Biology of the Cell (2025) - First Lecture Summary
Table of Contents
- Table of Contents
- Course Introduction
- Fundamental Concepts in Cell Biology
- Chemistry of DNA and RNA
- Polynucleotide Formation
- Double-Stranded DNA Structure
- The Central Dogma of Biology
- History of Cell Discovery
Course Introduction
This is the first and only biological course for first-year medical students at Bar-Ilan University. The lecturer opened by acknowledging the diverse backgrounds of students, some with prior biology education from high school and others without, which is why the course starts with very basic concepts.
Administrative Information
- Teaching Staff: The semester is divided between three lecturers:
- The current lecturer
- Dr. Shai
- Dr. Michael Blank
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Attendance: Checked during the first 15 minutes of each class.
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Communication: “Our emails are in the syllabus and on the faculty website… you can contact us, as I wrote in the introduction on the website. We will be in touch with class representatives, so it’s preferable to direct general questions through them.”
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Recordings: “There is a Zoom recording happening right now.”
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Supplementary Sessions: “We did them last year; if needed this year - we’ll do it.”
- Examinations:
- A mid-term exam will take place immediately after Passover, “it’s literally the first day back to studies… the material covers only the first three weeks.”
- Exam purpose: “This exam is seriously for your benefit, it’s to get you up to speed.”
- Exam format: “All your exams until the clinical stage will be multiple-choice like this.”
- Safety net grade: “The safety net grade means it can’t harm you. You can even completely ignore this exam, but I strongly advise against it.”
Course Textbook
The lecturer emphasized the importance of the course textbook:
“The course textbook isn’t just for this course; it’s also for the molecular biology course… There are copies in the library from both the sixth and seventh editions, but most importantly, there’s a PDF version. The green cover is what’s in the library; the purple cover is the PDF that’s circulating online.”
Regarding using the book: “We’re not allowed to distribute the most advanced version to you, but from the publisher’s perspective, they would like all of you to rush out and buy such a book and have it at home… When I was a first-year biology student, I bought the old edition of this. It’s fun to flip through it.”
The lecturer clarified: “What’s on the exam won’t be things that appear only in the book and weren’t mentioned… I strongly recommend looking at the book as well.”
Course Structure
The lecturer explained the course structure: “I’ve arranged the PowerPoints by lectures – Lecture 1, Lecture 2. I don’t know if it exactly corresponds to the classes… but I do expect you to go over the summary a bit before coming to the next class.”
He continued: “What we’re dealing with here, although it’s a cell biology course, is largely an introduction to biology. You have five courses that are direct continuations of this next year.”
Regarding the course level: “Last year, organic chemistry came before this and provided some foundation. We no longer have that, so we’re starting from very basic concepts.”
Fundamental Concepts in Cell Biology
Importance of the Cell
The lecturer opened with a quote from E.B. Wilson: “The key to every biological problem must ultimately be sought in the cell.” He explained that this is “an appropriate motto for our book.”
The lecturer referred to a historical image of cell division from 1900, where one can see “cell division… chromosomes… cell nucleus… and what I work on in my research…”
Chemistry of DNA and RNA
Nucleotide Structure
The lecturer began explaining the chemical structure of nucleotides: “In this initial image, I don’t understand what’s happening here… it looks like Lego blocks.” He explained that this was a simplified representation and moved on to a more detailed explanation.
A nucleotide consists of three main components:
- Phosphate group:
- Contains negative charges
- Can have one, two, or three phosphate groups
O ‖ O=P-O- ‖ O - Sugar (Pentose):
- Composed of five carbon atoms
- Forms a ring structure with oxygen
5'CH₂ | 4'C—O | \ 3'C 1'C | | 2'C—C - Nitrogenous Base:
- Contains ring structures with double bonds and nitrogen molecules
- Forms chemical bonds crucial for all biological functions
Nitrogenous Bases
The lecturer explained: “Five nitrogenous bases that are the building blocks of DNA and RNA… In DNA, there’s thymine… In RNA, there’s uracil… which replaces thymine.”
The five nitrogenous bases are:
- Adenine (A) - Purine
N—C—N ‖ ‖ C C—N | | N═C—N - Guanine (G) - Purine
O ‖ C—N ‖ \ N—C N | ‖ C═N—C | NH₂ - Cytosine (C) - Pyrimidine
NH₂ | N═C | \ O═C N | H - Thymine (T) - Pyrimidine (in DNA)
CH₃ | C═C | \ O═C N \ | N—H | O - Uracil (U) - Pyrimidine (in RNA)
H | C═C | \ O═C N \ | N—H | O
The lecturer emphasized: “Regarding the names, you don’t need to memorize the names by heart; we’ll soon have a nomenclature slide—a table with the names. You need to understand the principle… If there’s a question about this, you’ll be given the information.”
