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molecular genetics Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

NUCLEIC ACIDS

A

A group of chemicals in cell that allow the transmission of
inherited information.

polymers of nucleotides

DNA – deoxyribose nucleic acid

RNA - ribose nucleic acid

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2
Q

NUCLEOTIDES

A

Nucleic acids are the genetic material of the cell and are composed of recurring monomeric units called nucleotides

Each nucleotide is comprised of three principal components:

5-carbon pentose sugar (pentagon)
Phosphate group (circle)
Nitrogenous base (rectangle)

Both the phosphate group and nitrogenous base are attached to the central pentose sugar

The nitrogenous base is attached to the 1’– carbon atom (right point)
The phosphate base is attached to the 5’– carbon atom (left point)

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3
Q

what are nulceotides made up of

A

Made up of:

a carbon sugar (ribose or deoxyribose)

a phosphate group

a nitrogen base (guanine, adenine, thymine, cytosine,
uracil)

The bonds within the nucleotide are covalent bonds.

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4
Q

BONDING IN DNA

A

The phosphate groups join nucleotides together by
bonding the C3 of one sugar with the C5 of an
adjacent sugar.

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5
Q

COMPLIMENTARY BASE PAIRING

A

C and G bond in DNA and RNA

A and T bond in DNA

A and U bond in RNA

The base pairs are held by weak hydrogen bonds.

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6
Q

DNA

A

Deoxyribose nucleic acid

DNA carries the genetic message for the functioning of the
organism.

A gene is a length of DNA that codes for a polypeptide,
which forms a protein. So DNA codes for the synthesis
of proteins.

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7
Q

WHERE IS DNA IS FOUND

A

Chromosomes in the nucleus of eukaryotes and in the
plastids of prokaryotes

In mitochondria

In chloroplasts

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8
Q

WHAT IS DNA MADE OF

A

The 5-carbon sugar is deoxyribose. The sugars are
labelled 1’ to 5’.

The shape of the molecule is a twisted ladder called a
double helix.

The sides of the ladder are made of deoxyribose –
phosphate – deoxyribose - phosphate etc.

The rungs of the ladder are made up of two bases which
always pair adenine with thymine (A-T) and guanine
with cytosine (G-C)

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9
Q

DNA STRUCTURE

A

The two nucleotide strands of DNA run in opposite directions (called anti-parallel). (5’ – 3’ down one strand and 3’ – 5’ down the other).

One turn of the helix contains 10 nucleotides.

Three DNA bases (called a triplet) code for one amino
acid

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9
Q

DNA STRUCTURE

A

The two nucleotide strands of DNA run in opposite directions (called anti-parallel). (5’ – 3’ down one strand and 3’ – 5’ down the other).

One turn of the helix contains 10 nucleotides.

Three DNA bases (called a triplet) code for one amino
acid

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10
Q

Sizes of DNA

A

Viruses
5-200 kilo
base pairs (kb)

Bacteria
500-5000 kb

Yeast
13,500 kb

Fruit fly
165,000 kb

Human
2,900,000 kb

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11
Q

HISTORY OF DNA

A

The structural organisation of the DNA molecule was correctly proposed in 1953 by James Watson and Francis Crick

  • constructed models to quickly visualise and assess the viability of potential structures
  • Their efforts were guided by an understanding of molecular distances and bond angles developed by Linus Pauling, and were based upon some key experimental discoveries:
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12
Q

making DNA models

A

Using trial and error, Watson and Crick were able to assemble a DNA model that demonstrated the following:

DNA strands are antiparallel and form a double helix
DNA strands pair via complementary base pairing (A = T ; C Ξ G)
Outer edges of bases remain exposed (allows access to replicative and transcriptional proteins)

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13
Q

As Watson and Crick’s model building was based on trial and error, a number of early models possessed what faults:

A

The first model generated was a triple helix
Early models had bases on the outside and sugar-phosphate residues in the centre
Nitrogenous bases were not initially configured correctly and hence did not demonstrate complementarity

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14
Q

The Rosalind Franklin Controversy

A

The final construction of a correct DNA molecule owed heavily to the X-ray crystallography data generated by Franklin

This data confirmed the arrangement of the DNA strands into a helical structure
The data was shared without Franklin’s knowledge or permission and contributed profoundly to the final design
Hence, Franklin is now recognised as a key contributor to the elucidation of DNA structure

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15
Q

PACKAGING OF DNA

A

Prokaryote – circular

Eukaryote – DNA wound around histone proteins – bead
like, made up of 8 molecules. There are other histones on the
outside of the DNA. Collectively known as a nucleosome.

