central dogma

Central dogma in one line: information usually flows from…

DNA -> RNA -> protein.

Transcription vs translation: what's the difference?

Transcription: DNA -> RNA. Translation: RNA -> protein.

Gene expression basically means…

Using a gene to make a functional product (usually a protein).

Trap: every gene makes a protein. True or false?

False.

DNA is mainly for… and proteins are mainly for…

DNA stores information; proteins do most of the work in cells.

If a cell wants MORE of a protein, the fastest lever is usually to…

Make more mRNA (increase transcription) or translate more of the mRNA.

DNA vs RNA: 2 easiest differences to remember.

DNA has deoxyribose + T; RNA has ribose + U.

RNA is usually single-stranded. Why does that matter?

It can fold into shapes and act as a messenger/helper molecule.

Where does DNA -> RNA (transcription) happen in eukaryotes?

In the nucleus.

Where does RNA -> protein (translation) happen in eukaryotes?

At ribosomes in the cytoplasm (or on rough ER).

Prokaryote bonus: transcription and translation can happen…

At the same time (coupled).

The 'alphabet' of DNA is…

A, T, C, G.

The 'alphabet' of RNA is…

A, U, C, G.

Codon means…

A 3-base sequence on mRNA that codes for an amino acid (or stop).

Anticodon means…

A 3-base sequence on tRNA that pairs with an mRNA codon.

The genetic code is described as 'degenerate'. That means…

Multiple codons can code for the same amino acid.

But the genetic code is NOT 'ambiguous' because…

Each codon specifies only one amino acid (or stop).

Central dogma: DNA -> {{c1::RNA}} -> {{c2::protein}}.

Central dogma: DNA -> RNA -> protein.

Transcription = DNA -> {{c1::RNA}}; translation = RNA -> {{c2::protein}}.

Transcription = DNA -> RNA; translation = RNA -> protein.

The molecule that carries the message from DNA to ribosomes:

mRNA

The RNA that brings amino acids to the ribosome:

tRNA

The RNA that forms the core of ribosomes:

rRNA

DNA strands are antiparallel. That means…

One runs 5'->3' and the other runs 3'->5'.

Polymerases add nucleotides to the… end.

3' end.

So new DNA/RNA is synthesized in which direction?

5' -> 3'.

To synthesize 5'->3', the polymerase must READ the template…

3' -> 5'.

In transcription, which DNA strand is used as the template?

The template (antisense) strand.

The mRNA sequence is complementary to the… strand.

Template strand.

The mRNA sequence matches the… strand (except U for T).

Coding (sense) strand.

Quick rule: coding strand vs template strand.

Coding = same as mRNA (T->U swap). Template = complementary to mRNA.

DNA base pairing: A pairs with… and C pairs with…

T; G.

RNA base pairing with DNA during transcription: A pairs with…

U (in RNA).

Trap: RNA polymerase needs a primer like DNA polymerase. True or false?

False.

Promoter is basically…

A DNA sequence where RNA polymerase (and factors) bind to start transcription.

Trap: the promoter gets transcribed into mRNA. True or false?

False (usually).

Terminator is basically…

A sequence that signals transcription to stop.

Start codon is on… (DNA or RNA?)

mRNA (codon).

Start codon is usually…

AUG (codes for methionine).

Stop codons do what?

Tell the ribosome to stop translation (no amino acid).

There are 3 stop codons:

UAA, UAG, UGA.

Trap: a stop codon codes for a special 'stop amino acid'. True or false?

False.

Reading frame means…

How you group bases into codons (triplets) starting from a start point.

Why is AUG a big deal beyond 'start'?

It sets the reading frame.

If you see a DNA sequence and they ask for mRNA, the fastest method is:

Find the coding strand and swap T -> U (or complement the template).

Quick check: if a DNA strand is labeled 5'->3' and it's the template, the mRNA will be…

Complementary and antiparallel (so read the template 3'->5').

Polymerases {{c1::synthesize}} nucleic acids 5'->3' by adding to the {{c2::3'}} end.

Polymerases synthesize nucleic acids 5'->3' by adding to the 3' end.

In transcription: mRNA is complementary to the {{c1::template}} strand and matches the {{c2::coding}} strand (T->U).

In transcription: mRNA is complementary to the template strand and matches the coding strand (T->U).

Start codon (standard):

AUG

How many bases in one codon?