Nucleotide Nomenclature
The lecturer presented a nomenclature table and said: “Here’s a real table, as it appears in these panels… The most important thing is this: When a nitrogenous base is attached to a sugar only, it’s called a nucleoside. You don’t need to remember, okay? When we have all three components… base, sugar, and phosphate… it’s called a nucleotide.”
He added: “Do a sample here, catch biological researchers in the faculty or doctoral students in the faculty, and ask them what’s the difference between guanine and guanosine, they won’t remember. Okay? But they know the principle.”
| Base | Nucleoside | Nucleotide (with phosphate) |
|---|---|---|
| Adenine (A) | Adenosine | Adenosine monophosphate (AMP) |
| Guanine (G) | Guanosine | Guanosine monophosphate (GMP) |
| Cytosine (C) | Cytidine | Cytidine monophosphate (CMP) |
| Thymine (T) | Thymidine | Thymidine monophosphate (TMP) |
| Uracil (U) | Uridine | Uridine monophosphate (UMP) |
Differences Between DNA and RNA
The lecturer explained the two main differences:
- In the sugar:
- RNA has a hydroxyl group (-OH) at the 2’ position
- DNA has just a hydrogen (-H) at the 2’ position
- DNA sugar is called deoxyribose; RNA sugar is ribose
- The ‘D’ in DNA stands for deoxyribonucleic acid, and the ‘R’ in RNA stands for ribonucleic acid
- In the nitrogenous bases:
- DNA: A, G, C, and T
- RNA: A, G, C, and U (uracil replaces thymine)
Polynucleotide Formation
Linking of Nucleotides
The lecturer explained the process of connecting nucleotides: “A very basic principle in biology… there would be no life on Earth if a mechanism hadn’t developed, and it took a long time to develop, a mechanism that knows how to connect nucleotides to each other, one after another…”
He showed the chemical process: “What happened here… a bond formed between the free nucleotide up there, between its position three, this OH. Remind you, nucleophilic attack, have you already learned?… Nucleophilic attack is something that will come out of all your backgrounds, but look, it’s also the answer to most questions in the field.”
“A phosphodiester bond is formed here… you don’t need to memorize the name, but you’ll encounter it endlessly, you’ll encounter phosphodiester bonds endlessly, and that’s what builds the chain.”
The chemical reaction can be represented as:
5' 5'
| |
-O-P=O -O-P=O
| |
O O
| |
CH₂ CH₂
| |
O Base₁ O Base₁
/ \ / \
| | | |
| | | |
O O + O O
| |
CH₂ CH₂
| |
O Base₂ O Base₂
/ \ / \
| | → | |
| | | |
O O O O
| |
H P=O
|
O
|
CH₂
|
O Base₃
/ \
| |
| |
O O
|
H
|
3'
Chain Directionality
The lecturer emphasized the importance of directionality: “Now, what have we got? A chain of two nucleotides… and here’s a free five prime end, five prime, five prime, or five tag, and here’s a free three tag end. That’s the whole teaching.”
“Even if we stop now, and you run away, you’ve learned a very, very important principle in biology… the connection of nucleotides… they always connect five to three.”
Regarding chain length: “What’s the length of these chains? In your body? DNA, a DNA molecule… very, very, very long… millions, tens of millions, hundreds of millions… what limits it is the length of a chromosome, because in a chromosome, there’s one DNA molecule… in RNA, they reach thousands, tens of thousands, in some cases hundreds of thousands, in DNA we reach millions of nucleotides.”
Double-Stranded DNA Structure
The Double Helix
The lecturer explained: “Do we have to believe in it blindly? Is it always, always true?… In biology, exceptions can be found for almost everything.”
Regarding the DNA structure: “The two strands interact with each other and are kept at the same distance from each other by many, many hydrogen bonds that are weaker… and what’s written here, the connection here between the nitrogenous base, whatever it may be, the connection to sugar is always on carbon number one.”
The lecturer emphasized the founding principle: “The secret of the ability to transfer genetic information… one strand of DNA dictates the sequence in the other strand… the possibility of transferring this information is built on the fact that one strand complements the other strand.”
“In terms of numbers, always the number of nucleotides with A in each strand will be equal to T… because G always pairs with C and A with T, so we can reach the equation G=C, A=T.”
In mathematical terms:
- $A = T$
- $G = C$
- $A + G = T + C$
- $\frac{A + T}{G + C}$ = ratio unique to each species
DNA Replication
The lecturer explained the replication process: “All living cells, from the simplest to your cells, replicate their genetic information… in something called ‘templated polymerization’, a template… replication according to an existing template.”
“I have here two red strands of DNA… once I’ve separated them, each red strand can serve as a template for building… a new strand.”
