatus → trans side of Golgi apparatus
What is nondisjunction in meiosis?
incorrect segregation of homologous chromosomes or sister chromatids → one daughter cell ends up with 2 copies of related genetic material and the other receives zero.
What does angiogenesis mean? What is it necessary for?
formation of new blood vessels → necessary for most tumors to grow
What would be the effect if the cell was stuck in G1?
remaining in G1 would significantly affect membrane transport (surface area is too small compared to volume)
What are the spindle fibers made of? What is their role? When does this happen?
Spindle fibers are made of microtubules
They attach to the centromeres → kinetochores are the attachment points; this happens in prophase!!!
What is the role of centrioles?
they are the ones that create the spindle fibers and align at two poles of the cell
What is synapsis?
pairing of homologous chromosomes
What is the zona pellucida?
glycoproteins on ovum for sperm binding
What is the corona radiata?
layer of cells that adhered to the oocyte during ovulation
What is a Double crossover?
two recombination events → “middle” portion of each chromosome is exchanged, while the ends remain the same.
What is the one organ that is generated from 2 different germ layers?
Adrenal glands come from both the ectoderm (adrenal medulla) and the mesoderm (adrenal cortex)
What is necrosis?
process of cell death as a result of injury
Dilate bronchi and pupils: parasympa or sympa NS?
Sympa!
What is retrograde neurotransmission?
refers to the process by which a retrograde messenger, such as anandamide or nitric oxide, is released by a postsynaptic dendrite or cell body, and travels “backwards” across a chemical synapse to bind to the axon terminal of a presynaptic neuron.
What is the Downstroke of action potential?
Repolarization
Can the TLC of the lungs be measured?
No because of residual volume
How are the lungs of premature babies different?
They lack surfactant
What does a virus being dormant mean?
the virus’ inserts its genetic material into the host cells, but the genes aren’t expressed. BUT, an infection might be active without symptoms → the genes ARE being expressed, but maybe they code for non-harmful proteins, hence the lack of symptoms.
If plants are genetically modified, is this innate or active immunity?
innate
Where is bile produced, stored, and concentrated?
Bile is produced in the liver, stored and concentrated in the gallbladder, and released in the duodenum through the biliary tree upon stimulation by CCK
Where does protein digestion start? Where do carbs and fat digestions start?
Protein digestion starts in the stomach; carbohydrate and fat digestion starts in the mouth
What happens when the stomach secretes too much HCl?
the enzymes for absorption in the rest of the digestive tract will not work because the pH will be too low
Under normal conditions, the nephron creates urine that is hyper or hypo tonic to the blood?
Hyper
What are the 3 portal systems?
Kidneys (different types of transfer in each cap bed: filtration + reabsorption/secretion)
Hypophyseal (between hypothalamus and anterior pituitary)
Hepatic (between gut tube and liver)
What are the 5 layers of the epidermis from highest to lowest? (Come, Let’s Get Sun Bathed)
Stratum Corneum Stratum Lucidum Stratum Granulosum Stratum Spinosum Stratum Basale
Where are Ach receptors located in the muscle cell?
Sarcolemma
What is the difference between a frequency of summation and tetanus?
frequency of summation (describes muscle): neuron fires in succession, and muscle does not have time to relax fully
tetanus (describes muscle): max contraction of the muscle
What will be the effect of having an excess X chromosome?
Excess X chromosomes will have mild phenotypic consequences because of dosage compensation
What part of the muscle cell releases the Ca2+?
The sarcoplasmic reticulum
What will increase the force of a muscle contraction?
An increase in the number of cells contracting
What energy source does the muscle utilize when O2 runs out?
creatine
myoglobin
What is Endochondral ossification?
cartilage into bone → long bonds
What is Intramembranous ossification
mesenchyme into bone → this is how the skull is formed
What is the hallmark of a dominant trait?
2 parents with a trait have offspring without the trait
What is the hallmark of a recessive trait?
2 parents without a trait have offspring with the trait
What is an example of the founder effect?
sending a small population to Mars
What are 2 examples of genetic drift?
people with a certain type of alleles die, random mutations, etc.
What is directional evolution?
a drastic and extreme change in phenotype.
