Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What are exergonic reactions

A

Reactions in which total free energy of the product is less than total free energy of reactant, Delta G is -ve

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are endergonic reactions

A

Reactions in which total free energy of products is more than the reactants, Delta G is + ve

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What do Delta G values towards zero signify?

A

These are characteristic of readily reversible reactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How do we determine Delta G for a reaction?

A

Delta G = - R T ln K (eq) kJ/mol
R = Universal gas constant
T = Absolute temperature (Kelvin)
K (eq) = Product/Substrate concentration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How does the body compensate for the many unfavourable reactions necessary for life

A

By coupling an exergonic reaction (favourable) with an endergonic reaction (unfavourable)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are amphipathic molecules?

A

Molecules that are hydrophobic and hydrophilic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Differentiate acids and bases based on proton donation

A

Acids donate protons, bases accept protons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Most abundant protein in vertebrates

A

Collagen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Deficiency of what vitamin can cause weak collagen

A

Ascorbic Acid - Vitamin C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Types of tertiary structure

A

Fibrous protein - Collagen, Kerain

Globular protein - Myoglobin, Haemoglobin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are salt bridges in proteins

A

Electrostatic interaction between unlike charges

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What catalyzes DNA replication

A

DNA dependant - DNA polymerase, requires RNA primers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Limitation of DNA polymerase

A

Can only add to 3’ end, called leading strand. Other strand is replicated in short fragments called Okazaki fragments.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Central dogma?

A

DNA - Transcription - mRNA - Translation - Protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Nucleoside vs nucleotide

A 
Nucleoside = Base + Sugar
Nucleotide = Nucleoside + Phosphate group
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is DNA polymerisation

A

Formation of a phosphodiester bond between the 3’ OH group and 5’ Triphosphate group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Name a HIV drug that is a nucleotide analogues

A

Zidovudine or Azidothymidine. Lack a 3’ OH group and hence terminate chain elongation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What direction is DNA polymerase exonuclease activity?

A

3’ to 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are the stable RNAs

A

tRNA, mRNA and rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Types of RNA Polymerase

A

Pol I, Pol II and Pol III. Pol II synthesizes all mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Transcription steps

A

RNA polymerase detects initiation sites and binds to to these. Requires transcription factors
DNA chain separation
Initiation - Selection of first nucleotide
Elongation - Addition of further nucleotide
Termination - Release of finished RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is the TATA box

A

Sequence of TATAT around 25 nucleotides before transcriptional start. RNA Pol II specific promoter. This is recognised by TATA box Binding Protein (TBP), part of TFIID - General transcription factor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is the direction of newly synthesized RNA strand

A

5’ to 3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What are transcription factors

A

DNA binding proteins that regulate transcription positively or negatively

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What happens when a ligand (steroid) binds to steroid receptors

A

Steroid receptors consists of three domains: transactivation domain, DNA-binding domain, ligand-binding domain. Steroid binds to the ligand-binding domain. This causes it to move into the nucleus and bind to DNA at steroid-response element (SRE)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is splicing

A

Removal of non-coding regions (introns) from coding regions (exons)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

How is mRNA processed

A

GTP cap is added to 5’ end

Poly A-tail is added to 3’ end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Properties of genetic code

A 
64 possible combinations
20 amino acids
AUG - Start
UAA, UAG, UGA - Stop
Unambiguous, degenerate, universal
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Function of Aminoacyl-tRNA Synthetases

A

Aminoacyl-tRNA Synthetase bind amino acids to their corresponding tRNA molecule. ATP for energy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Ribosomal subunits in eukaryotes

A

60s - Large

40s - Small

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Initiation of translation

A

GTP hydrolysed to provide energy
40s subunit moves from 5’ end of mRNA to find AUG. UAC tRNA brings Methionine. 60s subunit joins assembly and initiator tRNA is located at P site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Elongation of translation

A

Elongation factor - 1 alpha (EF-1alpha) brings the next aminoacyl-tRNA to Aminoacyl site
Anticodon base pairs with codon
GTP hydrolysed, elongation factor released
Elongation factor - Beta Gamma regenerates EF-1 Alpha to pick up next tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What catalyzes peptide bond formation in translation

