Exam one prep Genetics

What is a Chromatin?

DNA associated with proteins, especially histones, packaged into a chromosome structure.

Homologous chromosomes are

Key distinction: Homologs are one chromosome from each parent. They are similar, but not necessarily identical.

Chromosomes that contain the same genes in the same order but may carry different alleles

A diploid cell has

Two sets of chromosomes

Notation: 2n

A haploid cell has:

One set of chromosomes

Notation: n

Examples: sperm and egg cells are — in humans

Sister chromatids are:

Identical copies of a chromosome produced by DNA replication

Sister chromatids are produced…

during S phase.

The centromere is:

The region of a post-replication chromosome where sister chromatids are attached

The centromere is a chromosome region important for

sister-chromatid attachment and chromosome movement.

Homologous chromosomes are

a pair of chromosomes, one inherited from each parent, that contain the same genes in the same order but may contain different alleles.

Sister chromatids are

Identical copies of the same chromosome produced during DNA replication and initially attached at the centromere.

Homologous chromosomes vs. sister chromatids…. homologs

One maternal + one paternal

Same genes

May have different alleles

Exist as a pair

Homologous chromosomes vs. sister chromatids.. sister chromatids

Copies of one chromosome

Same DNA sequence, barring replication errors

Usually genetically identical

Produced during S phase

If 2n = 12, how many chromosomes are in a haploid gamete

6

2n = 12 → n = 6

Major difference between prokaryotic and eukaryotic cells

Eukaryotic cells usually have their DNA in a nucleus, while prokaryotic cells do not

Structure found in both prokaryotic and eukaryotic cells

Ribosome

use ribosomes to make proteins.

Eukaryotic chromosomes are typically:

Linear and associated with histone proteins

Eukaryotic nuclear chromosomes are generally

linear DNA molecules wrapped around histone proteins.

Central dogma

DNA → RNA → protein

DNA
↓ transcription
RNA
↓ translation
PROTEIN

Transcription

the first step of gene expression, where an RNA polymerase enzyme copies a specific segment of DNA into a complementary RNA molecule, usually messenger RNA (mRNA)

Translation

RNA is used to produce a protein

Which type of RNA carries genetic information from DNA to the ribosome?

messenger RNA (mRNA)

mRNA

carries coding information

tRNA

brings amino acids

rRNA

forms much of the ribosome

Codon

A sequence of three nucleotides that corresponds to an amino acid or stop signal

Example:

mRNA: 5' — AUG — 3'
          ↑
       codon

AUG codes for methionine and commonly serves as the start codon.

Molecule directly assembled during translation

Protein

Four major biological macromolecules

Carbohydrates, lipids, proteins, and nucleic acids

Protein monomers

Amino acids

Nucleic-acid monomers

Nucleotides

Nucleotides are joined by

Phosphodiester bonds

example of Phosphodiester bonds

Sugar — phosphate — sugar — phosphate — sugar
↑

(———)

Amino acids are joined by:

Peptide bonds

A covalent bond involves:

The sharing of electrons between atoms

Hydrogen bonds are:

Weaker and involve attractions between opposite partial charges

Hydrogen bonds are important in what

DNA base pairing.

Primary protein structure

The sequence of amino acids in the polypeptide chain

Alpha helices and beta sheets

The three-dimensional shape of a single polypeptide chain

Quaternary structure

A protein is made of more than one polypeptide subunit

Diploid cell

Contains two sets of chromosomes, one from each parent

Haploid cell

One set of chromosomes

Homologous chromosomes

Chromosomes carrying the same genes in the same order, potentially with different variants

After DNA replication, a chromosome consists of:

Two sister chromatids

Very important exam distinction of chromatids and chromosomes

Before replication:       After replication:

     |                         X
 one chromosome          one chromosome
 one chromatid           two chromatids

The X is still ONE chromosome, because it has one centromere.

 If an organism has a diploid chromosome number of 12, its haploid number is

6

2n = 12 → n = 6

If an organism has 10 chromosomes in its haploid cells, then its diploid body cells have:

20

n = 10 → 2n = 20

If an organism has diploid cells with 2n = 8, how many chromosomes are found in a haploid cell of this same organism?

Answer: 4 chromosomes

2n = 8 → n = 4

If an organism has haploid cells with n = 7, how many chromosomes would be found in a diploid cell of this same organism? How many homologous pairs? 

• Diploid = 14 chromosomes

• Homologous pairs = 7 pairs

n = 7 → 2n = 14

Cell contains 6 duplicated chromosomes. How many chromatids?

12 chromatids

Each duplicated chromosome = 2 chromatids.

6 chromosomes × 2 chromatids = 12 chromatids

Cell contains 4 unreplicated chromosomes. How many chromatids?

4 chromatids

Each unreplicated chromosome consists of one chromatid.

A diploid organism is 2n = 10. Just before DNA replication, how many chromosomes does each cell contain? How many chromatids? How many pairs of homologs? 