Which protein structure is the most important for enzymatic function? Why?
the tertiary structure
Most inactive enzymes have modifications of the active site, which is part of the tertiary structure
What is a lysosome? What process is it involved in?
membrane bound structures containing enzymes to break down substrates and waste products → involved in phagocytosis
The more nitrogen in a molecule, the more…?
Basic
Is tyrosine hydrophilic of phobic?
Phobic
Which is more conformationally demanding: alpha helix or beta sheet?
Alpha helix
What kind of secondary structure do amyloid plaques have?
Aggregates of beta sheets with hydrophobic residues
When the pH is below the pKa of an amino acid, is it deprotonated or protonated?
Protonated
Which 2 aas have a chiral center in their side chain?
Isoleucine and threonine
What is Km equal to?
k2 + k3/k1
What is the equation to calculate V from Vmax and Km?
V = Vmax . [S] / (Km + [S])
When does an enzyme need to be tightly bound to its substrate?
when it needs a more tightly controlled catalytic environment. If you have a substrate that can easily react with something you don’t want it to, it makes sense to bind it really tightly to hide it from the external environment → the enzyme as protecting it while it reacts.
How does the graph for V vs [S] look when the substrate induces cooperative binding?
the [S] vs V plot is sigmoidal (instead of hyperbolic) because after 1 molecule binds, the affinity increases and v increases (Km does NOT)
What are the reactants when beta amylase cleaves amylose?
Maltoses
What are the reactants when alpha amylase cleaves amylose?
maltose + glucose
What is a furanose?
carbohydrate with a 5-membered ring
What is a pyranose?
carbohydrate with a 6-membered ring
What is an aldose?
carbohydrate with only one aldehyde group
What vitamin is cholesterol a precursor to?
Vitamin D
What are glycerophospholipids made of?
polar head group (glycerol) and 2 fatty acids + phosphodiester bond to head group
Can tryacylglycerol H bond?
Nope
What are trans fats?
Unsaturated fatty acids
Usually, does adding double and triple bonds increase boiling point?
Yes
What increases the fluidity of the membrane: saturated or unsaturated fatty acids?
Unsaturated
What are the molecules least likely to contain aromatic rings?
Carbs
How is cDNA formed?
from processed mRNA by reverse transcription
When does cytosine become uracil?
In the presence of heat
What energy form is necessary for DNA replication?
ATP
What can a thymine dimer be caused by?
UV light
How do restriction enzymes work?
They cleave DNA at specific sites: they recognize and cleave palindromic regions of DNA → regions in which 2 complementary strands have the same sequence
What is the order to remember the 4 types of DNA repairs?
- Proofreading
- Mismatch
- Nucleotide excision
- Base excision
At which point in the cell cycle would a DNA double-strand break, if left unrepaired, affect both chromatids in a pair of sister chromatids?
G1, because it happens before the S phase, in which synthesis takes place.
What is the difference between B-DNA and Z-DNA (not biologically relevant)?
order of major and minor grooves and how spaced out they are
In PCR, when are low and high temperatures needed?
Low: enzyme activity High: DNA denaturation = separating the 2 strands
How many base pairs in the human genome?
3 million
What is the theoretical maximum recombination frequency?
50%!!
What is the start codon?
AUG
When determining the mRNA sequence, how should it match the DNA?
it should match antiparallel → 5’ → 3’ on the DNA will match the 3’ → 5’ on the mRNA
What would happen if antisense mRNA is present in the cytoplasm?
it will bind to the newly synthesized mRNA, form a double stranded RNA molecule → cannot be transcribed by ribosome
Where does a mutation need to be to modify the amount of protein produced?
The promoter site
Does mRNA happen prior or after the ribosomal units binding?
mRNA binding precedes the binding of the 2 ribosomal units!
What happens if there is deamination of DNA adenosine?
It incorrectly pairs with cytosine
What happens if thymine in DNA is in its enol form?
It incorrectly pairs with guanine
What does the RNA do to protect itself?
Single stranded nucleic acids are especially vulnerable to attack, so the RNA usually assumes a 3D conformation in a very tight hairpin loop or lariat where RNA binds to itself.