To avoid tangling, DNA needs to be coiled into
chromosomes for cell division. To do this, the beaded
nucleosomes coil tightly to form chromatin fibres.

Looped domains form and these attach to non-histone
protein structures. The looped domains coil and fold further
to form chromosomes.

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16
Q

Exons

A

coding regions on DNA – code for proteins

Only about 10% of the human genome are exons.

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17
Q

Introns

A

non-coding regions on DNA

Some introns are used as regulators of gene expression, as
telomeres and genes for tRNAs. Most introns seem to have no
function at all.
During protein synthesis the introns are edited out so that only
coding regions (exons) are used.
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18
Q

telomeres

A

regions of repetitive DNA located at each end of a chromatid and function to prevent chromosomal deterioration

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19
Q

limited capacity on cell divison

A

During DNA replication, the extreme ends of the telomere cannot be copied and so the telomere gets marginally shorter
- This occurs because the terminal RNA primer on the lagging strand cannot be replaced (no 3’-attachment point for DNA pol I)

The progressive shortening of telomeres is associated with ageing (senescence), age-related diseases and mortalilty

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20
Q

telomerase

A

Telomeres can be lengthened by the enzyme telomerase, allowing for continued cell division past the Hayflick limit

Permanent activation of telomerase can cause cells to become immortal and leads to cancer (uncontrolled cell division)
Many cancer researchers are currently investigating the viability of telomerase inhibitor drugs as a treatment for cancers

21
Q

hayflick limit

A

Cells have a limited capacity for cellular division

  • Hayflick limit = ~ 40 – 60 divisions for a typical human cell
22
Q

what are introns

A

Introns often constitute highly repetitive sequences
(tandem repeats) that may make up almost 50% of the
genome.

Typically between 5 and 300 base pairs per repeat and may
be duplicated as many as 105 times.

These regions used to be referred to as ‘junk DNA’.

Tandem repeats are used in DNA profiling because they
are highly variable.

23
Q

RNA

A

RIBOSE NUCLEIC ACID - RNA

Differs from DNA:

Sugar is ribose instead of deoxyribose.

Base uracil instead of thymine.

Single strand instead of double helix.

Less stable than DNA

Much smaller (DNA is a thousand to a million times
larger).
24
Q

MESSENGER RNA (mRNA)

A

Carries genetic info from the nucleus to the ribosome.

Long string of nucleotides.

Sets of three nucleotides are called codons. Each codon
codes for a specific amino acid.

25
Q

TRANSFER RNA (tRNA)

A

Transport amino acids to their correct position on the mRNA
strand. Each amino acid has a specific tRNA activating enzyme.

Clover leaf shape. Double stranded, with base pairing.

Contain:
Carrier end for binding to the specific amino acid

A triplet of bases called the anticodon that binds to the codon
from mRNA

Ribosome site for attaching to the ribosome

Enzyme site for the tRNA activating enzyme

26
Q

RIBOSOMAL RNA (rRNA)

A

Makes up part of the structure of ribosomes, the site of

protein synthesis.

27
Q

DNA REPLICATION

A 
The two strands of DNA coil up into a helix. Each of the
two DNA strands will go into forming a chromatid. In
cell division (mitosis and meiosis) these two strands
appear as sister chromatids joined at a centromere.

DNA replication is semi-conservative as each of the
new chromatids is contains a strand of the original DNA

DNA replication is initiated at many points along the
chromosome in eukaryotes.

28
Q

POLYMERASE CHAIN REACTION (PCR)

A

Technique used to make millions of copies of DNA from a
small sample. For example, the DNA taken from a crime
scene may be present in too small a quantity to allow a
DNA profile to be done, so it is copied many times first.

PCR uses heat rather than helicase to unwind the helix and
Taq polymerase to add nucleotides.

29
Q

GENE EXPRESSION OVERVIEW

A
  1. A section of DNA (called a transcription unit) that
    codes for the polypeptide unzips
  2. A copy of the transcription unit is made called mRNA
    (Transcription)
  3. mRNA moves out of nucleus to ribosomes
  4. Three bases code for a specific amino acid
  5. Amino acids are assembled in correct order by
    carrier tRNA to make the polypeptide chain
    (Translation)
  6. Several polypeptides join together to make a protein
30
Q

GENE EXPRESSION

A

The three bases that code for an amino acid are called:

Triplets on DNA

Codon on mRNA

Anticodons on tRNA

Each triplet codes for one amino acid. Most amino acids have
more that one triplet that codes for it.(the code is said to be
degenerate). Eg the codons GCU, GCC, GCA and GCG all
code for the amino acid alanine.