A

Peptidyl transferase catalyses peptide bond formation between Peptidyl and Aminoacyl site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Termination of translation

A

Release factor (RF) binds stop codon
GTP hydrolysed
rRNA, mRNA and tRNA dissociate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is a polysome

A

A cluster of ribosomes held together by a strand of mRNA which each is translating

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Common post translation modifications

A

Proteolysis - Cleaving polypeptide allows fragments to fold into different shapes
Glycosylation - Adding sugars
Phosphorylation - Added phosphate group alter shape of protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Cofactors vs Coenzymes

A

Cofactors - Metal ions

Coenzymes - Organic molecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What are metalloproteins

A

Metal cofactors form a metal coordinating centre in the enzyme. This is called metalloprotein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What are prosthetic groups

A

Tightly bound coenzymes such as Haem group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Apoenzyme vs Holoenzyme

A

Apoenzyme is an inactive enzyme

Holoenzyme = Apoenzyme + Cofactor, catalytically active

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Common coenzyme for redox reactions

A

Nicotinamide adenine dinucleotide, NAD+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

What are Isozymes

A

Isozymes are isoforms of enzymes, they catalyse the same reaction but have different properties and structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Example of Isozyme

A

Lactate dehydrogenase, 2 subtypes -
Heart - Promotes aerobic metabolism
Muscle - Promotes anaerobic metabolism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What is a kinase enzyme

A

Kinase is an enzyme that adds a Phosphate group - Phosphorylation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What is a Phosphatase

A

Phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester

46
Q

What are Zymogens

A

Inactive precursors of enzymes. Transformed into active enzymes by cleavage of covalent bond. Ex: Trypsinogen and Chymotrypsinogen

47
Q

What is Vmax and Km in enzymatic behaviour

A

Vmax is the maximum rate an enzyme can operate at

Km is the concentration of solutes at which half Vmax is obtained

48
Q

What does a low Km signify?

A

An enzyme with a low Km requires little substrate to work at half maximum velocity

49
Q

Glucokinase vs Hexokinase

A

Glucokinase Km = 5 mM Glucose. Hence it’s involved in homeostasis as it can sense high concentrations of glucose. Maturity Onset Diabetes is caused by the lack of Glucokinase activity. Hexokinase in RBC has a Km = 0.05mM Glucose. Useful in energy production during low Glucose levels.

50
Q

What is Prolyl Hydroxylase

A

Uses Oxygen as a substrate to regulate Hypoxia Inducible Factor. Has a high Km for Oxygen; this keep is sensitive to fluctuations. Absence leads to expression of genes for surviving Hypoxia - RBC synthesis, angiogenesis and anaerobic survival pathways

51
Q

Orthosteric vs Allosteric inhibition

A

Orthosteric - Inhibitor binds to active site

Allosteric - Inhibitor binds to site other than catalytic centre

52
Q

Competitive vs noncompetitive inhibitor graphs

A

Km changes in competitive inhibition; using Ethanol to treat Methanol poisoning
No change in Km in non-competitive inhibition

53
Q

What are allosteric enzymes

A

Allosteric enzymes don’t follow Michaelis-Menten kinetics. Increasing substrate concentration results in sigmoidal curve. Ex: Haemoglobin

54
Q

What involves exercise, Anabolism or Catabolism

A

Anabolism

55
Q

Process from oxidised precursor to reduced biosynthetic products

A

Anabolism

56
Q

Process from reduced fuel to oxidised product

A

Catabolism

57
Q

Fate of glucose in the body

A

Can be stored as glycogen, starch and sucrose
Aerobic glycolysis to Pyruvate
Anaerobic glycolysis to Lactate
Oxidation through the pentose phosphate pathway - Ribose-5-phosphate (precursor for nucleotide synthesis and DNA repair)

