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MCAT prep > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Differentiate between hydrolysis and dehydration.

A 
Hydrolysis = breaking macromolecules into their products USING WATER 
Dehydration = molecules into macromolecules RELEASING WATER
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2
Q

Describe the function of lipids.

A
  • energy storage
  • cellular organization and structure
  • precursor molecules for vitamins and hormones
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3
Q

What class of lipid has most energy storage than any other macromolecule? Why?

A

Fatty acids because they have long carbon chains

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4
Q

How much energy is produced from fatty acids when oxidized?

A

9 Kcals

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5
Q

What are triglycerides functions?

A
  • store energy (adipocytes)

- thermal insulation and padding

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6
Q

What are the simplest forms of phospholipids?

A

phosphatidic acids (phosphatids)

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7
Q

What are sphingolipids? Where are they found?

A

Instead of a glycerol backbone of a lipid, have an amino alcohol (sphingosine)
-found in membranes

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8
Q

What is cholesterols main functions?

A

membrane stability/fluidity and precursor to most steroid hormones

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9
Q

What are eicosanoids? Give example of one.

A

Released from cell membranes as local hormones for regulation of blood pressure, temperature and smooth muscle contraction
-ex = prostaglandins

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10
Q

In regards to lipoproteins, When will the lipoprotein be LESS DENSE? (i.e. a VLDL or LDL)

A

when there is MORE LIPID than there is PROTEIN

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11
Q

What is the generic molecular formula for carbohydrates?

A

Cn(H2O)n

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12
Q

Why are carbohydrates good for energy storage too?

A

They have carbon chains and are easily stackable

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13
Q

Glycogen is what type of carbohydrate?

A

Branched polymer with alpha-linkages

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14
Q

Which cells in the body absorb glucose AGAINST their concentration gradient?

A

epithelial cells in the digestive tract and the proxima tubule of the kidney

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15
Q

Differentiate between amylopectin and amylose (2 types of starch).

A 
amylose = branched or not with alpha-linkages
amylopectin =  always branched
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16
Q

How is cellulose different than glycogen?

A

Cellulose is only found in plants, and is used as more of a structural material rather than storage, due to their BETA-linkages

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17
Q

Nucleotides are composed of…?

A
  • a 5 carbon pentose sugar
  • nitrogenous base
  • phosphate group
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18
Q

What are the PURINES? Describe their structure.

A

Adenine and Guanine

-DOUBLE ringed structure

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19
Q

What are the PYRIMIDINES? Describe their structure.

A

Cytosine and Thymine

-SINGLE ringed structure

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20
Q

How many bonds are between Adenine and Thymine? Between Guanine and Cytosne?

A

2 between A and T

3 between G and C

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21
Q

In what direction does the DNA polymerase synthesize DNA?

A

5’ —> 3’

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22
Q

What is the phosphodiester bond?

A

bond between the phosphate group of one nucleotide and the 3rd Carbon of pentose sugar on next one.

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23
Q

How is RNA different from DNA?

A
  • 2nd Carbon on pentose is NOT deoxygenated
  • single stranded
  • contains pyrimidine uracil instead of thymine
  • moves through nuclear pores; not contained in nucleus
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24
Q

How does a peptide bond have double bond character?

A

The Nitrogen likes 4 bonds, and the Oxygen attracts electron density, which gives a partial negative and electrons then delocalize.

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25
Q

How is a peptide bond formed?

A

Via dehydration, creating an amide

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26
Q

Describe the secondary structure of proteins.

A

a single chain forms distinct shapes - alpha helix of beta sheets.
-responsible for overall conformation of protein

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27
Q

Describe the tertiary structure of proteins.

A
  • 3D structure of protein

- Disulphide bonds, ionic interactions, H-bonds and hydrophobic bonding

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28
Q

Describe the quaternary structure of proteins.

A

2+ polypeptides come together and bind

-same forces acting on that as are in tertiary structure.

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29
Q

How does hydrophobic bonding occur?

A

salvation layer pushing the non polar molecules to the middle.
-occurs because it allows a decrease in size of highly ordered solvate later, which increases entropy.

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30
Q

What are the 5 denaturing agents and what forces they disrupt?

A
  1. Urea – H bonds
  2. Salt or pH change – ionic bonds
  3. Mercaptoethanol – disulphide bonds
  4. organic solvents – hydrophobic forces
  5. Heat – all of the above
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31
Q

How is the Vmax of enzyme kinetics PROPORTIONAL to the concentration of enzyme?

A

because as you increase the concentration of substrate, that increases the rate of reaction, but until the enzyme is saturated.

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32
Q

What is the Kcat of enzyme kinetics?