31
Q

START AND STOP SEQUENCES

A

There are a few triplet codes that make up the START
and STOP sequences for polypeptide chain formation
(denoted below in the mRNA form):

START: AUG (met)

STOP: UAA, UAG, UGA

32
Q

TRANSLATION

A

Requires:

mRNA

tRNA

Amino acids

Ribosomes - Ribosomes composed
of approximately 60 percent
ribosomal RNA (rRNA) and 40
percent protein.

Ribosomes are composed of the
two ribosomal subunits (one
small and one large).

33
Q

STEPS IN TRANSLATION

A
  1. Initiation:
  2. Elongation:
  3. Termination:
34
Q

INITIATION

A
  1. Initiation: The start of translation brings together mRNA with the start codon (AUG), a tRNA bearing the start amino acid of a polypeptide (methionine), and ribosomes
35
Q

Elongation

A
  1. Elongation: In the elongation stage of translation, amino acids are added one by one by tRNAs as the ribosome moves along the mRNA, as follows:

The tRNA brings the appropriate amino acid up to the ribosome.

The anticodon on the tRNA matches with the codon on the mRNA.

The new amino acid is then joined to the polypeptide chain.

As each new amino acid is joined, the ribosome nudges the mRNA strand along three ‘notches’ and the next tRNA falls into place.

A peptide bond forms between adjacent amino acids.

The tRNA is released

36
Q

Termination

A
  1. Termination: The final stage of protein synthesis occurs when the ribosome reaches a stop codon. The polypeptide chain disconnects
37
Q

POLYSOMES

A

Several ribosomes can translate an mRNA at the same
time, forming what is called a polysome.

More than one ribosome can translate a mRNA at a time,
making it possible to produce many polypeptides
simultaneously from a single mRNA.

38
Q

THE OPERON THEORY HYPOTHESIS

A

Hypothesis put forward by Jacobs and Monod to explain why E. coli produces an enzyme galactosidase which breaks down lactose only when lactose is present.

39
Q

THE OPERON THEORY

A

One section of DNA that codes for the enzyme is called the Structural gene.

Situated close to this is another section of DNA called the Operator gene. This activates the structural gene when the enzyme is needed.

The operator gene is controlled by the Regulator gene situated further down the DNA chain. This produces a Repressor substance which turns the operator gene off (so no enzyme is made, called Gene
Repression).

When an enzyme is needed, the repressor substance is
inhibited. Therefore, the operator gene can now turn on the
structural gene and the enzyme is made, (called Gene
Induction)

It has been found that lactose itself can inactivate the repressor
by combining with it.

40
Q

Operator gene

A

activates the structural gene when the enzyme is needed.

controlled by the Regulator gene which is situated further down the DNA chain.

41
Q

gene repression

A

regulator gene produces a Repressor substance which turns the operator gene off (so no enzyme is made, called Gene Repression).

It has been found that lactose itself can inactivate the repressor
by combining with it.

42
Q

gene induction

A

When an enzyme is needed, the repressor substance from the regulator gene is
inhibited. Therefore, the operator gene can now turn on the
structural gene and the enzyme is made, (called Gene
Induction)

43
Q

EPIGENETICS

A

Study of how environmental factors can:

Turn genes on and off

Affect how cells read genes

44
Q

DNA methylation

A

A process where methyl groups are added to the bases cytosine and adenine in DNA. Methylation modifies the function of the DNA, typically acting to suppress gene transcription. Eg preventing a cell from reverting to a stem cell or converting into a different cell type.

45
Q

Histone modification

A

DNA is wrapped around histones so alterations in the

histone can affect the activity of the DNA.

46
Q

transcription

A

the process where a DNA sequence (gene) is copied into a complementary RNA sequence by RNA polymerase

47
Q

transcription process

A

RNA polymerase unwinds and separates the DNA strands and synthesises a complementary
RNA copy from one of the DNA strands

When the DNA strands are separated, ribonucleoside triphosphates align opposite their exposed complementary base partner

RNA polymerase removes the additional phosphate groups and uses the energy from this cleavage to covalently join the nucleotide to the growing sequence

Once the RNA sequence has been synthesised, RNA polymerase detaches from the DNA molecule and the double helix reforms

48
Q

translation Mnemonic

A 
Messenger RNA  (goes to…)
Ribosome  (reads sequence in …)
Codons  (recognised by …)
Anticodons  (found on …)
Transfer RNA  (which carries …)
Amino acids  (which join via …)
Peptide bonds  (to form …)
Polypeptides

Mnemonic: Mr Cat App

49
Q

ribosomes

A

free ribosomes synthesise proteins for use primarily within the cell

bound ribosomes synthesise proteins primarily for secretion or for use in lysosomes

Biology- IB (10 decks)

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