58
Q

How is glucose transported into cells

A

Via Na+/Glucose symporters

Passive facilitated diffusion glucose transporters

59
Q

How many ATP generated at the end of Glycolysis

A

2 net ATP, 2 used in the process, 4 produced

60
Q

Control points in Glycolysis

A

Hexokinase, Phosphofructokinse and Pyruvate kinase

61
Q

Key enzyme controlling rate of substrate movement along glycolytic pathway

A

Phosphofructokinase

62
Q

What inhibits phosphofructokinase

A

ATP - Energy abundance slows glycolysis
Citrate - TCA intermediate, slows downstream pyruvate entry to TCA cycle
H+ - Slows glycolysis if too much lactic acid produced

63
Q

What activates phosphofructokinase

A

AMP - Energy is needed

64
Q

What is energy charge

A

Ratio of ATP/AMP is energy charge. This controls phosphofructokinase

65
Q

What happens to the products of glycolysis

A

4ATP - Energy, 2 pyruvate as substrate for TCA cycle, 2 NADH+ for the electron transport chain and ATP synthesis

66
Q

What happens if mitochondrial metabolism is inhibited by lack of oxygen

A

NADH is used to ferment pyruvate to lactic acid

67
Q

Why do cancer patients lose weight

A

Due to the Warburg effect, upregulation of anaerobic glycolysis in cancer cells. High glucose demand

68
Q

Anaerobic respiration

A

Pruvate to Lactate

69
Q

Where does the TCA cycle occur in the Mitochondria

A

Inner membrane and matrix

70
Q

How does Pyruvate, ADP and P get into the matrix

A

pH gradient drive Pyruvate and phosphate (P) import

Voltage gradient drives ADP-ATP exchange

71
Q

What catalyzes pyruvate to acetyl-CoA

A

Pyruvate dehydrogenase complex (PDC)

72
Q

Yields in oxidative decarboxylation of pyruvate

A

CO2, NADH + H+ and Acetyl-CoA

73
Q

Only enzyme of TCA cycle not in mitochondrial matrix

A

Succinate dehydrogenase, located in inner mitochondrial membrane which oversees Succinate + FAD = Fumarate + FADH2

74
Q

Each turn of TCA cycle involves

A

3 NADH, 3 H+, GTP, FADH2, CO2

75
Q

What can inhibit TCA cycle

A

High levels of ATP, NADH, acetyl-CoA

76
Q

What can stimulate TCA cycle

A

High levels of ADP, NAD+

77
Q

New yield of glucose to acetyl-CoA to TCA cycle

A

6-2 = 4 ATP, 10 NADH, 10 H+, 2 FADH2, 6 CO2

78
Q

Can males have Pyruvate dehydrogenase complex deficiency

A

No as it’s present on the X chromosome. XY leads to still born whereas XX is survivable. Females be mosaic

79
Q

Why does pyruvate dehydrogenase complex deficiency lead to persistent lactic acidosis

A

As Pyruate can’t be oxidatively decarboxylated to Acetyl-CoA to enter the TCA cycle. Pyruvate is instead fermented to lactate

80
Q

What is hereditary leiomyomatosis and renal cell cancer

A

Defect in fumarate hydratase. Fumarate can’t be converted to Malate, causing a buildup of Fumarate in the mitochondria. Leads to tumours which can metastasize to kidney

81
Q

Essence of oxidative phosphorylation

A

Electrons from NADH and FADH2 are used to reduce O2 to H2O. This energy is used to pump H+ from membrane to the intermembrane space. Protons flow back across the membrane, following their concentration gradient. Energy of proton flow is used to phosphorylate ADP to ATP

82
Q

How does NADH form cytoplasm get in

A

Via Glycerol-3-Phosphate and Malate-Aspartate shuttle
Oxaloacetate is converted to Malate using NADH + H+. This is transferred to the mitochondrial matrix via Malate transporters. Malate enters TCA cycle to be converted to Oxaloacetate and release of NADH + H+

83
Q

Transfer potentials in oxidative phosphorylation

A

Electron transfer potential of NADH+ and FADH2 is converted to phosphoryl transfer potential of ATP