• Chromosomes = 10

• Chromatids = 10

• Homologous pairs = 5

2n = 10

5 homologous pairs:

| |   | |   | |   | |   | |
↑     ↑     ↑     ↑     ↑
5 homologous pairs

11. A diploid organism is 2n = 10. Just before DNA replication, how many chromosomes does each cell contain? How many chromatids? How many pairs of homologs? 

12. A cell from the same organism from Question 11 above has completed DNA replication. How many chromosomes does this cell contain? How many chromatids? How many pairs of homologs?

• Chromosomes = 10

• Chromatids = 20

• Homologous pairs = 5

      X       X
      X       X
      X       X
      X       X
      X       X

10 chromosomes
20 chromatids
5 homologous pairs

⭐ Critical rule

DNA replication doubles the number of chromatids, NOT the number of chromosomes.

What components make up a nucleoside?

A nitrogenous base + pentose sugar

(blank) =
nitrogenous base
      +
pentose sugar

What makes up a nucleotide?

nitrogenous base + pentose sugar + one or more phosphate groups

(blank) =
base + sugar + phosphate(s)

Purines number of rings

two

Pyrimidines number of rings

one

Purines DNA bases

• Adenine (A)

• Guanine (G)

Pyrimidines DNA and RNA bases

DNA:

• Cytosine (C)

• Thymine (T)

RNA:

• Cytosine (C)

• Uracil (U)

Where are the base and phosphate attached for Nitrogenous base

The —- base is covalently attached to the 1′ carbon of the pentose sugar.

Where are the base and phosphate attached for phospate

The — is attached to the 5′ carbon of the sugar in a nucleotide.

The 3′-OH participates in forming the phosphodiester bond with the next nucleotide.

BASE

|

1'

/ \

4' 2'

| |

5' 3'

| |

PHOSPHATE OH

DNA vs. RNA Nucleotides

Similarities

Both contain:

• A phosphate group

• A pentose sugar

• A nitrogenous base

• Nucleotides connected by phosphodiester bonds

• A 5′ → 3′ direction

DNA vs. RNA Nucleotides DNA differences

Deoxyribose
Has T
Usually double-stranded
More chemically stable

DNA vs. RNA Nucleotides RNA differences

	Ribose
	Has U
	Usually single-stranded
	Less chemically stable

The key sugar difference is the 2′ carbon DNA vs. RNA RNA differences

2′ carbon → OH

The key sugar difference is the 2′ carbon DNA vs. RNA DNA differences

2′ carbon → H

Why are double-stranded nucleic-acid strands antiparallel?

The two strands run in opposite directions because nucleotides have directional 5′ and 3′ ends, and complementary bases can pair properly only when the strands are oriented antiparallel.

Strand 1: 5' ───────────── 3'
                 ↓
Strand 2: 3' ───────────── 5'

How do you identify 5′ and 3′ ends? 5′ end

is associated with the 5′ carbon, typically bearing a phosphate.

How do you identify 5′ and 3′ ends? 3′ end

The 3′ end has a free 3′-OH group.

RNA vs. DNA Primary structure

Both DNA and RNA have a sequence of nucleotides connected by phosphodiester bonds.

DNA Primary structure

5'—A—G—C—T—3'

RNA Primary structure

5'—A—G—C—U—3'

RNA vs. DNA Secondary Structure DNA

typically a double helix with two complementary strands.

RNA vs. DNA Secondary Structure RNA

usually single-stranded, but can fold back on itself to form structures such as:

      ┌───┐
──────┘   └──────
       hairpin

—- secondary structure results from complementary base pairing within the — molecule.

Hydrogen bonding

bonds form between complementary bases.

DNA:

A ═══ T
G ≡≡≡ C

• A–T → 2 hydrogen bonds

• G–C → 3 hydrogen bonds

Base stacking

Adjacent bases stack on top of each other inside the DNA helix.

Base stacking involves favorable interactions between neighboring aromatic bases and is a major contributor to DNA stability.

Exam point: DNA stability comes from both hydrogen bonding and base-stacking interactions

Why is RNA less stable than DNA?

RNA has a 2′-OH

RNA's ribose has a 2′-OH, whereas DNA has a 2′-H.

The 2′-OH can participate in chemical reactions that promote cleavage of the RNA backbone.

2. RNA is usually single-stranded

DNA's double-stranded structure provides substantial structural stability. RNA is commonly single-stranded and therefore more chemically accessible.

3. DNA uses thymine instead of uracil

DNA's use of thymine helps with repair because cytosine can spontaneously deaminate into uracil. If DNA normally used uracil, the cell would have more difficulty recognizing which uracils resulted from normal base composition versus cytosine damage.

Biggest reason to remember

The 2′-OH of RNA is a major chemical reason RNA is less stable than DNA.

Eukaryotic DNA Compaction

Eukaryotic DNA is packaged into chromatin, which consists of DNA associated with proteins, especially histones. DNA wraps around histone proteins to form nucleosomes, producing a more compact structure. During different stages of the cell cycle, the degree of DNA compaction changes. DNA is relatively accessible as chromatin during much of interphase but becomes highly condensed into visible chromosomes during cell division.