3

Main enzyme for transcription is…

RNA polymerase.

RNA polymerase uses what building blocks?

Ribonucleotides (ATP, UTP, CTP, GTP).

Transcription makes RNA from a…

DNA template.

In eukaryotes, transcription needs help from… (broad term)

Transcription factors.

What is a transcription factor (in plain words)?

A protein that helps control transcription by binding DNA.

Transcription starts at the…

Promoter region (DNA).

Transcription ends at a…

Terminator / termination signal.

Eukaryotes separate transcription and translation because…

Transcription is in the nucleus; translation is in the cytoplasm.

Prokaryotes can start translating an mRNA while it's still being transcribed because…

They don't have a nucleus.

In eukaryotes, the first RNA made from a protein-coding gene is called…

pre-mRNA (primary transcript).

3 main processing steps for eukaryotic pre-mRNA:

5' cap, splicing, poly-A tail.

5' cap does what? (high-level)

Protects mRNA and helps ribosome bind/start translation.

Poly-A tail does what? (high-level)

Helps mRNA stability and export; affects translation efficiency.

Trap: poly-A tail is copied directly from a DNA stretch of T's. True or false?

False (the tail is added).

Splicing means…

Removing introns and joining exons together.

Introns vs exons: which are usually kept in mature mRNA?

Exons.

Trap: introns are translated into protein. True or false?

False (normally).

Alternative splicing is useful because…

One gene can make multiple protein variants.

Where does mRNA splicing happen (eukaryotes)?

In the nucleus.

After processing, mRNA must leave the nucleus through…

Nuclear pores.

RNA polymerase reads the DNA template strand in which direction?

3' -> 5'.

If the coding DNA strand is 5'-ATG GAA TTT-3', the mRNA is…

5'-AUG GAA UUU-3'.

If you're given the template DNA strand and asked for mRNA, what must you do?

Complement it AND reverse direction to write mRNA 5'->3'.

Transcription uses base pairing rules, but the output is…

RNA, so it uses U instead of T.

RNA polymerase makes a single RNA from a DNA region called a…

Gene (transcription unit).

In eukaryotes, mRNA is usually… (one gene -> one mRNA)

Monocistronic (one mRNA codes for one protein).

In prokaryotes, an mRNA can be…

Polycistronic (can code for multiple proteins).

Operon (basic meaning) is…

A cluster of genes controlled together by one promoter (common in prokaryotes).

Trap: splicing is a normal step for prokaryotic mRNA. True or false?

False (in basic pre-med level).

If a question mentions 'TATA box' or many transcription factors, think…

Eukaryotic transcription.

RNA polymerase vs ribosome: who does what?

RNA polymerase makes RNA; ribosome makes protein.

If you see 'nucleus' in a gene-expression question, your first thought should be…

Transcription and RNA processing.

Eukaryotic pre-mRNA processing: {{c1::5' cap}} + {{c2::splicing}} + {{c3::poly-A tail}}.

Eukaryotic pre-mRNA processing: 5' cap + splicing + poly-A tail.

Splicing removes {{c1::introns}} and joins {{c2::exons}}.

Splicing removes introns and joins exons.

Prokaryotes can couple transcription and translation because they have no {{c1::nucleus}}.

Prokaryotes can couple transcription and translation because they have no nucleus.

Process that removes introns from pre-mRNA:

Splicing

Enzyme that makes RNA from DNA:

RNA polymerase

Translation happens on…

Ribosomes.

Ribosomes are made of…

rRNA and proteins.

Ribosome reads the mRNA in which direction?

5' -> 3'.

The polypeptide chain grows in which direction?

From N-terminus to C-terminus.

Start codon does two things: it says 'start' and it…

Sets the reading frame.

Which RNA carries amino acids?

tRNA.

Which RNA carries the message?

mRNA.

Which RNA is the main structural/catalytic part of ribosomes?

rRNA.

tRNA is 'charged' when it…

Has an amino acid attached.

The enzyme that attaches an amino acid to tRNA is…

Aminoacyl-tRNA synthetase.

Why is aminoacyl-tRNA synthetase so important?

Because it ensures the correct amino acid matches the codon (via tRNA).

Stop codons are recognized by…

Release factors (not tRNA).

A site, P site, E site: A stands for…

Aminoacyl site (incoming tRNA).

A site, P site, E site: P stands for…

Peptidyl site (holds the growing chain).