A

The number of substrate molecules one active site can convert to product in a given unit of time when an enzyme is saturated.
Vmax/[E]t

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33
Q

What is the Michaelis constant (Km)?

A
  • the concentration of substrate at which the reaction rate is 1/2Vmax
  • Km is INVERSLY proportional to enzyme-substrate affinity.
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34
Q

Differentiate between co-substrates and prosthetic groups (types of co enzymes)

A

Co-substrates: reversibly bind to enzyme and transfer chemical group to another substrate
Prosthetic groups: covalently bond to enzyme in reaction

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35
Q

What are the 4 types of enzyme regulation?

A
  • Proteolytic cleavage (peptide bonds cleaved)
  • Reversible covalent modification (phosphorylation and de-phos)
  • Control proteins ( g-proteins or calmodulin)
  • Allosteric interactions
36
Q

How do competitive inhibitors affect Km or Vmax? Do they bind to active site or not?

A

Bind to active site

-INCREASE Km, Vmax unaffected

37
Q

How do noncompetitive inhibitors affect Km or Vmax? Do they bind to active site or not?

A

Not active site, bind to the complex or just enzyme

-DECREASE Vmax, Km unaffected

38
Q

How do uncompetitive inhibitors affect Km or Vmax? Do they bind to active site or not?

A

Not active site, bind to complex

-DECREASE Km and DECREASE Vmax

39
Q

How do mixed inhibitors affect Km or Vmax? Do they bind to active site or not?

A

Not active site, bind to the complex or just enzyme

-INCREASE or DECREASE Km, DECREASE Vmax

40
Q

Differentiate Lyases and Ligases -type enzymes.

A
  • Lyases (aka synthase): catalyze reactions where functional groups are added - does NOT need ATP
  • Ligases: catalyze condensation reactions coupled with hydrolysis of high energy molecules - DOES REQ. ATP.
41
Q

How do histones cause DNA not to be transcribed?

A

Give proteins a positive charge that attracts the net negative charge of the DNA

42
Q

What are the nucleosomes?

A

8 histones with DNA wrapped around them

43
Q

What is chromatin made up of?

A

The nucleosomes (of histones and DNA)

44
Q

Differentiate DNA methylation and histone acetylation.

A 
Methylation = DNA cannot be transcribed
Acetylation = DNA can be transcribed
45
Q

Describe the 3 stages in transcription.

A
  1. Initiation: Promoter tells where to transcribe, RNA polymerase starts
  2. Elongation: creates an antisense (-) template strand and a (+) coding strand
  3. Termination: rho proteins dissociate
46
Q

What are the 2 post-transcriptional modifications?

A
  • 5’ cap: protect against degradation and serves as attachment site in protein synthesis
  • Poly A tail: protect against degradation and aids in transport to cytoplasm
47
Q

What are the differences between splicing and alternative splicing?

A
  • Splicing: removes introns and keeps axons, uses small nuclear ribonucleoproteins (snRNP’s)
  • Alternative splicing: incorporate sequences into mature RNA
48
Q

The triplet code of the genome means…?

A

It is degenerative: more than one series of nucleotides may code for the same amino acid sequence
It is unambiguous: any single series of 3 nucleotides will code for one amino acid

49
Q

What are the stop codons? The start codons?

A

STOP: UAA, UGA, UAG
START: AUG

50
Q

What amino acid starts every protein for translation?

A

Methionine, (5’-CAU-3’)

51
Q

What enzyme is important in stringing all the amino acids together?

A

peptides transferase

52
Q

What are all the components in the replisome of DNA (origin of replication)?

A
  1. DNA helicase: unwinds DNA
  2. DNA polymerase: synthesizes new DNA strand
  3. Primase: creates primer to start replication
  4. DNA ligase: attaches fragments after replication
53
Q

What are the defining features of all the stages in mitosis?

A
  1. Prophase: sister chromatids joined together. Nucleolus disappears
  2. Metaphase: chromosomes align in middle
  3. Anaphase: sister chromatids split.
  4. Telophase: nuclear membrane and nucleolus form. Cytokinesis continues
54
Q

What is the difference between missense and nonsense mutation?

A

Missense: when a base substitution changes a codon. Can be neutral or have profound effects
Nonsense: Change in nucleotide sequence creates a stop codon.

55
Q

What makes meiosis 1 and its steps different from the meiosis 2 and mitosis?

A

In prophase 1, homologous chromosomes line up at the middle and exchange nucleotides (called genetic recombination)

56
Q

What is nondisjunction?

A

When in anaphase 1 or 2, the centromere of any chromosome does NOT split.

  • in 1, 1 cell has 2 extra chromatids
  • in 2, 1 cell has 1 extra chromatid
57
Q

In gametogenesis, in which stages are the sperm haploid and diploid?