The lecturer explained semi-conservative replication: “It’s called semi-conservative replication… half-conservative, keeping one strand exactly as it is and complementing what’s missing.”
“DNA taken in a test tube can be dissolved without affecting the covalent bonds at all; the two strands separate from each other by heating… close to boiling, the strands separate, if we let it cool down, they’ll find each other again.”
Original DNA:
5'-ATGCTAGCTAGCT-3'
3'-TACGATCGATCGA-5'
After separation:
5'-ATGCTAGCTAGCT-3'
+
3'-TACGATCGATCGA-5'
After replication:
5'-ATGCTAGCTAGCT-3' (Original strand)
3'-TACGATCGATCGA-5' (Newly synthesized strand)
5'-ATGCTAGCTAGCT-3' (Newly synthesized strand)
3'-TACGATCGATCGA-5' (Original strand)
Replication Fork
“We have something called a replication fork… the main lecturer in genetics was shocked that the cohort before you hadn’t heard of a replication fork.”
The lecturer explained the replication process in cells: “Something ensures separation… it’s an enzyme… an enzyme that can open a helix… there’s one strand where the polymerase, which is the enzyme that polymerizes, that inserts a nucleotide, can run without interruption; on the other strand, each time it’s needed, it’s only exposed when the replication fork opens.”
“This whole process is happening all the time in your body; cells divide, before they divide, they must duplicate their genetic information and ensure that both daughter cells receive exactly the same information.”
5' --------------------------> 3'
| | | | | | | | |
A--T G--C C--G T--A G--C
| | | | | | | | |
3' <-------------------------- 5'
↓
↓ (Helicase opens the double helix)
↓
5' -----------------> 3'
| | | | | |
A--T G--C C--G
| | |
| | |
3' <----------------- 5'
↓
↓ (DNA polymerase adds nucleotides)
↓
5' -----------------> 3'
| | | | | |
A--T G--C C--G
| | | | | |
T A C G G C
| | | | | |
3' <----------------- 5'
The Central Dogma of Biology
Three Main Processes
The lecturer presented the central dogma: “The central dogma of biology… a fundamental concept describing the flow of genetic information in living cells… this is where everything begins and ends… the take-off and landing of everything. Everything in biology begins and ends with the central dogma, with this flow direction, from DNA to RNA to proteins.”
The three stages of the central dogma are:
- DNA → DNA (Replication):
- “DNA replication is actually replication, duplication of DNA, this matter of separation and building an additional strand, it’s something that living cells must all do.”
- DNA → RNA (Transcription):
- “A process called ‘Transcription’… The name from the language academy is, I think, ‘tiatouk’ (תיעתוק), with a ‘taf’. But most Israelis say ‘shiatouk’ (שיעתוק), the important thing is that you know it’s transcription… There’s an enzyme that reads the double-stranded DNA here, it knows which strand, which strand to use as a template.”
- RNA → Protein (Translation):
- “The information from RNA is transferred to protein in a process called translation. What is a protein? Again, a polymer… a very long chain with directionality.”
Replication
↗ ↘
DNA -------→ DNA
|
| Transcription
↓
RNA
|
| Translation
↓
Protein
Exceptions to the Central Dogma
The lecturer mentioned an exception: “In the system, there are exceptions… HIV-1… it has all sorts of envelopes, and inside it has an inner vault called a capsid. Inside this capsid, the genome of the virus is in the form of RNA… inside that, there are also copies of a special enzyme encoded by the virus. This enzyme, it’s the enzyme that goes against the dogma. It’s called reverse transcriptase… and it goes from this RNA to DNA, meaning it goes against the current.”
“Is the virus even a living organism? This question will be deferred to the microbiology course… because if it’s some kind of parasite, is it a molecular parasite, viruses exploit the system of the cell they invade.”
General flow: DNA → RNA → Protein
Exception (HIV): RNA → DNA → RNA → Protein
↑
Reverse Transcriptase
History of Cell Discovery
At the end of the lecture, the lecturer returned to a historical topic: “Who was the first to discover this? Robert Hooke, England, sixteen hundred and something… You can read his book, you can find his book as a PDF on the internet, such old English, amazing.”
“This microscope, you see here, a lamp and some kind of water container that magnifies, so that the sample can be seen here, the maximum magnification he managed to reach then… fifty times, and he was the first to identify cells.”
“Look at his quote… he received an appointment from the King of England, it was the first time that this book he published… became a bestseller… all of high society flocked, the nobles flocked to him to see through the microscope, ticks, all sorts of things he managed to magnify, but he also identified these, so these are the first cells and that’s where the name came from.”
The lecturer concluded by saying that the next class will begin on Wednesday at 12:15.