What does it say about the cellular environment if a cell lyses?
it was in a hypotonic environment
Which are the most rapid molecules in the cell membrane?
lipids moving within the plane of the membrane
What should the temperature be when 2 DNA strands have weak pairing?
Lower than normal because higher temperatures disrupts the H bonds
What is mesenchymal tissue?
Embryonic connective tissue
What do tendons connect?
Bones and muscles
What is chondrin? What cells secrete it?
The elastic matrix that makes up cartilage
Chondrocytes secrete it
What do ligaments connect?
Bones and bones
What does a flexor muscle do?
Decreases the angle across a joint
What does an extensor muscle do?
Increases the angle across a joint
What does an abductor muscle do?
Moves a part of the body away from the midline
What does an adductor muscle do?
Moves a part of the body toward the midline
In which parts of the body do medial and lateral rotation happen?
Limbs
Which one is easier to establish: paternity or maternity?
Paternity is easier to establish than maternity because to establish maternity either the child’s alleles must be compared to both mother and father, or mitochondrial DNA must be used
What is pinocytosis?
Mode of endocytosis in which the cell inputs large amounts of water
Does the mitochondria use more maternal or paternal DNA?
more maternal DNA than paternal DNA, but still uses both
What are the 3 factors affecting membrane fluidity? Explain
- Temperature: low decreases it, high increases it
- Cholesterol: at low temps in increases it, at high it decreases it
- Fatty acids: saturated decreases it, unsaturated increases it
Where are sphingomyelins found?
In myelin producing cells and myelin: Schwann cells (PNS) and oligodendrocytes (CNS)
What is a ceramide?
Sphingosine backbone bound to a fatty acid residue that has an amide
Is tryacylglycerol hydrolizable?
Yes
What is a phosphodiester bond?
P bonded to:
2 OR
=O
OH
What is the lipid bilayer like?
It has phospholipids with head groups pointing on the inside and outside of the cell and the hydrophobic tails connecting in the middle of the membrane
Are sphingolipids hydrolizable?
Yes
What is the structure of a wax?
Ester with two very long R groups on each side
What kind of biomolecules are prostaglandins? What is their role?
Lipids
Autocrine and paracrine hormones that regulate cAMP levels
What is the structure of steroids like?
3 cyclohexane rings + 1 cyclopentane ring
What is the role of terpenes?
Signaling molecules
In the nephron, where is Na+ resorption active?
Thick segment of ascending limb of the loop of Henle
What is the difference in sugars in DNA and RNA?
DNA contains the sugar deoxyribose, while RNA contains the sugar ribose. The only difference between ribose and deoxyribose is that ribose has one more -OH group than deoxyribose, which has an H attached to the second (2’) carbon in the ring.
Is cellulose digestible by humans? Why?
No because of beta linkage
What are amylose annd amylopectin?
Starches to store carbs
What does amylopectin’s structure resemble?
Glycogen
What is the role of the epithelial cells in the lungs?
They are responsible for the cough reflex, and are not responsible for alveolar gas exchange
In what embryogenesis stage are the 3 germ layers formed?
Gastrulation
How to pick the best PCR primer?
Should have the most C and G to be more tightly bound
Does Km depend on substrate concentration?
No
Does transport capacity depend on substrate concentration?
Yes
What does Km represent?
Substrate concentration at which the reaction rate is 1/2 of Vmax
What kind of amino acids are used during ribosomal protein synthesis?
L-isomers!!
How do bacteria adapt to a new environment?
Regulation and control of gene expression
Which is expressible: euro or heterochromatin???
Eurochromatin!
How will have fewer pigments of a certain color affect the signals sent to the brain regarding that color?
Fewer signals will be sent
How to go from Fischer to Haworth?
- Find carbon #5 –> the O on it, will be part of the ring
- C5 will be on the left of it in the ring
- Everything on the right hand side in the Fisher projection will go down on the Haworth
- CH2OH is always UP on C5
- The OH on C1 will either go up or down: racemic mixture
What is the difference between alpha and beta D glucose?
Alpha: OH points down on C1
Beta: OH points up on C1
What is the difference between D and L glucose?
Different stereochemistry at all Cs
Which 5 amino acids are charged at physiological pH?
Negative: glutamic acid and aspartic acid
Positive: histidine, arginine, and lysine