Eukaryotic DNA Compaction Visualization

DNA
↓
DNA wrapped around histones
↓
NUCLEOSOMES
↓
more compact chromatin
↓
highly condensed chromosome

2n = 6 Cell in G1

• Chromosomes = 6

• Chromatids = 6

2n = 6 Cell in G2 after S phase

• Chromosomes = 6

• Chromatids = 12

X X X X X X

Anaphase Question

You see 8 chromosomes moving toward opposite sides during anaphase.

At anaphase, sister chromatids have separated. Each separated chromatid is now considered an individual chromosome.

• Total chromosomes during anaphase = 8

• Chromosomes present during metaphase = 4

• Ploidy back in prophase = 2n = 4, assuming ordinary mitosis of a diploid cell

METAPHASE:

X X
X X
↑
4 chromosomes
8 chromatids


ANAPHASE:

← | | | | | | | | →
8 chromosomes total

A diploid cell contains homologous pairs before anaphase, but after mitosis and cell division are completed, the daughter cells no longer contain homologous pairs

False.

In normal mitosis, daughter cells retain the same chromosome number and homologous pairs as the original cell.

Example:

Parent: 2n = 6

        ↓ mitosis

Daughter 1: 2n = 6
Daughter 2: 2n = 6

Mitosis produces genetically similar daughter cells with the same ploidy.

DNA replication happens during S phase in both prokaryotic and eukaryotic cells.

This is true for eukaryotic cell-cycle terminology, but the statement is misleading for prokaryotes.

Correction: DNA replication occurs in both prokaryotes and eukaryotes, but G1, S, G2, and M are eukaryotic cell-cycle stages and are not normally used to describe the prokaryotic cell cycle.

In most cells of multicelled organisms, DNA replication happens after the cell has spent 24 hours in G1.

False.

Cells do not universally spend 24 hours in G1. The duration of G1 varies greatly depending on cell type and conditions.

Correct: DNA replication occurs during S phase, after G1.

DNA polymerase enzymes catalyze a phosphodiester bond between the 3′ carbon of an already-incorporated nucleotide and the 3′ carbon of an incoming nucleotide.

False.

DNA polymerase catalyzes a bond between the 3′-OH of the existing strand and the 5′ phosphate of the incoming nucleotide.

Existing DNA:
          3'-OH
             ↓
5'—DNA—DNA—DNA—OH

                 +
         incoming nucleotide
               5'-P
                 ↓

                bond

Mitosis vs. Cell Division Similarity

Both are processes involved in producing new cells.

Mitosis vs. Cell Division Difference

Mitosis specifically refers to nuclear division and separation of duplicated chromosomes.

Cell division/cytokinesis refers to the physical division of the cell into daughter cells

Mitosis

nucleus/chromosomes

Cytokinesis

cytoplasm/cell physically divides

DNA polymerase uses

a template strand to determine which nucleotide should be incorporated into the new DNA strand. Hydrogen bonds between complementary bases help position the incoming nucleotide opposite the template. DNA polymerase requires a free 3′-OH group of the deoxyribose sugar on the growing strand to add the next nucleotide.

Essential fact

DNA polymerase adds to the 3′-OH → DNA grows 5′ → 3′.

Initiator Proteins vs. Helicase Similarity

Both participate in initiating DNA replication at the origin of replication.

Initiator Proteins vs. Helicase Differnce

Initiator proteins recognize/bind the origin and help begin assembly of the replication machinery.

Helicase unwinds the DNA double helix by separating the two strands.

Origin
  ↓
Initiator proteins
  ↓
Helicase recruited/activated
  ↓
DNA unwinds

70% GC vs. 20% GC DNA DNA molecule A (70% G/C) is generally more

thermally stable.

Why?

• G–C base pairs have 3 hydrogen bonds

• A–T base pairs have 2 hydrogen bonds

• GC-rich DNA also tends to have stronger base-stacking interactions

G ≡ C    3 H-bonds

A = T    2 H-bonds

So GC-rich DNA generally requires more energy to separate.

Eukaryotic Cell Cycle interphase G1

Growth

• Cell grows

• Performs normal cellular functions

• Makes proteins and organelles

Eukaryotic Cell Cycle interphase S

Synthesis

• DNA replication

• Each chromosome becomes duplicated

Eukaryotic Cell Cycle interphase G2

Growth/Preparation

• Additional growth

• Protein synthesis

• Preparation for mitosis

INTERPHASE

┌──────┬──────┬──────┐

│ G1 │ S │ G2 │

└──────┴──────┴──────┘

↑ ↑ ↑

grow DNA prepare

copy for M

↓

Mitosis

DNA Replication Fork

replication fork

↓

Template 1: 3' ======================= 5'

\

\ HELICASE

/

/

Template 2: 5' ======================= 3'

How to determine 5′ and 3′

The two DNA strands are antiparallel.

If one template is:

3' ───────── 5'

the complementary strand must be:

5' ───────── 3'

DNA polymerase can only synthesize DNA:

5′ → 3′