84
Q

What does a negative redox potential mean

A

Tend to donate electrons, strong reducers; NAD+

85
Q

What does a positive redox potential mean

A

Tend to gain electrons, strong oxidisers; O2

86
Q

What is the chemiosmotic hypothesis

A

Action of ATP synthase is coupled with that of a proton gradient. It is the action of proton gradient that causes a proton motive force that allows ADP + Pi = ATP

87
Q

Where do electrons from NADh and FADH2 enter the electron transport chain

A

Complex 1 and 2 (2 is succinate dehydrogenase part of TCA cycle), all located on inner mitochondrial membrane

88
Q

What are cytochromes

A

Proteins that contain a haem group as a functional co-factor. The Fe(II) can take up and release electrons

89
Q

What pump is used to synthesize ATP

A

ATP synthase, Mitochondrial ATPase, F1F0ATPase

90
Q

What can inhibit oxidative phosphorylation

A

Cyanide (CN-), Azide (N3-) and Carbon Monoxide can inhibit transfer of electron from complex IV to O2

91
Q

What does brown adipose tissue contain

A

Uncoupling protein (UCP) = Thermogenin, generates heat by short-circuiting mitochondrial battery

92
Q

How does non-shivering thermogenesis work

A

Protons that are pumped out into the intermembrane space flow back across the concentration gradient via Uncoupling Protein (UCP) instead of ATP synthase. This leads to generation of heat. Free fatty acids required

93
Q

What can proton leak (non-shivering thermogenesis) be used for

A

Anti-obesity therapy, 2,4 - Dinitrophenol (DNP) can be used to create artifical proton leak, metabolic rate up

94
Q

How does ecstasy (MDMA)cause death

A

Ecstasy targets UCP-3, involved in skeletal muscle thermogenesis. MDMA causes death by hyperthermia and rhabdomyolysis

95
Q

1 glucose molecule yields how many ATP

A

30 - 32 ATP molecules

96
Q

Normal presentation of diabeties

A

Breath smells funny, deep breathing and urine positive for glucose/ketones

97
Q

Osmotic symptoms

A

Increased glucose in blood (hyperglycaemia), stimulates the thirst centre in the brain. This causes polyuria and nocturia.

98
Q

Typical signs of undiagnosed diabetes in young

A

Dehydrated, polyuria, nocturia, vomiting, muscle waste

99
Q

What can cause insulin resistance

A

Obesity as person have excessive fat stores, it wouldn’t make sense for body to response to Insulin, whose function is to make more energy stores.

100
Q

What makes diabetic person nausea

A

Body used triglycerides as a source of fuel as glucose can’t be absorbed into cells. This is broken down into glycerol, fatty acids and ketones. Ketones are strongly acidic, dissociate and release protons

101
Q

What causes Kussmauls breathing

A

Increase H+ ions, due to ketoacidosis drives reaction of
H + HCO3 - H2CO3 - CO2 + H2O to the right
However, CO2 is constantly blown off as a deep sighted respiration (Kussmauls breathing)

102
Q

Can raised creatine kinase be physiological

A

Never, signifies damage to muscle tissue

103
Q

Function of cholesterol in plasma membrane

A

Provide structure and fluidity

104
Q

How are lipids transported

A

Via lipoproteins

105
Q

Which is the densest lipoprotein

A

High density lipoprotein - Least triglyceride content

106
Q

Earliest visible lesions in atherosclerosis

A

Fatty streaks, consists of foam cells

107
Q

Ideal total cholesterol levels

A

< 5 mmol/L

108
Q

Normal total HDL cholesterol levels

A

0.9 - 1.6 mmol/L

109
Q

What leads to lipoproteins eventually attracting macrophages

A

Cholesterol from liver is transported on VLDL. Triglycerides are slowly stripped away leading to formation of IDL and LDL. If not enough LDL is cleared, this accumulates and gets oxidised. This triggers macrophages to mediate inflammation and swallow LDL becoming foam cells. This inflammation inhibits reverse cholesterol transport, starting a vicious feedforward

110
Q

Mode of action of statins

A

Express more LDL receptors to increase reverse cholesterol transport and decrease cholesterol synthesis from acetate. Also less inflammation

Principles (14 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions