Biology and Chemistry Interactions

This set of flashcards covers key concepts in biology, particularly the interaction of chemistry with biological molecules, the significance of ATP and NADH, oxygen metabolism, DNA structure and function, and gene regulation.

ATP

Universal energy currency of the cell that releases energy when hydrolyzed to ADP + Pi.

NADH

An electron carrier in metabolism that stores energy as high-energy electrons used to make ATP.

Oxidative phosphorylation

Process occurring in mitochondria where ATP synthesis is driven by proton gradients.

Chemiosmosis

The mechanism of ATP synthesis where protons flow back through ATP synthase, driving ADP + Pi to ATP.

Bohr Effect

Phenomenon where decreased pH (increased H⁺, CO₂) leads to reduced O₂ affinity of hemoglobin.

Myoglobin (Mb)

A molecule that stores oxygen in muscle tissues.

Hemoglobin (Hb)

A tetrameric protein that transports oxygen in the blood, from lungs → tissue

Sigmoidal O₂-binding curve

The characteristic curve of hemoglobin that reflects cooperativity in oxygen binding.

T state

The tense state of hemoglobin with low O₂ affinity, stabilized by ionic interactions.

R state

The relaxed state of hemoglobin with high O₂ affinity that forms upon oxygen binding.

Sickle cell anaemia

A genetic disorder caused by an amino acid substitution in hemoglobin leading to sickle-shaped red blood cells.

Quinine

A drug that accumulates in the malaria parasite vacuole, blocking hemozoin formation and killing the parasite.

Polynucleotide

A long chain of nucleotides forming DNA, consisting of a sugar, phosphate, and nitrogenous base.

Complementary base pairing

The pairing of A with T and G with C that ensures accurate DNA replication.

Supercoiling

The overwinding or underwinding of DNA that affects its transcription and replication.

Genome

The complete set of DNA within an organism, containing genes and regulatory sequences.

Operon

A cluster of genes transcribed together, allowing coordinated control of gene expression.

Negative control (lac operon)

Mechanism where the lac repressor binds the operator to block transcription.

Positive control (lac operon)

Mechanism where CRP–cAMP complex enhances RNA polymerase binding under low glucose conditions.

Glycolysis

Glucose to pyruvate

Glycolysis occurs

in systole

Anaerobic conditions for NADH

NADH → NAD⁺ via lactate dehydrogenase

Aerobic conditions of NADH

NADH oxidised in mitochondria

Anaerobic metabolism

• Pyruvate → lactate

• Regenerates NAD⁺

• No additional ATP beyond glycolysis

Aerobic metabolism

• Pyruvate → acetyl-CoA → TCA cycle

• produces NADH and FADH₂

• Feed into oxidative phosphorylation

ATP generation

• ETC creates a proton gradient

• ATP synthase uses electrochemical potential to make ATP
  NADH oxidation is key to energy yield

Mutation in sickle cell anamia

Glu → Val

What are the consequences of the mutation in sickle cell anaemia?

• Reduced oxygen delivery

• Causes cell rigidity and blockage of capillaries

Parasites convert heme into

hemozoin

DNA replication is

• semi-conservative

• driven by dNTP hydrolysis

• Requires template strand

Topoisomerases

• Changes DNA topology

• removes supercoils

Gel electrophoresis

separates topoisomers by shape and charge

Nucleosomes

• DNA wrapped around histones

• First level of DNA compaction

Transcription

• DNA to mRNA

• Catalysed by RNA polymerase

Translation

mRNA → protein

uses tRNAs and genetic code

Lac permease

transports lactose

β-galactosidase

cleaves lactose → glucose + galactose

What is the net yield of glycolysis?

2 ATP, 2 NADH, 2 pyruvate per glucose

Does glycolysis require oxygen?

No

Why is NADH re-oxidised to NAD⁺?

To allow glycolysis to continue

What role does NADH play in ATP synthesis

Donates electrons to the ETC

When does HbS polymerise most?

In the deoxygenated (T) state

How do chloroquine and quinine work

Inhibits hemozoin formation

Components of DNA?

Antiparallel, right handed double helix

Why are major and minor grooves important

protein recognition and binding

Why do grooves exist

• DNA bases attach to sugars asymmetrically

• When double helix forms, the backbones aren’t opposite each other

Major groove

• Wide and deep

• Exposes more chemical information from base pairs

Minor groove

• Narrow and shallow

• purpose is for structural interactions and non-specific binding

What is DNA melting?

Strand separation

What is annealing?

Re-association of complementary strands

What does semi-conservative replication mean?

Each daughter DNA contains one old strand

What drives DNA synthesis energetically

dNTP hydrolysis

What is a promoter consensus?

Idealised sequence recognised by RNA polymerase

What are the E. coli promoter consensuses?

-35: TTGACA, -10: TATAAT

mRNA’s role

template for protein synthesis

What sugar does the lac operon metabolise

lactose

what does lac permease do?

Imports lactose via proton symport

What is the lac repressor?

Protein that blocks transcription in absence of lactose

What is the inducer of the lac operon

Allolactose

Why is glucose preferred over lactose

more energy efficient