A
  • Spermatagonium and primary spermatocytes are HAPLOID

- secondary spermatocytes and spermatids are DIPLOID

58
Q

In gametogenesis in females, where is the process first halted?

A 
The oogonium (haploid) goes through mitosis and produces primary oocytes (haploid). 
-It is halted in prophase 1 until menstruation starts
59
Q

In gametogenesis in females, where is the process halted for the second time?

A

After primary oocytes go through rest of meiosis 1, creates secondary oocytes that are halted in metaphase 2. Completes meiosis 2 when sperm fertilizes

60
Q

Glycolysis converts….? In the..?

A

Glucose into pyruvate. Glycolysis just happens in cytosol

61
Q

What is produced form glycolysis?

A
  • 2 3-Carbon pyruvate molecules
  • 2 ATP (4 in total)
  • 2 NADH
62
Q

Does glycolysis happen anaerobically or aerobically?

A

both!

63
Q

What is the main function of fermentation?

A

To regenerate NAD+ from NADH

64
Q

What is the function of the Pentose-phosphate pathway?

A
  • To generate NADPH, used for many metabolic or structural components.
  • To generate 5-Carbon sugars for DNA and RNA
65
Q

What is the function of chylomicrons?

A

Transport lipids from the intestines to the liver

66
Q

Differentiate between VLDLs and HDL’s?

A

VLDL’s transport lipids and cholesterol to other parts of the body from the liver.
HDL’s pick up fatty acids and bring them back to the liver.

67
Q

What does insulin promote in the body?

A
  • Glycolysis in all tissues
  • Glycogenesis in the liver and muscles
  • Fatty acid synthesis in liver
  • storage in the adipocytes
68
Q

What does the glucagon promote in the body?

A
  • Glycogenolysis in the liver and muscle
  • Gluconeogenesis in liver
  • Beta oxidation in all tissues
  • Fatty acid release from adipocytes
69
Q

What makes ATP an energy molecule?

A

The hydrolysis of the phosphoanhydride bond, as it is is spontaneous and exothermic

70
Q

What are the products of the citric aid cycle?

A

1 ATP
3 NADH
1 FADH2

71
Q

Describe the electron transport chain.

A
  • Complex 1 (ubiquinone). 4 protons across the membrane from NADH
  • Complex 2 (Q). No protons across membrane. FADH2 provides electrons
  • Complex 3 (cytochrome c). 4 protons across membrane from QH2
  • Complex 4. 2 protons across the membrane from cytochrome c, electrons then put onto O2
72
Q

Out of the whole aerobic respiration cycle, how many ATP’s are produced?

A

36

73
Q

1 NADH molecule produces how many ATP’s? How about FADH2?

A

1 NADH produces 2-3 ATP’s.

1 FADH2 produces 2 ATP.

74
Q

What does the extraction technique utilize to separate compounds?

A

Solubility

75
Q

In extraction, what is the main component to think about?

A

Weak acids/bases bind STRONG compounds, and Strong acids/bases will bind BOTH strong and weak compounds

76
Q

Is crystallization efficient to fully seperate compounds?

A

No

77
Q

The beads in column chromatography are…?

A

Polar! So non-polar molecules will elute first because they won’t stick around

78
Q

How is paper chromatography different than the other forms?

A

The non-polar phase is MOBILE (paper is put into non-polar solvent, which travels up paper so the non-polar molecules come with)

79
Q

What is the Rf value used in paper chromatography?

A

distance of compound / distance of solvent

80
Q

How does size-exclusion chromatography seem backwards?

A

Because LARGE molecules elute first, b/c they dont penetrate into the stationary phase like small molecules can

81
Q

In gel electrophoresis, what will the bands near the top represent, the bottom?

A

Near the top = larger masses of nucleic acids/ proteins

Near the bottom = smaller masses

82
Q

How are proteins separated based on their isoelectric points?

A

In a stable pH gel, poteins in the pH region BELOW their pI are (+) and will move toward the more (-) cathode. At their pI, the protein will stop

83
Q

A Northern blot visualizes…..?

A Souther blot visualizes…?

A 
Northern = RNA
Southern = DNA
84
Q

What is a defining feature of a restriction/recognition site? (For restriction enzymes to notice)

A

They are usually palindromic

85
Q

What is recombinant DNA?

A

When the SAME endonuclease cleaves 2 DNA fragments that can then by joined together

86
Q

What is the innovative thing about DNA polymerase?

A

The polymerase enzyme used is heat resistant!
-so can denature DNA, add primers and enzyme, and polymerase will bind to desired DNA strand to trasncribe
(will double DNA each cycle)

MCAT prep (4 decks)

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